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Octet System Data Acquisition User Guide

1. Lg CAUsers Owner Documents Contracting Forte Bio User_Guides Data and methods Quant 96 data higG ProG Q Quantitation Runtime Binding Chart ston x lt Current Binding Charts Sensors to Chart Plate Status a Plate Legend Sample Column 1 SelectAll Ss i Selected Sample Column 2 i y 3 7 Solecte Sample Column 3 A A Processing Semple Column 4 B B Sample Column 5 c c Processed Sample Column 6 Reserved Semple Column 7 D D O Basen Sample Column 8 E E F F SensorFail c c L Subtract reference sensors H H Experiment Progress Step 8 of8 120s 120s Elapsed exp time 0 21 55 Total experimenttime 0 21 55 Flip Data 40 35 30 E25 E p 520 a 15 A A 10 ir 05 0 0 0 10 20 30 40 50 60 70 80 90 100 110 120 Time sec Sensor A1 Sensor B1 Sensor C1 Sensor D1 Sensor E1 Sensor F1 Sensor G1 Sensor H1 Figure 5 53 Runtime Binding Chart 4 Optional Click View gt Instrument Status to view the log file see Figure 5 54 The experiment temperature is recorded at the beginning of every experiment as well as each time the manifold picks up a new set of biosensors Instrument events such bio sensor pick up manifold movement integration time biosensor ejection and sample plate temperature are recorded in the log file WARNING Do not open the Octet instrument door when an experiment is in progress If the door is opened the data from the active acquisition st
2. Plate Definition sensor Assignment Review Experiment Run Experiment od In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and rightclick to enter modify well data Read Head 8 Channels 16 Channels Sample Plate Table i Concentration units ug ml Zi Export Import Assay Settings pem Basic Quantitation ler Sample 1D Replicate Group type one ig ml platen Factor Information ot gtr Om Unknown n a 2 Time 5 Saipa 07 Unknown n a 2 al P ag Control n a n a Quantitation 120 400 Qc ee e Fa E9 Control n a nja OKE Control n a n a Os Control n a n a K Control n a n a m Control n a n a o9 Control n a n a QA Control n a nia Sample Plate 8 c cono n a n a Sample Plate 384 wells e Sa ma E W123 45 6 7 8 9101112131415161718192021222324 om Control n a nja AODOOOOOOOOO90BOBO0000000 Ox Control n a n a BOOQOOQOQOQQOQQOQQQQOQOQQQQQQQQ 3010100101010101 010510 10 1001010101010 DOQQQ 999898589 OQQQQ0QQ EOQOOQOOOOOO0OOOOO000000 FIOOOOOOOOOOOOOOOOO000O FOOOODOOOOOOOBO OOOO0000O HOOOOQOOOOOOOOOOOOOOOO00OO NOOOOWO O O O O OO000000O JIOOOOOOOOOOOOOOOOOOOO000O KOOOOOOO OOO0OO0 O OO000000Q LOQOQQQQQQQQQQQQQQQQQQQQQ MOQCOOOOOOOOO0OOOOO0O00000 NOQOOOOOOOOOOOOOOOOOO000OO LMOODDDOOO OO O0 O OO000000O POQQOOQOOOQOOQOOQOOOOO0009 IO Standar
3. Legend Unassigned sensors BY Missing sensors Legend O Unassigned Samples Pie charts Assay Sample Plate Step Name Step Type SensorType Al 1 equilibration 3 Custom AHC Anti higG F 1 1 AS Loading I Loading AHC Anti hlgG F 1 AJ 1 Baseline b Baseline AHC Anti hlgG F 1 A13 1 Association I Association AHC Anti hlgG F 1 Ag 4 Dissociation A Dissociation AHC Anti higG F s 1 Al 2 Regeneration J Custom AHC Anti higG F 1 AS 2 Neutralization 3 Custom AHC Anti higG F 1 Al 2 Regeneration F Custom AHC Anti hlgG F H 1 A5 2 Neutralization Custom AHC Anti higG F 1 io Al 2 Regeneration E Custom AHC Anti hlgG FL J 1 AS 2 Neutralization Custom AHC Anti hlgG F k Al 1 equilibration Custom AHC Anti hlgG F M A5 1 Loading Uf Loading AHC Anti hlgG F NIOC Ag 1 Baseline b Baseline AHC Anti hlgG F O A13 1 Association IE Association AHC Anti hlgGF _ Pi C C a SFERRARE Poet AINSA na nA i m X D i AA j N Legend O Unassigned Samples Pie charts Figure 8 52 Review Experiment Window SAVING EXPERIMENTS After an experiment is run the software automatically saves the experiment information that you specified sample plate definition biosensor assignment assay settings to an experiment method file fmf If you set up an experiment but do not start the run you can manually save the experiment method To manually save an exper
4. j issii G2 Protein A Legend O Unassigned sensors R Missing sensors aT Remove Fill Fill Plate A3 Protein A B3 Protein A Sensor Tray Sensor Tray V Replace sensors in tray after use of 2 F oi 2 3 4 5 6 7 8 9 10 11 12 wel SensorType Lot Number Information aAOOCOOCOCOOOCOOO pea B1 Protein A B m C C C C1 Protein A E mnir D1 Protein A COOOL UL E1 Protein A oAB OOOO e G1 ProteinA eDOCOCOOOCOOCOO mea A2 Protein A F T C B2 Protein A E moomoo C2 Protein A csOOUL Ei JIL Proteins H E H C E2 Protein A F2 Protein A j ici G2 Protein A Legend O Unassigned sensors B Missing sensors a ea Remove Fill Fil Plate A3 Protein A B3 Protein A Figure 5 48 Example Assay Using One Partial Biosensor Tray and Biosensors from a Second Tray To restore biosensors that have been removed select the columns to restore and click Fill To restore all sensors on the plate click Fill Plate NOTE If multiple biosensor trays are used only the first biosensor tray can be a partial tray During the experiment the software prompts you to insert the appropriate tray in the Octet instrument Octet System Data Acquisition User Guide Release 7 1 page 114 Chapter 5 Quantitation Experiments Octet RED96 QK and QK REVIEWING EXPERIMENTS Before running an experiment you can review the sample plate layout and the biosensors assigned
5. Defining a Kinetic Assay page 247 Assay Steps List New Assay Move Up Move Down Remove Replicate Pp me Assay Sample Step Name Step Type Sensor Type Assay Time 1 1 Equlibration Custom SA Streptavidin p 1 2 F Equlibration Loading SA Streptavidin 1 3 EProA Immobilization Baseline SA Streptavidin 2 1 4 resin Z Association SA Streptavidin i ssociation 1 3 Dissociation Z Association SA Streptavidin 1 ti F Regeneration Custom SA Streptavidin 1 12 n Neutralization 2 Custom SA Streptavidin 1 11 F Custom SA Streptavidin 1 12 b Custom SA Streptavidin 1 11 Regeneration J Custom SA Streptavidin Assay Steps List New Assay Move Up Move Down Remove Replicate Re ime Assay Sample Step Name Step Type Sensor Type Assay Time 1 1 Equlibration Custom SA Streptavidin la i 2 ProA Immobilization LZ Loading ESA Streptavidin i 3 Baseline ke Baseline SAHC Anti hlgG Fc Ca 1 4 Association a Association EP EHE Aa 1 3 Dissociation Association ESSA Super Streptavi 1 1 Regeneration 3 Custom E Custom 1 12 Neutralization 3 Custom sAHC Beta 1 1 11 Regeneration Custom 1 12 Neutralization J Custom 1 11 Regeneration 32 Custom SA Streptavidin Figure 7 34 Editing an Assay Step Name top or Sensor Type bottom in the Assay Steps List To reorder or remove an assay step 1 Select a step row in the Assay Steps List
6. Reference Positive Control Negative Control Legend Unassigned sensors 583 Missing sensors f E Ve 71 Figure 5 36 Populating the Sensor Tray Map with First Biosensor Type 4 Select the columns in the Sensor Tray Map that should contain the second biosensor type right click and select the second biosensor type see Figure 5 38 The Sensor Type column will update accordingly Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 103 Sensor Tra Sensor Tray v aes sensors in tray after use of 2 E Miall Cancar Tuna Lot auto assign Anti Human IgG Fc Anti Mouse IgG Fv Protein A Protein G Protein L SA Streptavidin Residual Protein A Anti Penta HIS Custom HCO deggie Positive Control Legend Unassigned sensors Missing sensors p Negative Control Figure 5 37 Populating the Sensor Tray Map with Second Biosensor Type 5 Repeat this column selection and assignment process for all other biosensor types to be used in the experiment The software will automatically update the number of bio sensor trays needed and biosensor assignments in all trays according to the column assignments made in Tray 1 In the example shown in Figure 5 38 Protein A and Protein G biosensor types are used for a multiple analyte experiment using two replicates Three heterogeneous biosensor trays will be needed for the experiment Octet Syste
7. Choose an option to start Es New Quantitation Experiment fat Basic Quanttaton Basic Quantraton wth Regeneration Advanced Quantitation Roe AEA Basic Kinetics O Standard Contor O Unassigned 5 O unom Reference Reseweu Figure 6 1 Selecting an Experiment Type in the Experiment Wizard for Octet RED384 4 Click the 5 arrow The Experiment window displays Figure 6 1 right DEFINING THE SAMPLE PLATE Table 6 3 lists the steps to define a sample plate Table 6 3 Defining a Sample Plate Step See Page 1 Select the instrument read head configuration 8 or 16 channels 143 2 Select the sample plate format 96 or 384 wells 144 3 Designate the samples 144 4 Annotate the samples optional 157 5 Save the sample plate definition optional 163 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 143 Read Head Configuration and Plate Layout The Octet read head contains the collection optics If the read head is set to 8 channels one column of 8 biosensors interrogate 8 plate wells If the read head is set to 16 channels two columns of biosensors interrogate 16 wells Figure 6 1 The read head configuration and the plate format 96 or 384 wells determine the plate lay out Figure 6 2 8 Channel Read Head 16 Channel Read Head 7 8 9 10 11 12 5 6
8. page 168 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Plate Definition Sensor Assignment Review Experiment Q Run Experiment In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and right click to enter modify well data Read Head i 8Channels 16 Channels Sample Plate Table Concentration units ug mi A Export l Import Assay Settings z Well Sample ID Replicate Group Type Conc mI Dilution Factor Information Assay Basic Quantitation i ee aim Standard Assay Single analyte Time s Shake speed Quantitation 120 400 m Sample Plate Sample Plate 384 wells P1234567 8 9 10111213141516171819 AIOOOOOO OOO OOOO0000O gt E IBIOOOOOOOOOOOOOO000OG c OOOOOOOOOOOO000000G DOOQOOO0O0O000000000000q EIOOOOOOOOOOOO000000G IFFOOCOOOOQCOOOOOO0 0000 IFIOOOOOOCOOOOO0OO000G HOOOOOOQCOOOOO000000G NOOOOOOOOQOO9ONOOOOd YIOOOOOOOOOOOOOOOOOOG KOOOOOOOOOOOO0O0000G LOOQOQOQOQQOQOQQQQQ0Q000000Q MOOOOOOQOOOOQO0O0000000qQ NOOQOQOQOQOQOQ0Q0Q000000000q o O0O0O0O000000000000000q P O00000 000000000000q IO Standard IO Control ite Unas O Lnknom _Reteense O ress D Assay Parameters Available Assays Assay Parameters Basic Quantitation with Regeneration Single analyte Multi E High sensitivity assay
9. v Localhost 20002 Figure B 18 Authentication Server Dialog Box Click Default to recall the default server settings of localhost and Port 2002 Localhost lf the local computer is to be used as the GxP Server module host select the Localhost check box Change the Port number if needed Remote host on same subnet lIf the GxP Server module is hosted on the same subnet deselect the Localhost check box and click Find A list of potential GxP Server module addresses will be listed Choose the desired location from the list and click OK Octet System Data Acquisition User Guide Release 7 1 page 376 Chapter B 21 CFR Part 11 Software Administrator Options Choose Server Address Ees More than one server was found Please choose one 192 168 1 78 JRICHARDS 192 168 1 78 JRICHARDS Figure B 19 GxP Server Address Search Results Remote host on another subnet lf the GxP Server module is hosted on a differ ent subnet deselect the Localhost check box Enter the IP address of the com puter hosting the GxP Server module Connection to server Server address 192 168 1 78 Figure B 20 Manual Entry of Remote Host Address When the GxP Server module host location has been selected or entered click OK to save changes and exit the Authentication Server dialog box The GxP Server module location will now be listed as the Server in t
10. 96 well 96 Wel 384 well 384 well koc a Reagent Plate 384 wells A5 Protein A 7 Cs ProteinA OE5 ProteinA G5 ProteinA I5 Proteina K5 Protein A M5 ProteinA O5 Protein A OA ProteinA C7 ProteinA QE ProteinA OG Protein A OI ProteinA OK ProteinA OM ProteinA 0 ProteinA AI 1X Kinetics Buffer C9 1X Kinetics Buffer 00000000000 OOO0Q00Q000000 OQQQQQ 0700101010 ORDR RaRa POZErAAA TFOAOANMOQODS MOOOOQOOOOOOOOOOOOOOO00000 O Unassigned Import Export Remove O Unassigned Import Export Remove Figure 8 27 Modifying the Reagent Plate 4 Select a reagent plate format 96 Well or 384 Well and click OK 5 Select the Reagent Plate radio button above the plate table This will display the Reagent Plate Table 6 Inthe Reagent Plate Map right click a column to use and select Buffer Activation Quench Load Wash or Regeneration from the shortcut menu see Figure 8 28 The well designations appear in the Reagent Plate Table Repeat this step to define other wells in the reagent plate Octet System Data Acquisition User Guide Release 7 1 Working with a Reagent Plate page 301 Plate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered Highlight one or more wells on t
11. Zrzxc IrIronmoow gt 00000860008 0008008008000080 0E0808080808 N KS IPC Legend Unassigned samples 6 0 0909 0 090 9000909090909 g Figure 8 49 Assay Sensor Type Reassignment 3 Repeat the previous steps to assign locations for the remaining biosensor types in the tray D IMPORTANT Ensure that the biosensor types selected in the Assay Definition window have assigned column s in the Sensor Assignment window or the experiment cannot be run Using Partial Biosensor Trays If you remove biosensors from the Sensor Tray Map and there are not enough remaining biosensors for the experiment the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay s The experiment in the example shown in Figure 8 50 includes two assays and Tray 1 does not include enough biosensors for the experiment To view the additional biosensor tray that is required for the assay select Tray 2 from the Sensor Tray drop down list Figure 8 50 top The Sensor Tray Map will then display the additional biosensors required for the assay Figure 8 50 bottom If necessary change the location of these biosensors Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 321 Sensor Tray v Replace sensors in tray after use Sensor Tray of 2 10 11 12 o SEERE BA
12. Task Export Option Export Result Destination Text EMF WMF Data BMP JPG or PNG Save the vV Click File gt Creates a tab delimited text binding Browse to file of the numerical raw data data select a folder from each biosensor Open and enter a file the file with a text editor name such as Notepad Export the v Click File gt Creates a graphic image Runtime Browse to Binding select a folder Chart toa and enter a file graphic file name Octet System Data Acquisition User Guide Release 7 1 page 338 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Table 8 11 Runtime Binding Chart Export Options Continued Task Export Option Export Result Destination Copy the vV Clipboard Copies the chart to the sys Runtime tem clipboard Binding Chart Print the v Printer Opens the Print dialog box Runtime Binding Chart MANAGING EXPERIMENT METHOD FILES After you run an experiment the Octet System Data Acquisition software automatically saves the method file fmf which includes the sample plate definition biosensor assign ment and the run parameters An experiment method file provides a convenient initial template for subsequent experiments Open a method fmf and edit it if necessary NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the s
13. Time 8 Shake speed Quantitation 120 a 400 Ez L Figure 5 27 Assay Parameters Basic Quantitation Assay Table 5 6 Basic Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte and For multi analyte experiments using multiple biosensor types Replicates per sen per sample well and the number of replicate assays in each well sor type per biosensor type Quantitation Time s The duration of data acquisition seconds while the biosensor is incubated in sample NOTE A subset of data points may be selected for processing during data analysis Quantitation Shake The sample platform orbital shaking speed rotations per min speed rpm ute Octet System Data Acquisition User Guide Release 7 1 Managing Assay Parameter Settings page 93 Basic Quantitation with Regeneration Assay Parameters r Assay Parameters Available Assays Assay Parameters Bf Standard Assay Basic Quantitation with Regeneration Z High sensitivity assay with regeneration E Protein L Standard range D Multiple analyte Replicates per sensortype 1 Single analyte Time s Quantitation 120 Shake speed woo S Regeneration 5 400 p lt gt 4 gt 15 00 et kp lt gt KIG Neutralization 5 400 4 M Pre condi
14. Aligning Data by a Selected Step To align the binding data to the beginning of a user selected step in the Runtime Binding Chart see Figure 7 57 right click a step and select Align to Step lt number gt To remove the step alignment right click the step and select Unaligned ao ii mio mo 2 5 m 1 Align to Step 5 Dissociation Unaligned 2 0 g ne Properties z 5 Export Data ait S Undo Zoom 40 Fullscale lt Autoscale 0 5 oe ya ie l wt 1 0 500 1000 1500 2000 2500 3000 Time sec Sensor A1 Sensor B1 Sensor C1 Sensor D1 Sensor E1 Figure 7 57 Runtime Binding Chart Aligning the Data to a User Selected Step Extending or Skipping an Assay Step During acquisition the duration of the active step may be extended You can also terminate the active step and begin the next step in the assay NOTE If the step you want to extend or terminate includes biosensors used in Parallel Reference Double Reference or Average Reference subtraction meth ods the data will not be analyzed To extend the duration of the active step 1 Inthe chart window click the Extend Current Step button 2 Inthe Extend Current Step dialog box see Figure 7 58 enter the number of seconds to extend the step and click OK Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 271 r Dl Extend Current Step
15. Octet System Data Acquisition User Guide Release 7 1 ForteBio Inc 1360 Willow Road Suite 201 Menlo Park CA 94025 888 0CTET QK 650 322 1360 O r e B O www fortebio com A Division of Pall Life Sciences Copyright 20110 ForteBio Inc All rights reserved page 1 Table of Contents Chapter 1 WeICOMG ss csicciecen sce veseeee sane 7 About the Octet System 000s ee aee 8 What s New in the Octet System Data Acquisition Software Release 7 1 8 What s New in the Octet System Data Acquisition software Release 7 0 12 Conventions and Symbols Used in This Guide 13 ForteBio Technical Support 13 Chapter 2 Octet System Specifications 15 Octet RED96 System Specifications 16 Octet RED384 System Specifications 18 Octet QK System Specifications 21 Octet QK System Specifications 23 Octet QK384 System Specifications 25 Chapter 3 Getting Started 29 Starting the Octet System and Data Acquisition Software 0eeeees 30 Software Overview seee cece ees 31 Main Menu and Toolbar 31 View Menu ccc c cee e eee e eens 34 Status Bar ccc estes eetine saa 38 Instrument Status Window 39 Experiment Wizard 0000 40 Octet System Data Acquisition Options 40 Setting the Plate Temperature 43 Changing the Plate Temperature for Individual Exper
16. Sampling Format Required plate 96 well black flat bottom polypro pylene microplate Greiner Bio One 655209 SBS standard microplate Single sample plate capacity Sample Volume 180 220 uL well 96 well plate Sample Types Purified samples common culture media crude lysates Biosensor Type Disposable single use fiber optic biosensors with optional reuse by regeneration and or re racking Biosensor Tray Type 8 x 12 format 96 biosensor tip tray green color Optics and Mechanics 8 channel biosensor manifold Optical interferometer One spectrometer shared by eight biosensors Throughput Up to eight biosensors in parallel maximum of 96 tests unattended One 96 well plate and one biosensor tray at once Orbital Flow Capacity Static or 100 1 500 rpm Temperature Range Ambient 4 C 40 C 1 C increments Dimensions 18 6 H x 17 W x 20 8 D 47 cm H x 43 cm W x 53 cm D Weight 54 Ib 24 5 kg Electrical Requirements Mains AC 100 240 V 5 0 2 0 A 50 60 Hz single phase Power consumption 120 W 240 W peak Octet System Data Acquisition User Guide Release 7 1 Octet QK System Specifications page 23 OCTET QK SYSTEM SPECIFICATIONS Jort Bio Optics 8 channel biosensor manifold Black 96 well sample plate Biosensor Tray Orbital shaker Waste Compartment Figure 2 4 Octet QK Instrument Door Closed Left or O
17. Starting a Quantitation Experiment page 141 STARTING A QUANTITATION EXPERIMENT NOTE Before starting an experiment check the plate temperature displayed in the status bar Confirm that the temperature is appropriate for your experi ment and if not set a new temperature If the Octet System Data Acquisition software is closed the plate temperature will reset to the default startup value specified in the Options dialog box when the software is relaunched You can start a quantitation experiment using one of the following options e Launch the Experiment Wizard e Open a method file fmf by clicking File gt Open Method File Method files may be saved and recalled using the File menu and are automatically saved when an experi ment is run For more details on method files see Managing Experiment Method Files on page 205 Onthe menu bar click Experiment gt Templates gt Quantitation NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Starting an Experiment Using the Experiment Wizard To start an experiment using the Experiment Wizard 1 If the Experiment Wizard is
18. The following General Settings are available on the Run Experiment Tab Table 5 12 General Settings Item Description Machine name The computer name that controls the Octet instrument and acquires the data User name The user logon name Description A user specified description of the assay or assay purpose The description is saved with the method file fmf Octet System Data Acquisition User Guide Release 7 1 page 122 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Stopping an Experiment To stop an experiment in progress click x or click Experiment gt Stop The experiment is aborted The data for the active biosensor is lost the biosensor is ejected into the waste tray and the event is recorded in the experimental log NOTE After the experiment is run the software automatically saves the exper iment method fmf MANAGING RUNTIME BINDING CHARTS If the Open runtime charts automatically check box is selected in the Run Experiment window the Runtime Binding Charts are automatically displayed when data acquisition starts see Figure 5 55 The Runtime Binding Chart window displays the current step number time remaining for the current step total elapsed experimental time and total experiment time The Runtime Binding Chart is updated at the start of each experimental step The active biosensor column is color coded A green B magenta C orange D purple E olive F
19. Designating a Reference Biosensor During Acquisition To designate a reference biosensor during acquisition 1 Inthe Sensors to Chart list or the Sensor Tray right click a biosensor and select Refer ence see Figure 5 57 Current Binding Charts Sensors to Chart Sample Column 1 Select All Sample Column 2 5 Al Sample Column 3 Rae BI Sample Column 4 angor Sample Column 5 Sensor C1 Sample Column 6 SensorD1 pa c L Sample Column sensor E1 Reference Sample Column 8 BSensor F1 i sensor G1 sensor H1 Subtract reference sensors Figure 5 56 Designating a Reference Biosensor in the Runtime Binding Chart The selected biosensor will be shown with an R in the Sensors to Chart list and Sensor Tray see Figure 5 57 2 Click the Subtract reference sensors check box see Figure 5 57 Current Binding Charts Sensors to Chart Plate Status Sample Column 1 Selecta Sensor Tray Sample Column 2 FSensorai F 1234567 8 9 101112 Sample Column 3 A Lil EEHEHE Sample Column 4 e a B Ej HEHHEE Sample Column 5 ensor Sample Column 6 c m Titi HE Sample Column 7 Sensor E1 D EEHEEHE Sample Column 8 sensor F1 E Ha BEERS a Bsensor Gi F SERRE sensor H1 G rT ETLLiLLe v Subtract reference sensors H Figure 5 57 Subtract Reference Sensors check box in the Runtime Binding Chart NOTE Subtracting reference data in the Runtime Binding Chart only makes a
20. Desktop 5 Libraries 1 Documents Music 5 Pictures a Videos al Filename 96 standard plate csv aa Save as type csv Files csv x Hide Folders Cancel L Figure 7 20 Export Plate Definition Window Octet System Data Acquisition User Guide Release 7 1 page 234 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Importing a Plate Definition To import a plate definition 1 In the Sample Plate Definition window see Figure 7 19 on page 233 click Import Sample Plate 96 wells O Unassigned Import Export Remove Figure 7 21 Sample Plate Map Import Button 2 Inthe Import Plate Definition window see Figure 7 22 select the plate definition csv and click Open 3 Import Plate Definition go k Forte Bio gt ty Search Data and met P Organize 7 New folder 0 0 Arrange by Folder 7 E Desktop Data and methods J Downloads Recent Places Name Date modified Type k Favorites Documents library 4 96 standard plate csv 4 22 2011 6 34PM Microsoft Excel Cq E Desktop t Libraries Documents J My Documents JL Public Documents Music 5 Pictures A Videos RE m r CSV Files csv Bd Ki File name 96 standard plate csv Figure 7 22 Import Plate Definition Window NOTE You can also create a csv file for import Figure 7 23 s
21. Figure 6 14 Concentration Representation in Dilution Series 4 Click OK The Sample Plate Table will display the dilution factors entered Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 155 Editing a Dilution Factor in the Sample Plate Table To edit a dilution factor in the Sample Plate Table 1 Inthe Sample Plate Table see Figure 6 15 double click a cell in the Dilution Factor column for the desired unknown 2 Enter the new value the default dilution factor is 1 Sample Plate Table Concentration units g ml Z Export Import Well Sample ID Replicate Group Type Conc pg ml Dilution Factor Information a Oa3 Standard 200 n a c Standard 100 n a E3 Standard 50 n a O G3 Standard 25 n a O13 Standard 10 n a OK3 Standard 5 n a 1 O M3 Standard 2 5 n a 03 Standard 1 Q A5 Unknown n a Undo cs Unknown n a Cut E5 Unknown n a cs Unknown n a Copy O s Unknown n a Paste Oks Unknown n a Delete Ms Unknown n a 05 Unknown n a Select All Ov Unknown n a Right to left Reading order oc Wissen Te j Show Unicode control characters QE Unknown n a Qa Ueci GE Insert Unicode contro character Or Unknown n a Open IME OK Unknown n a Reconversion Om Unknown n a Figure 6 15 Sample Plate Table Shortcut Menu of Edit Commands NOTE Edit commands Cut Copy Paste Delete and shortcut keys
22. Annotating Samples 00 82 Replicate GroupS 0 cceceeeees 84 Managing Sample Plate Definitions 88 Exporting a Plate Definition 88 Importing a Plate Definition 89 Managing Assay Parameter Settings 91 Modifying Assay Parameter Settings 91 Viewing User Modifiable Assay Parameter SOQHINGS ie s csctieee Aiea E 91 Assigning Biosensors to Samples 96 Biosensor Assignment in Single Analyte Experiments 0 ccc cece ec eee ees 96 Biosensor Assignment in Multiple Analyte Experiment e ccc cee ce ceeees 99 Biosensor Regeneration 111 Using Partial Biosensor Trays 112 Reviewing Experiments 114 Saving Experiments 0000 114 Running a Quantitation Experiment 116 Loading the Biosensor Tray and Sample PIG otras anc e ER 116 Starting an Experiment 117 Run Experiment Window Settings 119 Stopping an Experiment 122 Managing Runtime Binding Charts 122 Opening a Runtime Binding Chart 123 Viewing Reference Subtracted Data 123 Viewing Inverted Data 125 Magnifying the Runtime Binding Chart 125 Scaling a Runtime Binding Chart 126 Adding a Runtime Binding Chart Title 126 Selecting a Runtime Binding Chart Legend 126 Viewing Multiple Runtime Binding Charts 127 Exporting or Printing the Runtime Binding Chart arerin 127 Managing Experiment Method Files 128 Custom
23. B10 OOOOO000OO Figure 7 14 Replicate Groups Displayed in Sample Plate Map The Sample Plate Table will update with the Replicate Group names entered see Figure 7 15 Sample Plate Table Concentration units pg ml RA Molar concentration units mM Well Sample ID Replicate Group Type Conc pg ml MW kD Molar Conc nM Information a A4 Association 1 Sample 10 150 66 67 1X Kinetics Buffer B4 Association 2 Sample 5 150 33 33 1X Kinetics Buffer C4 Association 3 Sample 25 150 16 67 1X Kinetics Buffer D4 Association 4 Sample 1 25 150 8 333 1X Kinetics Buffer E4 Association 5 Sample 0 625 150 4 167 1X Kinetics Buffer F4 Association 6 Reference 1X Kinetics Buffer G4 Association 6 Reference 1X Kinetics Buffer H4 Association 6 Reference 1X Kinetics Buffer AS5 Association 1 Sample 10 150 66 67 1X Kinetics Buffer B5 Association 2 Sample 5 150 33 33 1X Kinetics Buffer cs Association 3 Sample 25 150 16 67 1X Kinetics Buffer D5 Association 4 Sample 1 25 150 8 333 1 Kinetics Buffer Q E5 Association 5 Sample 0 625 150 4 167 1X Kinetics Buffer F5 Association 6 Reference 1X Kinetics Buffer G5 Association 6 Reference 1X Kinetics Buffer H5 Association 6 Reference 1X Kinetics Buffer Figure 7 15 Replicate Groups in Sample Plate Table Assigning Replicate Groups in the Sample Plate Table To assign Replicate Groups in the Sample Plate Table 1 Double click the desired cell in the Re
24. FiPate iiid oo BSS eee poe 8 ea A meat 1 B 1E IC D E F E G DDD EES BBS HE Fe ss Ls es Legend _ Unassigned sensors 83 Missing sensors Remove Fill Fill Plate Figure 7 41 Changing Biosensor Location Method 2 Click Fill Plate to return the Sensor Tray Map to the default layout Using Heterogenous Trays If heterogenous biosensor trays will be used the column location of each biosensor type in the tray can be identified in the Sensor Assignment Tab Assignment of biosensors that will not be used in the assay enables the software to auto assign the biosensors that will be used in the assay by biosensor type There are two ways to change the biosensor type Select a column in the Sensor Tray Map right click and select a biosensor type from the drop down list Figure 7 42 left The associated wells in the Sensor Type col umn will automatically populate with the biosensor type selected Select a cell in the Sensor Type table column click the down arrow and select a bio sensor type from the drop down list Figure 7 42 right All other wells in the same column of the Sensor Tray Map as the selected cell will automatically populate with the biosensor type selected Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 255 Sensor Tray E i V Replace sensors in tray after use Well Sensor T Lot N
25. Octet QK Octet RED384 Significant digits 4 2 Q O Octet RED _ Octet QK384 v Web Server 8080 10 Octet RED96 Octet QKe Connect as 192 168 1 78 192 168 1 75 Figure 3 17 Selecting the Web Server in the Options Dialog Box 3 Click File gt Options to access the Options dialog box again A Web Server URL will now be listed under the Connect as box Figure 3 18 Note this URL as it will be needed to access the experiment remotely Octet System Data Acquisition User Guide Release 7 1 page 46 Chapter 3 Getting Started v Web Server Connect as Port 8080 192 168 1 78 Refresh s 10 192 168 1 75 http JRICHARDS 8080 ___ Web Server URL Figure 3 18 Web Server URL 4 Start the experiment in the Octet System Data Acquisition software as you normally would 5 Opena web browser on a remote computer or device that is on the same network as the Octet system NOTE The remote computer or device must be on the same network as the Octet system or connected to the network the instrument is on via VPN 6 Enter the Web Server URL in the browser window or click the Web Server URL link in the Options dialog box The experiment in progress will display Figure 3 19 Octet System Data Acquisition User Guide Release 7 1 Monitoring Experiments Remotely page 47 ForteBio DataAcquisition Mozilla Firefox File Edit View H
26. Status automation interface command 350 status bar described 38 figure 38 hiding 34 showing 34 Status Bar menu 34 Step Data List displaying step types figure 305 Step Name arrow 246 Step Name drop down list 246 step types activation 237 303 applying a threshold 238 304 assigning to columns in sample plate 242 307 association 236 302 changing 246 311 copying kinetics 384 305 kinetics 96 240 creating 237 303 custom 237 303 defining 236 kinetics 384 305 kinetics 96 240 deleting 240 305 dissociation 236 302 editing 240 305 loading 236 302 quenching 237 303 requirements for kinetics assays 236 302 step types sample for kinetic assays 236 steps adding to assays 245 310 copying between assays 243 308 replicate 244 309 Stop automation interface command 350 Stop menu 36 Stop Shaker menu 36 stopping experiment 36 experiment in progress 266 331 quantitation 384 199 quantitation 96 122 sample plate shaker 36 Subtract Reference Biosensor check box 268 332 Subtract reference sensors check box 124 201 268 333 symbols electrical hazard 13 fuse 13 heat hot 13 system preferences setting 40 system specifications Octet QK 23 Octet System Data Acquisition User Guide Release 7 1 page 35 Octet QKe 21 Octet RED96 16 18 25 T Tab menu 383 TCP IP socket 346 TCP IP socket connection connecting 348 technical support contacting 13 Temperature field a
27. To change projects during a user session 1 Click Security gt Change Projects A list of projects assigned to your user account will be shown with the active project highlighted Window Help Verify Document View Audit Trail Change Project none Change Password Receptor Ligand screen Server Administration Antigen Antibody screen Lock Application Cell Culture screen Logoff Figure 4 22 Changing Projects 2 Select the desired project from the list The selected project will now become the active project for the user session Octet System Data Acquisition User Guide Release 7 1 Compliance Features page 65 Changing the User Password To change the user password 1 Initiate a new user session with your existing password 2 When the software launches click Security gt Change Password The Change Password dialog box will display Current password New password Confirm new password Password reminder Figure 4 23 Change Password Dialog Box 3 Enter the Current password for your user account Click for a password reminder 4 Enter the New Password and Password reminder optional 5 Click OK to save changes and exit Locking the Application The Data Acquisition or Data Analysis software can be locked during a user session to pre vent another user from interrupting a session or experiment When the application is locked any experiments start
28. data points per second and monitors faster binding events better than a slower acquisition rate A lower acquisition rate allows the software enough time to perform more averages of the collected data Typically more averaging leads to reduced noise and thus better signal to noise ratios Therefore the frequency setting should be determined based on consider ation of the binding rate the amount of signal generated in your assay and some experi mentation with the settings The following Advanced Settings are available for the Octet384 system Table 6 11 Advanced Settings Octet RED384 Item Description Acquisition rate High sensitivity quantitation 2 0 Hz averaging by 50 The average of 50 data frames is reported as one data point Two data points are reported per second Standard quantitation 5 0 Hz averaging by 20 The average of 50 data frames is reported as one data point Five data points are reported per second e High concentration quantitation 10 0 Hz averaging by 5 The average of 5 data frames is reported as one data point Ten data points are reported per second Sensor off set Recommended sensor offset Quantitation 3 mm mm Default Sets the acquisition speed and sensor offset at the default settings The following Advanced Settings are available for the OctetQK384 system Table 6 12 Advanced Settings Octet QK384 Item Description Acquisition rate High sensitivity quantitation 0
29. startup temperature user option 42 Status automation interface command 350 status bar described 38 figure 38 hiding 34 showing 34 Status Bar menu 34 Step Data List displaying step types figure 305 Step Name arrow 246 Step Name drop down list 246 step types activation 237 303 applying a threshold 238 304 assigning to columns in sample plate 242 307 association 236 302 changing 246 311 copying kinetics 384 305 kinetics 96 240 creating 237 303 custom 237 303 defining 236 kinetics 384 305 kinetics 96 240 deleting 240 305 dissociation 236 302 editing 240 305 loading 236 302 quenching 237 303 requirements for kinetics assays 236 302 step types sample for kinetic assays 236 steps adding to assays 245 310 copying between assays 243 308 replicate 244 309 Stop automation interface command 350 Stop menu 36 Stop Shaker menu 36 stopping experiment 36 experiment in progress 266 331 quantitation 384 199 quantitation 96 122 sample plate shaker 36 Subtract Reference Biosensor check box 268 332 Subtract reference sensors check box 124 201 268 333 symbols electrical hazard 13 fuse 13 heat hot 13 system preferences setting 40 system specifications Octet QK 23 Octet System Data Acquisition User Guide Release 7 1 page 35 Octet QKe 21 Octet RED96 16 18 25 T Tab menu 383 TCP IP socket 346 TCP IP socket connection connecting 348 technical supp
30. 09 1X Kinetics Buffer Buffer A11 1 Kinetics Buffer Buffer C11 1X Kinetics Buffer Buffer E11 1X Kinetics Buffer Buffer G11 1X Kinetics Buffer Buffer 111 1X Kinetics Buffer Buffer K11 1X Kinetics Buffer Buffer M11 1X Kinetics Buffer Buffer O11 1XKinetics Buffer Buffer A13 human IgG Group 1 Sample 40 C13 human IgG Group 2 Sample 20 E13 human IgG Group 3 Sample 10 G13 human IgG Group 4 Sample 5 1113 humanlgG Group 5 Sample 25 K133 humanlgG Group amp Sample 1 25 M13 human IgG Group Sample 0 625 013 1XKinetics Buffer Reference A15 human lgG Group 1 Sample 40 C15 humanlgG Group 2 Sample 20 E15 human lgG Group 3 Sample 10 G15 human IgG Group 4 Sample 5 ON5 humanlgG Group 5 Sample 25 KI5 human IgG Group 6 Sample 1 25 M15 human IgG Group Sample 0 625 Figure 8 18 Replicate Groups in Sample Plate Table Assigning Replicate Groups in the Sample Plate Table To assign Replicate Groups in the Sample Plate Table 1 Double click the desired cell in the Replicate Group table column 2 Enter a group name see Figure 8 19 Octet System Data Acquisition User Guide Release 7 1 page 294 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Sample Plate Concentration units pg ml v P Reagent Plate Molar concentration units mM Well Sample ID Replicate Group Type Conc ug ml MW kD Molar OM Proteina Load 12 5 O0 Proteina Load 12 5 AQ 1X Kin
31. 290 Replicate Groups assigning in the Sample Plate Table quantitation 384 162 quantitation 96 87 defined 226 quantitation 384 159 quantitation 96 84 displayed in Sample Plate Map quantitation 384 figure 161 quantitation 96 figure 86 displayed in Sample Plate Table quantitation 384 figure 161 quantitation 96 figure 86 Replicate Groups displayed in Sample Plate Map figure 229 Replicate Groups in Sample Plate Table figure 229 replicate steps All steps option 244 309 Append as new assay option 244 309 Append to current assay option 244 309 Offset steps option 244 309 options table 244 309 Sample steps only option 244 309 Sample steps will be adjusted by vertically by one row option 244 309 Sample steps will be adjusted by X column option 244 309 Replicate Steps dialog box figure 243 requirements for reserved wells 72 reserved column changing location quantitation 384 146 quantitation 96 72 Reserved Well requirements 72 146 reserved well requirements 72 Detection quantitation 384 146 quantitation 96 72 Octet System Data Acquisition User Guide Release 7 1 page 28 Neutralization quantitation 384 146 quantitation 96 72 Regeneration quantitation 384 146 quantitation 96 72 reserved wells 72 reserved type of well 71 145 Reset automation interface command 349 Reset menu 36 resetting Octet instrument 36 Restart Server desktop icon figure 399
32. 350 status bar described 38 figure 38 hiding 34 showing 34 Status Bar menu 34 Step Data List displaying step types figure 305 Step Name arrow 246 Step Name drop down list 246 step types activation 237 303 applying a threshold 238 304 assigning to columns in sample plate 242 307 association 236 302 changing 246 311 copying kinetics 384 305 kinetics 96 240 creating 237 303 custom 237 303 defining 236 kinetics 384 305 kinetics 96 240 deleting 240 305 dissociation 236 302 editing 240 305 loading 236 302 quenching 237 303 requirements for kinetics assays 236 302 step types sample for kinetic assays 236 steps adding to assays 245 310 copying between assays 243 308 replicate 244 309 Stop automation interface command 350 Stop menu 36 Stop Shaker menu 36 stopping experiment 36 experiment in progress 266 331 quantitation 384 199 quantitation 96 122 sample plate shaker 36 Subtract Reference Biosensor check box 268 332 Subtract reference sensors check box 124 201 268 333 symbols electrical hazard 13 fuse 13 heat hot 13 system preferences setting 40 system specifications Octet QK 23 Octet System Data Acquisition User Guide Release 7 1 page 35 Octet QKe 21 Octet RED96 16 18 25 T Tab menu 383 TCP IP socket 346 TCP IP socket connection connecting 348 technical support contacting 13 Temperature field accessing 12 temperature range Octet Q
33. EB AQ 1X Kinetics Buffer Buffer Undo C9 1X Kinetics Buffer Buffer Cut E9 1X Kinetics Buffer Buffer G9 1X Kinetics Buffer Buffer Copy 19 1XKinetics Buffer Buffer Paste K9 1X Kinetics Buffer Buffer Delete M9 1X Kinetics Buffer Buffer 09 1X Kinetics Buffer Buffer Select All A11 1X Kinetics Buffer Buffer Right to left Reading order C Me Ancus Baner Elia Show Unicode control characters E11 1X Kinetics Buffer Buffer G11 1x Kinetics Buffer Buffer Insert Unicode control character 111 1X Kinetics Buffer Buffer Open IME K11 1X Kinetics Buffer Buffer Reconvercidn M11 1X Kinetics Buffer Buffer Figure 8 21 Sample Plate Table Editing Sample Data Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sample Plate Table To view edit com mands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the right click menu used to designate sample types MANAGING SAMPLE PLATE DEFINITIONS NOTE After you define a sample plate you can export and save the plate defi nition for future use Octet System Data Acquisition User Guide Release 7 1 Managing Sample Plate Definitions page 297 Exporting a Plate Definition To export
34. Execute C Program Files ForteBio 7 CFR FBServer7 FBServer exe 42 s gt i fortebio com ForteBio Inc lt Back Next gt Cancel Figure B 14 Installation Progress Octet System Data Acquisition User Guide Release 7 1 page 374 Chapter B 21 CFR Part 11 Software Administrator Options The installation wizard displays the Completing the ForteBio GxP Server 7 0 Setup Wiz ard dialog box Figure B 15 73 ForteBio GxP Server 7 0 Setup ojia Completing the ForteBio GxP Server 7 0 Setup Wizard ForteBio GxP Server 7 0 has been installed on your computer Click Finish to dose this wizard Figure B 15 Completing the ForteBio GxP Server Software 7 0 Setup 7 Click Finish to complete the installation ADMINISTRATOR ACCOUNT SETUP To set up the administrator account 1 Launch the Data Acquisition or Data Analysis software by double clicking on the desk top icon Data Data Analysis Acquisition 7 0 CFR11 7 0 CFR11 Figure B 16 Data Acquisition and Data Analysis Desktop Icons The Login dialog box will display Octet System Data Acquisition User Guide Release 7 1 Administrator Account Setup page 375 Figure B 17 Login Dialog Box 2 Select a Server location by clicking Browse The Authentication Server dialog box will display la Authentication Server Connection to server Server address localhost
35. Octet System Data Acquisition User Guide Release 7 1 page 180 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Sensor Tray Sensor Tray Trayi of2 a v Replace sensors in tray after use Well Sensor Type auto assign Anti Human IgG Fc Anti Mouse IgG Fv Protein A Protein G Protein L SA Streptavidin Residual Protein A Anti Penta HIS Custom Reference Legend Unassigned sensors BRI Missing sensors Positive Control Figure 6 42 Populating the Sensor Tray Map with Second Biosensor Type 5 Repeat this column selection and assignment process for all other biosensor types to be used in the experiment The software will automatically update the number of bio sensor trays needed and biosensor assignments in all trays according to the column assignments made in Tray 1 In the example shown in Figure 6 43 Protein A and Protein G biosensor types are used for a multiple analyte experiment using two replicates Three heterogeneous biosensor trays will be needed for the experiment Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 181 Pite Definition Sensor Assignment Review Experiment Q Run Experiment vo In this step sensors are assigned to samples If you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be
36. Plate Definition Sensor Assignment Review Experiment Q Run Experiment Assay Settings Assay Basic Quantitation Standard Assay Single analyte Time s Shake speed Quantitation 120 200 Sample Plate Sample Plate 96 wells ADOOOOOOOOOOO BOOOOOOOO8O0O0O O OOOO 0000 ODOOOOOOOOO D EOOOOOO OQOO0O F G 010101 DIDI DIO 10101010 0101011101 101010 H OO OO O OOOC l O Standard Control IQ Unassigned QO Unknown e Reference Reserved In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and right click to enter modify well data Sample Plate Table Concentration units ugm x Export l Import Well Sample ID Replicate Group Type Conc pg ml Dilution Factor h G4 Unknown a 2 a ja H4 Unknown n a 2 ce AS Unknown n a 2 B5 Unknown n a 2 acs Unknown n a 2 5 Unknown n a 2 e5 Unknown nja 3 O Fs Unknown n a 2 Okei Unknown n a 2 O HS Unknown n a 2 OAs Unknown n a 2 B Unknown n a 2 oc Unknown n a 2 De Unknown n a 2 OE Unknown n a 2 Fe Unknown nja 2 ce Unknown n a 2 e 6 Unknown n a 2 LLLI a n a E va va J Oam m a r a z Figure 5 13 Designate Controls or Reference Wells NOTE Shift clicking in the Sample Plate Map mimics the head of the in
37. eter 169 Quantitation Time parameter 169 Single Analyte parameter 169 quantitation 96 Multiple Analyte and Replicates per Sensor Type parameter 92 Quantitation Shake Speed param eter 92 Quantitation Time parameter 92 Single Analyte parameter 92 Quantitation Shake Speed quantitation 384 209 quantitation 96 132 Quantitation Time quantitation 384 209 quantitation 96 132 Single Analyte quantitation 384 208 quantitation 96 131 Octet System Data Acquisition User Guide Release 7 1 page 7 basic quantitation assay parameters listed table quantitation 384 208 quantitation 96 131 Basic Quantitation with Regeneration shortcut menu option 166 Basic Quantitation with Regeneration assay parameter 133 210 Basic Quantitation with Regeneration assay parameters Neutralization Time and Shake speed 134 211 Post condition sensors 134 211 Pre condition sensors 134 211 quantitation 384 170 Multiple Analyte parameter 170 Neutralization Time and Shake Speed parameter 170 Post condition sensors parameter 171 Precondition sensors parameter 171 Regeneration Cycles parameter 171 Regeneration Time and Shake Speed parameter 170 Single Analyte parameter 170 quantitation 96 93 Multiple Analyte parameter 93 Neutralization Time and Shake Speed parameter 93 Post condition sensors parameter 94 Precondition sensors parameter 94 Quantitation Time and Shake speed 93 Regeneration
38. l this step will prevent data analysis if these sensors are to be used in Parallel Reference Double Reference or Average Reference subtraction methods Assay 1 Step 2 Duration s 600 Budbro E C Ce Figure 7 58 Extend Current Step Dialog Box Terminating a Step to Begin the Next Step To terminate a step and begin the next step in the assay 1 Inthe chart window click the Go to Next Step button 2 Inthe Data Acquisition dialog box click OK Magnifying the Runtime Binding Chart To magnify the chart press and hold the mouse button while you draw a box around the chart area to magnify To undo the magnification right click the chart and select Undo Zoom Scaling a Runtime Binding Chart To scale the Runtime Binding Chart 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box select Fullscale or Autoscale Adding a Runtime Binding Chart Title To add a Runtime Binding Chart title 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box enter a graph title or subtitle Selecting a Runtime Binding Chart Legend To select a Runtime Binding Chart legend 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box see Figure 7 59 select one of the fol lowing legends Sensor Location Sample ID Sensor Information e Concentration Dilution Octet System Data Acquisition User Guide Re
39. page 84 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Replicate Groups When samples are assigned to a Replicate Group the Octet System Data Analysis software will automatically calculate statistics for all samples in that group The average binding rate average concentration and corresponding standard deviation as well CV are presented in the Results table for each group see Figure 5 16 Protein Group 1 0 66 0 01 1 5 604 5 17 8 29 Protein Group 1 0 66 0 01 1 5 604 5 17 8 29 Protein Group 1 0 66 0 01 1 5 604 5 17 8 29 Protein Group 1 0 66 0 01 15 604 5 17 8 29 Anti Hu Group 2 0 6589 0 0052 0 8 602 5 915 15 Anti Hu Group 2 0 6589 0 0052 0 8 602 5 9 15 15 AntiHu Group 2 0 6589 0 0052 08 602 5 9 15 1 5 AntiHu Group 2 0 6589 0 0052 0 8 602 5 9 15 1 5 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 24 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 2 4 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 24 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 24 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2 2 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2 2 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2 2 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2 2 Figure 5 16 Replicate Group Result Table Statistics NOTE Replicate Group information can also be entered in the Results table in the Octet System Data Analysis software Assigning Replicate Groups in the Sample Plate Map To assign Replicate Groups in the
40. 0 H H H 0 200 400 600 800 1000 1200 1400 1600 1800 2000 Time sec Figure 1 7 Kinetic Experiment Running Chart Align at Specified Time The Align at Time dialog box displays Figure 1 8 Align at Time x Figure 1 8 Align at Time Dialog Box b Specify the time point you want to align to and click OK The running chart aligns to the time point you specify 6 Made changes to only permit samples in the sample plate 7 Added printing for the Assay Definition tab via File gt Print amp File gt Print Preview Octet System Data Acquisition User Guide Release 7 1 page 12 Chapter 1 welcome WHAT S NEW IN THE OCTET SYSTEM DATA ACQUISITION SOFTWARE RELEASE 7 0 Table 1 2 describes new features available in the Octet System Data Acquisition software Release 7 0 Table 1 2 Octet System Data Acquisition Software New Features for Release 7 0 New Feature Description User defined default start up temperature Allows you to define the default start up temperature for all experiments To access the Temperature field click File gt Options NOTE To change the default setting you must restart the Octet System Data Acqui sition software after entering the new value Post condition biosensors Sample plate temperature recorded in log file Post condition biosensors after Basic Quantitation with Regeneration or Advanced Quantitation experiments allowing re racked tips to be stored in a r
41. 169 Quantitation Shake Speed param eter 169 Quantitation Time parameter 169 Single Analyte parameter 169 quantitation 96 Multiple Analyte and Replicates per Sensor Type parameter 92 Quantitation Shake Speed param eter 92 Quantitation Time parameter 92 Single Analyte parameter 92 Quantitation Shake Speed quantitation 384 209 quantitation 96 132 Quantitation Time quantitation 384 209 quantitation 96 132 Single Analyte quantitation 384 208 quantitation 96 131 Octet System Data Acquisition User Guide Release 7 1 page 7 basic quantitation assay parameters listed table quantitation 384 208 quantitation 96 131 Basic Quantitation with Regeneration shortcut menu option 166 Basic Quantitation with Regeneration assay parameter 133 210 Basic Quantitation with Regeneration assay parameters Neutralization Time and Shake speed 134 211 Post condition sensors 134 211 Pre condition sensors 134 211 quantitation 384 170 Multiple Analyte parameter 170 Neutralization Time and Shake Speed parameter 170 Post condition sensors parameter 171 Precondition sensors parameter 171 Regeneration Cycles parameter 171 Regeneration Time and Shake Speed parameter 170 Single Analyte parameter 170 quantitation 96 93 Multiple Analyte parameter 93 Neutralization Time and Shake Speed parameter 93 Post condition sensors parameter 94 Precondition sensors parameter 94 Quantitation T
42. 266 Octet RED listed table 266 Octet RED384 listed table 330 Octet RED96 listed table 266 Sensor offset Octet QKe 121 Align to Step menu 270 aligning binding data to the beginning of a user selected step 270 334 All steps option 244 309 analysis options viewing 40 analyzing quantitative experiment 68 140 216 276 annotating individual wells in the sample plate table kinetics 384 289 kinetics 96 226 quantitation 384 157 quantitation 96 82 one or more wells 82 225 288 annotations entering 225 288 quantitation 384 157 quantitation 96 82 Append as new assay option 244 309 Append to current assay option 244 309 Append to current assay option 243 Application Locked dialog box figure 66 applications closing 34 Arrange Icons menu 37 arranging window icons 37 Assay Definition tab 237 Assay Definition window 237 Assay number 267 assay parameter settings modifying quantitation 384 167 quantitation 96 91 assay parameter values editing quantitation 384 208 quantitation 96 131 assay parameters Advanced Quantitation quantitation 96 94 Basic Quantitation for 384 model 169 for 96 model 92 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Assay Parameters box 91 assay parameters Basic Quantitation Multiple Analyte quantitation 384 209 quantitation 96 132 Quantitation Shake Speed Octet System Data Acquisition User Guide Release 7 1 page 4 quantitation
43. 96 wells Reagent Plate 384 wells Modit y a ae a E 2 456 4 EXOT SOME EEE n I I oq A f BOOQOOOOQONOO 5 COMOOOOOOOOOD DOOQOQQQQQQQQQ k EOQQOOOOOOOOOD FOOQQQQQQQQQQ l GOOOQOQOOQQQQQQQQ i HOOOQOOOQOQOOQOQOQQQQ 96 well Format Reagent Plate 384 well Format Reagent Plate Figure 6 30 Example Reagent Plate Layouts for an Advanced Quantitation Experiment 16 Channel Read Head To remove well designations select the column s and click Unassigned or right click and choose Clear Data Saving a Reagent Plate Definition Exporting and saving a reagent plate definition is done in the same manner as you would for sample plates For details Managing Sample Plate Definitions on page 163 MANAGING ASSAY PARAMETER SETTINGS Modifying Assay Parameter Settings You can modify the assay parameter settings during sample plate definition However the changes are only applied to the current experiment To save modified parameter settings you must define a new assay For details on creating a new assay see Custom Quantitation Assays on page 206 Viewing User Modifiable Assay Parameter Settings To view the user modifiable settings for an assay click Modify in the Assay Settings box The Assay Parameters box will display Figure 6 31 The settings available are experiment dependent Octet System Data Acquisition User Guide Release 7 1
44. Advanced Settings Octet QK Octet RED and Octet RED96 Item Description Acquisition rate e High sensitivity kinetics 0 3 Hz averaging by 40 The Octet QKS average of 40 data frames is reported as one data point One data point is reported every 3 3 seconds Standard kinetics 0 6 Hz averaging by 5 The aver age of five data frames is reported as one data point One data point is reported every 1 6 seconds Acquisition rate e High sensitivity kinetics 2 Hz averaging by 50 The Octet RED96 average of 50 data frames is reported as one data point Two data points are reported per second Standard kinetics 5 Hz averaging by 20 The average of 20 data frames is reported as one data point Sensor offset mm Recommended sensor offset Large molecule kinetics 4 Octet QK only mm Default Sets acquisition rate and sensor offset to the defaults Stopping an Experiment To stop an experiment in progress click xX or click Experiment gt Stop The experiment is aborted The data for the active biosensor is lost the biosensor is ejected into the waste tray and the event is recorded in the experimental log NOTE After the experiment is run the software automatically saves the exper iment method fmf Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 267 MANAGING THE RUNTIME BINDING CHART If the Open runtime charts automatically check box i
45. Basic Quantitation with Regeneration Enzyme 120 1000 I High Snoey assay with regeneration 2nd Butter 120 z 1000 E Protein L Standard range IE Standard Assay Detection 120 a 1000 E My Basic Quant with Regen Assay amp Advanced Quantitation Time 3 Shake speec E Immunogenctty Enzyme Linked Regeneration 5 E 1000 E Residual Protein A j l E Standard Assay Neutralization 5 t 1000 E Three Step Assay Pre condition sensors Post condition sensors Bf My Advanced Quant Assay m g Regeneration cycles Single analyte Multiple analyte Replicates per sensor type 1 Buffer 120 t 1000 t V Reuse Buffer 4 EHLE Regeneration Blue indicates a ForteBio built in assay and cannot be modified or deleted bine anew Figure 5 65 Assay Parameters Advanced Quantitation L Table 5 17 Advanced Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte For multi analyte experiments using multiple biosensor types per and Replicates per sample well and the number of replicate assays in each well per sensor type biosensor type SampleTime s and The duration of data acquisition in seconds while the biosensor is Shake speed rpm incubated in sample and the sample platform orbital shaking s
46. Custom AHC Anti hlgG Fe Capture 1 AS 1 Loading I Loading ASA Streptavidin 1 Ag 1 Baseline k Baseline 2AHC Anti hlgG Fc Capture 1 A13 1 Association a Association Ann Ici i ala 1 Ag 1 Dissociation kK Dissociation SSA Super Streptavidin 1 Al 2 Regeneration 3 Custom Custom 1 A5 2 Neutralization 3 Custom 2AHC Beta 1 0 29 00 Figure 8 38 Selecting an Assay Sensor Type NOTE The Sensor Type for the assay must be selected or changed from the Assay Steps List Changing the Sensor Type from the Sensor Assignment Tab will not update the assay Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 311 Editing an Assay To edit the step type or the biosensor type In the Assay Steps List To change the step type click the Step Name arrow and select a step name from the drop down list Figure 8 39 top To change the biosensor type click the Sensor Type arrow for any step in the assay and select a sensor type from the drop down list Figure 8 39 bottom The biosensor type will automatically update for every assay step gt NOTE The Step Name drop down list includes only the step types defined in the Step Data List Assay Steps List NewAssay Move Up Move Down Remove Replicate Pe ime Assay Sample Plate Step Name Step Type Sensor Type Assay Time i Al 1 equilibration 3 Custom AHC Anti hlgG Fe Capture 1 AS 1 Leq
47. Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Octet System Data Acquisition User Guide Release 7 1 page 156 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Designating Controls or Reference Wells Controls are samples of known concentration that are not used to generate a standard curve A reference well contains sample matrix only and is used to subtract non specific binding of the sample matrix to the biosensor During data analysis data from reference wells can be subtracted from standards and unknowns to correct for background signal To designate controls select the control wells and click Control below the Sample Plate Map or right click and select Control Positive and Negative Control types can also be assigned using this menu To designate reference wells select the reference wells and click the Reference but ton below the Sample Plate Map or right click the selection and choose Reference The wells are marked in the Sample Plate Map and the Sample Plate Table is updated see Figure 6 15
48. Data Acquisition icon 8 Data Analysis 21 CFR Part 11 software overview 52 Data Analysis icon 8 data column displaying acquisition 267 331 quantitation 384 199 quantitation 96 122 data display significant digits 42 data file location and name settings quantitation 384 listed 196 quantitation 96 listed 119 Data File repositories setting Data File repositories 347 data files kinetics data repository 41 quantitation data repository 41 Use extended sample types 42 Use old 5 0 file format for FRD files 42 data preferences setting 40 DataAcquisition CFR 7_0_0_x exe 366 default biosensor columns 252 316 default locations for reserved wells in a 96 well sample plate map figure 72 default server settings localhost 54 Port 2002 54 default temperature value saving 44 default temperature defining new 44 default Tray Format 101 default user group privileges 385 default user groups 388 default windows Octet System Data Acquisition software 31 Default advanced settings 121 defining custom assays quantitation 384 206 quantitation 96 129 kinetic assays 236 new assay 35 new assay figure 130 207 new default temperature 44 reagent plates quantitation 384 166 sample plates kinetics 384 278 kinetics 96 218 quantitation 384 142 quantitation 96 70 samples by entering sample information figure 284 step types 237 303 kinetics 384 305 kinetics 96 240 defining step types 236 Delayed experiment start
49. Figure B 54 ForteBio GxP Server Desktop Icon The ForteBio GxP Server Configuration window will display E ForteBio GxP Server Configuration 7 0 0 Connection to clients l Localhost Port 20002 E aAPPM Test v Support UDP ping for discovery Users Groups Projects Constants Events Login Name Full Name Group Privileges Password Age Info Administrator Administrator Administrator admin review change plate 4 days 00 47 57 Default administrator user PSmith Paul Smith Lab User run 2 days 02 45 25 JBlack John Black Developer change plate run 1 day 04 34 45 RBrown Richard Brown Supervisor review 2 days 01 43 06 Figure B 55 GxP Server Configuration Window Use of the User Groups Projects Constants and Events tabs are described in Accessing Administrator Options on page 381 Server Testing The GxP Server module can be tested to ensure it is accessible and functioning properly 1 In the Connections to Clients box make changes to the server settings if needed Connection to clients E Localhost Port 20002 Aep Aest Support UDP ping for discovery lt Figure B 56 Connections to Clients Box 2 Click Apply amp Test If the GxP Server module is found and functioning properly the fol lowing message will display Octet System Data Acquisition User Guide Release 7 1 page 398 Chapter B 21 CFR Part 11 Software Administr
50. G Clear Data SE 4 By value 200 H Copy to Clipboard Dilution series FA aa v Extended Sample Type Replicate Group m SENTRE A Bape ee Unknown Reference EPN Series operator formation serie s1 Dilution orientation 833 O Right 888 O Left Down g Up Goc acns Figure 5 7 Sample Plate Map Assigning a Standard Concentration 2 Select the By value option and enter the starting concentration value 3 Click OK The Sample Plate Table will display the standard concentrations entered Editing an Individual Standard Concentration To enter or edit an individual standard concentration in the Conc column of the Sample Plate Table double click the value and enter a new value see Figure 5 8 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 77 Sample Plate Table Concentration units pg ml k A Export Import Well Sample ID Replicate Group Type Conc g ml Dilution Factor Information OA OBI oc Oot GEI OF Oai OHI Oa2 B2 c D2 OE2 Ore IF Ore Oa OB3 Standard 1 n a Standard nia Standard 100 Undo Standard 50 Standard 25 ae Standard 10 Copy Standard 5 Paste Standard 2 5 Delete Standard 1 Standard 200 Select All Standard 100 Standard 50 Standard 25 Right to left Reading order Show Unicode control characters Standard 10 Insert Unic
51. O O O O O t Shake i BOO OOOOOOOOO pecans tea im beset COOOOQQOOOCOL D OO O OO O qQ Add Step Definition E OOOO OQOOOG FOO O OOO U e GOOO Q OOOd issociatk Loading ae time HOOO OOO R custom i Assayed samples O Unassigni Time s Shake speed Figure 7 24 Creating an Assay Step Type 3 Apply a threshold to the step a In the Step Data List click the Threshold check box The Threshold Parameters dialog box displays see Figure 7 25 b Set the threshold parameters refer to Table 7 4 for the parameter definitions Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 239 D Pite Definition Assay Definition Sensor Assignment Review Experiment Run Experiment f In this step the assay steps will be assembled from the Step Data List Select a group of sensors and append the currently selected step into the current assay with a double click or right click for more options Time in s Shake speed in rpm Sample Plate 96 wells Step Data List WM iij2 3 4 6 6 7 8 9 10 11 12 l Copy l Remove Threshold Params A O O O O O O Name Time Shake speed Type Threshold BOOOOOOQO0O000 Baseine 00 120 b Besse T cC 1 1 101010101019 gt Association 300 1000 Association DOOOCOOOO ate E OOOOO F O Assa
52. Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 81 Designating Controls or Reference Wells Controls are samples of known concentration that are not used to generate a standard curve A reference well contains sample matrix only and is used to subtract non specific binding of the sample matrix to the biosensor During data analysis data from reference wells can be subtracted from standards and unknowns to correct for background signal To designate controls select the control wells and click Control below the Sample Plate Map or right click and select Control Positive and Negative Control types can also be assigned using this menu To designate reference wells select the reference wells and click the Reference but ton below the Sample Plate Map or right click the selection and choose Reference The wells are marked in the Sample Plate Map and the Sample Plate Table is updated see Figure 5 12
53. Release 7 1 page 10 connecting Automation Client example application 348 Octet instrument to computer 30 to a TCP IP socket connection locally using localhost 348 Connections to Clients box figure 397 constants changing 394 creating new 393 deleting 394 viewing 394 Constants tab figure 392 constants administrator listed table 393 contacting ForteBio technical support 13 Control well type 218 kinetics 384 280 quantitation 384 145 quantitation 96 71 control type of well 71 145 controls 156 defined 81 156 designating 156 quantitation 384 156 quantitation 96 81 conventions used in this guide 13 copying assay steps 243 308 Runtime Binding Chart kinetics 384 338 kinetics 96 273 quantitation 384 205 quantitation 96 128 step type kinetics 384 305 kinetics 96 240 creating csv file for import 90 assay step type figure kinetics 384 303 kinetics 96 238 different types of assay steps 237 303 new constants 393 new user account 384 new user group 389 step types 237 303 Current Binding Charts box 331 custom assays defining quantitation 384 206 quantitation 96 129 selecting quantitation 384 214 quantitation 96 137 custom biosensors 48 custom steps 237 303 D Data Acquisition 21 CFR Part 11 software overview 52 Data Acquisition desktop icon 30 Data Acquisition Software New Features 12 Data Acquisition User Guide menu 38 Octet System Data Acquisition User Guide Release 7
54. Restart Server window figure 399 restarting the GxP Server module 398 Resume automation interface command 350 resuming user session 66 Reuse Buffer parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Review Experiment window 114 191 258 322 Review Experiment window figure 114 191 259 323 reviewing experiments kinetics 96 258 Run automation interface command 349 Run Experiment tab 117 Run Experiment window Octet RED RED96 and QKe figure 117 194 Run Experiment window settings 2nd Plate Name Barcode 119 196 Assay Type 119 196 Auto Increment File ID Start 120 197 Experiment Run Name 119 196 Plate Name Barcode 119 196 Quantitation Data Repository 119 196 Run Experiment window Octet RED and Octet RED96 figure 262 326 run name 264 328 run settings quantitation 384 Delayed Experiment Start 197 Start After setting 197 quantitation 96 Delayed Experiment Start 120 Start After setting 120 run settings listed quantitation 384 197 quantitation 96 120 running experiment settings 119 196 Runtime Binding Chart adding title 271 336 quantitation 384 203 quantitation 96 126 copying kinetics 384 338 kinetics 96 273 exporting to a graphic file 273 337 exporting to a graphic or data file 127 204 272 337 magnifying 271 335 quantitation 384 202 quantitation 96 125 managing Octet System Data Acquisition User Guide Release 7 1 page 29 kinetics
55. Review Experiment Q Run Experiment In this step sensors are assigned to samples Sensor Tray v Replace sensors in tray after use y 5 6 9 10 11 12 Well Sensor Type Lot Number Information A Al_ Ant HumanigGFc Td B1 Anti Human IgG Fc B C1 Anti Human IgG Fc D1 Anti Human IgG Fc Cc E1 Anti Human IgG Fc D S C U E m F1 Anti Human IgG Fc G1 Anti Human IgG Fc ENOTO H1 Anti Human IgG Fc A2 Anti Human IgG Fc F SoG Bn B2 Anti Human IgG Fc as C2 Anti Human IgG Fc G SED fe D2 Anti Human IgG Fc HITE LIL IMSL IL E2 Anti Human IgG Fc F2 Anti Human IgG Fc Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate rammoad X i icc G2 Anti Human IgG Fc Legend Unassigned sensors Missing sensors ii i A a H2 Anti Human IgG Fc Remove Fi FalPhate A3 Anti Human IgG Fc B3 Anti Human IgG Fc Sample Plate c3 Anti Human IgG Fc a of 10 1 12 D3 Anti Human IgG Fc O E3 Anti Human IgG Fc F3 Anti Human IgG Fc O G3 Anti Human IgG Fc H3 Anti Human IgG Fc O A4 Anti Human IgG Fc B4 Anti Human IgG Fc O C4 Anti Human IgG Fc O Anti Human IgG Fc Anti Human IgG Fc O Anti Human IgG Fc Anti Human IgG Fc Legend Unassigned samples D4 E4 F4 G4 Anti Human IgG Fc O O O O H4 Anti Human IgG Fc AS BS Anti Human IgG Fc
56. Save the sample plate definition optional 296 Defining Step Types Table 8 3 lists the example step types to define a kinetic assay Use these examples as a starting point to create your own step types Table 8 3 Sample Step Types for Kinetic Assays Step Type Step Description Association Calculates the kops Select this step type when binding the second pro tein of interest analyte to the biosensor This step should be performed at 1 000 rpm Dissociation Calculates the kg Select this step type when monitoring the dissociation of the protein complex This step should be performed at 1 000 rpm Baseline Can be used to align the data Select this step type when establishing the biosensor baseline in the presence of buffer This step can be performed with no flow 0 rpm However if the baseline step directly precedes an association step perform the baseline step at 1 000 rpm IMPORTANT An assay must include a baseline step fol lowed by a set of association dissociation steps to be ana lyzed The Octet System Data Analysis software recognizes the baseline association dissociation step series during processing Data cannot be processed if this sequence is not included in the assay setup Loading Not used in data analysis Select this step type when binding the first protein of interest ligand to the biosensor NOTE This step may be performed offline outside the Octet instrument Octet System Da
57. Standard range V Pre condition sensors Post condition sensors Standard Assay Regeneration cycles 3 Ea vanced Quantitation E Immunogencity Enzyme Linked Residual Protein A Standard Assay Three Step Assay Description Enter a short description of the assay here Shake speed a ma Quantitation 120 400 os ewe por pr g m re eed re oun oe po ee w a owe fons om pn Blue indicates a ForteBio built in assay and cannot be modified or deleted oie remove L d Figure 6 69 Assay Parameters Basic Quantitation with Regeneration Table 6 17 Assay Parameters Basic Quantitation with Regeneration Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte For multi analyte experiments using multiple biosensor types per and Replicates per sample well and the number of replicate assays in each well per sensor type biosensor type Quantitation The duration of data acquisition in seconds while the biosensor is Time s and Shake incubated in sample and the sample platform orbital shaking speed rpm speed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incuba
58. Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate Sensor Tray Sensor v Replace sensors in tray after use of 2 Tray Drop 3 0 11 2 EE Type Lot Number Information Down I an IgG Fc List B1 Anti Human IgG Fc C1 Anti Human IgG Fc D1 Anti Human IgG Fc E1 Anti Human IgG Fc F1 Anti Human IgG Fc G1 Anti Human IgG Fc H1 Anti Human IgG Fc A2 Anti Human IgG Fc B2 Anti Human IgG Fc C2 Anti Human IgG Fc D2 Anti Human IgG Fc E2 Anti Human IgG Fc F2 Anti Human IgG Fc G2 Anti Human IgG Fc H2 Anti Human IgG Fc Remove Fill Fill Plate A3 Anti Human IgG Fc B3 Anti Human IgG Fc Legend _ Unassigned sensors R3 Missing sensors Pite Definition Sensor Assignment Review Experiment Run Experiment f In this step sensors are assigned to samples Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate Sensor Tray ripe may2 7 Replace sensors in tray after use of 2 Pai a ES Well Sensor Type Lot Number Information B1 _ Anti Human IgG Fc BL B1 Anti Human IgG Fc C1 Anti Human IgG Fc Di ail D1 Anti Human IgG Fc EL E1 Anti Human IgG Fc I F1 Anti Human IgG Fc FO so G1 Anti Human IgG Fc HL H1 Anti Hu
59. The Set Well Data dialog box displays see Figure 6 13 Octet System Data Acquisition User Guide Release 7 1 page 154 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Sample Plate Sample Plate 384 wells y 123456 7 8 9101112131415161718192021222324 AMOOOOQOO CLS 2244454454555 50900 BIOOOCOOOCO Standard O clOOOCOO O DIO00000 Unknown re EIOOOOOOC Control 0 s Negative Control 8 HIOOOOOOC Positive Control oO P aoa Reference O 4 Set Well Data Q la hl M CSV ERE Set Well Data Copy to Clipbo P V Extended Samy Well Information Dilution Factor Unknown only Sample ID o By value 2 Dilution series Replicate Group oO SAO vals 1 erie X Well Information EI im a erie 2 Dilution orientation 2338 Right 8882 Left g Down g Up A d Figure 6 13 Sample Plate Map Setting a Dilution Factor or a Serial Dilution To assign a dilution factor to selected wells 1 Inthe Set Well Data dialog box see Figure 6 13 select the By Value option 2 Enter the dilution factor value and click OK To assign a serial dilution to selected wells 1 Inthe Set Well Data dialog box see Figure 6 13 select the Dilution series option 2 Enter the starting dilution select a series operator and enter a series operand 3 Select the appropriate dilution orientation see Figure 6 14 Highest Concentration Lowest Concentration
60. The reagent plate format 96 or 384 well and the read head configu ration 8 or 16 channels determine the reagent plate layout For more details see Read Head Configuration and Plate Layout on page 143 To define a reagent plate 1 Select the Reagent Plate radio button above the plate map to display the Reagent Plate Map Figure 6 29 2 Click Modify to display the Modify Plates dialog box Reagent Plate 7 Sample Plate 384 wells Reagent Plate 384 wells Modify Plates Wi234 5678 5 Sample Plate Reagent Plate 96 Well 96 well 384 well 384 well Standard Control IIO Unassigned O Unknown I Reference O Reserved Figure 6 29 Modifying the Reagent Plate 3 Select a reagent plate format 96 Well or 384 Well and click OK 4 Inthe Reagent Plate Map right click a column to use and make a selection on the shortcut menu that appears e Advanced Quantitation Select Detection Basic Quantitation with Regeneration Select Regeneration or Neutraliza tion Repeat this step to set both the regeneration and neutralization reagent columns The Reagent Plate Map then shows where to dispense the reagents in the plate Figure 6 30 Octet System Data Acquisition User Guide Release 7 1 Managing Assay Parameter Settings page 167 Reagent Plate Reagent Plate Sample Plate 96 wells Reagent Plate 96 wells Sample Plate
61. assigning biosensors quantitation 384 177 quantitation 96 99 used with Replicate Groups quantitation 384 163 quantitation 96 88 Multiple Analyte parameter Advanced Quantitation quantitation 384 171 quantitation 96 94 133 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 multiple runtime binding charts 12 N Negative Control well type kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 Neutralization reserved well requirements quantitation 384 146 quantitation 96 72 Neutralization Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Neutralization Time and Shake speed parameter 134 211 Neutralization Time s and Shake speed 136 213 New Experiment Wizard menu 217 277 New Experiment Wizard menu 35 new features Octet System Data Acquisition software 12 New Group dialog box figure 389 New Kinetics Experiment menu 217 277 New Quantitation Experiment 69 141 New Window menu 37 non adjacent steps selecting 243 308 O Octet instrument cleaning 340 342 resetting 36 Octet instrument labels 13 Octet instrument power supply back panel 341 344 Octet instrument to computer connecting 30 Octet instrument side panel removed 343 Octet System Data Acquisition User Guide Release 7 1 page 21 Octet QK ins
62. be sent in any order The command or response is terminated with a new line CR LF sequence Parameters containing embedded spaces must be enclosed in double quotes Response items containing embedded spaces will be enclosed in double quotes Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 357 REVISIONS 1 0 lees Info commands mand Version of the API described in this header file cons 8 cons cons cons cons cons cons cons cons Parameter switches for the Run char char char char char First release Added Added Added t char AUT API VERSION tatus return values UT _OK UT _STOPPED UT RUNNING UT WAITING p plate file parameter to Run and GetMethod u use last sensor tray option to the Run com SetValue command to set the temperature target char AUT BUS char char AUT EOL const char AUT SWI required const char AUT SWI iment data option const char AUT SWI iment name in the const char AUT SWI after method file const char AUT SWI plate optional const char AUT SWI AUT_SWITCH_BARCODE const char AUT SWI plate optional const char AUT SWI optional const char AUT SWI window optional const char AUT SWI as it was left aft const char AUT SWI tus information A A A A AUT _LOADSENSORS A A A x a ae a O
63. black G red H blue within the Sensor Tray Map Used sensor columns that are inactive are colored black Active sample columns are colored green Each data acquisition step is represented by Sample Column X in the Current Binding Charts box To selectively display acquisition data for a particular acquisition step 1 Click the corresponding Sample Column number 2 Select a sub set of sensors for a displayed column under Sensors to Chart box see Figure 5 55 WARNING Do not close the Runtime Binding Chart window until the experi D ment is complete and all data is acquired If the window is closed the charts are not saved To remove the chart from view minimize the window The Octet System Data Acquisition software saves the Runtime Binding Chart as dis played at the end of the experiment For example modifying a chart by hiding the data for a particular biosensor will cause this data not to be included in the bitmap image generated at the end of the run Octet System Data Acquisition User Guide Release 7 1 Managing Runtime Binding Charts page 123 L g CAUsers Owner Documents Contracting Forte Bio User_Guides Data and methods Quant 96 data higG ProG Q Quantitation Runtime Binding Chart tela Current Binding Charts Sensors to Chart Plate Status a z EE Plate Legend Sample Column 1 SelectAll ensor Tray amea 7 __ Sample Plate ee Sample Column 2 _ YI 0114 d 456 Selecta Samp
64. loa Standard n a OH Standard na Oa Standard na B2 Standard ne Oc SAR Fa Sample Plate lopez Standard n a Sample Plate 96 wells OE Standard na Wit2 3 4 6 6 7 8 9 0 1 12 ge Bendar we andar a AOOOOOQOOQOOQOQO Ore Standard ve Oa Standard ni BOOOOOOOOOSO ge COOOOOOOOOSOA es n tane a DOOOOCOQOQQOQOQOQQO On Sinara ne F3 Standard E OOOOOOCO00O So Sindor Ke FIOOOOOOOOOOOY ee m GOOOOOCOC0CO0O Standard HOOQOOOOOOOO Button T O Sender conoi CE Unassigned Figure 5 4 Plate Definition Window Designating Standards To remove a well designation select the well s and click Unassigned Or right click the well s and select Clear Data Assigning Standard Concentrations Using a Dilution Series To assign standard concentrations using a dilution series 1 Inthe Sample Plate Map select the standard wells right click and select Set Well Data The Set Well Data dialog box displays see Figure 5 5 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 75 Sample Plate Sample Plate 96 wells y DE a a a ee E E A A Standard B Unknown Control r al nd c Negative Control Set Well Data D RESEUEES TG Concentration jig ml Standard only v E Reference By value Set Well Data F Clear Data Dilution series Replicate Gi R G Copy to Clipboard eup Starting value
65. or E drive 2 Double click DataAcquisition CFR 7_0_0_x exe to launch the installation wizard see Figure B 1 3 Data Acquisition 7 0 Setup a Welcome to the Data Acquisition 7 0 Setup Wizard for 21 CFR part 11 This wizard will quide you through the installation of Data Acquisition 7 0 It is recommended that you close all other applications before starting Setup This will make it possible to update relevant system files without having to reboot your computer Click Next to continue Figure B 1 Data Acquisition 7 0 for 21 CFR Part 11 Software Setup Wizard 3 Click Next to display the Choose Install Location dialog box Figure B 2 Octet System Data Acquisition User Guide Release 7 1 Installing the Data Acquisition 7 0 21 CFR Part 11 Software page 367 lt 3 Data Acquisition 7 0 Setup Choose Install Location Choose the folder in which to install Data Acquisition 7 0 Setup will install Data Acquisition 7 0 in the following folder To install in a different folder dick Browse and select another folder Click Next to continue Destination Folder Program Files ForteBio 7 DataAcquisition7 0 0 89 Space required 66 3MB Space available 177 2GB ForteBio Inc www Fortebio com Figure B 2 Choose Install Location Dialog Box The default location for the software on the local machine is C Program Files Forte Bio DataAcquisition7 4 Click Next to
66. quantitation 96 93 Quantitation Time assay parameter quantitation 384 209 quantitation 96 132 Quantitation Time parameter quantitation 384 169 quantitation 96 92 quantitative experiment analyzing 68 140 216 276 setting up 68 140 216 276 Quench well type kinetics 384 281 kinetics 96 218 quenching steps 237 303 R raw reference subtracted data viewing quantitation 384 201 quantitation 96 123 read head configuration kinetics 384 278 quantitation 384 143 reagent plate defining quantitation 384 166 modifying quantitation 384 299 Octet System Data Acquisition User Guide Release 7 1 page 26 reagent plate definitions saving 301 Reagent Plate Map 166 Reagent Plate Map figure 166 300 Reagent Plate radio button 166 reagent plates loading kinetics 384 324 Received well type quantitation 384 145 quantitation 96 71 recommended sensor offset 198 330 Reference well type 218 kinetics 384 280 quantitation 384 145 quantitation 96 71 reference biosensors designating 105 110 182 187 257 258 321 designating during acquisition 268 333 reference biosensors designating during acquisition quantitation 384 201 quantitation 96 124 Reference menu 124 201 268 333 reference wells defined 81 156 designating quantitation 384 156 quantitation 96 81 reference type of well 71 145 reference subtracted data viewing kinetics 384 332 kinetics 96 268 reference subtracted data viewing quant
67. setting 265 329 Delayed Experiment Start setting quantitation 384 197 quantitation 96 120 deleting constants 394 factory loaded biosensor types 49 projects 392 step types 240 305 Octet System Data Acquisition User Guide Release 7 1 page 12 user account 386 user group 390 Description setting 121 199 331 designating controls quantitation 384 156 quantitation 96 81 controls figure 81 156 reference biosensor during acquisition 268 333 reference biosensors 105 110 182 187 257 321 reference biosensors during acquisition quantitation 384 201 quantitation 96 124 reference wells quantitation 384 156 quantitation 96 81 reference wells figure 81 156 samples kinetics experiments 218 unknowns quantitation 384 153 quantitation 96 78 well type kinetics 384 282 well types kinetics experiments 282 designating reference biosensors 258 designating standards quantitation 384 148 quantitation 96 73 designating well types kinetics 96 219 Detection 95 136 172 213 Detection reserved well requirements quantitation 384 146 quantitation 96 72 Detection Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Detection Time and Shake speed parameter 136 213 determining the GxP Server module host location 52 developing the automation client 347 dialog boxes Options 41 setting default temperature 44 Temperature Setting 43 digital signatures
68. 00000 00000 0090000000 0000000900 00900000000 0090000000 Feeeeoeoeeeee 009000000 s eeeeeeeee 0000000 9 e 0e0000000 Biosensors interrogate 8 wells in a column one column Biosensors interrogate 16 wells in two columns Col is interrogated at a time umns 1 amp 2 are interrogated at the same time Columns 3 amp 4 are interrogated at the same time and so on Figure 6 2 Color Coded Wells Display How Biosensors Interrogate a 96 well Plate 8 Channel or 16 Chan nel Read Head 8 Channel Read Head 16 Channel Read Head 9 10 11 12 13 14 15 16 19 20 21 22 23 24 22 PI 2 22 23 24 Ryze etter Yo Biosensors interrogate 8 wells in a column one column Biosensors interrogate 16 wells in two columns Col is interrogated at a time umns 1 amp 2 are interrogated at the same time Columns 3 amp 4 are interrogated at the same time and so on Figure 6 3 Color Coded Wells Display How Biosensors Interrogate a 384 well Plate 8 Channel or 16 Channel Read Head Octet System Data Acquisition User Guide Release 7 1 page 144 Chapter 6 Quantitation Experiments Octet RED384 and QK384 NOTE Keep the read head configuration in mind when laying out the sample plate While reading a 384 well sample plate both the 8 channel and 16 chan nel read heads can freely step through the plate by either moving left or right to step across columns or step one row up or down Changing the Plate Format To
69. 1 page 11 Data Acquisition User Guide opening online version 38 Data Acquisition icon 8 Data Analysis 21 CFR Part 11 software overview 52 Data Analysis icon 8 data column displaying acquisition 267 331 quantitation 384 199 quantitation 96 122 data display significant digits 42 data file location and name settings quantitation 384 listed 196 quantitation 96 listed 119 Data File repositories setting Data File repositories 347 data files kinetics data repository 41 quantitation data repository 41 Use extended sample types 42 Use old 5 0 file format for FRD files 42 data preferences setting 40 DataAcquisition CFR 7_0_0_x exe 366 default biosensor columns 252 316 default locations for reserved wells in a 96 well sample plate map figure 72 default server settings localhost 54 Port 2002 54 default temperature value saving 44 default temperature defining new 44 default Tray Format 101 default user group privileges 385 default user groups 388 default windows Octet System Data Acquisition software 31 Default advanced settings 121 defining custom assays quantitation 384 206 quantitation 96 129 kinetic assays 236 new assay 35 new assay figure 130 207 new default temperature 44 reagent plates quantitation 384 166 sample plates kinetics 384 278 kinetics 96 218 quantitation 384 142 quantitation 96 70 samples by entering sample information figure 284 step types 237 303 kineti
70. 121 198 329 M Machine drop down list 63 Machine name setting 121 199 330 magnification undoing 125 202 271 335 magnifying Runtime Binding Chart 271 335 quantitation 384 202 quantitation 96 125 Main Menu Octet System Data Acquisition software 31 main screen Octet System Data Acquisition software 31 main toolbar hiding 34 showing 34 managing experiment method files 128 274 338 quantitation 384 205 quantitation 96 128 Runtime Binding Chart kinetics 96 267 managing experiment method files 274 manually save an experiment 259 323 mechanics Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 menu bar Octet System Data Acquisition software 32 menu commands listed 33 34 35 36 method file fmf 68 140 216 276 method file fmf described 32 method files closing 33 saving 33 saving all 33 Modify Plates dialog box 166 modifying assay parameter settings quantitation 384 167 quantitation 96 91 reagent plate quantitation 384 166 299 molar concentration units 222 284 Octet System Data Acquisition User Guide Release 7 1 page 20 molar concentration assigning kinetics 96 221 molecular weight assigning kinetics 96 221 monitoring experiments remotely 45 Multiple Analyte assay parameter quantitation 384 209 quantitation 96 132 Multiple Analyte experiments assigning biosensors quantitation 384
71. 144 removing quantitation 384 149 153 quantitation 96 74 78 reagent plates quantitation 384 167 removing controls or reference wells quantitation 384 157 quantitation 96 81 well information tooltip 241 well types Activation kinetics 384 281 kinetics 96 218 Buffer kinetics 384 280 kinetics 96 218 Control kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 designating kinetics 384 282 kinetics 96 219 designating kinetics experiments 282 for kinetics experiments 220 282 Load kinetics 384 281 kinetics 96 218 Negative Control kinetics 384 280 quantitation 384 145 quantitation 96 71 Positive Control kinetics 384 280 quantitation 384 145 quantitation 96 71 Quench kinetics 384 281 kinetics 96 218 Received quantitation 384 145 quantitation 96 71 Reference kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 Regeneration kinetics 384 281 kinetics 96 218 removing designated type 220 Sample kinetics 384 280 Octet System Data Acquisition User Guide Release 7 1 page 39 kinetics 96 218 Standard quantitation 384 145 quantitation 96 71 Unknown quantitation 384 145 quantitation 96 71 Wash kinetics 384 281 kinetics 96 218 well volumes Octet QK384 20 27 Octet RED384 20 27 wells annotating 82 225 288 annotating individual kinetics 384 289 kinetics 96 226 quantitation 384 157 quantitation 96 82 assigning dilution factor quantitati
72. 177 quantitation 96 99 used with Replicate Groups quantitation 384 163 quantitation 96 88 Multiple Analyte parameter Advanced Quantitation quantitation 384 171 quantitation 96 94 133 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 multiple runtime binding charts 12 N Negative Control well type kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 Neutralization reserved well requirements quantitation 384 146 quantitation 96 72 Neutralization Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Neutralization Time and Shake speed parameter 134 211 Neutralization Time s and Shake speed 136 213 New Experiment Wizard menu 217 277 New Experiment Wizard menu 35 new features Octet System Data Acquisition software 12 New Group dialog box figure 389 New Kinetics Experiment menu 217 277 New Quantitation Experiment 69 141 New Window menu 37 non adjacent steps selecting 243 308 O Octet instrument cleaning 340 342 resetting 36 Octet instrument labels 13 Octet instrument power supply back panel 341 344 Octet instrument to computer connecting 30 Octet instrument side panel removed 343 Octet System Data Acquisition User Guide Release 7 1 page 21 Octet QK instrument 23 biosensor tray type 24 bios
73. 2 Click the Move Up Move Down or Remove button located above the list D IMPORTANT An assay must have a baseline step followed by a set of associa tion dissociation steps to be analyzed The Octet System Data Acquisition software recognizes the baseline association dissociation set of steps Adding an Assay Through Replication A sample plate can include multiple assays that are the same replicates or different Each assay utilizes a new set of biosensors Replicates within a single assay will therefore use the same biosensor and replicates in different assays will use different biosensors To add a replicate assay to a plate 1 Inthe Assay Steps List select the steps to copy and click Replicate e To select adjacent steps press and hold the Shift key while you click the first and last step in the selection To select non adjacent steps press and hold the Ctrl key while you click the steps 2 Inthe Replicate Steps dialog box click the Add as a new assay option Figure 7 35 Octet System Data Acquisition User Guide Release 7 1 page 248 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Assay Steps List Move Up co Assay Sample Step Name Step Type Sensor Type Assay Time 1 Equlibration _y Custom SA Streptavidin pa FeAlmmabilizaton Loading S Replicate Steps Replication Type Add as a new assay Append to current assay Offset steps Sample steps onl
74. 2 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2 2 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2 2 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2 2 Figure 6 19 Replicate Group Result Table Statistics NOTE Replicate Group information can also be entered in the Results table in the Octet System Data Analysis software Assigning Replicate Groups in the Sample Plate Map To assign Replicate Groups in the Sample Plate Map 1 Select the samples to group right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 6 20 enter a name in the Replicate Group box and click OK Octet System Data Acquisition User Guide Release 7 1 page 160 Chapter 6 Quantitation Experiments Octet RED384 and QK384 E Set Well Data Well Information Dilution Factor Unknown only Sample ID E By value 2 Ab1 F Dilution series Replicate Group W i 1 g f I v Well Information Sample Diluent series operand 2 Dilution orientation 333 Right Left 8 Down Up k 4 Figure 6 20 Add Replicate Group from the Sample Plate Map 3 Repeat the previous steps to assign new samples to the existing Replicate Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and D calculate statistics for samples that use the same Repl
75. 3 Hz averaging by 40 The average of 40 data frames is reported as one data point One data point is reported every 3 3 seconds Standard quantitation 0 6 Hz averaging by 5 The average of 5 data frames is reported as one data point One data point is reported every 1 6 seconds Sensor off set Recommended sensor offset Quantitation 3 mm mm Default Sets the acquisition speed and sensor offset at the default settings Octet System Data Acquisition User Guide Release 7 1 Managing Runtime Binding Charts page 199 The following General Settings are available on the Run Experiment Tab Table 6 13 General Settings Item Description Machine name The computer name that controls the Octet instrument and acquires the data User name The user logon name Description A user specified description of the assay or assay purpose The description is saved with the method file fmf Stopping an Experiment To stop an experiment in progress click xX or click Experiment gt Stop The experiment is aborted The data for the active biosensor is lost the biosensor is ejected into the waste tray and the event is recorded in the experimental log NOTE After the experiment is run the software automatically saves the exper iment method fmf MANAGING RUNTIME BINDING CHARTS If the Open runtime charts automatically check box is selected in the Run Experiment window the Runtime Binding Charts are automati
76. 36 figure 36 list of menu commands 36 Instrument Status menu 34 instrument status log figure 119 196 263 327 Instrument Status window 36 described 39 figure 39 logging 36 inverted data viewing in the Runtime Binding Chart 269 334 K kinetic data analysis 40 kinetics assays building 248 defining 236 step type requirements 236 302 kinetics data repository 264 328 kinetics data repository user option 41 kinetics experiments designating samples 218 designating well types 282 Plate Definition window 282 starting 384 277 96 217 L launching the Octet System Data Acquisition software 30 legend for Runtime Binding Chart selecting 271 336 quantitation 384 203 quantitation 96 126 license information displaying 38 list options available for events 396 listing windows currently open in the Main Screen 37 Load well type kinetics 384 281 kinetics 96 218 loading biosensor tray kinetics 384 324 kinetics 96 260 quantitation 384 193 quantitation 96 116 reagent plates kinetics 384 324 sample plate kinetics 384 324 Octet System Data Acquisition User Guide Release 7 1 page 19 kinetics 96 260 quantitation 384 193 quantitation 96 116 steps 236 302 LoadSensors 353 Localhost option 347 localhost default server settings 54 locking Data Acquisition software 65 Data Analysis software 65 logging in the Instrument Status window 36 Login dialog box administrator session figure
77. 378 user session figure 56 Lot Number column 252 lower acquisition rate 121 198 329 M Machine drop down list 63 Machine name setting 121 199 330 magnification undoing 125 202 271 335 magnifying Runtime Binding Chart 271 335 quantitation 384 202 quantitation 96 125 Main Menu Octet System Data Acquisition software 31 main screen Octet System Data Acquisition software 31 main toolbar hiding 34 showing 34 managing experiment method files 128 274 338 quantitation 384 205 quantitation 96 128 Runtime Binding Chart kinetics 96 267 managing experiment method files 274 manually save an experiment 259 323 mechanics Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 menu bar Octet System Data Acquisition software 32 menu commands listed 33 34 35 36 method file fmf 68 140 216 276 method file fmf described 32 method files closing 33 saving 33 saving all 33 Modify Plates dialog box 166 modifying assay parameter settings quantitation 384 167 quantitation 96 91 reagent plate quantitation 384 166 299 molar concentration units 222 284 Octet System Data Acquisition User Guide Release 7 1 page 20 molar concentration assigning kinetics 96 221 molecular weight assigning kinetics 96 221 monitoring experiments remotely 45 Multiple Analyte assay parameter quantitation 384 209 quantitat
78. 384 209 quantitation 96 132 Quantitation Time quantitation 384 209 quantitation 96 132 Single Analyte quantitation 384 208 quantitation 96 131 Assay Parameters Advanced Quantitation Standard Assay figure 94 135 171 212 Assay Parameters Basic Quantitation Assay figure 92 131 169 208 Assay Parameters Basic Quantitation with Regeneration figure 93 133 170 210 Assay Settings box 91 Assay Step Definition dialog box 303 assay step name changing figure 247 311 assay steps adding 243 308 copying 243 308 inserting 245 310 removing 247 311 reordering 247 311 assay times updating figure 242 307 Assay Type setting Run Experiment window settings kinetics 384 328 kinetics 96 264 quantitation 384 196 quantitation 96 119 assays adding steps 245 310 adding to sample plates 248 313 assigning biosensors to samples 249 313 automatic addition of sensor tray maps 256 320 building 241 changing biosensor locations 252 257 changing biosensor type 320 copying steps between 243 308 editing 246 311 example using one partial biosensor try and biosensors from a second tray quantitation 384 190 quantitation 96 113 removing steps 247 311 reordering steps 247 311 replicating steps 244 309 starting new 244 309 assigning account details 385 biosensors in Multiple Analyte experiments quantitation 384 177 quantitation 96 99 biosensors in single analyte experiments quantitati
79. 384 317 kinetics 96 254 partial biosensor trays kinetics 384 320 kinetics 96 256 quantitation 96 112 V Verify Digital Signature dialog box figure 60 verifying digital signatures 60 Version automation interface command 349 View menu described 34 figure 34 list of menu commands 34 viewing analysis options 40 Audit Trail 62 available types of biosensors 48 constants 394 events 395 events for a specific project or computer 63 group settings 390 inverted data displayed in the Runtime Binding Chart 269 334 multiple Runtime Binding Charts kinetics 384 336 kinetics 96 272 quantitation 384 204 quantitation 96 127 project settings 391 raw reference subtracted data quantitation 384 201 quantitation 96 123 reference subtracted data kinetics 384 332 kinetics 96 268 quantitation 384 201 quantitation 96 123 templates 260 324 user account settings 386 user options 40 user modifiable settings for an assay quantitation 384 167 quantitation 96 91 W warm up time 30 Wash well type kinetics 384 281 kinetics 96 218 waste container emptying 340 for the Octet instrument figure 341 web browser opening 38 remote view of experiment 47 Web Server check box 45 URL figure 46 user option 43 Octet System Data Acquisition User Guide Release 7 1 page 38 weight Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instru
80. 4 200 80 60 5 225 100 80 6 250 120 100 7 300 130 100 Octet System Data Acquisition User Guide Release 7 1 Octet QK System Specifications page 21 OCTET QK SYSTEM SPECIFICATIONS Optics 8 channel biosensor manifold Black 96 well sample plate Biosensor Tray Orbital shaker Waste Compartment Figure 2 3 Octet QK Instrument Door Closed Left or Open Right Table 2 4 Octet QK System Specifications Item Description Equipment Classifications Product Classification Class 1 Detachable power cord Installation Overvoltage Category Category II Pollution Degree Degree 2 EMC Classification Group I Class A ISM Equipment EN55011 emissions EN61326 immunity Environmental Storage Temperature 20 to 70 C Optimum Operating Temperature 22 4 C Safe Operating Temperature 15 to 30 C Humidity Non condensing 10 to 80 Relative Humidity Indoor Use Only Operating Altitude 0 to 2 000 meters Compliance CE CSA Octet System Data Acquisition User Guide Release 7 1 page 22 Cc hapter 2 Octet System Specifications Table 2 4 Octet QK System Specifications Continued Item Description Capabilities Protein quantitation Kinetic and affinity analyses kops Kar kg Kp Binding specificity and cooperativity Kinetic screening of proteins peptides and other biomolecules Biosensor re racking Recommended analyte molecular weight of 5 000 Da or higher
81. 4 4 GxP Server Address Search Results Remote host on another subnet lf the GxP Server module is hosted on a differ ent subnet deselect the Localhost check box Enter the IP address of the com puter hosting the GxP Server module Octet System Data Acquisition User Guide Release 7 1 Selecting a Server Location page 55 J X Authentication l l Connection to server Server address 192 168 1 78 Figure 4 5 Manual Entry of Remote Host Address When the GxP Server module host location has been selected or entered click OK to save changes and exit the Authentication Server dialog box The GxP Server module location will now be listed as the Server in the Login box Figure 4 6 Login Dialog Box Displaying GxP Server Location Octet System Data Acquisition User Guide Release 7 1 page 56 Chapter 4 21 CFR Part 11 Compliance STARTING A USER SESSION gt NOTE Before starting your first user session please contact your administra tor to determine the GxP Server module host location that should be used To start a user session 1 Launch the Data Acquisition or Data Analysis software by double clicking on the desk top icon Data Data Analysis Acquisition 7 0 CFR11 7 0 CFR11 Figure 4 7 Data Acquisition and Data Analysis Desktop Icons The Login dialog box will display om A 2 fort sio E Server localhost 20002 User Pas
82. 47 40 Ready to move to sample location A1 14 47 40 Moving to sample location A1 14 47 41 Arrived at sample location A1 14 47 41 Waiting to start sample location A1 14 47 41 Processing sample location Al 14 47 51 Sample completed location A1 SF 14 47 51 Waiting to start new step 14 47 51 Starting new step 14 47 52 Ready to move to sample location A2 14 47 52 Moving to sample location A2 14 47 53 Arrived at sample location A2 14 47 53 Waiting to start sample location A2 14 47 53 Processing sample location A2 LJ u gt v Auto scroll to bottom Figure 8 57 Instrument Status Log Octet System Data Acquisition User Guide Release 7 1 page 328 Chapter 8 Kinetics Experiments Octet RED384 and QK384 WARNING Do not open the Octet instrument door when an experiment is in progress If the door is opened the data from the active biosensors is lost The data already acquired is saved however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning Run Experiment Window Settings The following Data File Location and Name settings are available on the Run Experiment Tab Table 8 6 Data File Location and Name Item Description Assay type The name of the selected assay Kinetics data The location where the subdirectory will be created The subdirectory repository contains
83. 5 10 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 79 Sample Plate Sample Plate 96 wells F i 2 3 4 5 A AA 9 10 na 12 ADOC a B DA IS Unknown Cc I 1 Control Negative Control D O Positive Control E O OO Reference F OLDI 1 Set Well Data z G O q cari Set Well Data kesal H 00004 Copy to Clipboard an ol Extended Sample T yell Information ae Factor Unknown only Tl Unknown Reference O Resen DRAE By value 2 Dilution series Replicate EEE Starting value 1 Wel Information Lx Dilution orientation 888 Right 8888 Left g Down g Up L Figure 5 10 Sample Plate Map Setting a Dilution Factor or a Serial Dilution To assign a dilution factor to selected wells 1 Inthe Set Well Data dialog box see Figure 5 10 select the By Value option 2 Enter the dilution factor value and click OK To assign a serial dilution to selected wells 1 Inthe Set Well Data dialog box see Figure 5 10 select the Dilution series option 2 Enter the starting dilution select a series operator and enter a series operand 3 Select the appropriate dilution orientation see Figure 5 11 Highest Concentration Lowest Concentration Figure 5 11 Concentration Representation in Dilution Series 4 Click OK The Sample Plate Table will display t
84. 63 enter the number of seconds to extend the step and click OK lt nl Extend Current Step Extending this step will prevent data analysis if these sensors are to be used in Parallel Reference Double Reference or Average Reference subtraction methods Assay 1 Step 2 Duration s 600 ubro o E CE Ce Figure 8 63 Extend Current Step Dialog Box To terminate a step and begin the next step in the assay 1 Inthe chart window click the Go to Next Step button 2 Inthe Data Acquisition dialog box click OK Magnifying the Runtime Binding Chart To magnify the chart press and hold the mouse button while you draw a box around the chart area to magnify To undo the magnification right click the chart and select Undo Zoom Scaling a Runtime Binding Chart To scale the Runtime Binding Chart 1 Right click the Runtime Binding Chart and select Properties 2 Inthe Runtime Graph Properties dialog box select Fullscale or Autoscale Octet System Data Acquisition User Guide Release 7 1 page 336 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Adding a Runtime Binding Chart Title To add a Runtime Binding Chart title 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box enter a graph title or subtitle Selecting a Runtime Binding Chart Legend To select a Runtime Binding Chart legend 1 Right click the chart and select Properties 2 Inthe Runtime Graph
85. 67 m LS Figure 7 5 Entering Molecular Weight and Molar Concentration from the Sample Plate Map The information displays in the Sample Plate Table see Figure 7 6 Octet System Data Acquisition User Guide Release 7 1 page 222 Chapter 7 Kinetics Experiments Octet RED96 QK and QK 3 Inthe Sample Plate Table select the sample concentration units and the molar con centration units Sample Plate Table Concentration units pg ml EA Concentration Molar concentration units nM units Well Sample ID Replicate Group Type Conc pg ml MW kD Molar Conc nM Information F3 Buffer G3 Buffer H3 Buffer O A4 Sample 150 66 67 l B4 Sample 150 33 33 c4 Sample 150 16 67 D4 Sample 150 8 333 E4 Sample 150 4167 Fa Reference G4 Reference H4 Reference P O45 Sample 150 66 67 s5 Sample 150 33 33 oa Sample 150 16 67 l s Sample 150 8 333 E5 Sample 150 4 167 Fs Reference G5 Reference 45 Reference as Sample 150 66 67 B6 Sample 150 33 33 acs Sample 150 16 67 Ops Sample 150 8 333 OES Sample 150 4 167 Fe Reference Ld Figure 7 6 Entering Molecular Weight and Molar Concentration from the Plate Table Assigning User Specified Sample Concentrations To assign sample concentrations using a dilution series 1 Inthe Sample Plate Map select the desired wells right click and select Set Well Data The Set Well
86. 7 0 Setup Ee x J Choose Install Location Choose the folder in which to install Data Analysis 7 0 Setup will install Data Analysis 7 0 in the following folder To install in a different folder click Browse and select another folder Click Next to continue Destination Folder C Program Files ForteBio 7 DataAnalysis7_0_0_29 Space required 57 4MB Space available 177 2GB ForteBio Inc www fortebio com Figure B 7 Choose Install Location Dialog Box Octet System Data Acquisition User Guide Release 7 1 page 370 Chapter B 21 CFR Part 11 Software Administrator Options The default location for the software on the local machine is C Program Files Forte Bio DataAnalysis7 5 Click Next to accept this path location The Choose Start Menu Folder dialog box displays Figure B 8 i Data Analysis 7 0 Setup e Choose Start Menu Folder Choose a Start Menu folder for the Data Analysis 7 0 shortcuts Select the Start Menu folder in which you would like to create the program s shortcuts You can also enter a name to create a new folder Fortebio ACT by Sage Premium Administrative Tools Bonjour Print Services Corel DVD MovieFactory Lenovo Edition DivX Plus Dropbox FileZilla FTP Client FileZilla Server ForteBio ForteBio Inc www fortebio com Figure B 8 Choose Start Menu Folder Dialog Box The default Start Menu folder is ForteB
87. 7 18 Sample Plate Table Editing Sample Data Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sample Plate Table To view edit com mands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the right click menu used to designate sample types MANAGING SAMPLE PLATE DEFINITIONS NOTE After you define a sample plate you can export and save the plate defi nition for future use Octet System Data Acquisition User Guide Release 7 1 Managing Sample Plate Definitions page 233 Exporting a Plate Definition To export a plate definition 1 Inthe Sample Plate Map click Export see Figure 7 19 Sample Plate 96 wells O Unassigned Import Export Jf Remove Figure 7 19 Sample Plate Map Export Button 2 Inthe Export Plate Definition window see Figure 7 20 select a folder enter aname for the plate csv and click Save EY Export Plate Definition 6 O JL Forte Bio tt Search Data and met P Organize New folder 3E a a Favorit s i Favorites Documents library Bronce by Fobier B Desktop Data and methods E a Downloads Name Date modified Type Recent Places
88. 8Channels 16 Channels Sample Plete Teble Concentration units ug ml z Epot impor Assay Settings l fi _ Moai Well Sample ID Replicate Group Type Conc pg ml Dilution Factor Information eae Sta cane ody DA Standard 200 na parga oc Standard 100 nja Time s Shake speed e Standard 50 ma Quantitation 120 400 oa Standard 25 Wa j on Standard 10 nja OK Standard 5 na Omi Standard 25 nja Oo Standard 1 n a OA Standard 200 nja c3 Standard 100 nja OE Standard 50 nja Oa Standard 25 na Sample Plate elk Standard 10 nja z OK Standard 5 nja Sample Plate 384 wells Pike sede wa P1234567 8 9 1011121314151617 18192021 222324 003 Standard 1 n a Al00000E O O0OOOCO Standard e jelefel ele Unknown OOOOO O00000 Control SSsss Negative Control O00000 Positive Control O09 Set Well Data Clear Data vozzrzc ronmoow OOOO O O O vV Extended Sample Types 00000 Copy to Clipboard OOOO000Cd O Standard Control ite Unassigned O Unknown Reference O Reserved Figure 6 12 Plate Definition Window Designate Unknown Wells To remove a well designation select the well s and click Unassigned Or right click the well s and select Clear Data Assigning a Dilution Factor or Serial Dilution to Unknowns To assign a dilution factor or serial dilution to unknowns 1 In the Sample Plate Map select the unknown wells see Figure 6 12 2 Right click and select Set Well Data
89. 96 267 opening 268 332 quantitation 384 200 quantitation 96 123 printing 273 338 scaling 271 335 quantitation 384 202 quantitation 96 126 selecting legend 271 336 quantitation 384 203 quantitation 96 126 updating kinetics 384 331 kinetics 96 267 quantitation 384 199 quantitation 96 122 viewing inverted data 269 334 viewing multiple kinetics 384 336 kinetics 96 272 quantitation 384 204 quantitation 96 127 Runtime Binding Chart figure 118 195 263 327 Runtime Binding Chart Export options copy the Runtime Binding Chart to a graphic file quantitation 384 205 quantitation 96 128 export the Runtime Binding Chart to a graphic file quantitation 384 204 quantitation 96 127 print the Runtime Binding Chart to a graphic file quantitation 384 205 quantitation 96 128 save the binding data quantitation 384 204 quantitation 96 127 Runtime Binding Chart options listed table quantitation 384 204 quantitation 96 127 Runtime Binding Chart window figure 267 332 Runtime Binding Chart copying quantitation 384 205 quantitation 96 128 Runtime Binding Chart enhanced legend options 12 Runtime Binding Chart printing 128 205 Runtime Graph Properties dialog box 126 203 271 336 S Sample well type kinetics 384 280 kinetics 96 218 sample plate loading kinetics 384 324 kinetics 96 260 quantitation 384 193 quantitation 96 116 Octet System Data Acquisition User Guide Release 7 1 pag
90. ABE BeeeeL Legend O Unassigned sensors Ry Missing sensors Remove Fill Fill Plate Sensor Tray c5 DS E5 FRARRQRS Well Sensor 7 Tray 1 fas Jac em B5 Lot Number Information AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti higG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti higG Fc Capture AHC Anti hIgG Fc Capture v Replace sensors in tray after use Sensor Tray of2 3 4 5 6 Well Sensor Type Lot Number Information ADOC Al AHC Anti higG Fc Capture BOOL CHO gt EOL a csOOL I HOOL __ Unassigned sensors Legend RRA Missing sensors Remove Fill Fill Plate B1 cl D1 El F1 G1 H1 A2 B2 C2 D2 E2 F2 G2 H2 A3 B3 AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture AHC Anti higG Fc Capture AHC Anti hIgG Fc Capture AHC Anti hIgG Fc
91. Analysis Software User Guide gt NOTE Before starting an experiment check the sample plate temperature dis played in the status bar Confirm that the temperature is appropriate for your experiment and if not set a new temperature If the Octet System Data Acquisi tion software is closed the plate temperature will reset to the default startup value specified in the Options window when the software is relaunched Octet System Data Acquisition User Guide Release 7 1 Starting a Basic Kinetics Experiment page 277 STARTING A BASIC KINETICS EXPERIMENT You can start a kinetics experiment using one of the following options Launch the Experiment Wizard Open a method file fmf by clicking File gt Open Method File Method files may be saved and recalled using the File menu and are automatically saved when an experi ment is run For more details on method files see Managing Experiment Method Files on page 338 On the menu bar click Experiment gt Templates gt Kinetics NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Starting an Experiment Using the Experiment Wizar
92. Analysis 6 Analyze the binding data Octet System Data Analysis eo B 7 Generate a report Software User Guide For more details on how to prepare the biosensors see the appropriate biosensor product insert Octet System Data Acquisition User Guide Release 7 1 Starting a Quantitation Experiment page 69 STARTING A QUANTITATION EXPERIMENT NOTE Before starting an experiment check the plate temperature displayed in the status bar Confirm that the temperature is appropriate for your experi ment and if not set a new temperature If the Octet System Data Acquisition software is closed the plate temperature will reset to the default startup value specified in the Options dialog box when the software is relaunched You can start a quantitation experiment by one of the following methods e Launch the Experiment Wizard e Open a method file fmf by clicking File gt Open Method File Method files may be saved and recalled using the File menu and are automatically saved when an experi ment is run For more details on method files see Managing Experiment Method Files on page 128 Onthe menu bar click Experiment gt Templates gt Quantitation NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non
93. Anti Human IgG Fc Unassigned samples c5 Anti Human IgG Fc DS Anti Human TG Fe m rommoonwr O O Legend Figure 5 33 Sensor Assignment Window for Basic Quantitation Using the Multiple Analyte Option There are two ways to assign biosensors e Select a column in the Sensor Tray Map right click and select a biosensor type from the drop down list see Figure 5 34 left Select a cell in the Sensor Type table column click the down arrow and select a bio sensor type from the drop down list see Figure 5 34 right Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 101 Sensor Tray v Replace sensors in tray after use W 12 3 4 5 6 7 o 10 11 12 auto assign Anti Human IgG Fc Anti Mouse IgG Fv Protein A Protein G Protein L SA Streptavidin Residual Protein A Anti Penta HIS Custom Reference Positive Control Negative Control Remove Sample Fill Missing sensors Set Sensor Data Copy to Clipboard Lot Number Information Well Sensor Type A1 Anti Human IgG Fc B1 A auto assign C1 Alu g D1 pAnti Mouse IgG Fv E1 Protein A Protein G F1 A protein L G1 ASA Streptavidin H1 AResidual Protein A A2 aAnti Penta HIS B2 pCustom C2 JA D2 A E2 A Figure 5 34 Changing Biosensor Types in the Sensor Tray Map left and Sensor Type Column right B
94. Anti Penta HIS High sensitivity Anti Penta HIS Standard range E High sensitivity Human IgG quantitation IE Human IgG Quantitation E Immunogenicity Direct detection E Murine IgG Quantitation E Protein L Standard range E Standard Assay D Basic Quantitation with Regeneration E High sensitivity assay with regeneration B Protein L Standard range E Standard Assay My Basic Quant with Regen Assay Advanced Quantitation E Immunogenctty Enzyme Linked E Residual Protein A E Standard Assay Z Three Step Assay Duplicate Remove Assay Parameters Name Description My Basic Quant Assay Enter a short description of the assay here Quantitation Blueindicates a ForteBio built in assay and cannot be modified or deleted Single analyte Multiple analyte Replicates per s sor type Time s 120 Shake speed 400 Figure 6 67 Defining a New Assay Octet System Data Acquisition User Guide Release 7 1 page 208 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Editing Assay Parameters To edit assay parameters 1 Inthe Edit Assay Parameters dialog box confirm that the new assay is selected in Available Assays see Figure 6 67 bottom 2 Modify the assay parameters as needed A complete list of parameters for each type of quantitation experiment follows this procedure 3 C
95. Appendix B 21 CFR Part 11 Software Administrator OPTIONS sein dice tiinteadesadiecteaves 365 Installing the Data Acquisition 7 0 21 CFR Part 11 Software 366 Installing the Data Analysis 7 021 CFR Part 11 SoftWare oiai a naasiri tangine 369 Installing the ForteBio GxP Server Module371 Administrator Account Setup 374 Starting an Administrator User Session 378 Accessing Administrator Options 381 Administrator Tabs 2 04 383 User Account Administration 384 Group Administration 388 Project Administration 390 Administrator Constants 392 Event Log ccce cee e eee eeees 394 Accessing the GxP Server Module Directly396 Restarting the GxP Server Module 398 Octet System Data Acquisition User Guide Release 7 1 page 7 CHAPTER 1 Welcome Ab t the Oct t Systemi icicscvceadover cad ateasar acer eicemetendeseterekiaceeaeadenands 8 What s New in the Octet System Data Acquisition Software Release 7 1 5 8 What s New in the Octet System Data Acquisition software Release 7 0 12 Conventions and Symbols Used in This Guide eee c eee cence eee e een eee es 13 ForteBio Technical SUPPOrt sererrererstrek t strt eee eee e nent eee eee PERES EERENS EEES 13 Welcome to the ForteBio Octet System Data Acquisition User Guide This guide explains how to Operate the Octet instrument Set up and run
96. Baseline 600 1200 be Baseline r DO OOOQOOOO0O O Disocoton 610M Aneosebon T EO O O00000089 Newser 10 oem F F Q O O O O O Equilibration2 10 1000 F Custom D GOO OQOSOOQOOOOOO sewsseneu NewAssay Move Up Mave Down el H Q O Q O Assay Sample Step Name Step Type Sensor Type Assay Time A Assayed samples O Unassigned samples 1 i Equilibration Custom SA Streptavidin 0 00 30 New Assay Step m r Figure 7 29 Assigning a Step Type to a Column in the Sample Plate 3 Repeat the previous steps to define each step in the assay As each step is added the total Experiment and Assay Time update see Figure 7 30 Assay Steps List Sa Tilt R z xp time le xperimen New Assay Move Up _ Move Down Remove Replicate D Tm pernime Assay Sample Step Name Step Type Sensor Type Assay Time 1 Equlibration 3 Custom SA Streptavidin 1 2 ProA Immobilization Loading SA Streptavidin 1 3 Baseline ke Baseline SA Streptavidin 1 4 Association Association SA Streptavidin 1 3 Dissociation Association SA Streptavidin 1 11 Regeneration 3 Custom SA Streptavidin 1 12 Neutralization 3 Custom SA Streptavidin 1 11 Regeneration 3 Custom SA Streptavidin 1 12 Neutralization J Custom SA Streptavidin 1 11 Regeneration 3 Custom SA Streptavidin 1 12 Neutralization J Custom SA Streptavidin 1 13 50 Total Assay Time Figure 7 30 Experi
97. Definition window kinetics 384 297 kinetics 96 233 quantitation 384 163 quantitation 96 88 exporting binding data 127 204 plate definition kinetics 384 297 kinetics 96 233 quantitation 384 163 quantitation 96 88 Runtime Binding Chart to a data file 127 204 272 337 Runtime Binding Chart to a graphic 127 204 272 337 Runtime Binding Chart to a graphic file 273 337 Exporting dialog box figure 127 204 Extend Current Step button 270 Extend Current Step dialog box figure 271 335 extending duration of the active step 270 335 F factory loaded biosensor types deleting 49 FBServer7 folder installation location 381 FBServerConfig exe file 381 File Compliant figure 62 File History menu 34 File menu described 32 figure 33 list of menu commands 33 File menu commands listed table 33 File Not Compliant figure 62 File Type selection figure 61 Fill Plate menu 253 316 Filtering threshold parameter 239 305 Flip Data check box 125 269 334 Flip Data function viewing inverted data 269 ForteBio GxP Server 7 0 exe 372 ForteBio GxP Server desktop icon figure 397 ForteBio GxP Server module installing 371 Octet System Data Acquisition User Guide Release 7 1 page 17 ForteBio technical support contacting 13 ForteBio Web Site menu 38 fractional use of regeneration and neutralization wells figure 112 189 Fuse symbol 13 G general settings kinetics 384 330 GetMethodInfo auto
98. ForteBio UK Ltd ForteBio 1360 Willow Road 83 Victoria Street Aria Biotechnology Co Ltd Suite 201 Suite 407 917 Halley Road Bldg 4 Menlo Park CA 94025 London SW1H OHW Zhangjiang High Tech Park USA UK Shanghai China 201203 Tel 1 650 322 1360 Tel 44 0 20 31784425 Tel 86 21 51320387 Fax 1 650 322 1370 Fax 44 0 20 31787070 E mail info fortebio com E mail info fortebio com E mail info fortebio co uk Octet System Data Acquisition User Guide Release 7 1 page 14 Chapter 1 welcome Octet System Data Acquisition User Guide Release 7 1 page 15 CHAPTER 2 Octet System Specifications Octet RED96 System Specifications 0 cece cece cece eee eee ence ee eee eneenens 16 Octet RED384 System Specifications 22 0 0 cece cece cee cence eee ence een e ee eneeeees 18 Octet QKe System Specifications 6 cece cece cece cence nee ene ee eee eeneenens 21 Octet QK System Specifications 0 ccc cece cece cece ene ene e ene ne ene neeneenees 23 Octet QK384 System Specifications 0 cece cece cece nee cnet e ene ne en eeeees 25 Octet System Data Acquisition User Guide Release 7 1 page 16 Chapter 2 Octet System Specifications OCTET RED96 SYSTEM SPECIFICATIONS Optics 8 channel biosensor manifold Black 96 well sample plate Biosensor Tray Orbital shaker Waste Compartment Figure 2 1 Octet RED96 Instrument Door Closed Left or Open Right Table 2 1
99. G1 SA Streptavidin H1 SA Streptavidin A2 SA Streptavidin L i ia B2 sa Streptavidin IIL IL S 7m C2 SA Streptavidin D2 SA Streptavidin E2 SA Streptavidin F2 SA Streptavidin G2 SA Streptavidin H2 SA Streptavidin Remove Fill Fill Plate A3 SA Streptavidin B3 SA Streptavidin roaTmmMovaWr Y JI Legend _ Unassigned sensors RI Missing sensors Sample Plate C3 SA Streptavidin VW 12 3 4 6 6 7 8 9 0 11 12 D3 SA Streptavidin AOOOOOQO OO E Emn BOOOO0 e 24 oS COOSOCOOO JOO DIOCCO0O OO EIOOCO0O OO FIOOCOOOO CO GO OOCO00O CO HI OOO000 OO Legend Unassigned samples Figure 7 36 Sensor Assignment Window Hover the cursor over a well in the Sensor Tray Map or Sample Plate Map to display a tool tip with sample or biosensor information see Figure 7 37 Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 251 Sample ID Dissociation Well Info 1X Kinetics Buffer Legend Unassigned samples Figure 7 37 Tool Tip of Well Information Replacing the Biosensors in the Biosensor Tray After an assay is completed the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container To return the biosensors to the tray click the Replace sensors i
100. Guide Release 7 1 page 5 Managing Experiment Method Files 274 Chapter 8 Kinetics Experiments Octet RED384 and QK384 275 Introduction 0 0 cece cece eee eee 276 Starting a Basic Kinetics Experiment 277 Starting an Experiment Using the Experiment Wizard 006 277 Defining the Sample Plate 278 Read Head Configuration and Plate Changing the Sample Plate Format 280 Designating Samples 280 Selecting Wells in the Sample Plate Map 281 Designating Well Types 282 Entering Sample Information 283 Replicate GrOupS 0 ceceeues 289 Editing the Sample Table 295 Managing Sample Plate Definitions 296 Exporting a Plate Definition 297 Importing a Plate Definition 298 Working with a Reagent Plate 299 Saving a Reagent Plate Definition 301 Defining a Kinetic Assay 4 302 Defining Step Types 006 302 Building an Assay a nn 306 Assigning Biosensors to Samples 313 Reviewing Experiments 322 Saving Experiments 0eeeeeee 323 Saving an Experiment to the Template Folde soap o age 324 Running a Kinetics Experiment 324 Loading the Biosensor Tray Sample and Reagent Plates nanaonan 324 Starting the Experiment 325 Run Experiment Window Settings 328 Stopping an Experiment 331 Managing the Runtime Bind
101. Homogeneous trays Voi2 3 45 67 3 wi 2 oe Type Lot Number information R ABUIGUUCIICI ITI eas Bs pOTOLULULILLILILIL e Pans cmomaHULULLILILILIL a protena DEMAM ILILILILIL ei mene ERRERBOUWUWUWUUUL m mma FpgmOUUUOLLLIL 2 erena sOGGooo Shee HELI I een i Legend _ Unassigned sensors RR Missing sensors z ee Remove Fill Fill Plate A3 Protein A B3 Protein A Figure 5 45 Tray Selection 7 To designate reference biosensors select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during acquisition 8 Optional Double click in any cell in the Lot Number column to enter a biosensor lot number All wells in the Lot Number column for the biosensor type selected will automatically populate with the lot number entered 9 Optional Double click in a cell in the Information column to enter biosensor informa tion for a particular cell NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 111 NOTE For greater clar
102. IgG Standard 200 Standard 200 n a p B1 IgGStandard 100 Standard 100 n a O C1 IgG Standard 50 Standard 50 nja D1 IgG Standard 25 Standard 25 n a O El IgGStandard 10 Standard 10 n a O F1 IgGStandard 5 Standard 5 n a Figure 5 21 Export Button in Sample Plate Table 2 In the Export Plate Definition window see Figure 5 22 select a folder enter a name for the plate csv and click Save Octet System Data Acquisition User Guide Release 7 1 Managing Sample Plate Definitions page 89 m 2 Export Plate Definition go JL Forte Bio 4s Search Data and met Organize New folder JE i Favorites m Documents library E Desktop Data and methods J Downloads Arrange by Folder 7 Name Date modified Type Recent Places W Desktop Ti Libraries _ Documents Music 5 Pictures A Videos E m r Filename 96 standard plate csv aa Save as type csv Files csv z L Figure 5 22 Export Plate Definition Window Importing a Plate Definition To import a plate definition 1 Inthe Sample Plate Table see Figure 5 23 click Import Sample Plate Table Concentration units pg ml v Export Import Well Sample ID Replicate Group Type Conc ig ml Dilution Factoi O Al IgGStandard 200 Standard 200 nja p O B1 IgGStandard 100 Standard 100 n a O C1 IgG Standard 50 Standard 50 n a D1 IgG Standard 25
103. Kinetics Experiments Octet RED384 and QK384 There are two ways to change the biosensor type Select a column in the Sensor Tray Map right click and select a biosensor type from the drop down list Figure 8 47 left The associated wells in the Sensor Type col umn will automatically populate with the biosensor type selected Select a cell in the Sensor Type table column click the down arrow and select a bio sensor type from the drop down list Figure 8 47 right All other wells in the same column of the Sensor Tray Map as the selected cell will automatically populate with the biosensor type selected Sensor Tray T V Replace sensors in tray after use Well Sensor T Lot Number Information AE a Ye T Al AHC Anti hIgG Fc Capture A auto assign Hepes a i SA Streptavidin ic Ai niac re Capture B AHC Anti higG Fc Capture ci iar org 5 Fi Amine Reactive Cc APS Aminopropylsilane Fl Aca Super Streptavidin AR Amine Reactive G1 ACustom D SSA Super Streptavidin AHC Beta 1 E Custom OMA F AHC Beta 1 pP Reference G Positive Control H Negative Control i Remove egeng Fill ig sensors Ba Set Sensor Data Sample Copy to Clipboard Figure 8 47 Sensor Assignment Window Changing the Biosensor Type The biosensor types shown in the Sensor Assignment window were specified previously in the Assay Definition window and default locations are assigned automatically To assign biosensor types for
104. Missing sensors remove a mPa Figure 6 37 Replace Sensors in Tray After Use Check Box NOTE Biosensors can be regenerated up to a max of 11 times per experiment Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 177 Biosensor Assignment in Multiple Analyte Experiments In a multiple analyte experiment more than one biosensor type is assigned to the same sample allowing multiple analytes to be analyzed in a single experiment NOTE For multiple analyte experiments the Multiple Analyte option must be selected in the Assay Parameters dialog box For more information please see Managing Assay Parameter Settings on page 167 Click the Sensor Assignment tab or click the arrow to access the Sensor Assignment window see Figure 6 35 The software generates a color coded Sensor Tray Map and Sample Plate Map that shows how the biosensors are assigned to the samples by default In the example shown in Figure 6 35 one replicate had been previously selected with the Multiple Analyte assay parameter option Plate Definition Sensor Assignment Review Experiment Run Experiment Oo In this step sensors are assigned to samples Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate Sensor Tray v Replace sensors in tray
105. OK The Data Acquisition or Data Analysis software will now launch and start the adminis trator session During the session the administrator account and project selected at login display in the software status bar Experiment Not Started Plate temp 30 C Project Antigen Antibody screen amp User Administrator Figure B 29 Status Bar Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 381 NOTE Administrator and user sessions are automatically locked after a period of inactivity set using the UserldleMin constant Please see Administrator Constants on page 392 for more information The Login dialog box will dis play anda message indicating the session has been locked will be shown You can choose to log back into the session or log off at this time Administrator and user sessions will not be locked during experimental data acquisition ACCESSING ADMINISTRATOR OPTIONS The 21 CFR Part 11 software Server Administration options allow administrators to mange users groups projects and constants and view associated events These options can be accessed in the Data Acquisition and Data Analysis software or by launching the ForteBio GxP Server module directly Data Acquisition and Data Analysis softwareClick Security gt Server Administra tion Window Help Verify Document View Audit Trail Change Project G Change Password Server Adminis
106. Octet RED 121 Activation well type 218 kinetics 384 281 activation steps 237 303 active biosensor column 122 199 267 331 Active Channels threshold parameter 239 304 active method file closing 33 active steps extending duration 270 335 Add Sensor dialog box figure 49 Adding 49 adding biosensor type 49 replicate assay to a plate 247 312 Replicate Groups from the Sample Plate Map kinetics 384 291 kinetics 96 228 quantitation 384 figure 160 quantitation 96 figure 85 Runtime Binding Chart title 271 336 quantitation 384 203 quantitation 96 126 Octet System Data Acquisition User Guide Release 7 1 page 2 sample annotations from the Sample Plate Map kinetics 96 figure 225 adjacent steps selecting 243 308 administrator account setting up 374 administrator constants listed table 393 administrator password changing 387 administrator user session starting 378 administrator username selection figure 379 Advanced Quantitation shortcut menu option 166 Advanced Quantitation assay parameters 94 135 171 212 2nd Buffer Time and Shake speed 136 213 Buffer Time and Shake speed 135 212 Detection Time and Shake speed 136 213 Enzyme Time and Shake speed 136 213 Offline 136 213 Pre condition sensors 136 213 quantitation 384 2nd Time and Shake Speed param eter 172 Buffer Time and Shake Speed pa rameter 172 Detection Time and Shake Speed parameter 172
107. Octet RED384 instrument automation 19 capabilities 18 compliance 18 dimensions 20 electrical requirements 20 environment 18 equipment classifications 18 mechanics 19 optics 19 sample types 19 sampling format 19 weight 20 Octet RED384 instrument figure 18 Octet RED384 stage platform figure 193 Octet RED96 instrument biosensor tray type 17 19 26 biosensor type 17 19 26 capabilities 17 compliance 16 dimensions 17 electrical requirements 17 environment 16 equipment classifications 16 mechanics 17 optics 17 orbital flow capacity 17 20 27 sample types 17 sampling format 17 sampling volume 17 temperature range 17 throughput 17 19 26 weight 17 Octet RED96 instrument figure 16 Octet RED96 system specifications displayed figure 18 listed table 16 18 25 Octet system biosensor stage left and sample stage right figure 325 Octet System Data Acquisition software Main Menu 31 main toolbar 32 new features 12 starting 30 toolbar 31 Octet System Data Acquisition software Main Screen 31 Octet System Data Acquisition analysis options viewing 40 Octet system described 8 Offline parameter 136 213 Advanced Quantitation quantitation 384 172 quantitation 96 95 Offset steps option 244 309 Offset steps check box 243 Open Experiment menu 268 332 Open Experiment menu 33 Open Method File menu 33 Open runtime charts automatically setting 120 197 265 329 Open runtime
108. Octet RED96 System Specifications Item Description Equipment Product Classification Class 1 Detachable power cord Classifications Installation Overvoltage Category Category II e Pollution Degree Degree 2 EMC Classification Group Class A ISM Equipment EN55011 emissions EN61326 immunity Environmental Storage Temperature 20 to 70 C e Optimum Operating Temperature 22 4 C Safe Operating Temperature 15 to 30 C e Humidity Non condensing 10 to 80 Relative Humidity Indoor Use Only e Operating Altitude 0 to 2 000 meters Compliance CE CSA Octet System Data Acquisition User Guide Release 7 1 Octet RED96 System Specifications page 17 Table 2 1 Octet RED96 System Specifications Continued Item Description Capabilities Protein quantitation Kinetic and affinity analyses kops Ka Kg Kp Binding specificity and cooperativity Kinetic screening of proteins peptides and other biomole cules Small molecule and fragments screening and kinetic analy sis Recommended analyte molecular weight of 150 Da or higher Sampling Format Required plate 96 well black flat bottom polypropylene microplate Greiner Bio One 655209 or similar SBS stan dard microplate Single sample plate capacity Sampling Volume 180 220 uL well 96 well plate Sample Types Biosensor Type Purified samples common culture media crude lysates Disposable single use fiber
109. Offline incubation is best performed on the ForteBio Sidekick biosensor immobilization station Reuse Buffer Allows buffer wells to be reused If unselected the number of buf fer columns must equal the number of sample columns If selected the number of buffer columns may be less than the number of sample columns as the buffer columns are reused Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incubated in regeneration buffer to speed rpm remove bound analyte Neutralization The duration time and shaking speed of the neutralization step Time s and Shake where the biosensor is incubated in neutralization buffer after the speed rpm regeneration step Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For example an acidic pre conditioning buffer maximizes the binding competence of Protein A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Octet System Data Acquisition User Guide Release 7 1 page 214 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Table 6 18 Advanced Quantitation Assay Parameters Parameter Description The numbe
110. Open runtime charts automatically setting 120 197 265 329 Open runtime charts automatically check box 267 Octet System Data Acquisition User Guide Release 7 1 page 23 Open runtime charts automatically option 326 Open Windows menu 37 opening dialog box to select an experiment method file 33 Edit Assay Parameters dialog box 35 Experiment Wizard 35 online Data Acquisition User Guide 38 Runtime Binding Chart 268 332 quantitation 384 200 quantitation 96 123 Sensor Types dialog box 35 Temperature Setting dialog box 35 web browser 38 optics Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 Options dialog box displayed figure 41 setting FRD file format to the earlier 5 0 for mat 34 significant digits 34 viewing analysis options 41 Options dialog box figure 41 Options dialog box Automation Interface selection figure 347 Options menu 34 orbital flow capacity Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 20 27 organizing windows in a cascade arrangement 37 P panel Octet instrument removing 343 parameter settings assay modifying quantitation 384 167 quantitation 96 91 parameter values editing quantitation 384 208 quantitation 96 131 partial biosensor trays using 256 kinetics 384 320 password reminder user and administrator figure 57 plate definition exporting k
111. Quantitation Assays 129 Defining a Custom Assay 129 Editing Assay Parameters 131 Octet System Data Acquisition User Guide Release 7 1 page 3 Selecting a Custom Assay 137 Chapter 6 Quantitation Experiments Octet RED384 and QK384 139 INCrOCUCTION 0 6 ec ccc cece eens 140 Starting a Quantitation Experiment 141 Starting an Experiment Using the Experiment Wizard 006 141 Defining the Sample Plate 142 Read Head Configuration and Plate LAYOUT sirar errada bias naseadie diets 143 Changing the Plate Format 144 Designating Samples 144 Selecting Wells in the Sample Plate Map 148 Designating Standards 148 Designating Unknowns 153 Designating Controls or Reference Wells 156 Annotating Samples 157 Replicate GroupS ceeeeues 159 Managing Sample Plate Definitions 163 Exporting a Plate Definition 163 Importing a Plate Definition 164 Working with a Reagent Plate 165 Saving a Reagent Plate Definition 167 Managing Assay Parameter Settings 167 Modifying Assay Parameter Settings167 Viewing User Modifiable Assay Parameter SCttiNGS 1 0 cece ccc e eee ene a 167 Assigning Biosensors to Samples 173 Biosensor Assignment in Single Analyte Experiment S oniran isorinis 173 Biosensor Assignment in Multiple Analyte Experiments
112. Quench NOOOOO00O0 o P Regeneration Set Well Data Clear Data Copy to Clipboard Reference Sample Ou Unassigned l Import Export T Remove ii r Figure 8 6 Designating a Well Type in the Plate Definition Window To remove a well designation in the Sample Plate Map select the well s and click Remove Or right click the well s and select Clear Data see Figure 8 7 Sample Plate 384 wells Sample Plate 384 wells 2345 6 7 8 9 1011121314151617 18192021 222324 vi 23456789 1011 121314151617 18192021 222324 AWMOOOOCOVCOOOOOO OOO0C00C007D A ie nen a cee D O000d BIOQCOQOOOOOOOOOOOCOOOOOO0OO B Sample DOOQOOO0OO COOOOOOCOOOOOOPO OOO0000OO CE Reference DOOOOO0OO Aeee AENEAN EEEE SEE 2 eE E D DOQOQQQQQQ EOOCQOQOQOQOOOQOQOOOQOOOQOQOQQQOQOQOQ EgO Control DOOQOQOQQOQQQ F OOQOQOOQOOQOQOOQOQOOQOQOOQOQOQQOQQ0Q00Q000Q FIO _ Negative Control DOOOOO0OO 6OOOODOODOOOOO OO OO0O00000Q GJE a DOOOOO0OO HOOQOQCOQOOOOOOOOOOCOOOOCO00OG HC Positive Control DOOOOO0OO OCOOOQOODOODOOO O OOOC0000OG O DOOOOOO0OO SOOODOOOOOOOOOOOOCOOOOOO0OO s Buffer DOOOOO0OO K QOOOCOODOPODO9O OOOOO000O KIE Activation DOQOOOO0OQ Mesettetetet tot tot etet tot totototelotetotets LQ DOQQQQQQ M QOOWOOOOOOO BOOOWOOOO000OQ MEO Quench DOOOOOOO NOQOOQOOOOOOOOOOOOOOOOOOOOO NOO Load SODOOOCOOCOODOOO O OO000000O oe P OOOQQQQQQQQQQQ
113. Release 7 1 1 Multiple instruments can co exist on the same computer 2 The fmf file is saved in the experiment folder as read only 3 Added the Sample Plate and Sensor Tray Print button on the Plate Definition tab and the plate map The associated table information prints after you click Print Figure 1 1 Octet System Data Acquisition User Guide Release 7 1 What s New in the Octet System Data Acquisition Software Release 7 1 page 9 Sample Plate 96 wells O Unassigned Import J Export Remove rink Reagent Plate 96 wells Figure 1 1 Sample Plate and Sensor Tray Print Button 4 Added a new Regeneration step that is similar to regeneration in Quantitation a On the Plate Definition tab assign wells as Regeneration or Neutralization Figure 1 2 an a a ro e z a Reference Control Buffer Activation Quench Load Wash Regeneration Neutralization Set Well Data Clear Data Copy to Clipboard Extended Sample Types Figure 1 2 Regeneration Step b Click Add Figure 1 3 to display the Add Step Definition dialog box Figure 1 4 Octet System Data Acquisition User Guide Release 7 1 page 10 Chapter 1 welcome Step Data List Add Copy l Remove l Regeneration Params jl Threshold Params Name Time Shake speed Type Threshold Baseline 60 1000 a Baseline DO gt Feaeneration 30 40
114. Run Experiment 9 Plate Definition In this step sensors are assigned to samples Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Oo Only the first sensor tray can be a partial plate Sensor Tray 7 Replace sensors in tray after use Tray Format Heterogeneous trays 5 Well Sensor Type Lot Number Information 2 3 4 6 7 m E E A1 Anti Human IgG Fc B1 Anti Human IgG Fc 7 A BEDENEN JL C1 Anti Human IgG Fc coo0g0ma0OULL E atuen gr aaa LILI Ja F G 8 mW Anti Human IgG Fc Anti Human IgG Fc ill lig JE H1 Anti Human IgG Fc A2 Anti Human IgG Fc O C E E E B2 Anti Human IgG Fc C2 Anti Human IgG Fc E C L D2 Anti Human IgG Fc HHOGOSSOO00A 2 seer 3 F2 Anti Human IgG Fc x 5 G2 Anti Human IgG Fc Legend im Unassigned sensors R3 Missing sensors H2 Anti Human gG Fc Fil Fill Plate A3 Anti Human IgG Fc B3 Anti Human IgG Fc Sample Plate C3 Anti Human IgG Fc 6 7 8 9 10 11 12 D3 Anti Human IgG Fc OC E3 Anti Human IgG Fc F3 Anti Human IgG Fc O G3 Anti Human IgG Fc H3 Anti Human IgG Fc O A4 Anti Human IgG Fc B4 Anti Human IgG Fc O O C4 Anti Human IgG Fc 0000000 rae E4 Anti Human IgG Fc 00000000 r Anti Human IgG Fc G4 Anti Human IgG Fc 00000000 Ha Ant Human 196 Fc O000 00 enum B5
115. Server desktop icon Octet System Data Acquisition User Guide Release 7 1 Restarting the GxP Server Module page 399 Restart Server Figure B 59 Restart Server Desktop Icon The Restart Server window will display momentarily as the GxP Server module restarts 2 3 Restart Server oe LE CMDLINE Starting service x 5 Figure B 60 Restart Server Window Octet System Data Acquisition User Guide Release 7 1 page 400 Chapter B 21 CFR Part 11 Software Administrator Options Octet System Data Acquisition User Guide Release 7 1 page 1 Index Symbols csv file for import creating 90 Numerics 21 CFR Part 11 compliant features accessing 59 2nd Buffer Time and Shake speed parameter 136 213 2nd plate name barcode 264 328 2nd Plate Name Barcode setting Run Experiment window settings quantitation 384 196 quantitation 96 119 2nd Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 384 Well format option 280 384 well Format Reagent Plate figure 167 96 Well format option 280 96 well Format Reagent Plate figure 167 A About ForteBio Data Acquisition menu 38 accessing GxP Server module directly 396 accessing Temperature field 12 account details assigning 385 acquisition for a data column displaying 267 331 quantitation 384 199 quantitation 96 122 acquisition options 40 Acquisition rate advanced sett
116. T 29 Set Well Data Well Information Concentration ug ml Standard only T JOO Clear Data Sample ID By value 120 B91 Copy to Clipboard Dilution series S 2o Extended Sample Types Replicate Group Starting value 1 SPOOOOOOOOOO00OG Series operator T PIOQQQQGAQGGGAGAGE _welinformation les operand 2 Dilution orientation 888 Right 888g Left 4 Down Up Figure 6 10 Sample Plate Map Assigning a Standard Concentration 2 Select the By value option and enter the starting concentration value 3 Click OK The Sample Plate Table will display the standard concentrations entered Editing an Individual Standard Concentration To enter or edit an individual standard concentration in the Conc column of the Sample Plate Table double click the value and enter a new value see Figure 6 11 Octet System Data Acquisition User Guide Release 7 1 page 152 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Sample Plate Table Concentration units ug ml A Export Import Well Sample ID Replicate Group Type Conc ug ml Dilution Factor Informatio A Standard 200 n a c Standard 100 n a Ob Standard nin Oa Standard 25 Undo on Standard 10 Cut OK Standard 5 c Om Standard 2 5 opy oi Standard 1 Paste Oa Standard 200 Delete c Standard 100 Select All OB Standard 50 aise Oc Standard 25 Right to left Reading order
117. The duration of data acquisition seconds while the biosensor is incubated in sample NOTE A subset of data points may be selected for processing during data analysis Quantitation Shake The sample platform orbital shaking speed rotations per min speed rpm ute Octet System Data Acquisition User Guide Release 7 1 page 170 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Basic Quantitation with Regeneration Assay Parameters 4 Assay Parameters Available Assays Assay Parameters Basic Quantitation with Regeneration Single analyte Multiple analyte Z High sensitivity assay with regeneration Replicates per sensortype 1 E Protein L Standard range Bf Standard Assay Time s Quantitation 120 Shake speed woo S Regeneration 5 400 p lt gt f gt Py AC EL kp lt gt al Neutralization 5 400 4 M Pre condition sensors Postcondition sensors Regeneration cycles 3 ESE lt L Figure 6 33 Assay Parameters Basic Quantitation with Regeneration Table 6 7 Assay Parameters Basic Quantitation with Regeneration Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte For multi analyte experiments using multiple biosensor types per and Replicates per sample well and the number of replicate assays in each well per
118. Time and Shake Speed parameter 172 Enzyme Time and Shake Speed pa rameter 172 Multiple Analyte parameter 171 Neutralization Time and Shake Speed parameter 172 Offline parameter 172 Post condition sensors parameter 173 Pre condition sensors parameter 173 Regeneration cycles parameter 173 Regeneration Time and Shake Speed parameter 172 Reuse Buffer parameter 172 Sample Time and Shake Speed pa rameter 172 Single Analyte parameter 171 quantitation 96 94 2nd Time and Shake Speed param eter 95 Buffer Time and Shake Speed pa rameter 95 Detection Time and Shake Speed parameter 95 Enzyme Time and Shake Speed pa rameter 95 Multiple Analyte parameter 94 133 Neutralization Time and Shake Speed parameter 95 Offline parameter 95 Post condition sensors parameter 96 Pre condition sensors parameter 96 Regeneration cycles parameter 96 Regeneration Time and Shake Speed parameter 95 Reuse Buffer parameter 95 Sample Time and Shake Speed pa rameter 95 Single Analyte parameter 94 Octet System Data Acquisition User Guide Release 7 1 page 3 Regeneration cycles 137 214 Regeneration Time and Shake speed 136 213 Sample Time and Shake speed 212 Advanced Quantitation Quantitation 384 Experiment 142 advanced run experiment settings 120 197 329 advanced settings Acquisition rate Octet QKe 121 Acquisition rate Octet RED 121 Default 121 Octet QKe listed table
119. Tray button and select a tray number from the drop down list The Sensor Tray Map and table for the tray selected will be shown and biosensor assignments can be changed as needed see Figure 5 39 Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 105 Sensor Tray Sensor Tray v Replace sensors in tray after use e of 3 Tray Format Heterogeneous trays iT 1 T Type Lot Number Information a Tray 3 B rotein A C1 Protein A D1 Protein A E1 Protein A F1 Protein A G1 Protein A H1 Protein A A2 Protein A B2 Protein A C2 Protein A L D2 Protein A HiT E2 Protein A La Feet F2 Protein A G2 Protein A H2 Protein A Remove Fill Fill Plate A3 Protein G B3 Protein G Legend _ Unassigned sensors R3 Missing sensors Figure 5 39 Tray Selection 7 To designate reference biosensors select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during acquisition 8 Optional Double click in any cell in the Lot Number column to enter a biosensor lot number All wells in the Lot Number column for that biosensor type will automatically populate with the lot number entered 9 Optional Double c
120. Well Information y Series operand 2 Dilution orientation 2888 Orem 888 Oet Well Data Sample only g Down Up Molecular Weight and Molecular Weight kD Gs Molar Concentration Molar Concentration nM la L Figure 8 8 Entering Molecular Weight and Molar Concentration from the Sample Plate Map The information displays in the Sample Plate Table see Figure 8 9 3 In the Sample Plate Table select the sample concentration units and the molar con centration units Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 285 Sample Plate Concentration units pg ml v Concentration Reagent Plate Molar concentration units nM X units Well Sample ID Replicate Group Type Conc pg ml MW kD Molar Conc nM Information OK Proteina Load 12 5 OM Proteina Load 12 5 O07 Proteina Load 12 5 A9 1XKinetics Buffer Buffer C9 1XKinetics Buffer Buffer E9 1XKinetics Buffer Buffer G9 1XKinetics Buffer Buffer 19 1XKinetics Buffer Buffer K9 1X Kinetics Buffer Buffer M9 1X Kinetics Buffer Buffer 09 1XKinetics Buffer Buffer A11 1X Kinetics Buffer Buffer C11 1X Kinetics Buffer Buffer E11 1X Kinetics Buffer Buffer G11 1X Kinetics Buffer Buffer 11 1X Kinetics Buffer Buffer K11 1X Kinetics Buffer Buffer M11 1X Kinetics Buffer Buffer 8 011 1X Kinetics Buffer Buffer Base IgG Sample 40 150 266 7 C13 human IgG Sample 20 150 133 3 E13 huma
121. a View and process the raw data Analyze the data Octet System Data Analysis Software User Guide gt NOTE Before starting an experiment check the sample plate temperature dis played in the status bar Confirm that the temperature is appropriate for your experiment and if not set a new temperature If the Octet System Data Acquisi tion software is closed the plate temperature will reset to the default startup value specified in the Options window when the software is relaunched Octet System Data Acquisition User Guide Release 7 1 Starting a Basic Kinetics Experiment page 217 STARTING A BASIC KINETICS EXPERIMENT You can start a kinetics experiment using one of the following options e Launch the Experiment Wizard e Open a method file fmf by clicking File gt Open Method File Method files may be saved and recalled using the File menu and are automatically saved when an experi ment is run For more details on method files see Managing Experiment Method Files on page 274 On the menu bar click Experiment gt Templates gt Kinetics NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indica
122. a plate definition 1 Inthe Sample Plate Map click Export see Figure 8 22 Sample Plate 384 wells W123 4 5 6 7 8 9 101112131415161718 192021222324 AMQOOOOOOOOBOOOOOOOO0OO0000O OOO000O OOOO00O O Unassigned Import Export Remove Figure 8 22 Sample Plate Map Export Button 2 Inthe Export Plate Definition window see Figure 8 23 select a folder enter a name for the plate csv and click Save a EY Export Plate Definition go m Forte Bio gt r Search Data and met P Organize 7 New folder Documents library Data and methods W Favorites E Desktop J Downloads Name lt Recent Places E Desktop t Libraries _ Documents Music amp Pictures B Videos Date modified Arrange by Folder 7 Type lt E File name 384 standard plate csv r oa Save as type csv Files csv Hide Folders Figure 8 23 Export Plate Definition Window Octet System Data Acquisition User Guide Release 7 1 page 298 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Importing a Plate Definition To import a plate definition 1 In the Plate Definition window see Figure 8 22 on page 297 click Import Sample Plate 384 wells J 1234567 8 9 101112131415161718192021 222324 Figure 8 24 Sample Plate Map Import Button 2 Inthe Import Plate Definition window see Figure 8 25
123. about the sample plate and its wells will be entered Highlight one or more wells on the sample plate and right click to enter modiify well data Sample Plate 96 wells Sample Plate Table aa Ra 7 a 9 10 11 12 Concentetioniants 2 Sample Reference Control Negative Control Positive Control Buffer fe Activation Molar concentration units Well Sample ID Pepica Group Type Conc uam MW 12 Molar Conc m Information Quench Load Wash Regeneration Set Well Data Clear Data Ozrammoonsry a Ui Copy to Clipboard vV Extended Sample Types Figure 7 3 Designating a Well Type in the Plate Definition Window To remove a well designation in the Sample Plate Map select the well s and click Remove Or right click the well s and select Clear Data see Figure 7 4 Sample Plate 36 wells Sample Plate 36 wells Pai 2 3 4 5 67 8 9 10 1 12 Wii2 3s 4 5 67 8 9 40 1 12 AMOOOOOQOOOOOD AOOG sam BOOOOOOQOOOOO BOOGE retre COOOOQQOOOCOO D COO qs lt a DOOO QQOCOOOD DOCCE necon EOOOOOOQOOOCOOD EOOGS urr FOOOOQQOOOOOD FOOGA activation GOOOSGQOOOOOD GOOG werh HOOO OOOCOOGD HOOG w Unassigned Import Export Remove Unassigned Regeneration Set Well Data Clear Data Copy to Clipboard Extended Sample Types Figure 7 4 Clearing Sample Data from a Sample Plate Octet System Data Acquisition U
124. and Sample Stage right IMPORTANT Ensure that the bottom of the sample plate and biosensor tray are flat on each stage 4 Close the Octet instrument door 5 Allow the plate to equilibrate The time required for temperature equilibration depends on the temperature that your application requires and the initial temperature of the sample plate For specific biosen sor rehydration times see the appropriate biosensor product insert Octet System Data Acquisition User Guide Release 7 1 Running a Quantitation Experiment page 117 Starting an Experiment To start the experiment 1 Click the Run Experiment tab or click the arrow gt to access the Run Experiment win dow see Figure 5 52 9 Plate Definition 9 Sensor Assignment Review Experiment Data File Location and Names Plate name barcode file prefix 110422 Auto incrementfile ID start 1 Data files will be stored as follows Assay type Basic Quantitation Standard Assay Quantitation data repository CAUsers Owner Documents ForteBio Experiment run name sub directory higG ProG Q O Run Experiment Prior to pressing Go confirm the Assay dl Total experiment time 0 18 40 Documents ForteBio higG ProG Q 110422_001 fra Documents ForteBio higG ProG Q 110422_002 frd Docurments ForteBio higG ProG Q 110422_003 frd Run Settings V Delayed experiment start Start after e 600 S F Shake sample plate wh
125. and Shake Speed parameter 93 Single Analyte parameter 93 133 Quantitation Time and Shake speed 133 170 210 Regeneration cycles 134 211 Regeneration Time and Shake speed 133 210 Basic Quantitation with Regeneration Quantitation Experiment 69 141 Basic Quantitation Quantitation Experiment 69 141 beginning an experiment 216 276 beginning the next step in the assay 271 335 binding data aligning kinetics 384 334 kinetics 96 270 exporting quantitation 384 204 quantitation 96 127 saving kinetics 384 337 kinetics 96 273 quantitation 384 204 quantitation 96 127 biosensor column active 122 199 267 331 biosensor columns default 252 316 biosensor pickup tips cleaning 343 biosensor regeneration described quantitation 384 188 Octet System Data Acquisition User Guide Release 7 1 page 8 quantitation 96 111 biosensor stage left and sample stage right figure 116 261 biosensor tray loading kinetics 384 324 kinetics 96 260 replacing biosensors 251 315 biosensor tray type 17 19 26 Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 biosensor tray loading quantitation 384 193 quantitation 96 116 biosensor type adding 49 changing figure 247 311 Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 removing 49 biosensor type changing in the Assay Definition window 258 322 biosensor type changing in the Se
126. and click Fill Or right click the selection and select Fill Figure 8 46 bottom left The software fills the selected columns in the tray Figure 8 46 bottom right Sensor Tray 7 Replace sensors in tray after use pogodi opoogo UUULULLI HHH IonmoovwvDb Legend _ Unassigned sensors R Missing sensors Remove J m J ripate Sensor Tray V Replace sensors in tray after use 7 A B c D E F G aR HEF EE Legend __ Unassigned sensors RJ Missing sensors Remove II Fill Fill Plate Figure 8 46 Changing Biosensor Location Method 2 Sensor Tray V sensors in tray after use VW iif2 3 4 5 6 7 8 9 10 11 12 Legend m Unassigned sensors bee Remove Ae Sensor Tray 7 Replace sensors in tray after use 7 A B Cc iD E F iG H Legend _ Unassigned sensors B Missing sensors renove C a Car Click Fill Plate to return the Sensor Tray Map to the default layout Using Heterogenous Trays If heterogenous biosensor trays will be used the column location of each biosensor type in the tray can be identified in the Sensor Assignment Tab Assignment of biosensors that will not be used in the assay enables the software to auto assign the biosensors that will be used in the assay by biosensor type Octet System Data Acquisition User Guide Release 7 1 page 318 Chapter 8
127. and select a biosensor type from the drop down list see Figure 6 35 left Selecta cell in the Sensor Type table column click the down arrow and select a biosensor type from the drop down list see Figure 6 35 right All wells in the Sensor Type column will automatically populate with the biosensor type selected Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 175 Sensor Tra Vv nel sensors in tray after use We ype EOL ears SN iad a Al P temo 910 11 12 B1 A auto assign A auto assign al F Anti Human IgG Fc D aAnti Mouse IgG Fv F Protein A B Anti Mouse IgG Fv Et A brotein G c i Protein A Fl A protein L Protein G G1 ASA Streptavidin D D 3 H1 AResidual Protein A Protein L A2 aAnti Penta HIS E D SA Streptavidin B2 Custom Residual Protein A C2 A F D Anti Penta HIS D2 A G I Custom ENA H C Reference Positive Control Negative Control Missing sensors Legend Rem Remove Fill 1 Set Sensor Data A Copy to Clipboard Figure 6 36 Changing Biosensor Types in the Sensor Tray Map left and Sensor Type Column right 161718192021 222324 2 To designate reference biosensors select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during a
128. as needed by selecting the biosensor type in the Sensor box and clicking Move Up or Move Down Octet System Data Acquisition User Guide Release 7 1 page 108 Chapter 5 Quantitation Experiments Octet RED96 QK and QK The order of biosensor types listed in the Sensor box will be used as the default tray assignment see Figure 5 43 F Tray Format Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical Homogeneous A different sensor tray is used for each sensor type Sensors Protein G Move Up L Figure 5 43 Biosensor Types List Order in Sensor Box 5 Click OK The software will automatically calculate the number of biosensor trays needed and assign biosensors types to each tray In the example shown in Figure 5 44 Protein A and Protein G biosensor types will be used for the multiple analyte experiment using two replicates Four homogeneous bio sensor trays two for each biosensor type will be needed for the experiment The Tray 1 Sensor Tray Map will be displayed by default Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 109 Pate Definition Sensor Assignment Review Experiment Q Run Experiment Sensor Tray Replace sensors in tray after use lt In this step sensors are assigned to samples If you have a partial sensor t
129. biosen cycles sor undergoes before reuse Advanced Quantitation Assay Parameters r j 7 Assay Parameters Available Assays Assay Parameters E Advanced Quantitation Single analyte Multiple analyte E Immunogencity Enzyme Linked Replicates per sensortype 1 Residual Protein A er j E BAECS imaisi a PISROR E Three Step Assay Sample 20 S 1000 F Offline Buffer 120 1000 V Reuse Buffer Enzyme 120 1000 F 2nd Buffer 120 1000 Detection 120 E 1000 _ Regeneration Time s Shake speed Regeneration 5 1000 Neutralization R 1000 Pre condition sensors _ Post condition sensors Regeneration cycles 3 Blue indicates a built in assay OK Cancel i Figure 6 34 Assay Parameters Advanced Quantitation Table 6 8 Advanced Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte For multi analyte experiments using multiple biosensor types per and Replicates per sample well and the number of replicate assays in each well per sensor type biosensor type Octet System Data Acquisition User Guide Release 7 1 page 172 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Table 6 8 Advanced Quantitation Assay Parameters Parameter Description SampleTime s and The duration o
130. chang ing system and software options Exit N A Closes the application after prompting users to save any changes View Menu The View menu allows users to show or hide the Toolbar and status windows A check mark next to the menu item indicates the option is currently shown Experiment Instrumen v Toolbar v Status Bar Y Instrument Status Figure 3 5 View Menu Table 3 2 View Menu Commands Menu Command Function Toolbar Shows or hides the Toolbar Status Bar Shows or hides the Status bar Instrument Status Displays the Instrument Status window Experiment Menu The Experiment menu provides access to the Experiment Wizard assay and experiment options as well as experiment templates Octet System Data Acquisition User Guide Release 7 1 Software Overview page 35 Instrument Security Window New Experiment Wizard Ctrl N Edit Assay Parameters Edit Sensor Types Set Plate Temperature Templates Skip Step Stop Figure 3 6 Experiment Menu Table 3 3 Experiment Menu Commands Menu Command Toolbar Button Function New Experiment Wizard Opens the Experiment Wizard Edit Assay Parameters N A Opens the Edit Assay Parameters dialog box to define a new assay edit an existing assay or remove an assay from the quantita tion application See Managing Assay Parameter Settings on page 167 for more information Edit Sensor Types N A Open
131. changes and exit Deleting a User Group 1 Right click on the group and select Delete Group from the Tab menu 2 Click OK in the dialog box displayed Project Administration The Projects Tab allows administrators to add and delete user projects Projects are selected when a new user session is initiated in the Data Acquisition or Data Analysis soft ware allowing all user system and software events for a particular project to be monitored Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 391 _E ForteBio GxP Server Admininstrati users Groups Projects Constants Events Name Info Receptor Ligand screen Affinity Screen Antigen Antibody screen Off rate determination Cell Culture screen Protein quantitation Figure B 44 Projects Tab Creating a New Project 1 Right click anywhere in the Projects Tab and select New Project from the Tab menu or double click in a blank area The New Project dialog box will display Project name Information Figure B 45 New Project Dialog Box 2 Enter the Project name and Information optional 3 Click OK to save changes and exit Viewing and Changing Project Settings 1 Right click on the project and select Edit Project from the Tab menu or double click on the project The Edit Project dialog box will display Octet System Data Acquisition User Guide Release
132. charts automatically check box 267 Octet System Data Acquisition User Guide Release 7 1 page 23 Open runtime charts automatically option 326 Open Windows menu 37 opening dialog box to select an experiment method file 33 Edit Assay Parameters dialog box 35 Experiment Wizard 35 online Data Acquisition User Guide 38 Runtime Binding Chart 268 332 quantitation 384 200 quantitation 96 123 Sensor Types dialog box 35 Temperature Setting dialog box 35 web browser 38 optics Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 Options dialog box displayed figure 41 setting FRD file format to the earlier 5 0 for mat 34 significant digits 34 viewing analysis options 41 Options dialog box figure 41 Options dialog box Automation Interface selection figure 347 Options menu 34 orbital flow capacity Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 20 27 organizing windows in a cascade arrangement 37 P panel Octet instrument removing 343 parameter settings assay modifying quantitation 384 167 quantitation 96 91 parameter values editing quantitation 384 208 quantitation 96 131 partial biosensor trays using 256 kinetics 384 320 password reminder user and administrator figure 57 plate definition exporting kinetics 384 297 kinetics 96 233 quantitation 384 163 quantitation 96 88 impo
133. command or response is terminated with a new line CR LF sequence Parameters containing embedded spaces need to be enclosed in double quotes Automation Interface Control Setup Before the Octet System Data Acquisition software can be controlled using an automation interface the correct automation options must be set To do this go to File gt Options Figure A 1 and select the appropriate port in the Automation box NOTE The Octet System Data Acquisition software can be controlled via auto mation interface through a serial port RS 232 or a TCP IP socket Octet System Data Acquisition User Guide Release 7 1 Design of the Automation Interface page 347 r Options Data Files Quantitation data repository C Temp _ Kinetics data repository C Temp Use old 5 0 file format for FRD files Use extended sample types Startup Simulation Temperature 30 Lal oc Tf no instrument is connected the application is configured using the properties of the selected instrument aaa Octet QK Octet RED384 Significant digits 4 es 2 OctetRED Octet Qk384 Octet RED96 Octet QKe Web Server Port 8080 192 168 1 78 Refresh s 10 192 168 1 75 Automation TCP IP Port 20000 Localhost E Serial RS232 Port 5 Figure A 1 Options Dialog Box Automation Interface Selection S NOTE The Localhost opt
134. done for 77 Sleep 200 if SendRecv pPort AUT_CMD_STATUS AUT_EOL csResp return false int nStart 0 CString csStatus csResp Tokenize nStart if csStatus AUT _OK break SUCCESS else if csStatus AUT STOPPED break SUCCESS else if csStatus AUT RUNNING else if csStatus AUT WAITING else if csStatus AUT _LOADSENSORS if LoadSensors pPort return false else if csStatus AUT BUSY else if csStatus AUT ERROR return false bool LoadSensors CCmdTransport pPort if SendRecv pPort AUT_CMD_PRESENT AUT_EOL csResp return false if csResp AUT _OK return false Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 355 if WaitNotBusy pPort return false At this point the robot replaces the sensor tray AfxMessageBox Robot changes sensor tray if SendRecv pPort AUT CMD RESUME AUT EOL csResp return false if csResp AUT OK return false return WaitNotBusy pPort bool WaitNotBusy CClientResponder pPort CCountdownTimer Timer c_uBusyTimeoutMS CString csResp while Timer IsDone Sleep 200 if SendRecv pPort AUT _CMD_ STATUS AUT EOL csResp return false int nStart 0 CString csStatus csResp Tokenize nStart if csStatus AUT OK returni trus else if csStatus AUT_STOPPED return fals
135. during operation of the instrument ForteBio recommends saving a copy of the system log to better assist our technical support staff in diagnosing the issue The instrument log automatically resets when the Octet System Data Acquisi tion software application is closed Octet System Data Acquisition User Guide Release 7 1 page 40 Chapter 3 Getting Started Experiment Wizard The Experiment Wizard guides users through the complete set up of an experiment Using the wizard is described in detail in the Quantitation and Kinetics experiment chapters D Experiment Wizard Choose an option to start a New Quantitation Experiment fal Basic Quantitation Basic Quantitation with Regeneration Advanced Quantitation eek New Kinetics Experiment Basic Kinetics Figure 3 13 Experiment Wizard OCTET SYSTEM DATA ACQUISITION OPTIONS Acquisition options allow users to set system and data preferences for quantitation and kinetic data acquisition To view user options Figure 3 14 click File gt Options from the Main Menu Octet System Data Acquisition User Guide Release 7 1 Octet System Data Acquisition Options page 41 gt Options Data Files Quantitation data repository C Temp iii Kinetics data repository C Temp i aii l Use old 5 0 file format for FRD files Use extended sample types Startup Simulatio
136. example an acidic pre conditioning buffer maximizes the binding competence of Protein A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Regeneration The number of regeneration neutralization cycles that a biosen cycles sor undergoes before reuse NOTE In an Advanced Quantitation experiment this option is only available if the first step biosen sor incubation in sample is performed online ASSIGNING BIOSENSORS TO SAMPLES After the sample plate is defined biosensors must be assigned to the samples Biosensor Assignment in Single Analyte Experiments In a single analyte experiment only one biosensor type is assigned to each sample and only one analyte is analyzed per experiment NOTE For single analyte experiments the Single Analyte option must be selected in the Assay Parameters dialog box For more information please see Managing Assay Parameter Settings on page 91 Click the Sensor Assignment tab or click the arrow to access the Sensor Assignment window see Figure 5 30 The software generates a color coded Sensor Tray Map and Sample Plate Map that shows how the biosensors are assigned to the samples by default Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 97 Piate Definition Sensor Assignment
137. fmf Protein L biosensor_16CH_96W fmf Protein L biosensor_8CH_96W fmf Templates Skip Step Stop Figure 6 55 Experiments in the Template Folder Octet System Data Acquisition User Guide Release 7 1 Running a Quantitation Experiment page 193 RUNNING A QUANTITATION EXPERIMENT D IMPORTANT Before starting an experiment ensure that the biosensors are properly rehydrated For details on how to prepare the biosensors see the appropriate biosensor product insert Loading the Biosensor Tray Sample and Reagent Plates To load the biosensor tray sample plate and reagent plate 1 Open the Octet instrument door lift the handle up and present the instrument stage click the Present Stage button EJ 2 Place the biosensor tray sample plate and reagent plate on the appropriate stage so that well A1 is located at the upper right corner see Figure 6 56 a Place the rehydration plate and biosensor tray on the biosensor stage left plat form b Place the sample plate on the sample stage middle platform c Optional Place the reagent plate on the reagent stage right platform if you are using a reagent plate Well A1 Position Figure 6 56 Octet Instrument t Stage Platform IMPORTANT Ensure that the bottom of the sample plate reagent plate bio sensor tray and rehydration plate are flat on each stage 3 Click E to close the Octet instrument door 4 Allow the pla
138. heterogenous trays 1 Select the column location of the biosensor type see Figure 8 48 Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 319 Sensor Tray v Replace sensors in tray after use F i 2 3 4 5 6 7 8 9 100 1 12 Well Sensor Typ Lot Number Information AOO OOM mom E E AHC Anti hIgG Fc Capture es DPpM rram anc antehigG Fc Capture OO AKC AntehigG Fc Capture cHoOOEs AH Ant higG Fe Capture DOO OOoo AHC AntrhigG Fc Capture LS E F G LIL _ Iai TL AC Ant higG Fc Capture gt AC Ant higG Fe Capture _ _ _ me ANC AnthgG Fe Capture M anc anthias Fc Capture m e as L eee AHC Anti higGFcCapturey H O O E C E AHC Anti hIgG Fc Capture ey p AHC Anti hIgG Fc Capture lt Legend __ Unassigned sensors R Missing sensors AHC Anti higG Fc Capture AHC Anti hIgG Fc Capture Remove m mpate A3 AHC Anti hIgG Fc Capture B3 AHC Anti hIgG Fc Capture Figure 8 48 Selecting a Sensor Tray Column 2 Right click in the Sensor Tray Map or click in a cell in the Sensor Type table column and select a biosensor type from the drop down list The biosensor type associated with the assay will shift location accordingly see Figure 8 49 In the example shown AHC is the Sensor Type used for the current ass
139. hour warm up time It is recommended that you leave the instrument on for a minimum of eight hours prior to use 3 Launch the Octet System Data Acquisition software by double clicking on the Data Acquisition desktop icon Data Acquisition Figure 3 1 Desktop Icon Octet System Data Acquisition User Guide Release 7 1 Software Overview page 31 NOTE When using the CFR 11 version of the Octet System Data Acquisition software users are required to log in and start a user session before the soft ware will launch Please refer to Starting a User Session on page 56 for more information SOFTWARE OVERVIEW Launching the application displays the Octet System Data Acquisition software Main Screen Screen components along with the default windows displayed are shown in Figure 3 2 Main EF octet Data Acquisition 7 00 65 ens Menu File View Experiment Instrument Security Window Help _ aman PEL 23 fort so Toolbar 16 0 Waiting to initialize 16 07 24 Initializing 16 07 27 Instrument intialzed 16 07 27 Ready Instrument Status Window Status Bar sument Ready Experiment Not Started Plate temp 30 C Experiment Wizard Figure 3 2 Main Screen Main Menu and Toolbar The Main Menu and Toolbar are located in the upper left corner of the Main Screen Figure 3 3 Men
140. includes reference biosensors you can display reference subtracted data in the chart by clicking the Subtract Reference Biosensor check box in the chart window To view raw data remove the check mark next to this option Reference biosensors can be designated e During experiment setup in the Sensor Assignment tab e During acquisition in the Runtime Binding Chart Sensors to Chart box e During analysis in the Data Selection tab Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 333 Designating a Reference Biosensor During Acquisition To designate a reference biosensor during acquisition 1 In the Sensors to Chart list or the Sensor Tray right click a biosensor and select Refer ence see Figure 8 59 Current Binding Charts Kinetics Assay 1 Kinetics Assay 2 Sensors to Chart SelectAll sensor as Sensor A iSensor B6 Sensor 57 PSensor C6 Sensor c7 sensor Reference sensor F6 Sensor F sensor G6 isensor G sensor H6 sensor H __ Subtract reference sensors Figure 8 59 Designating a Reference Biosensor in the Runtime Binding Chart The selected biosensor will be shown with an R in the Sensors to Chart list and Sensor Tray see Figure 8 60 2 Click the Subtract reference sensors check box see Figure 8 60 Current Binding Charts Kinetics Assay 1 Kinetics Assay 2 Sensors to Chart Sensor As Sensor A iSensor B6 Se
141. it may require more than one tray of sensors to complete the experiment This can be detected at the start of the experiment by checking the tN response from the GetMethodInfo command If N is greater than 1 then the exper iment requires more than one tray of sensors to complete If this is the case initially the experiment will start as before but halfway through the exper iment the Status command will return LoadSensors indicating that the first tray of sensors has been exhausted and another tray of sensors needs to be loaded At this point you must issue the Present command to allow access to the sensor plate polled for completion and then once the new sensor tray is in place the Resume command must be sent to resume the experiment Connecting to Data Acquisition SEND Version r n RECV 6 1 0 30 Pegasys 1 0 SEND Status r n RECV OK Preparing for an Experiment SEND Cleanup RECV OK SEND GetMethodInfo mC MethodFiles Q002 fmf r n RECV OK p96 0 t2 s Anti Human IgG Fc Starting the Experiment SEND Run mC MethodFiles Q002 fmf bP0001 s r n RECV OK Getting Information about the Experiment SEND GetRunInfo r n RECV OK n Experiment 2 p fbdata Quantitation Experiment 2 r n Octet System Data Acquisition User Guide Release 7 1 page 354 Chapter A Using Octet384 Systems with an Automation Interface Monitoring the Experiment bool MonitorExperiment CCmdTransport pPort Poll the experiment until it is
142. kinetics 384 330 GetMethodInfo automation interface command 349 GetRunInfo automation interface command 349 GetRunInfo command 347 Gradient threshold parameter 239 305 group administration 388 group settings changing 390 viewing 390 Groups tab figure 388 GxP Server Address search results figure 54 GxP Server Configuration window figure 397 GxP Server module accessing directly 396 restarting 398 H Heat hot symbol 13 Help menu described 38 figure 38 list of menu commands 38 heterogeneous biosensor trays assigning biosensors quantitation 384 178 quantitation 96 101 using kinetics 384 317 kinetics 96 254 hiding main toolbar 34 status bar 34 higher acquisition rate 120 197 329 Homogeneous biosensor trays assigning biosensors quantitation 384 183 quantitation 96 106 icons Data Acquisition 8 Data Analysis 8 Import button 89 Import button figure 234 Import Plate Definition window quantitation 384 164 quantitation 96 89 Import Plate Definition window figure 234 importing plate definitions kinetics 384 298 kinetics 96 234 Octet System Data Acquisition User Guide Release 7 1 page 18 importing plate definition quantitation 384 164 quantitation 96 89 inserting assay steps 245 310 installing Data Acquisition 7 0 CFR Part 11 software 366 Data Analysis 7 0 CFR Part 11 software 369 ForteBio GxP Server 372 ForteBio GxP Server module 371 Instrument menu described
143. layout Sensor Tray Sensor Tray M Replace sensors in tray after use v Replace sensors in tray after use PW i234 6 6 7 8 8 0 12 F ri 2 3 4 5 6 7 e 10 11 e AES B O c LJ D LJ E O F m cmon G O HEE Legend Unassigned sensors RA Missing sensors Legend __ Unassigned sensors RA Missing sensors Remove Fu __FilPlate Remove Fu _FilPate Figure 7 40 Changing Biosensor Location Method 1 Method 2 1 Inthe Sensor Tray Map select all of the columns and click Remove Figure 7 41 top left Or right click the selection and select Remove All columns will be shown as Miss ing Figure 7 41 top right 2 Select the column s to use and click Fill Or right click the selection and select Fill Figure 7 41 bottom left The software fills the selected columns in the tray Figure 7 41 bottom right Octet System Data Acquisition User Guide Release 7 1 page 254 Chapter 7 Kinetics Experiments Octet RED96 QK and QK oe in tray after use pl in tray after use 7 E 7 A cl Ee ES eel EES Eee Es Ee BL B Ess 5 Es Es Bs BB c ggZ gt OOL DD Eee Es Es EQUOUULUUOUOO ERB RE Bee ae ees FODOUUOUULOUOOo F Ee FS ES sOOOCOCOO0OO0007 scBkSeEsenogEs HODOOOOOOOOO He Be ed Ee Ee EF eB Legend Unassigned sensors A Missing sensors Legend Unassigned sensors B Missing sensors Remove a a Remove Fu
144. login Instrument Ready Experiment Not Started Plate temp 35 C Project Antigen Antibody screen amp User JBlack John Black Octet System Data Acquisition User Guide Release 7 1 Software Overview page 39 Instrument Status Window The Instrument Status window displays a log of all instrument activity 2 Instrument Status sien x Hl 14 47 39 Sensor 7 Integration Time 1 0 ms H 14 47 39 Sensor 8 Integration Time 1 0 ms H 14 47 40 Picking sensors completed location A1 14 47 40 Plate temperature 30 C 14 47 40 Ready to move to sample location A1 14 47 40 Moving to sample location A1 14 47 41 Arrived at sample location A1 14 47 41 Waiting to start sample location A1 14 47 41 Processing sample location Al 14 47 51 Sample completed location A1 E 14 47 51 Waiting to start new step 14 47 51 Starting new step 14 47 52 Ready to move to sample location A2 14 47 52 Moving to sample location A2 14 47 53 Arrived at sample location A2 14 47 53 Waiting to start sample location A2 E 14 47 53 Processing sample location A2 LJ ii gt v Auto scroll to bottom Save to File Figure 3 12 Instrument Status Window Selecting the Auto Scroll to bottom check box will auto scroll the log to display the most current events Clicking Save to File will save a copy of the instrument log NOTES 9 Ifa problem occurs
145. mi x Export Import Well Sample ID Replicate Group Type Conc jig ml Dilution Factor Information OA hig Standard 200 n a humanigG M oc Standard 100 n a E Standard 50 n a ci Standard 25 n a on Standard 10 n a OK Standard 5 n a Figure 8 14 Add Sample Annotations in the Sample Plate Table Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sample Plate Table To view edit com mands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Replicate Groups Replicate Groups enable data to be organized into custom groups during data analysis see Figure 8 15 Octet System Data Acquisition User Guide Release 7 1 page 290 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Index Include Color SensorLocation Sensor Type SensorInfo Replicate Group Baseline Loc lt 2 x E c SA Streptavidin 3 C3 a x ae c2 SA Streptavidin 3 c3 220 x E 2 SA Streptavidin 4 D3 23 x D2 SA Streptavidin 4 D3 24 x E2 SA Streptavidin 5 E3 25 x E2 SA Streptavidin 5 E3 2 x ae 2 SA Streptavidin 6 F3 27 x ae 2 SA Streptavidin 6 F3 2 x E c2 SA Streptavidin 6 G3 2
146. minute with the door open Biosensor Pickup Tips Sample Platform Biosensor Platform Figure 9 1 Octet Instrument Emptying the Waste Container To empty the waste container 1 Press on the container to open it Figure 9 2 2 Pull the container out and completely remove it from the instrument 3 Remove the container insert with the biosensor tips and dispose of both in a biohazard container suitable for sharp objects NOTE ForteBio recommends that the waste container be emptied after every run of a 96 biosensor tray Octet System Data Acquisition User Guide Release 7 1 Octet RED96 and Octet QK Systems page 341 Waste container Figure 9 2 Waste Container for the Octet Instrument Replacing Fuses Octet RED96 and Octet QK Systems only Two replaceable fuses are located on the left back panel of the Octet instrument power supply Figure 9 3 WARNING Turn off and unplug the instrument before replacing the fuses octet fort sio www fortebio com Instrument 1360 Willow Road Suite 201 Menlo Park CA 94025 USA Power Supply TOSE RINA Power OFF ON Replace with same type and rating as marked r Ne remplacer le fusible que par un fusible de EEE type et de m me puissance FOAL asov 100 240 V Max 5A 50 60 Hz Model Octet RED MANHUNT om _CE Figure 9 3 Octet Instrument Power Supply Back Panel To replace the fuses 1 Using a small screw
147. only Events in the Audit Trail can be sorted by clicking on any of the column headers Date Time Project 2011 04 24 12 07 24 Antigen Antibody screen 2011 04 13 22 33 48 Antigen Antibody screen 2011 04 13 21 52 57 Antigen Antibody screen 2011 04 13 21 14 37 2011 04 13 21 12 48 2011 04 05 13 54 51 2011 04 05 10 16 25 2011 04 05 10 16 17 2011 04 05 10 15 54 2011 04 05 10 15 45 2011 04 05 10 13 41 2011 04 05 10 13 32 2011 04 05 10 02 13 2011 04 04 12 59 34 Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Figure 4 19 Audit Trail Events Sorted by Date Time Machine JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS Action User login User logout User login User logout User login User logout User login User logout User login User logout User login User logout User login User logout Description a m By default the events initially displayed in the Audit Trail will be those associated with the project selected at login and the machine computer currently being used To view events for a specific project or computer click on the Project or Machine drop down list and select an entry B Audit Trail any Date Tim Antigen Antibody screen 2011 02 Cel
148. optic biosensors with optional reuse by regeneration and or re racking Biosensor Tray Type Optics and Mechanics 8 x 12 format 96 biosensor tip tray green color 8 channel biosensor manifold Optical interferometer Eight spectrometers one dedicated spectrometer per bio sensor Throughput Orbital Flow Capacity Up to 8 biosensors in parallel maximum of 96 tests unat tended One 96 well plate and one biosensor tray at once Static or 100 1 500 rpm Temperature Range Ambient 4 C 40 C 1 C increments Dimensions 18 6 H x 17 W x 20 8 D 47 cm H x 43 cm W x 53 cm D Weight 63 Ib 28 6 kg Electrical Requirements Mains AC 100 240 V 5 0 2 0 A 50 60 Hz single phase Power consumption 120 W 240 W peak Octet System Data Acquisition User Guide Release 7 1 page 18 Chapter 2 Octet System Specifications OCTET RED384 SYSTEM SPECIFICATIONS Biosensor tray amp rehydration plate Sample plate stage fort si Prt sio Reagent plate stage Biosensor chute to waste Automatic Sliding Door Figure 2 2 Octet RED384 Instrument Door Closed Left or Open Right Table 2 2 Octet RED384 System Specifications Item Description Equipment e Product Classification Class 1 Detachable power cord Classifications Installation Overvoltage Category Category II e Pollution Degree Degree 2 EMC Classification Group Class A ISM Equipment EN5
149. quantitation 384 157 quantitation 96 82 assigning dilution factor quantitation 384 154 quantitation 96 79 assigning serial dilution quantitation 384 154 quantitation 96 79 selecting in the Sample Plate Map kinetics 96 219 quantitation 384 148 quantitation 96 73 window icons arranging 37 Window menu described 37 list of menu commands 37 windows organizing in a cascade arrangement 37 tiling vertically 37 Octet System Data Acquisition User Guide Release 7 1 page 40 Octet System Data Acquisition User Guide Release 7 1 page 1 Index Symbols csv file for import creating 90 Numerics 21 CFR Part 11 compliant features accessing 59 2nd Buffer Time and Shake speed parameter 136 213 2nd plate name barcode 264 328 2nd Plate Name Barcode setting Run Experiment window settings quantitation 384 196 quantitation 96 119 2nd Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 384 Well format option 280 384 well Format Reagent Plate figure 167 96 Well format option 280 96 well Format Reagent Plate figure 167 A About ForteBio Data Acquisition menu 38 accessing GxP Server module directly 396 accessing Temperature field 12 account details assigning 385 acquisition for a data column displaying 267 331 quantitation 384 199 quantitation 96 122 acquisition options 40 Acquisition rate advanced settings Octet QK384 Kinetics 330 Octet
150. rToamoonyrp v Subtract reference sensors 2345 67 8 9 101112 Figure 7 55 Subtract Reference Sensors check box in the Runtime Binding Chart NOTE Subtracting reference data in the Runtime Binding Chart only makes a visual change to the data on the screen The actual raw data is unaffected and the reference subtraction must be repeated during data analysis if needed Viewing Inverted Data The data displayed in the Runtime Binding Chart can be inverted during real time data acquisition or data analysis after the experiment has completed To invert data select the Flip Data check box see Figure 7 56 Uncheck the box to return to the default data display Assay Step Status Experiment Progress Step 17 of 17 Step details Assay 3 of 3 Elapsedtime Total exp time 10s 0s be Equilibration 5190 5 5190 s 2 57 13 2 57 13 z_ e se a 0 0 0 5 Binding nm N o 2 5 1 WN 1 1 1 I 30 1 0 0 500 1000 1500 2000 2500 3500 Time sec 3000 Sensor A1 Sensor B1 Sensor C1 Sensor D1 Sensor E1 Sensor F1 Figure 7 56 Data Inverted Using Flip Data Function Extend Current Step gt Go to Next Step v Flip Data 4000 4500 5000 Sensor G1 Sensor H1 Octet System Data Acquisition User Guide Release 7 1 page 270 Chapter 7 Kinetics Experiments Octet RED96 QK and QK
151. select the plate definition csv and click Open 7 lt 2 Import Plate Definition g E Forte Bio tr Search Data and met P Organize New folder g OF amp a 3 k Favorites Documents library range by Folder EE Desktop Data and methods J Downloads Recent Places Name Date modified Type m 4 384 standard plate csv 4 22 2011 6 41PM _ Microsoft Excel C E Desktop I Libraries Documents J My Documents J Public Documents Music 5 Pictures a Videos B m r File name 384 standard plate csv v CSV Files csv mi cn Figure 8 25 Import Plate Definition Window NOTE You can also create a csv file for import Figure 8 26 shows the appro priate column information layout Octet System Data Acquisition User Guide Release 7 1 Working with a Reagent Plate page 299 A B 8 D 1 PlateWells 384 2 Well ID Replicate Group Group 3 A1 1X Kinetics Buffer Buffer 4 C1 1X Kinetics Buffer Buffer omy E1 1X Kinetics Buffer Buffer 6 G1 1X Kinetics Buffer Buffer 7 H 1X Kinetics Buffer Buffer 8 K1 1X Kinetics Buffer Buffer 9 M1 1X Kinetics Buffer Buffer 10 01 1X Kinetics Buffer Buffer 11 A3 1X Kinetics Buffer Buffer 12 c3 1X Kinetics Buffer Buffer 13 E3 1X Kinetics Buffer Buffer 14 G3 1X Kinetics Buffer Buffer 15113 1X Kinetics Buffer Buffer 16 K3 1X Kinetics Buffer Buffer 17 M3 1X Kinetics Buffer Buffer 18 03 1X Kinetics Buffer Buffer 19 AS
152. steps will be adjusted Horizontally by 1 verticaly by one rc Figure 8 36 Replicating Assay Steps by Appending Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 309 4 Click OK The step s appear at the end of the assay in the Assay Steps List Table 8 5 Replicate Steps Options Item Description Add as a new assay Adds the replicate step s as a new assay to the Assay Steps List Append to current assay Adds the replicate step s to the end of the current assay Offset steps Assigns the replicate steps to different columns in the sam ple plate Sample steps only Applies the offset to the sample plate only All steps Applies the offset to the sample plate and reagent plate Sample steps will be Specifies the column in which to add the new step s For adjusted horizontally by X example if a step in column 11 is copied and the replicate columns step should begin in column 12 enter 1 Enter 0 to apply the step s to the same columns Sample steps will be Choose this option to put the replicate step in the same adjusted vertically by one column but the next row row Starting a New Assay Anew assay will utilize a new set of biosensors To start a new assay using the next available sensor column 1 Select a column in the Sample Plate Map 2 Right click to view the shortcut menu and select Start New Assay see Figure 8 37 3 Add steps
153. the plate while plate until the experiment starts waiting Open runtime Displays the Runtime Binding Chart for the current biosensor dur charts auto ing data acquisition matically Automatically Saves an image jpg of the Runtime Binding Chart The binding save runtime data frd is saved as a text file regardless of whether a chart image is chart created Set plate tem Specifies a plate temperature and enters the temperature in the dia perature C log box If not selected the plate temperature is set to the default temperature specified in File gt Options The factory set default tem perature is 30 C NOTE If the actual plate temperature is not equal to the set plate temperature a warning displays and the Octet System Data Acquisition software provides the option to wait until the set temperature is reached before proceeding with the run continue without wait ing until the set temperature is reached or cancel the run Advanced settings are available for Octet RED384 and Octet QK384 systems The signal to noise ratio of the assay can be optimized by selecting different acquisition rates The acqui sition rate refers to the number of binding signal data points reported by the Octet system per second and is reported in Hertz per second A higher acquisition rate generates more data points per second and monitors faster binding events better than a slower acquisition rate A lower acquisition rat
154. the Sample Plate Table quantitation 384 162 quantitation 96 87 defined 226 quantitation 384 159 quantitation 96 84 displayed in Sample Plate Map quantitation 384 figure 161 quantitation 96 figure 86 displayed in Sample Plate Table quantitation 384 figure 161 quantitation 96 figure 86 Replicate Groups displayed in Sample Plate Map figure 229 Replicate Groups in Sample Plate Table figure 229 replicate steps All steps option 244 309 Append as new assay option 244 309 Append to current assay option 244 309 Offset steps option 244 309 options table 244 309 Sample steps only option 244 309 Sample steps will be adjusted by vertically by one row option 244 309 Sample steps will be adjusted by X column option 244 309 Replicate Steps dialog box figure 243 requirements for reserved wells 72 reserved column changing location quantitation 384 146 quantitation 96 72 Reserved Well requirements 72 146 reserved well requirements 72 Detection quantitation 384 146 quantitation 96 72 Octet System Data Acquisition User Guide Release 7 1 page 28 Neutralization quantitation 384 146 quantitation 96 72 Regeneration quantitation 384 146 quantitation 96 72 reserved wells 72 reserved type of well 71 145 Reset automation interface command 349 Reset menu 36 resetting Octet instrument 36 Restart Server desktop icon figure 399 Restart Server window figure 399 re
155. the analyte from the ligand Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 219 Selecting Wells in the Sample Plate Map There are several ways to select wells in the Sample Plate Map Click a column header or select adjacent column headers by click hold drag To select non adjacent columns hold the Ctrl key and click the column header Figure 7 2 left Click a row header or select adjacent row headers by click hold drag Figure 7 2 cen ter Click a well or draw a box around a group of wells Figure 7 2 right Sample Plate Sample Plate 96 wells 5 6 7 8 9 1 1 12 OOOOOOOO QOQOOOOOOOOO QOQOOOOOOOOO QOQOOOOOOOOO Q Q O 7 A B c D E F G H O Sendari i i 5 il O Sanders Controt_ O Unassigned O _ Unknown D eee Orne O tenown Reference O Reserved Figure 7 2 Selecting Wells in the Sample Plate Map NOTE Shift clicking in the Sample Plate Map mimics the head of the instru ment during the selection Designating Well Types In the Sample Plate Map select the wells right click and select a sample type see Figure 7 24 Octet System Data Acquisition User Guide Release 7 1 page 220 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Piate Definition Assay Definition Sensor Assignment Q Review Experiment Run Experiment Inthis step all the information
156. the bitmap image generated at the end of the run Sensor E3 sensor F3 iSensor G3 Sensor H3 sensor Ga SensorH4 roammooor noze at zonmonor N Subtract reference sensors Experiment Progress Step 4 of 4 1208 1208 Elapsed exp time 0 10 13 Total experimenttime 0 10 13 Lg CAUsers Owner Documents Contracting Forte Bio User_Guides Data and methods 384 04 27 11 384 Q hlgG Quantitation Runtime Binding Chart ston x Current Binding Charts Sensors to Chart Plate Status Plate Legend Select All Sensor Tray Sample Plate 1234567 8 9101112 12345678 9 101112191415161718192021222724 Selected Sensor Ad CEA EEEE C Sample Column 13 eoecscece Processed e oeeend Data Error e O Reseved E Sensor Fail Flip Data Binding nm NO hs 0 10 20 30 40 50 60 Time sec Sensor A3 Sensor B3 Sensor C3 Figure 6 60 Runtime Binding Chart Window Opening a Runtime Binding Chart After an experiment is run you can open and review the Runtime Binding Chart at any time 1 Click File gt Open Experiment 70 80 90 100 110 120 Sensor D3 2 Inthe dialog box that appears select an experiment folder and click Select Octet System Data Acquisition User Guide Release 7 1 Managing Runtime Binding Charts page 201 Viewing Reference Subtracted Data If the experiment includes reference biosensors you can d
157. the data frd files Click Browse to select another data loca tion NOTE It is recommended that you save the data to the local machine first then transfer to a network drive Experiment Specifies a subdirectory name for the data files frd The software Run Name generates one data file for each biosensor that includes the data from sub directory all steps the biosensor performs Plate name A user defined field where you can enter text or a barcode barcode barcode file reader required prefix 2nd Plate A user defined field where you can enter text or a barcode barcode name barcode reader required for a second plate This field is also used to generate the path of the saved directory Auto Incre Each file is saved with a number after the plate name For example if ment File ID the Auto Increment File ID Start number is 1 the first file name is Start xxx_001 frd Octet System Data Acquisition User Guide Release 7 1 Running a Kinetics Experiment page 329 The following Run Settings are available on the Run Experiment Tab Table 8 7 Run Settings Item Description Delayed experi Specifies a time delay for the start of the experiment Enter the num ment start ber of seconds to wait before the experiment starts after you click Q Start after Enter the number of seconds to delay the start of the experiment Shake sample If the experiment has a delayed start time this setting shakes
158. to each assay in the experiment In the Review Experiment window move the slider left or right to highlight the biosensors and samples in an assay or click the gt arrows to select an assay Slider Plate Definition Sensor Assignmeht Review Experiment Run Experiment wo In this step you can review thE steps that make up the experiment moving the slider to change the active step A 7 ssay g led foa Sensor Tray Sample Plate 96 wells y 4 2 3 a s E Tt UEU 8 10 11 y ft 2 3 4 e T 8 9 16 _ 41 nR A a A QQDDOOOOOOO BEODBOESOO B C OOOO O000O cC UE0D8B0O COOOODDOOOOOOOD DEUOBOEBOO DO QOOOOOO00CO EETA NAA E OOOOOOO0O0O F m a a a E F O OOOOOOO O00O cmrmogamgg G Q ODDOOOOOOO H E A E A E E HO O OO O O000O Legend Unassigned sensors BY Missing sensors Legend Unassigned Samples Pie charts Step Information Assay 3 Step 1 Type Sample Time 120s FlowRate 200 rpm Sensor Protein G Figure 5 49 Review Experiment Window SAVING EXPERIMENTS After a run the software automatically saves the experiment information that you specified sample plate definition biosensor assignment assay settings to an experiment method file fmf If you set up an experiment but do not start the run you can manually save the experiment method To manually save an exper
159. tray are flat on the stages Click ao to close the Octet instrument door 4 Allow the plate to equilibrate The time required for temperature equilibration depends on the temperature that your application requires and the initial temperature of the sample plate For specific biosen sor rehydration times see the appropriate biosensor product insert Starting the Experiment To start the experiment 1 Click the Run Experiment tab or click the arrow to access the Run Experiment window see Figure 8 55 Octet System Data Acquisition User Guide Release 7 1 page 326 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Plate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment Data File Location and Names Prior to pressing Go confirm the Assay Kinetics data repository CAUsers Owner Documents ForteBio cas Experiment run name sub directory Experiment_1 E Total experiment time Plate name barcode file prefix FB100 1 02 28 2nd Plate name barcode Auto increment file ID start 1 Data files will be stored as follows Docurnents ForteBio Experiment_1 FB100_001 fra Documents ForteBio Experiment_1 FB100_002 frd Documents ForteBio Experiment_1 FB100_003 frd Run Settings v Delayed experiment start 7 Open runtime charts automatically Start after s 300 F Automatically save runtime chart Shak
160. waste container To return the biosensors to the tray click the Replace sen sors in tray after use check box see Figure 5 32 Sensor Tray v Replace sensors in tray after use HOOO IEC Legend Unassigned sensors 683 Missing sensors Remove Fill Fill Plate Figure 5 32 Replace Sensors in Tray After Use Check Box NOTE Biosensors can be regenerated up to a max of 11 times per experiment Biosensor Assignment in Multiple Analyte Experiments In a multiple analyte experiment more than one biosensor type is assigned to the same sample allowing multiple analytes to be analyzed in a single experiment NOTE For multiple analyte experiments the Multiple Analyte option must be selected in the Assay Parameters dialog box For more information please see Managing Assay Parameter Settings on page 91 Octet System Data Acquisition User Guide Release 7 1 page 100 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Click the Sensor Assignment tab or click the 5 arrow to access the Sensor Assignment window see Figure 5 30 The software generates a color coded Sensor Tray Map and Sample Plate Map that shows how the biosensors are assigned to the samples by default In the example shown in Figure 5 30 one replicate had been previously selected with the Multiple Analyte assay parameter option Sensor Assignment Review Experiment Q
161. 0 Octet System Data Acquisition User Guide Release 7 1 page 262 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Plate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment Data File Location and Names Prior to pressing Go confirm the Assay Kinetics data repository CAUsers Owner Documents ForteBio cal Experiment run name sub directory higG ProA Kinetics Total experiment time Plate name barcode file prefix 110424 5 49 30 Auto increment file ID start 1 B Data files will be stored as follows Documents ForteBio higG ProA Kinetics 110424_001 frd Documents ForteBio higG ProA Kinetics 110424_002 frd Documents ForteBio higG ProA Kinetics 110424_003 frd Run Settings v Delayed experiment start v Open runtime charts automatically Start after s 600 gt 7 Automatically save runtime chart v Shake sample plate while waiting Set plate temperature C 30 Advanced Settings Acquisition rate Standard kinetics 5 0 Hz averaging by 20 Y l Default Warming changing these settings could affect assay signal to noise Ifyou are unsure of how to use these settings please consult the Data Acquisition User Guide General Information Username Owner Machine name JRICHARDS Description Figure 7 50 Run Experiment Window Octet RED96 2 Confirm the default sett
162. 0 Regeneration oO Figure 1 3 Regeneration Step Step Data List Add Button Add Step Definition a Figure 1 4 Add Step Definition Dialog Box c Select the Regeneration radio button and click OK d Click Regeneration Params Figure 1 5 Step Data List Copy J Remove J Regeneration Params l Threshold Params Name 7 Time Shake speed Type a Threshold Baseline 60 1000 a Baseline gt Feseneration 30 400 Regeneration O Figure 1 5 Regeneration Step Step Data List Regeneration Params Button The Regeneration Parameters dialog box Figure 1 6 displays where you can edit Regeneration parameters as necessary Regeneration Parameters Step Name Regeneration Time s Shake speed rpm Regeneration 5 40 Neutralization 5 d all gt D o Regeneration cydes 3 Total step time 30s R r 1 Figure 1 6 Regeneration Parameters Dialog Box 5 Added a new feature to align a Kinetic experiment at a given time a Right click the Kinetic experiment running chart and select Align at time Figure 1 7 Octet System Data Acquisition User Guide Release 7 1 What s New in the Octet System Data Acquisition Software Release 7 1 page 11 w o N n Align to Step 2 Loading 20 H Align at time 203 7 s N E Unaligned 215 Properties E Export Data poi 1 0 Undo Zoom 05 Fullscale Autoscale as eed ea eens
163. 000 0008000080000 N F 0000008000 F 000008000 6 000008000 1 000000000 Biosensors interrogate 8 wells in a column one column Biosensors interrogate 16 wells in two columns Col is interrogated at a time umns 1 amp 2 are interrogated at the same time Columns 3 amp 4 are interrogated at the same time and so on Figure 8 2 Color Coded Wells Display How Biosensors Interrogate a 96 well Plate 8 Channel or 16 Chan nel Read Head 8 Channel Read Head 16 Channel Read Head 9 10 11 12 13 14 15 16 1 167 ooe 12345 oY Ye 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Biosensors interrogate 8 wells in a column one column Biosensors interrogate 16 wells in two columns Col is interrogated at a time umns 1 amp 2 are interrogated at the same time Columns 3 amp 4 are interrogated at the same time and so on Figure 8 3 Color Coded Wells Display How Biosensors Interrogate a 384 well Plate 8 Channel or 16 Channel Read Head NOTE Keep the read head configuration in mind when laying out the sample plate While reading a 384 well sample plate both the 8 channel and 16 chan nel read heads can freely step through the plate by either moving left or right to step across columns or step one row up or down Octet System Data Acquisition User Guide Release 7 1 page 280 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Changing the Sample Plate Format To change the sample plate format
164. 0000000OLO H4 Protein A 0 00000000000000 A5 Protein A id lel Yerolerolelsleleler Ter 9 BS Protein A Legend Unassigned samples Se pox gt Figure 6 52 Fractional Use of Regeneration and Neutralization Wells Using Partial Biosensor Trays If you are using a partial tray of biosensors some biosensors are missing specify the miss ing columns in the Sensor Tray Map 1 Select the column s without biosensors and click Remove or right click the selection and select Remove If the number of specified biosensors in the Sensor Assignment tab is less than the number required to perform the assay the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay 2 To view the additional biosensor tray that is required for the assay select Tray 2 from the Sensor Tray drop down list Figure 6 53 In the example shown Tray 1 is a partial tray that does not contain enough biosensors for the assay To designate a second tray select Tray 2 from the Sensor Tray drop down list Figure 6 53 top The Sensor Tray Map will then display the additional biosensors required for the assay Figure 6 53 bot tom Octet System Data Acquisition User Guide Release 7 1 page 190 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Piate Definition Sensor Assignment Review Experiment Q Run Experiment In this step sensors are assigned to samples
165. 0c cece cneeneee 177 Biosensor Regeneration 188 Using Partial Biosensor Trays 189 Reviewing Experiments 191 Saving Experiments eee0eee 191 Running a Quantitation Experiment 193 Loading the Biosensor Tray Sample and Reagent Plates 0cceeeenees 193 Starting an Experiment 194 Run Experiment Window Settings 196 Stopping an Experiment 199 Managing Runtime Binding Charts 199 Opening a Runtime Binding Chart 200 Viewing Reference Subtracted Data 201 Viewing Inverted Data 202 Magnifying the Runtime Binding Chart 202 Scaling a Runtime Binding Chart 202 Adding a Runtime Binding Chart Title203 Selecting a Runtime Binding Chart Legend 203 Viewing Multiple Runtime Binding Charts 204 Octet System Data Acquisition User Guide Release 7 1 page 4 Exporting or Printing the Runtime Binding Managing Experiment Method Files 205 Custom Quantitation Assays 206 Defining a Custom Assay 206 Editing Assay Parameters 208 Selecting a Custom Assay 214 Chapter 7 Kinetics Experiments Octet RED96 QK and QK 215 Introduction 0 0 0 c cece cece eens 216 Starting a Basic Kinetics Experiment 217 Starting an Experiment Using the Experiment Wizard 0 008 217 Defining the Sample Plate 218 Designating Samples 218 Selecti
166. 0s Sianel A Show Unicode control characters OkK3 Standard 5 i tind Ich z Om Standard 25 nsert Unicode control character 0 03 Standard 1 Open IME Reconversion Figure 6 11 Sample Plate Table Shortcut Menu of Edit Commands NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 153 Designating Unknowns To designate unknowns in the Sample Plate Map select the wells to define as unknown right click and select Unknown The unknown wells are marked in the plate map and the Sample Plate Table is updated see Figure 6 12 Pate Definition Sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and right click to enter modify well data Read Head
167. 1 283 specifying concentration units 222 284 sampling format Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 sampling volume Octet RED96 instrument 17 Save All Method Files menu 33 Save Experiment menu 33 Octet System Data Acquisition User Guide Release 7 1 page 31 Save Method File As menu 33 Save Method File menu 33 Save to File menu 39 saved experiments in the Template folder figure 260 324 saving all method files 33 binding data 127 204 273 337 default temperature value 44 experiment method files 33 experiment method files to a new name 33 experiment methods 114 191 experiments manually 259 323 experiments to the factory installed Template folder kinetics 384 324 kinetics 96 260 quantitation 384 192 quantitation 96 115 modified parameter settings 91 167 reagent plate definition kinetics 384 301 quantitation 384 167 scaling Runtime Binding Chart kinetics 384 335 kinetics 96 271 quantitation 384 202 quantitation 96 126 screen components Octet System Data Acquisition software 31 Security menu availability 32 compliance features figure 59 described 36 figure 37 selecting adjacent steps to copy and add 243 308 concentration units 222 284 concentration units in the Plate Definition window figure 222 285 custom assays quantitation 384 214 quantitation 96 137 experiment m
168. 1 Click Modify above the plate map 2 In the Modify Plates dialog box select 96 Well or 384 Well format Sample Plate Sample Plate Sample Plate 96 wells Sample Plate 384 wells 12345678 9 10411213141516171819 2021222324 OQQQQQQQQQQQQQQQQQQQQQQQ OO0000 OO000 O 96 Well 96 Well 384 well 384 Well DOQOOOQOOOOOCOG EOOOQOQOQOOOOOOG DOOOO0000000000 HOQOQOQOOOOOOOOO Figure 8 4 Changing the Sample Plate Format Designating Samples NOTE It is important to define all of the wells that will be used in the assay Only wells that are selected and defined using one of the sample types in Table 8 2 will be included in the assay Table 8 2 displays the well types that can be assigned to a plate map Table 8 2 Types of Sample Wells Icon Description Sample Any type of sample For example an analyte Reference Reference sample For example a buffer only control biosensor that is used to correct for system drift Controls A control sample either positive or negative of known analyte compo sition Data from the well is not used to generate a standard curve dur ing analysis Positive Control A control sample that contains analyte of known concentration Negative Control A control sample known not to contain analyte Buffer Any type of buffer For example the buffer in a baseline association or dissociation step Octet System Data Acquisition User Guide Relea
169. 1 Default 121 Octet QKe listed table 266 Octet RED listed table 266 Octet RED384 listed table 330 Octet RED96 listed table 266 Sensor offset Octet QKe 121 Align to Step menu 270 aligning binding data to the beginning of a user selected step 270 334 All steps option 244 309 analysis options viewing 40 analyzing quantitative experiment 68 140 216 276 annotating individual wells in the sample plate table kinetics 384 289 kinetics 96 226 quantitation 384 157 quantitation 96 82 one or more wells 82 225 288 annotations entering 225 288 quantitation 384 157 quantitation 96 82 Append as new assay option 244 309 Append to current assay option 244 309 Append to current assay option 243 Application Locked dialog box figure 66 applications closing 34 Arrange Icons menu 37 arranging window icons 37 Assay Definition tab 237 Assay Definition window 237 Assay number 267 assay parameter settings modifying quantitation 384 167 quantitation 96 91 assay parameter values editing quantitation 384 208 quantitation 96 131 assay parameters Advanced Quantitation quantitation 96 94 Basic Quantitation for 384 model 169 for 96 model 92 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Assay Parameters box 91 assay parameters Basic Quantitation Multiple Analyte quantitation 384 209 quantitation 96 132 Quantitation Shake Speed Octet System Data Acquisition User Guide Rel
170. 1 version utilizes the ForteBio GxP Server module to manage the information recorded dur ing user sessions This chapter explains how to use the ForteBio GxP Server module compliance features and administrative functions specific to the 21 CFR Part 11 versions of the Data Acquisition and Data Analysis software FORTEBIO GXP SERVER MODULE When the Data Acquisition or Data Analysis 7 0 21 CFR Part 11 software is launched users are prompted to log on to the ForteBio GxP Server module This initiates a user session where all system software and user events are recorded During user sessions the GxP Server module manages and stores this recorded information User sessions are closed when the user logs out or a set period of inactivity is reached A new user session is initiated each time a user accesses the software SELECTING A SERVER LOCATION NOTES Please contact your administrator to determine the GxP Server module host location that should be used Once the GxP Server module host location is selected this location will be used as the default selection for the user account It does not need to be reselected each time a new user session is initiated Users must select the host location of the GxP Server module during the login process The GxP server can be run on the local host computer where the Data Acquisition or Data Anal ysis software is installed or from a network location Octet System Data Acquisition User Guide Re
171. 1 AHC Anti hIgG Fc Capture F1 AHC Anti higG Fc Capture G1 AHC Anti hIgG Fc Capture H1 AHC Anti hIgG Fc Capture A2 AHC Anti hIgG Fc Capture B2 AHC Anti hIgG Fc Capture C2 AHC Anti hIgG Fc Capture D2 AHC Anti hIgG Fc Capture E2 AHC Anti hIgG Fc Capture H m a E F2 AHC Anti hIgG Fc Capture a P ioci G2 AHC Anti hIgG Fc Capture Legend _ Unassigned sensors RR Missing sensors E c ani nic Fe Coture Remove Fil Fapiate A3 AHC Anti hIgG Fc Capture B3 AHC Anti hIgG Fc Capture Sample Plate C3 AHC Anti hIgG Fc Capture P1234567 8 9 101112131415161718192021222324 D3 AHC Anti higG Fc Capture slo 0006080 E3 AHC Anti hIgG Fc Capture B F3 AHC Anti higG Fc Capture jE 0 0 0808080808 G3 AHC Anti higG Fc Capture H3 AHC Anti higG Fc Capture IF OBB 9080888 A4 AHC Anti higG Fc Capture I 101 101 101 101 181 181 181 B4 AHC Anti hIgG Fc Capture H C4 AHC Anti hIgG Fc Capture l1 DODOS O0 OS O0O0 00 D4 AHC Anti hIgG Fc Capture J E4 AHC Anti hIgG Fc Capture K O CO 0Ce 0CEC80808 F4 AHC Anti hIgG Fc Capture L G4 AHC Anti hIgG Fc Capture bs D0 BlBl8080O0000 H4 AHC Anti higG Fc Capture fe LOL 101 10 101 101 L01 lero P Legend Unassigned samples Figure 8 41 Sensor Assignment Window Hover the cursor over a well in the Sensor Tray Map or Sample Plate Map to display a tool tip with sample or biosensor information see Figure 8 42 Sample Plate P 12345678 910111
172. 2 Well Sensor Type Lot Number Information E Anti Human IgG Fc E B1 Anti Human IgG Fc me ci mostra D1 Anti Human IgG Fc mm mE me Epo eres G1 Anti Human IgG Fc ma a M Anemon g6 Fe A2 Anti Human IgG Fc _ EE EE B2 Ant Human 196 Fc C2 Anti Human IgG Fc D2 Anti Human IgG Fc BAODEMEANN eee lt a a et dd F2 Anti Human IgG Fc G2 Anti Human IgG Fc H2 Anti Human IgG Fc Fill Fill Plate A3 Anti Human IgG Fc B3 Anti Human IgG Fc Sample Plate c3 Anti Human IgG Fc y 1234 6 141516171819 2021222324 D3 Anti Human IgG Fc A E3 Anti Human IgG Fc F3 Anti Human IgG Fc G3 Anti Human IgG Fc H3 Anti Human IgG Fc A4 Anti Human IgG Fc O 0 fe B4 Anti Human IgG Fc 0 0 lt ITaTmMmmMoVODS Legend _ Unassigned sensors R3 Missing sensors w 00000000000 0 0000000000000 000000000000000 a o pre N 0 C4 Anti Human IgG Fc D4 Anti Human IgG Fc E4 Anti Human IgG Fc F4 Anti Human IgG Fc G4 Anti Human IgG Fc H4 Anti Human IgG Fc A5 Anti Human IgG Fc BS Anti Human IgG Fc C5 Anti Human IgG Fc DS Anti Human IgG Fc ai 0 00 00 0000000 5 O 0 O O 0 0 0 Oo wOoZzZSerxec TreOmmoon Legend Unassigned samples Figure 6 35 Sensor Assignment Window for Basic Quantitation without Regeneration 1 Assign biosensors in one of two ways Select column s in the Sensor Tray Map right click
173. 2 257 removing biosensors 253 317 returning to default layout 253 316 Sensor Type arrow 246 Sensor Type table column 249 Sensor Types dialog box opening 35 Sensor Types dialog box figure 48 Sensors to Chart box figure 267 serial dilution assigning to selected wells quantitation 384 154 quantitation 96 79 serial dilution assigning to unknowns quantitation 384 153 quantitation 96 78 serial port RS 232 346 server location selecting 53 server testing 397 Set Plate Temperature setting kinetics 384 329 kinetics 96 265 quantitation 384 197 quantitation 96 120 Set Plate Temperature menu 35 Set Well Data dialog box 76 151 221 Set Well Data dialog box figure 290 setting assay step threshold parameters figure 239 304 plate temperature 43 system and data preferences 40 setting assay step threshold parameters figure 239 Setting Default Temperature dialog box 44 setting temperature figure 43 setting up administrator account 374 setting up quantitative experiment 68 140 216 276 Octet System Data Acquisition User Guide Release 7 1 page 33 settings advanced run experiment 120 197 329 shake sample plate while waiting setting 120 197 265 329 Shake Speed parameter quantitation 384 169 quantitation 96 92 shortcut keys 226 showing main toolbar 34 status bar 34 Signal Change threshold parameter 239 304 significant digits data display 42 user option 42 simulat
174. 2 assigning dilution factor quantitation 384 154 quantitation 96 79 assigning serial dilution quantitation 384 154 quantitation 96 79 selecting in the Sample Plate Map kinetics 96 219 quantitation 384 148 quantitation 96 73 window icons arranging 37 Window menu described 37 list of menu commands 37 windows organizing in a cascade arrangement 37 tiling vertically 37 Octet System Data Acquisition User Guide Release 7 1 page 40 Octet System Data Acquisition User Guide Release 7 1 page 1 Index Symbols csv file for import creating 90 Numerics 21 CFR Part 11 compliant features accessing 59 2nd Buffer Time and Shake speed parameter 136 213 2nd plate name barcode 264 328 2nd Plate Name Barcode setting Run Experiment window settings quantitation 384 196 quantitation 96 119 2nd Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 384 Well format option 280 384 well Format Reagent Plate figure 167 96 Well format option 280 96 well Format Reagent Plate figure 167 A About ForteBio Data Acquisition menu 38 accessing GxP Server module directly 396 accessing Temperature field 12 account details assigning 385 acquisition for a data column displaying 267 331 quantitation 384 199 quantitation 96 122 acquisition options 40 Acquisition rate advanced settings Octet QK384 Kinetics 330 Octet QK384 Quantitation 198 Octet QKe 121
175. 200 H Extended Sample Typ Series operator Well Information O stnaara cono O 4 Series operand 2 j C Unknown e Reference Dilution orientation 883 ORght 8883 O OLef Down up Coox ee i d Figure 5 5 Sample Plate Map Setting a Dilution Series 2 Select the Dilution Series option and enter the starting concentration value 3 Select a series operator enter an operand and select the appropriate dilution orienta tion see Figure 5 6 Highest Concentration Lowest Concentration Figure 5 6 Concentration Representation in Dilution Series 4 Click OK The Sample Plate Table will display the standard concentrations entered Octet System Data Acquisition User Guide Release 7 1 page 76 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Assigning a User Specified Concentration to Standards To assign a user specified concentration to standards 1 Inthe Sample Plate Map select the standard wells right click and select Set Well Data The Set Well Data dialog box displays see Figure 5 7 Sample Plate Sample Plate 96 wells 1 2 3 4 5 6 7 8 Te a A O r OOOO O Q BIO Ce virom OO CIOOCO contra OO D O Negative Control aa E O Positive Control Set Well Data Sm Reference s E O r Well Information Concentration ig ml Standard only 7 et Well Data 2 a
176. 2020 Copy Fl SA Streptavidin 10102020 pae Gi SA Streptavidin 10102020 Delete H1 SA Streptavidin 10102020 A2 SA Streptavidin 10102020 Select All B2 SA Streptavidin 10102020 z z C2 SA Streptavidin 10102020 Right to left Reading order D2 SA Streptavidin 10102020 Show Unicode control characters E2 SA Streptavidin 10102020 Insert Unicode control character F2 SA Streptavidin 10102020 o IME G2 SA Streptavidin 10102020 penaa H2 SA Streptavidin 10102020 Reconversion Figure 7 39 Entering or Editing Biosensor Information Changing the Biosensor Location If you prefer to not use the default biosensor columns you can select other column s to use There are two ways to do this Method 1 In the Sensor Tray Map Remove the columns you do not want to use The software automatically selects the next available column s Method 2 Remove all columns from the Sensor Tray Map then select the col umns you want to use Method 1 1 In the Sensor Tray Map see Figure 7 40 select the columns to not use and click Remove Or right click the selection and select Remove Figure 7 40 left The software automatically selects the next available biosensor columns in the tray Figure 7 40 right Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 253 2 Click Fill Plate to return the Sensor Tray Map to the default
177. 2131415161718192021222324 AWGOCOOO0G0GOG0OS Sample ID 1X Kinetics Buffer Buffer Legend Unassigned samples Figure 8 42 Tool Tip of Well Information Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 315 Replacing the Biosensors in the Biosensor Tray After an assay is completed the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container To return the biosensors to the tray click the Replace sensors in tray after use check box see Figure 8 43 Sensor Tray v Replace sensors in tray after use VW 1 2 3 4 ai 5 6 7 8 9 10 11 12 Legend Unassigned sensors B88 Missing sensors Remove Fill Fill Plate Figure 8 43 Replace Sensors in Tray After Use Check Box S NOTE Biosensors can be regenerated up to a max of 11 times per experiment Entering Biosensor Information To enter information about a biosensor 1 Optional Double click in any cell in the Lot Number column to enter the biosensor lot number All wells in the Lot Number column for that biosensor type will automatically populate with the lot number entered see Figure 8 44 2 Optional Double click a cell in the Information table column Enter or edit the biosen sor information as appropriate see Figure 8 44 NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x
178. 214 quantitation 96 137 experiment method file opening function 33 Experiment type for the Octet RED384 142 for the Octet RED96 70 in the Experiment Wizard 70 from a set of predefined ForteBio quantitation or kinetics method templates 35 molar concentration units 222 284 molar concentration units in the Plate Definition window figure 222 285 non adjacent steps to add and copy 243 308 project in the Audit Trail 63 Runtime Binding Chart legend kinetics 384 336 kinetics 96 271 quantitation 384 203 quantitation 96 126 server location 53 wells in the Sample Plate Map kinetics 384 282 Octet System Data Acquisition User Guide Release 7 1 page 32 kinetics 96 219 quantitation 384 148 quantitation 96 73 wells in the Sample Plate Map kinetics 384 281 selecting the Web Server in the Options dialog box figure 45 selectively display the acquisition for a data column 267 331 quantitation 384 199 quantitation 96 122 Send Commands Command Field figure 349 Sensor Assignment tab 48 96 100 173 177 303 Sensor Assignment window 96 100 173 177 303 displayed figure 250 314 Sensor Assignment Window for Basic Quantitation without Regeneration figure 97 100 174 177 sensor offset 198 330 Octet QK384 20 27 Octet RED384 20 27 Sensor offset Octet QKe advanced settings 121 Sensor Tray map color codes 122 199 267 331 sensor tray maps 256 automatically adding 2
179. 22 biosensor type changing in the Sensor Assignment window 254 318 biosensor types changing 246 311 biosensors assigning quantitation 384 173 quantitation 96 96 assigning to samples 249 313 automatically adding experiment tray maps 256 320 changing locations kinetics 96 252 changing type 320 designating reference 105 110 182 187 257 321 entering information 252 315 preparing 68 removing from sensor tray maps 253 317 replaying in the biosensor tray 251 315 viewing available 48 biosensors reference designating 258 browser window functions 47 Buffer well type kinetics 384 280 kinetics 96 218 Buffer Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Buffer Time and Shake speed parameter 135 212 building assays 241 By value option 76 151 222 285 C capabilities Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 22 Octet RED384 instrument 18 Octet RED96 instrument 17 Octet System Data Acquisition User Guide Release 7 1 page 9 cascade arrangement organizing windows 37 Cascade menu 37 Change Password dialog box figure 387 Change Projects menu 64 changing administrator password 387 assay step name figure 247 311 biosensor Location Method 1 253 316 biosensor location Method 2 254 317 biosensor type figure 247 311 biosensor type in the Assay Definition window 258 322 biosensor type
180. 36 Instrument Status menu 34 instrument status log figure 119 196 263 327 Instrument Status window 36 described 39 figure 39 logging 36 inverted data viewing in the Runtime Binding Chart 269 334 K kinetic data analysis 40 kinetics assays building 248 defining 236 step type requirements 236 302 kinetics data repository 264 328 kinetics data repository user option 41 kinetics experiments designating samples 218 designating well types 282 Plate Definition window 282 starting 384 277 96 217 L launching the Octet System Data Acquisition software 30 legend for Runtime Binding Chart selecting 271 336 quantitation 384 203 quantitation 96 126 license information displaying 38 list options available for events 396 listing windows currently open in the Main Screen 37 Load well type kinetics 384 281 kinetics 96 218 loading biosensor tray kinetics 384 324 kinetics 96 260 quantitation 384 193 quantitation 96 116 reagent plates kinetics 384 324 sample plate kinetics 384 324 Octet System Data Acquisition User Guide Release 7 1 page 19 kinetics 96 260 quantitation 384 193 quantitation 96 116 steps 236 302 LoadSensors 353 Localhost option 347 localhost default server settings 54 locking Data Acquisition software 65 Data Analysis software 65 logging in the Instrument Status window 36 Login dialog box administrator session figure 378 user session figure 56 Lot Num
181. 384 200 quantitation 96 123 printing 273 338 scaling 271 335 quantitation 384 202 quantitation 96 126 selecting legend 271 336 quantitation 384 203 quantitation 96 126 updating kinetics 384 331 kinetics 96 267 quantitation 384 199 quantitation 96 122 viewing inverted data 269 334 viewing multiple kinetics 384 336 kinetics 96 272 quantitation 384 204 quantitation 96 127 Runtime Binding Chart figure 118 195 263 327 Runtime Binding Chart Export options copy the Runtime Binding Chart to a graphic file quantitation 384 205 quantitation 96 128 export the Runtime Binding Chart to a graphic file quantitation 384 204 quantitation 96 127 print the Runtime Binding Chart to a graphic file quantitation 384 205 quantitation 96 128 save the binding data quantitation 384 204 quantitation 96 127 Runtime Binding Chart options listed table quantitation 384 204 quantitation 96 127 Runtime Binding Chart window figure 267 332 Runtime Binding Chart copying quantitation 384 205 quantitation 96 128 Runtime Binding Chart enhanced legend options 12 Runtime Binding Chart printing 128 205 Runtime Graph Properties dialog box 126 203 271 336 S Sample well type kinetics 384 280 kinetics 96 218 sample plate loading kinetics 384 324 kinetics 96 260 quantitation 384 193 quantitation 96 116 Octet System Data Acquisition User Guide Release 7 1 page 30 Sample Plate and Reagent Plat
182. 4 w WOOOOOOOOO O 00000008000 serve fi ESODO COLOQOO O Reference eke HOOHOOODOOOOGS Nesative Control OOO0O0O0O0000000 Positive Control Q Buffer 22220 Activation 208009008980 Quench 090000000000 Load 10110110 O leleletstetotetetoleteten O Wash Unassigned _ Import E Regeneration Reagent Plate 96 wells Set Well Data ates 3 4 45 6 Clear Data A O O O O Q Copy to Clipboard i id gyo eao BOOOOOOM Set Well Data ES resprre REARS LOL OOOO eaor O O Q O O Well Information Concentration g ml Standard only Sample ID v By value hig Replicate Group Dilution series Well Information v human IgG series operand 2 Dilution orientation 8838 right 8888 Left g Down Up Coox ca L d Figure 8 13 Add Sample Annotations from the Sample Plate Map Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 289 Annotating Wells in the Sample Plate Table To annotate an individual well in the Sample Plate Table 1 Double click the table cell for Sample ID or Well Information 2 Enter the desired information in the respective field see Figure 8 14 NOTE A series of Sample IDs may also be assembled in Excel and pasted into the Sample Plate Table Sample Plate Table Concentration units ug
183. 4 204 quantitation 96 127 Export Plate Definition window kinetics 384 297 kinetics 96 233 quantitation 384 163 quantitation 96 88 exporting binding data 127 204 plate definition kinetics 384 297 kinetics 96 233 quantitation 384 163 quantitation 96 88 Runtime Binding Chart to a data file 127 204 272 337 Runtime Binding Chart to a graphic 127 204 272 337 Runtime Binding Chart to a graphic file 273 337 Exporting dialog box figure 127 204 Extend Current Step button 270 Extend Current Step dialog box figure 271 335 extending duration of the active step 270 335 F factory loaded biosensor types deleting 49 FBServer7 folder installation location 381 FBServerConfig exe file 381 File Compliant figure 62 File History menu 34 File menu described 32 figure 33 list of menu commands 33 File menu commands listed table 33 File Not Compliant figure 62 File Type selection figure 61 Fill Plate menu 253 316 Filtering threshold parameter 239 305 Flip Data check box 125 269 334 Flip Data function viewing inverted data 269 ForteBio GxP Server 7 0 exe 372 ForteBio GxP Server desktop icon figure 397 ForteBio GxP Server module installing 371 Octet System Data Acquisition User Guide Release 7 1 page 17 ForteBio technical support contacting 13 ForteBio Web Site menu 38 fractional use of regeneration and neutralization wells figure 112 189 Fuse symbol 13 G general settings
184. 41 setting default temperature 44 Temperature Setting 43 digital signatures verifying 60 dilution factor assigning to selected wells quantitation 384 154 quantitation 96 79 dilution factor assigning to unknowns quantitation 384 153 quantitation 96 78 dilution factor editing in sample table quantitation 384 155 quantitation 96 80 dilution series assigning sample concentrations kinetics 384 286 kinetics 96 223 assigning standard concentrations quantitation 384 149 quantitation 96 74 Octet System Data Acquisition User Guide Release 7 1 page 13 Dilution Series option 75 223 dimensions Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 discontinuing user session 66 displaying acquisition for a data column 267 331 quantitation 384 199 quantitation 96 122 GxP Server location figure 377 Instrument Status window 34 license information 38 Octet System Data Acquisition software properties 38 step types figure 305 dissociation steps 236 302 E Edit Assay Parameters dialog box figure 129 206 Edit Assay Parameters dialog box opening 35 Edit Assay Parameters menu 35 edit commands 226 Edit Constant dialog box figure 394 Edit Project dialog box figure 392 Edit Sensor Types menu 35 editing assay parameter values quantitation 384 208 quantitation 96 131 assays 35 246 311 biosensor information figure 252 316
185. 46 and the Sensors box will be populated with the default biosensor type Octet System Data Acquisition User Guide Release 7 1 page 184 Chapter 6 Quantitation Experiments Octet RED384 and QK384 r Tray Format Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical Homogeneous A different sensor tray is used for each sensor type Sensors Am Add Remove Change Move Up Move Down Figure 6 46 Tray Format Dialog Box 2 Select Homogeneous Click Add to select the first biosensor type see Figure 6 47 r Tray Format Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical Homogeneous A different sensor tray is used for each sensor type Sensors Anti Mouse IgG Fv Protein A Protein G Protein L SA Streptavidin Residual Protein A Anti Penta HIS Custom Figure 6 47 Selecting a Biosensor Type in the Tray Format Dialog Box 3 Repeat this step to add any additional biosensor types that will be used in the experi ment To remove a biosensor type select a biosensor type in the Sensor box and click Remove 4 Adjust the order of biosensor types as needed by selecting the biosensor type in the Sensor box and clicking Move Up or Move Down Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 185 The o
186. 47 Octet System Data Acquisition User Guide Release 7 1 page 112 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Piate Definition Sensor Assignment Review Experiment Run Experiment In this step sensors are assigned to samples Regenerations fi Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Times ae will be reused Only the first sensor tray can be a partial plate ex Sensor Tray W Replace sensors in tray after use Poa 2 3 4 5 6 7 8 9 10 11 12 Well Sensor Type Lot Number Information A eal AL_JProtein a B1 Protein A B 2 B C1 Protein A D1 Protein A Cl 2 B E1 Protein A D A E E Fi Protein A as G1 Protein A EHHH H1 Protein A A2 ProteinA F E E B2 Protein A a ia C2 Protein A Gl CJ D2 Protein A H z 2 B E2 Protein A F2 Protein A ii G2 Protein A Legend i Unassigned sensors amp Missing sensors fell Pona Remove Fil l Fil Plate A3 Protein A B3 Protein A Sample Plate c3 ProteinA y 1 2 3 4 5 6 kd 8 R 1 1t i2 D3 Protein A A OOO00OO O60 E mm F3 Protein A BOOOOOOOO OQ amp rena COOOOO08O800O8 l m DOSOO00008 088 EOOO000008 0880 F OOO00008 088 CcOo OO GLI I IDIIDI I IOIO Is Legend Unassigned samples Figure 5 47 Fractional Use of Regeneration and Neutralization Wells Using Partial Bio
187. 5 n a H3 IgG Standard 1 Standard 1 n a A4 Abl Abl Unknown n a 2 B4 Ab2 Ab2 Unknown n a 2 C4 Ab3 Ab3 Unknown n a 2 D4 Ab4 Ab4 Unknown n a 2 E4 Abs Ab5 Unknown nja 2 F4 Ab Abb Unknown n a 2 G4 Ab Ab Unknown n a 2 a Figure 5 19 Replicate Groups in Sample Plate Table Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 87 Assigning Replicate Groups in the Sample Plate Table To assign Replicate Groups in the Sample Plate Table 1 Double click the desired cell in the Replicate Group table column 2 Enter a group name see Figure 5 20 Sample Plate Table Concentration units yoy Z Export Import Well Sample ID Replicate Group Type Conc ig ml Dilution Factor 4 O Al IgG Standard 200 Standard 200 n a E B1 IgG Standard 100 Standard 100 n a C1 IgG Standard Standard 50 n a D1 IgGStandard 25 Standard 25 n a E1 IgGStandard 10 Standard 10 n a O F1 IgGStandard 5 Standard 5 n a O G1 IgG Standard 2 5 Standard 25 n a Figure 5 20 Add Replicate Group from the Sample Plate Table NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context depen
188. 5011 emissions EN61326 immunity Environmental Storage Temperature 20 to 70 C Optimum Operating Temperature 22 4 C Safe Operating Temperature 15 to 30 C e Humidity Non condensing 10 to 80 Relative Humidity Indoor Use Only Operating Altitude 0 to 2 000 meters Compliance CE CSA Capabilities e Protein quantitation Kinetic and affinity analyses kops Kar Kg Kp Binding specificity and cooperativity e Kinetic screening e Small molecule kinetic analysis Octet System Data Acquisition User Guide Release 7 1 Octet RED384 System Specifications page 19 Table 2 2 Octet RED384 System Specifications Continued Item Description Sampling Format Required plates 96 well black flat bottom polypropylene microplate Greiner Bio One 655209 or similar SBS standard microplate 384 well black flat bottom polypropylene Greiner Bio One 781209 384 well black tilted bottom polypropylene ForteBio 18 5076 or 18 5080 SBS standard microplate e Two plate stations Test volume e 180 300 uL in a 96 well plate non destructive and recoverable e 80 130 uL in a 384 well plate non destructive and recoverable e 40 100 uL in a 384 well tilted bottom microplate 384TW non destructive and recoverable Sample Types Purified samples common culture media crude lysates Biosensor Type Disposable single use fiber optic biosensors with optional reuse by regenera
189. 56 320 changing biosensor locations 252 257 removing biosensors 253 317 returning to default layout 253 316 Sensor Type arrow 246 Sensor Type table column 249 Sensor Types dialog box opening 35 Sensor Types dialog box figure 48 Sensors to Chart box figure 267 serial dilution assigning to selected wells quantitation 384 154 quantitation 96 79 serial dilution assigning to unknowns quantitation 384 153 quantitation 96 78 serial port RS 232 346 server location selecting 53 server testing 397 Set Plate Temperature setting kinetics 384 329 kinetics 96 265 quantitation 384 197 quantitation 96 120 Set Plate Temperature menu 35 Set Well Data dialog box 76 151 221 Set Well Data dialog box figure 290 setting assay step threshold parameters figure 239 304 plate temperature 43 system and data preferences 40 setting assay step threshold parameters figure 239 Setting Default Temperature dialog box 44 setting temperature figure 43 setting up administrator account 374 setting up quantitative experiment 68 140 216 276 Octet System Data Acquisition User Guide Release 7 1 page 33 settings advanced run experiment 120 197 329 shake sample plate while waiting setting 120 197 265 329 Shake Speed parameter quantitation 384 169 quantitation 96 92 shortcut keys 226 showing main toolbar 34 status bar 34 Signal Change threshold parameter 239 304 significant digits
190. 69 frd 2 14 2011 12 08 PM FRD File 5 Pictures LABUSERO90811_068 frd 2 14 2011 12 08 PM FRD File B Videos LABUSERO90811_067 frd 2 14 2011 12 08 PM FRD File LABUSERO90811_066 frd 2 14 2011 12 08PM_ FRD File 83 Homegroup LABUSER090811_065 frd 2 14 2011 12 08 PM FRD File LABUSER090811_064 frd 2 14 2011 12 08 PM FRD File K u W Computer File name Data Files frd Figure 4 15 File Selection To change the file type available for selection click on the file type box and select a dif ferent format File name v Data Files rd Method File fmf Data Files frd XML Files xml ey A Files Figure 4 16 File Type Selection 3 Select the desired file and click OK A message will display in the Verify Digital Signature dialog box indicating file com pliance status Octet System Data Acquisition User Guide Release 7 1 page 62 Chapter 4 21 CFR Part 11 Compliance r Verify Digital Signature File Documents Contracting Forte Bio User_Guides Data and m Basic Quantitation Experiment cfr fmi This file is valid and has not been edited outside Fortebio software F Verify Digital Signature This file is not 21 CFR Part 11 compliant Fie Documents ForteBio Quantitation non CFR LABUSER090811_072 frd or was generated on a non 21 CFR Part 11 compliant system Figure 4 17 File Compliant top File Not Compliant bottom Viewi
191. 7 0 Setup Wizard This wizard will guide you through the installation of ForteBio GxP Server 7 0 It is recommended that you close all other applications before starting Setup This will make it possible to update relevant system files without having to reboot your computer Click Next to continue next gt Cancel Figure B 11 ForteBio GxP Server 7 0 Software Setup Wizard 4 Click Next to display the Choose Install Location dialog box Figure B 12 33 ForteBio GxP Server 7 0 Setup Choose Install Location Choose the folder in which to install ForteBio GxP Server 7 0 Setup will install ForteBio GxP Server 7 0 in the following folder To install in a different folder dick Browse and select another folder Click Next to continue Destination Folder C Program Files ForteBio 7 CFR FBServer 7 Space required 17 3MB Space available 177 2GB ForteBio Inc www fortebio com Figure B 12 Choose Install Location Octet System Data Acquisition User Guide Release 7 1 Installing the ForteBio GxP Server Module page 373 The default location for the software on the local machine is C Program Files Forte Bio DataAnalysis7 5 Click Next to accept this path location The Choose Start Menu Folder dialog box displays Figure B 13 33 ForteBio GxP Server 7 0 Setup e Choose Start Menu Folder Choose a Start Menu folder for the ForteBio GxP Server 7 0 shortcuts Sel
192. 7 1 page 392 Chapter B 21 CFR Part 11 Software Administrator Options rr Project name Receptor Ligand screen Information Affinity Screen Figure B 46 Edit Project Dialog Box 2 If needed modify the project settings 3 Click OK to save changes and exit Deleting a Project 1 Right click on the project and select Delete Project from the Tab menu 2 Click OK in the dialog box displayed Administrator Constants The Constants Tab allows administrators to set GxP Server module constant settings CredentialsTTL 5 PasswordMinLength 0 PasswordSecure 0 PasswordTTL 180 UserIdleMin 15 Figure B 47 Constants Tab Available administrator constants and their associated value ranges are shown in Table B 3 Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 393 Table B 3 Administrator Constants Constant Description Default Value Range Value CredentialsTTL The number of days that the 5 Minimum 0 server settings are stored in the no max value cache This allows the software to operate in case the server is tem porarily down PasswordMin Minimum number of characters 0 Minimum 0 Length that a password must contain no max value PasswordSecure Level of password complexity 0 0 1 Setting the constant to 0 has no password restrictions Setting the constant to 1 requires passwords to contain at least one alpha one numeric
193. 70 5 5270 s 25713 25713 ss Tenom e se os Go to Next Step Fip Data 3 0 Binding nm i S 0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 Time sec Sensor A1 Sensor B1 Sensor C1 Sensor D1 Sensor E1 Sensor F1 Sensor G1 Sensor H1 Figure 7 51 Runtime Binding Chart 4 Optional Click View gt Instrument Status to view the log file see Figure 7 52 The experiment temperature is recorded at the beginning of every experiment as well as each time the manifold picks up a new set of biosensors Instrument events such bio sensor pick up manifold movement integration time biosensor ejection and sample plate temperature are recorded in the log file lt 2 Instrument Status E i Hl 14 47 39 Sensor 7 Integration Time 1 0 ms H 14 47 39 Sensor 8 Integration Time 1 0 ms H 14 47 40 Picking sensors completed location A1 14 47 40 Plate temperature 30 C 14 47 40 Ready to move to sample location A1 14 47 40 Moving to sample location A1 14 47 41 Arrived at sample location A1 14 47 41 Waiting to start sample location A1 14 47 41 Processing sample location Al 14 47 51 Sample completed location A1 a 14 47 51 Waiting to start new step 14 47 51 Starting new step 14 47 52 Ready to move to sample location A2 14 47 52 Moving to sample location A2 14 47 53 Arrived at sample location A2 14 47 53 Waiting to start sample
194. 8 constants 394 group settings 390 project settings 391 projects during a user session 64 sample plate format kinetics 384 280 quantitation 384 144 sample plate format figure 144 280 user account passwords 387 user account settings 386 user password 65 well designations kinetics 384 295 kinetics 96 231 changing location of a reserved column quantitation 384 146 quantitation 96 72 changing projects figure 64 Choose Install Location dialog box figure 367 369 Choose Start Menu Folder dialog box figure 367 370 373 cleaning biosensor pickup tips 343 cleaning Octet instrument 340 342 Cleanup automation interface command 350 Close automation interface command 350 Close Method File menu 33 closing active method file 33 application 34 color codes 122 199 267 331 color coded wells displaying how biosensors interrogate a 384 well plate 8 channel or 16 channel read head 143 279 a 96 well plate 8 channel or 16 channel read head 143 279 compliance Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 compliant features 21 CFR Part 11 59 Conc column 76 151 concentration representation in dilution series figure 224 Concentration Units drop down list 73 Connect as IP address changing 45 Octet System Data Acquisition User Guide Release 7 1 page 10 connecting Automation Client example applic
195. 8 specifying analyte concentration 221 283 specifying concentration units 222 284 sampling format Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 sampling volume Octet RED96 instrument 17 Save All Method Files menu 33 Save Experiment menu 33 Octet System Data Acquisition User Guide Release 7 1 page 31 Save Method File As menu 33 Save Method File menu 33 Save to File menu 39 saved experiments in the Template folder figure 260 324 saving all method files 33 binding data 127 204 273 337 default temperature value 44 experiment method files 33 experiment method files to a new name 33 experiment methods 114 191 experiments manually 259 323 experiments to the factory installed Template folder kinetics 384 324 kinetics 96 260 quantitation 384 192 quantitation 96 115 modified parameter settings 91 167 reagent plate definition kinetics 384 301 quantitation 384 167 scaling Runtime Binding Chart kinetics 384 335 kinetics 96 271 quantitation 384 202 quantitation 96 126 screen components Octet System Data Acquisition software 31 Security menu availability 32 compliance features figure 59 described 36 figure 37 selecting adjacent steps to copy and add 243 308 concentration units 222 284 concentration units in the Plate Definition window figure 222 285 custom assays quantitation 384
196. 84 K ProA higG Kinetics Runtime Binding Chart eon x Current Binding Charts Plate Status Plate Legend Sensors to Chart Sensor Tray E Kinetics Assay 2 P 1234567 8910112 514151617 10192021222324 Selected A 99 e Processing B ood Processed 1 c g Reseved 1 O 6 od A 00000000000 Data Eror F ji Sensor Feil fal G H a Subtract reference sensors Assay Step Status Experiment Progress Step 11 of 11 Step details Assay 2 of 2 Elapsedtime Total exp time Exte 20 5 20 s Z squllibration 1840 5 1840 s 0 31 14 0 31 14 ir a A Trp Dota Binding nm N 0 200 400 600 800 1000 1200 1400 1600 meee Af gt eee 4 eee C4 me YA ee Ef ee Ft men Gf ner Ht BS BG 05 DG Se 5 een ES een G een ts Figure 8 56 Runtime Binding Chart 4 Optional Click View gt Instrument Status to view the log file see Figure 8 57 The experiment temperature is recorded at the beginning of every experiment as well as each time the manifold picks up a new set of biosensors Instrument events such bio sensor pick up manifold movement integration time biosensor ejection and sample plate temperature are recorded in the log file 22 Instrument Status eon x H 14 47 39 Sensor 7 Integration Time 1 0 ms Hl 14 47 39 Sensor 8 Integration Time 1 0 ms H 14 47 40 Picking sensors completed location A1 14 47 40 Plate temperature 30 C 14
197. 96 256 quantitation 96 112 V Verify Digital Signature dialog box figure 60 verifying digital signatures 60 Version automation interface command 349 View menu described 34 figure 34 list of menu commands 34 viewing analysis options 40 Audit Trail 62 available types of biosensors 48 constants 394 events 395 events for a specific project or computer 63 group settings 390 inverted data displayed in the Runtime Binding Chart 269 334 multiple Runtime Binding Charts kinetics 384 336 kinetics 96 272 quantitation 384 204 quantitation 96 127 project settings 391 raw reference subtracted data quantitation 384 201 quantitation 96 123 reference subtracted data kinetics 384 332 kinetics 96 268 quantitation 384 201 quantitation 96 123 templates 260 324 user account settings 386 user options 40 user modifiable settings for an assay quantitation 384 167 quantitation 96 91 W warm up time 30 Wash well type kinetics 384 281 kinetics 96 218 waste container emptying 340 for the Octet instrument figure 341 web browser opening 38 remote view of experiment 47 Web Server check box 45 URL figure 46 user option 43 Octet System Data Acquisition User Guide Release 7 1 page 38 weight Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 well designations changing kinetics 384 295 kinetics 96 231 defined
198. All Steps Sample steps will be adjuste Horizontally Vertically Figure 7 31 Replicating Assay Steps by Appending Octet System Data Acquisition User Guide Release 7 1 page 244 Chapter 7 Kinetics Experiments Octet RED96 QK and QK 4 Click OK The step s appear at the end of the assay in the Assay Steps List Table 7 5 Replicate Steps Options Item Description Add as a new assay Adds the replicate step s as a new assay to the Assay Steps List Append to current assay Adds the replicate step s to the end of the current assay Offset steps Assigns the replicate steps to different columns in the sam ple plate Sample steps only Applies the offset to the sample plate only All steps Applies the offset to the sample plate and reagent plate NOTE Reagent plates are only available when using an Octet384 or Octet QK384 instrument Sample steps will be Specifies the column in which to add the new step s For adjusted horizontally by X example if a step in column 11 is copied and the replicate columns step should begin in column 12 enter 1 Enter 0 to apply the step s to the same columns Sample steps will be Applies only to the Octet384 or Octet QK384 instruments adjusted vertically by one row Starting a New Assay A new assay will utilize a new set of biosensors To start a new assay using the next available sensor column 1 Select a column in the Sample
199. Assay oN E Anti Penta HIS High sensitivity 2 Anti Penta HIS Standard range E High sensitivity Human IgG quantitation Single analyte Multiple analyte Human IgG Quantitation Pe Immunogenicity Direct detection Murine IgG Quantitation Protein L Standard range Standard Assay mG o oge amp Basic Quantitation with Regeneration Quantitation 120 400 Z High sensitivity assay with regeneration i E Protein L Standard range E Standard Assay 2 My Basic Quant with Regen Assay amp Advanced Quantitation B B E Description Enter a short description of the assay here plicates per sensor type f1 E Immunogencity Enzyme Linked Residual Protein A Standard Assay Three Step Assay Blue indicates a ForteBio built in assay and cannot be modified or deleted Duplicate Remove Cancel L d Figure 5 63 Assay Parameters Basic Quantitation Assay Table 5 15 Basic Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Octet System Data Acquisition User Guide Release 7 1 page 132 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 15 Basic Quantitation Assay Parameters Continued Parameter Description Multiple analyte and For multi analyte experiments using multiple biosensor types Replicates per sen per
200. B5 Ab2 Unknown n a 2 Sample Diluent c5 Ab3 Unknown n a 2 Sample Diluent D5 Ab4 Unknown n a 2 Sample Diluent ES Ab5 Unknown n a 2 Sample Diluent F5 Abb Unknown n a 2 Sample Diluent G5 Ab Unknown n a 2 Sample Diluent OH5 Abs Unknown n a 2 Sample Diluent AB Abl Unknown n a 2 Sample Diluent BE Ab2 Unknown n a 2 Sample Diluent CB Ab3 Unknown n a 2 Sample Diluent D6 Ab4 Unknown n a 2 Sample Diluent E6 Ab5 Unknown n a 2 Sample Diluent F6 Abb Unknown n a 2 Sample Diluent G6 Ab Unknown n a 2 Sample Diluent E HE Abs Unknown n a 2 Sample Diluent A hlgG Positive Control n a n a 10 ug mL in B hlgG Positive Control n a n a 10 ug mL C hlgG Positive Control n a n a 10 ug mL D hlgG Positive Control n a nja 10 ug mL E higG Positive Control n a n a 10 ug mL v Figure 5 15 Adding Sample Annotations in the Sample Plate Table NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Octet System Data Acquisition User Guide Release 7 1
201. Buffer 1X Kinetics Buffer F Buffer 1X Kinetics Buffer q Copy to Clipboard Buffer 1X Kinetics Buffer V Extended Sample Types Buffer 1X Kinetics Buffer Sample 10 150 66 67 1X Kinetics Buffer L Figure 7 17 Sample Plate Table Well Designation Editing Sample Information To edit sample data in the Sample Plate Table double click a value and enter a new value see Figure 7 18 Octet System Data Acquisition User Guide Release 7 1 page 232 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Sample Plate Table Concentration units pg ml Z Molar concentration units m 7 Well Sample ID Replicate Group Type Conc ug ml MW kD Molar Conc nM Information A H3 Dissociation Buffer 1X Kinetics Buffer A4 Association 1 Sample 10 150 GEG 1S Kinatice Ruffa B4 Association 2 Sample 5 150 Undo C4 Association 3 Sample 25 150 Cut D4 Association 4 Sample 1 25 15 E4 Association 5 Sample 0 625 150 Copy F4 Association 6 Reference Paste G4 Association 6 Reference Delete H4 Association 6 Reference A5 Association 1 Sample 10 150 Select All O85 Association 2 Sample 5 150 Right to left Reading order ec Assocation i Sarie 26 150 Show Unicode control characters D5 Association 4 Sample 1 25 150 z 7 E5 Association 5 Sample 0 625 15 Insert Unicode control character F5 Association 6 Reference Open IME G5 Association 6 Reference R i econversion H5 Association 6 Reference Figure
202. C5 Anti Human IgG Fc DS Anti Human IaG Fc Figure 5 30 Sensor Assignment Window for Basic Quantitation without Regeneration 1 Assign biosensors in one of two ways Select a column s in the Sensor Tray Map right click and select a biosensor type from the drop down list see Figure 5 30 left Select a cell in the Sensor Type table column click the down arrow and select a biosensor type from the drop down list see Figure 5 30 right All wells in the Sensor Type column will automatically populate with the biosensor type selected Octet System Data Acquisition User Guide Release 7 1 Copy to Clipboard page 98 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Sensor Tra 7 V sia sensors in tray after use Wes Type Less ton mi at a F 12 3 4 7 8 9 10 1 12 B1 A auto assign ea cl A g A auto assign L Anti Mouse IgG Fv Dil A B Anti Human IgG Fc Protein A Anti Mouse IgG Fv EL Protein G e i E F1 A protein L Protein A G1 ASA Streptavidin D Protein G m Hi AResidual Protein A A2 pAnti Penta HIS E Protein L E E B2 Custom SA Gaepardin O la F Residual Protein A E D2 A G Anti Penta HIS E E2 A Custom H IL Reference E Legent Positive Control Missing sensors Negative Control Ren Remove Sample Fill A K Set Sensor Data Figure 5 31 Changing Biosensor Types in the Sensor Tray Map left and Sensor Type Column right 2 To designate reference biosensor
203. Capture AHC Anti hlgG Fc Capture AHC Anti hlgG Fc Capture Figure 8 50 Example Experiment Using Two Biosensor Trays insert the appropriate tray in the Octet instrument Reference Biosensors NOTE Up to two trays may be used per assay but only the first biosensor tray can be a partial tray During the experiment run the software prompts you to To designate reference biosensors select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during acquisition Octet System Data Acquisition User Guide Release 7 1 page 322 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Changing the Biosensor Type The biosensor type used in the assay must be selected in the Assay Definition window To change the biosensor type 1 Click the Assay Definition Tab 2 Inthe Assay Steps List click the cell in the Sensor Type column to change 3 Select from the drop down list see Figure 8 51 IMPORTANT Ensure that the same biosensor types are selected in both the Assay Definition and the Sensor Assignment windows or the experiment can not be run Assay Steps List s New Assay Move Up Move Down Remove Replicate Ee ime f Assay Sample Plate Step Name Step Type Sensor Type Assay Time 1 Al 1 equilibration 3 Custom AHC Anti hlgG Fe Cap
204. Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu Octet System Data Acquisition User Guide Release 7 1 page 316 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Figure 8 44 Entering or Editing Biosensor Information Changing the Biosensor Location Well Sensor Type Lot Number Information Al AHC Ant higG Fc Capture 10102020 B1 AHC Anti hIgG Fc Capture 10102020 Undo C1 AHC Anti hIgG Fc Capture 10102020 En D1 AHC Anti hIgG Fc Capture 10102020 E1 AHC Anti hIgG Fc Capture 10102020 Copy F1 AHC Anti hIgG Fc Capture 10102020 Paste G1 AHC Anti hIgG Fc Capture 10102020 Delete H1 AHC Anti hIgG Fc Capture 10102020 A2 AHC Anti hIgG Fc Capture 10102020 Select All B2 AHC Anti hIgG Fc Capture 10102020 Right to left Reading order E AC AnthIgG Fc Capture 10102020 Show Unicode control characters D2 AHC Anti hIgG Fc Capture 10102020 A E2 AHC Anti hIgG Fc Capture 10102020 Insert Unicode control character F2 AHC Anti hIgG Fc Capture 10102020 Open IME G2 AHC Anti hIgG Fc Capture 10102020 N H2 AHC Anti hlaG Fc Capture 10102020 If you prefer to not use the default biosensor columns you can select other column s to use There are two ways to do this Method 1 In the Sensor Tray Map Remove the columns y
205. Copy Remove Threshold Params_ lp B60000000000000000000000 Name Time Shake speed Type Threshold E O00000 equilibration 120 1000 33 Custom m S004 GOOOSOGOOOGO d Step Definition association Baseine N Dissocation Loading custom D x i Exp time Name Load Protein A Time 5 f Shake speed Assayed reagents O Unassigned reagents Figure 8 29 Creating an Assay Step Type Octet System Data Acquisition User Guide Release 7 1 page 304 Chapter 8 Kinetics Experiments Octet RED384 and QK384 3 Apply a threshold to the step a In the Step Data List click the Threshold check box The Threshold Parameters dialog box displays see Figure 8 30 b Set the threshold parameters refer to Table 8 4 for the parameter definitions Piate Definition Assay Definition Sensor Assignment Q Review Experiment Run Experiment f In this step the assay steps will be assembled from the Step Data List Select a group of sensors and append the currently selected step into the current assay with a double click or right click for more options Time in s Shake speed in rpm Sample Plate 384 wells Step Data List P1234567 8 9 101112131415161718192021222324 Add J Copy J Remove J Threshold Params AP000000 000000 00000000000 BOQOQOQOQOQOQQOQQQQQQQQQQQQ Name Time Shake speed Type
206. Custom Can be used for an activity not included in any of the above step types Activation Used when employing a reagent to chemically prepare the biosensor for loading Quenching Used to render unreacted immobilization sites on the biosensor inactive Creating Step Types Click the Assay Definition tab or click the 5 arrow to access the Assay Definition window see Figure 7 24 The Step Data List shows the types of assay steps that are available to build an assay By default the list includes a baseline step To create different types of assay steps 1 Click Add 2 In Assay Step Definition dialog box Figure 7 24 specify the step information a Choose a step type b Optional Edit the step name c Set the step time and shake speed Time range 2 to 48 000 seconds Shake speed range 100 to 1 500 rpm or 0 Octet System Data Acquisition User Guide Release 7 1 page 238 Chapter 7 Kinetics Experiments Octet RED96 QK and QK W Plate Definition B Assay Definition Sensor Assignment Review Experiment Run Experiment In this step the assay steps will be assembled from the Step Data List Select a group of sensors and append the currently selected step into the current assay with a double click or right click for more options pie Plate 96 wells Step Data List Tine MCE Shave speed PM 1 a a a a a a a a n Co Remove Threshold Params A
207. Cycles parameter 94 Regeneration Time and Shake Speed parameter 93 Single Analyte parameter 93 133 Quantitation Time and Shake speed 133 170 210 Regeneration cycles 134 211 Regeneration Time and Shake speed 133 210 Basic Quantitation with Regeneration Quantitation Experiment 69 141 Basic Quantitation Quantitation Experiment 69 141 beginning an experiment 216 276 beginning the next step in the assay 271 335 binding data aligning kinetics 384 334 kinetics 96 270 exporting quantitation 384 204 quantitation 96 127 saving kinetics 384 337 kinetics 96 273 quantitation 384 204 quantitation 96 127 biosensor column active 122 199 267 331 biosensor columns default 252 316 biosensor pickup tips cleaning 343 biosensor regeneration described quantitation 384 188 Octet System Data Acquisition User Guide Release 7 1 page 8 quantitation 96 111 biosensor stage left and sample stage right figure 116 261 biosensor tray loading kinetics 384 324 kinetics 96 260 replacing biosensors 251 315 biosensor tray type 17 19 26 Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 biosensor tray loading quantitation 384 193 quantitation 96 116 biosensor type adding 49 changing figure 247 311 Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 removing 49 biosensor type changing in the Assay Definition window 258 3
208. Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 209 Table 6 16 Basic Quantitation Assay Parameters Continued Parameter Description Multiple analyte and For multi analyte experiments using multiple biosensor types Replicates per sen per sample well and the number of replicate assays in each well sor type per biosensor type Quantitation Time s The duration of data acquisition seconds while the biosensor is incubated in sample NOTE A subset of data points may be selected for processing during data analysis Quantitation Shake The sample platform orbital shaking speed rotations per min speed rpm ute Octet System Data Acquisition User Guide Release 7 1 page 210 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Basic Quantitation with Regeneration Assay Parameters a Edit Assay Parameters Available Assays Assay Parameters Basic Quantitation Name My Basic Quant with Regen Assay IE Anti Penta HIS High sensitivity E Anti Penta HIS Standard range High sensitivity Human IgG quantitation Single analyte Multiple analyte Human IgG Quantitation E Replicates persensortype 1 2 Immunogenicity Direct detection Murine IgG Quantitation Time 8 Protein L Standard range La Standard Assay My Basic Quant Assay Regeneration 5 400 2 sic Quantitation with Regeneration aie High sensitivity assay with regeneration Siesia 5 4 ate Ea Protein L
209. Data dialog box displays see Figure 7 7 2 Select the By value option and enter the starting concentration value Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 223 Sample Plate 96 wells P12 3 4 8 7 8 9 10 47 12 AOOO sample aan B Reference D C Control fe D 0 Negative Control Positive Control p EOOod D uffer F e Activation D G G Quench e H Load fe O Unassigned Wash Regeneration Set Well Data Clear Data E Eg Copy to Cli v Extended s Well j Concentration ug ml Sample only A By value aol Dilution series PERAE EDI Starting value 1 Well Information y 2 a a Series operand 2 Dilution orientation 838 C Right 8883 O Left Well Data Sample only g Down g Up Molecular Weight kD 150 o Molar Concentration nM 66 67 o L d Figure 7 7 Sample Plate Map Assigning Sample Concentrations by Value 3 Click OK The Sample Plate Table will display the entered concentration Assigning Concentrations Using a Dilution Series To assign sample concentrations using a dilution series 1 Inthe Sample Plate Map select the wells right click and select Set Well Data The Set Well Data dialog box displays see Figure 7 8 2 Select the Dilution Series option and enter the starting concentration value Octet Sys
210. Enzyme Time and Shake Speed pa rameter 172 Multiple Analyte parameter 171 Neutralization Time and Shake Speed parameter 172 Offline parameter 172 Post condition sensors parameter 173 Pre condition sensors parameter 173 Regeneration cycles parameter 173 Regeneration Time and Shake Speed parameter 172 Reuse Buffer parameter 172 Sample Time and Shake Speed pa rameter 172 Single Analyte parameter 171 quantitation 96 94 2nd Time and Shake Speed param eter 95 Buffer Time and Shake Speed pa rameter 95 Detection Time and Shake Speed parameter 95 Enzyme Time and Shake Speed pa rameter 95 Multiple Analyte parameter 94 133 Neutralization Time and Shake Speed parameter 95 Offline parameter 95 Post condition sensors parameter 96 Pre condition sensors parameter 96 Regeneration cycles parameter 96 Regeneration Time and Shake Speed parameter 95 Reuse Buffer parameter 95 Sample Time and Shake Speed pa rameter 95 Single Analyte parameter 94 Octet System Data Acquisition User Guide Release 7 1 page 3 Regeneration cycles 137 214 Regeneration Time and Shake speed 136 213 Sample Time and Shake speed 212 Advanced Quantitation Quantitation 384 Experiment 142 advanced run experiment settings 120 197 329 advanced settings Acquisition rate Octet QKe 121 Acquisition rate Octet RED 121 Default 121 Octet QKe listed table 266 Octet RED listed table 266 Oc
211. ForteBio Data Acquisition or Data Analysis 7 0 21 CFR Part 11 software is installed Aremote host computer networked to a machine where the ForteBio Data Acquisi tion or Data Analysis 7 0 21 CFR Part 11 software is installed Upon launching the Octet System Data Acquisition or Data Analysis 7 0 CFR 11 software you are required to select the GxP Server module host location If the GxP Server module is installed in multiple locations you can select any host server The user session event record will be saved only to the host location selected making it possible to have records for the same user in multiple locations NOTE For administrators only To ensure that all records are saved to one location ForteBio recommends that administrators install a single copy of the ForteBio GxP Server module on the network that can then be accessed by all users Octet System Data Acquisition User Guide Release 7 1 page 372 Chapter B 21 CFR Part 11 Software Administrator Options To install the ForteBio GxP Server software 1 Navigate to the window listing the files located on the installation CD 2 Double click ForteBio GxP Server 7 0 exe to launch the installer 3 If prompted with the Do you want the following program from an unknown publisher to make changes to this computer message reply Yes The installation wizard should display Figure B 11 33 ForteBio GxP Server 7 0 Setup o e Welcome to the ForteBio GxP Server
212. G SAMPLE PLATE DEFINITIONS NOTE After you define a sample plate you can export and save the plate defi nition for future use Exporting a Plate Definition To export a plate definition 1 Inthe Sample Plate Table see Figure 6 24 click Export Sample Plate Table Concentration units yom M Export Import Well Sample ID Replicate Group Type Conc ig ml Dilution Factor Information a OA higG 1 Standard 200 n a human IgG OCI hlgG 2 Standard 100 n a human IgG OEI hgG 3 Standard 50 n a human IgG OGI hgG 4 Standard 25 n a human IgG on hlgG 5 Standard 10 nfa human IgG OKI higG 6 Standard 5 n a human IgG Figure 6 24 Export Button in Sample Plate Table 2 Inthe Export Plate Definition window see Figure 6 24 select a folder enter a name for the plate csv and click Save Octet System Data Acquisition User Guide Release 7 1 page 164 Chapter 6 Quantitation Experiments Octet RED384 and QK384 EX Export Plate Definition gO JL Forte Bio Search Data and met Organize 7 New folder z e amp Favorites Documents library W Desktop J Downloads Recent Places Arrange by Folder 7 Data and methods Name Date modified Type E Desktop Libraries Documents Music Pictures a Videos aa m r Filename 384 standard plate csv aa Save as type csv Files csv L Figure 6 25 Export Plate Defin
213. Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and group samples that use the same Replicate Group names spacing and capi talization must be identical For example samples assigned to Group 2 and group2 are treated as two groups Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 231 Editing the Sample Table Changing Sample Well Designations To change a well designation right click the well in the Sample Plate Table and make a new selection see Figure 7 17 Sample Plate Table Concentration units pg ml MA Molar concentration units nM Z We Type Conc ug ml MW kD Molar Conc nM Information ai gO Sample Buffer 1X Kinetics Buffer F Reference Buffer 1X Kinetics Buffer q O Control Buffer 1X Kinetics Buffer 7 H i Buffer 1X Kinetics Buffer 4 Negative Control Load 12 5 ug ml Pro amp Positive Control Load 12 5 ug ml Pro Oc Load 12 5 ug ml ProA c Buffer Load 12 5 ug ml ProA 5 Activation Load 12 5 ug ml Prod Load 12 5 ug ml ProA Oc Quench Load 12 5 ug ml ProA OHO Load Load 125uq mlProA 4 w Wash Buffer 1X Kinetics Buffer E R gt Buffer 1X Kinetics Buffer utter inetics Buffer d egeneration Butt 1 Kinetics Buff g Set Well Data Buffer 1X Kinetics Buffer E Clear Data
214. HC Beta 1 i 1 Regeneration 3 Custom 1 12 Neutralization 2 Custom 1 11 Regeneration J Custom SA Streptavidin Figure 7 46 Assay Definition Window Changing the Biosensor Type REVIEWING EXPERIMENTS Before running an experiment you can review the sample plate layout assays and assay steps as well as the biosensors assigned to each assay in the experiment In the Review Experiment window Figure 7 47 move the slider left or right to highlight the biosensors and samples associated with an assay step or click the e gt _arrows Alter natively select an assay step to view the biosensors and samples associated with it Octet System Data Acquisition User Guide Release 7 1 Saving Experiments page 259 iG DOO Slider Piate Definition Assay Definition Sensor Assfanment Review Experiment Run Experiment Oo In this step you can review the steps that male up the experiment moving the slider to change the active step Ses Jerem Q Lele azan Sensor Tray Sample Plate 96 wells y LJ 2 3 4 5 6 7 8 Ss 0 n 12 y 1 2 3 4 5 6 7 8 9 10 11 12 AGUS A OOS OOOOOOO s1000 BOOO S O0O00O cio COOOC SOOOOOOO DOUG DIOOOS SO000O EHUD EIOOO G O0000 FOU FOOOO OO00O GO H Baseline Assnciation f OOOOOOOO0COO OOOOOBOOOOO ke Baseline Asenciation HOS Legend Unassigned sensors je Missing sen
215. Info automation interface command 349 GetRunInfo command 347 Gradient threshold parameter 239 305 group administration 388 group settings changing 390 viewing 390 Groups tab figure 388 GxP Server Address search results figure 54 GxP Server Configuration window figure 397 GxP Server module accessing directly 396 restarting 398 H Heat hot symbol 13 Help menu described 38 figure 38 list of menu commands 38 heterogeneous biosensor trays assigning biosensors quantitation 384 178 quantitation 96 101 using kinetics 384 317 kinetics 96 254 hiding main toolbar 34 status bar 34 higher acquisition rate 120 197 329 Homogeneous biosensor trays assigning biosensors quantitation 384 183 quantitation 96 106 icons Data Acquisition 8 Data Analysis 8 Import button 89 Import button figure 234 Import Plate Definition window quantitation 384 164 quantitation 96 89 Import Plate Definition window figure 234 importing plate definitions kinetics 384 298 kinetics 96 234 Octet System Data Acquisition User Guide Release 7 1 page 18 importing plate definition quantitation 384 164 quantitation 96 89 inserting assay steps 245 310 installing Data Acquisition 7 0 CFR Part 11 software 366 Data Analysis 7 0 CFR Part 11 software 369 ForteBio GxP Server 372 ForteBio GxP Server module 371 Instrument menu described 36 figure 36 list of menu commands 36 Instrument Status menu 34 instr
216. JPG or PNG Save the vV Click File gt Creates a tab delimited text binding Browse to file of the numerical raw data data select a folder from each biosensor Open and enter a file the file with a text editor name such as Notepad Export the v Click File gt Creates a graphic image Runtime Browse to Binding select a folder Chart toa and enter a file graphic file name Copy the vV Clipboard Copies the chart to the sys Runtime tem clipboard Binding Chart Print the v Printer Opens the Print dialog box Runtime Binding Chart Octet System Data Acquisition User Guide Release 7 1 page 274 Chapter 7 Kinetics Experiments Octet RED96 QK and QK MANAGING EXPERIMENT METHOD FILES After you run an experiment the Octet System Data Acquisition software automatically saves the method file fmf which includes the sample plate definition biosensor assign ment and the run parameters An experiment method file provides a convenient initial template for subsequent experiments Open a method fmf and edit it if necessary NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Table 7 10 Managi
217. K Stopped Running Waiting LoadSensors Y Busy UT ERROR ERROR EAEn command TCH _ METHOD m df TCH FOLDER f hes al TCH EXPERIMENT e FMF file optional TCH _PLATEFILE p ai is loaded optional TCH_BARCODE b TCH _BARCODE1 l TEA optional TCH_BARCODE2 2 Id TCH _LOTNUMBER l fi TCH_SILENT s TCH USELAST u er last run optional TCH_VERBOSE v Id Resetting Presenting Method file to load Root folder for exper Overide for the exper Plate file to import Bar code of Sample Alias for Bar code of Reagent Lot number of sensors Don t open the runtime Reuse the sensor tray Send back verbose sta Octet System Data Acquisition User Guide Release 7 1 page 358 Chapter A Using Octet384 Systems with an Automation Interface Parameter switches for the SetValue command const char AUT SWITCH TEMPERATURE t Response parameter switches for the GetMethodInfo command const char AUT RESPONSE PLATEWELLS p const char AUT RESPONSE SENSORTRAYS t const char AUT RESPONSE SENSORTYPE ll oO const char AUT RESPONSE EXPTYPE const char AUT RESPONSE RERACKING ll K Response parameter switches for the GetRunInfo command const char AUT RESPONSE EXPNAME TR const char AUT RESPONSE EXPPATH ce oars const char AUT CMD VERSION Version Returns the version of t
218. K KKK KKK KKK KKK KK KKK KK KKK KKK KK KKKK KKK KK KKKEKK KK HEADER AutomationAPI h PURPOSE Defines the commands supported by the automation API AUTHOR BHI Nov 2008 ifndef INC_ANALYSIS AUTOMATIONAPI H define INC_ANALYSIS AUTOMATIONAPI H NOTES The automation interface is string based Commands and responses are strings one per line Bach command starts with the name of the command and may then be followed by required and ae optional parameters Bach parameter starts with a switch definition a la dos unix com mand line followed by the parameter itself This allows parameters to be sent in any order Octet System Data Acquisition User Guide Release 7 1 page 362 Chapter A Using Octet384 Systems with an Automation Interface The command or response is terminated with a new line CR LF sequence Parameters containing embedded spaces must be enclosed in double quotes Response items containing embedded spaces will be enclosed in dou ble quotes Version of thew API described in this header file const char AUT API VERSION 1 0 Status return values const char AUT OK OK const char AUT RUNNING Running const char AUT ERROR ERROR const char AUT BUSY Busy const char AUT _STOPPED Stopped Stopped by user const char AUT EOL an Parameter switche
219. K instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 Temperature Setting dialog box displayed figure 43 opening 35 temperature value default saving 44 temperature startup user option 42 Templates menu 35 templates viewing kinetics 384 324 kinetics 96 260 terminating a step in the assay 271 335 testing server 397 Threshold check box 238 threshold parameters Active Channels 239 304 Filtering 239 305 Gradient 239 305 listed table 239 304 Signal Change 239 304 Threshold Parameters dialog box 304 threshold applying to assay steps 238 304 throughput Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 Tile menu 37 tiling windows vertically 37 Toolbar menu 34 toolbar Octet System Data Acquisition software 31 tooltip of well information 241 Tray Format button 106 types of wells control 71 145 reference 71 145 reserved 71 145 standard 71 145 unassigned 71 145 Unknown 71 unknown 145 U Unaligned menu 270 334 unassigned type of well 71 145 UNC folder names 347 undo magnification 125 202 271 335 Unknown well type quantitation 384 145 quantitation 96 71 unknowns assigning a dilution factor quantitation 384 153 Octet System Data Acquisition User Guide Release 7 1 page 36 quantitation 96 78 assigning serial dilution quantitation 384 153 quantitation 96 78 designating quantitation 384 153 quantitation 96 78 upd
220. Log Port v Connect Run Experiment Experiment name E Show runtime window E Continue sensor tray from last run Method File Experiment folder ma Repetitions 1 gt Run Run Sequence Repetitions i __ Show runtime window o Continue sensor tray from last run x V Prompt for new plates within sequence Sequence Add Remove Move Up Move Down Run x Figure A 2 Automation Client Window 4 Select the TCP IP or RS 232 port selected previously in the Octet Data Acquisition soft ware Options dialog box Figure A 1 To connect locally using Localhost leave the Machine field blank 5 Click Connect If the port is successfully opened the automation client dialog will be minimized and remain minimized indicating that the connection succeeded and the port is open Oth erwise the automation client dialog will minimize and come back again indicating that the connection attempt failed Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 349 6 After a successful connection is established send the default Version command in the Send Commands Comman4d field and then click Send A response similar to the following should appear in the Response box Command Ferion fa Send Response PENEL ESES E Figure A 3 Send Commands Command Field Send Commands The response indicates that the Automation Client has connected to the Octet System Data Acquisiti
221. OOO000000 QOOOOQOO0O0O00O0O NOOQOQOQQOQOQOQOQOQOQQ0Q000000000009Q o OOOD OOQOQOQQ00000000000009 J POOOOOO000 000 000000000000 oS Experiment Wizard 2 E o Choose an option to start a9 New Quantitation Experiment Basic Quantitation Basic Quantitation with Regeneration advanced Quantitation 8K New Kinetics Experiment Basic Kinetics O vesina U aaa Rea i i Figure 8 1 Starting a Kinetics Experiment with the Experiment Wizard DEFINING THE SAMPLE PLATE The steps to define a sample plate include Step See Page 1 Select the instrument read head configuration 8 or 16 channels 278 2 Select the sample plate format 96 or 384 wells 280 3 Designate the samples 280 4 Save the sample plate definition optional 296 Read Head Configuration and Plate Layout The Octet read head contains the collection optics If the read head is set to 8 channels one column of 8 biosensors interrogate 8 plate wells If the read head is set to 16 channels two columns of biosensors interrogate 16 wells see Figure 8 2 The read head configuration and the plate format 96 or 384 wells determine the plate layout see example Figure 8 2 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 279 8 Channel Read Head 16 Channel Read Head 45 6 7 8 9 10 11 12 00000000 000000000 C O000008
222. Plate Map 2 Right click to view the shortcut menu and select Start New Assay see Figure 7 32 3 Add steps to the assay as described earlier Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 245 Sample Plate 96 wells A gt A e A Add Assay Step Insert Assay Step 10 11 12 Start New Assay Show Sample Types Show Pie Charts Copy to Clipboard Assayed samples O Unassigned samples Figure 7 32 Start New Assay Inserting or Adding an Assay Step To insert an assay step 1 Select a step in the Step Data List 2 Inthe Assay Steps List select the row above where you want to insert the step 3 Inthe Sample Plate Map right click the column to which the step will be applied and select Insert Assay Step The step is inserted into the Assay Steps List To add an assay step 1 Select a step type in the Step Data List 2 Inthe Sample Plate Map right click the column to which the step will be applied and select Add Assay Step The step is added to the end of the Assay Steps List Octet System Data Acquisition User Guide Release 7 1 page 246 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Selecting a Biosensor for the Assay To select the biosensor type associated with the assay click the Sensor Type arrow for any step in the assay and select a sensor type from the drop down list Figure 7 33 The biosensor type will a
223. Properties dialog box select one of the following legends Sensor Location Sample ID Sensor Information e Concentration Dilution BE Runtime Graph Properties Title Subtitle Legend Sensor Location Sensor Information Sample ID Concentration Dilution S Figure 8 64 Selecting a Runtime Binding Chart Legend NOTE Text for Sample ID Sensor Information or Concentration Dilution is taken from the Plate Definition and Sensor Assignment tabs and must be entered before the experiment is started 3 Click OK Viewing Multiple Runtime Binding Charts To view multiple Runtime Binding Charts click Window gt New Window Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 337 Exporting or Printing the Runtime Binding Chart To export the Runtime Binding Chart as a graphic or data file 1 Right click the chart and select Export Data 2 Inthe Exporting dialog box see Figure 8 65 select the export options and click Export r Exporting Export EMF ClipBoard OFile Printer Export Size K WMF Export Destination BMP JPG Browse Millimeters Width 152400 Figure 8 65 Exporting Dialog Box Inches 101 600 Large Font PNG Points Millimeters Table 8 11 Runtime Binding Chart Export Options Text Data
224. Protein A Load 20 C5 Protein A Load 4 4 gt 384 K method 4 export 3 Concentration ug ml Molecular Weight kD Molar Concentration M Information 12 5 12 5 z Figure 8 26 Example Plate Definition File csv WORKING WITH A REAGENT PLATE You can include an optional reagent plate in a Basic Kinetics experiment Using a reagent plate enables higher sample throughput since no reagents are included in the sample plate An experiment can include any combination of sample and reagent plate formats 96 or 384 well The reagent plate can be used for reagents but not samples references or controls S NOTE The reagent plate format 96 or 384 well and the read head configu ration 8 or 16 channels determine the reagent plate layout For more details see Read Head Configuration and Plate Layout on page 278 To modify a reagent plate 3 Click Modify Plates above the Sample Plate Map The Modify Plates dialog box dis plays see Figure 8 27 Octet System Data Acquisition User Guide Release 7 1 page 300 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Read Head E C 8 Channels 16 Channels Modify Plates g Sample Plate 384 wells F1i234567 1011121314151617 18192021222324 OQOQQOQ O00000 00000000Q Well Samp ID Replicate Group Al 1X Kinetids Buffer Sample Plate Reagent Plate OOOOOOOVOQ O O O O O
225. QK384 Quantitation 198 Octet QKe 121 Octet RED 121 Activation well type 218 kinetics 384 281 activation steps 237 303 active biosensor column 122 199 267 331 Active Channels threshold parameter 239 304 active method file closing 33 active steps extending duration 270 335 Add Sensor dialog box figure 49 Adding 49 adding biosensor type 49 replicate assay to a plate 247 312 Replicate Groups from the Sample Plate Map kinetics 384 291 kinetics 96 228 quantitation 384 figure 160 quantitation 96 figure 85 Runtime Binding Chart title 271 336 quantitation 384 203 quantitation 96 126 Octet System Data Acquisition User Guide Release 7 1 page 2 sample annotations from the Sample Plate Map kinetics 96 figure 225 adjacent steps selecting 243 308 administrator account setting up 374 administrator constants listed table 393 administrator password changing 387 administrator user session starting 378 administrator username selection figure 379 Advanced Quantitation shortcut menu option 166 Advanced Quantitation assay parameters 94 135 171 212 2nd Buffer Time and Shake speed 136 213 Buffer Time and Shake speed 135 212 Detection Time and Shake speed 136 213 Enzyme Time and Shake speed 136 213 Offline 136 213 Pre condition sensors 136 213 quantitation 384 2nd Time and Shake Speed param eter 172 Buffer Time and Shake Speed pa rameter 172 Detection
226. QQQQQQQQQOQQ PIC Wash O Unassigned l Import Export J Remove Q Regeneration Reac Set Well Data v Clear Data 9 w0 n 12 A Copy to Clipboard B Y Extended Sample Types Figure 8 7 Clearing Sample Data from a Sample Plate Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 283 Entering Sample Information NOTE You must specify sample analyte concentration and molecular weight otherwise the Octet System Data Acquisition software cannot com pute a Kpvalue If the sample concentration is not specified only kg and kops are calculated You can also annotate any well with Sample ID or Well Infor mation and assign Replicate Groups Assigning Molecular Weight and Molar Concentration 1 Inthe Sample Plate Map select the sample wells right click and select Set Well Data 2 Inthe Set Well Data dialog box enter the analyte molecular and molar concentration Figure 8 8 Octet System Data Acquisition User Guide Release 7 1 page 284 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Piate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered Highlight one or more wells on the sample plate and right click to enter modify well data Read Head 8 Channels 16 Channels Somple Plate Co
227. Release 7 1 page 29 kinetics 96 267 opening 268 332 quantitation 384 200 quantitation 96 123 printing 273 338 scaling 271 335 quantitation 384 202 quantitation 96 126 selecting legend 271 336 quantitation 384 203 quantitation 96 126 updating kinetics 384 331 kinetics 96 267 quantitation 384 199 quantitation 96 122 viewing inverted data 269 334 viewing multiple kinetics 384 336 kinetics 96 272 quantitation 384 204 quantitation 96 127 Runtime Binding Chart figure 118 195 263 327 Runtime Binding Chart Export options copy the Runtime Binding Chart to a graphic file quantitation 384 205 quantitation 96 128 export the Runtime Binding Chart to a graphic file quantitation 384 204 quantitation 96 127 print the Runtime Binding Chart to a graphic file quantitation 384 205 quantitation 96 128 save the binding data quantitation 384 204 quantitation 96 127 Runtime Binding Chart options listed table quantitation 384 204 quantitation 96 127 Runtime Binding Chart window figure 267 332 Runtime Binding Chart copying quantitation 384 205 quantitation 96 128 Runtime Binding Chart enhanced legend options 12 Runtime Binding Chart printing 128 205 Runtime Graph Properties dialog box 126 203 271 336 S Sample well type kinetics 384 280 kinetics 96 218 sample plate loading kinetics 384 324 kinetics 96 260 quantitation 384 193 quantitation 96 116 Octet System Data Acqui
228. Replicate Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and a group samples that use the same Replicate Group names spacing and capi talization must be identical For example samples assigned to Group 2 and group2 are treated as two groups Wells in the Sample Plate Map will show color coded outlines as a visual indication of which wells are in the same group see Figure 8 17 Octet System Data Acquisition User Guide Release 7 1 page 292 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Sample Plate 384 wells W123 4 5 6 7 8 9 101112131415161718 192021222324 AMOOOOOOOOOOO O0Q00O0 Figure 8 17 Replicate Groups Displayed in Sample Plate Map The Sample Plate Table will update with the Replicate Group names entered see Figure 8 18 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 293 Sample Plate Concentration units mMm z C Reagent Plate Molar concentration units Well Sample ID Replicate Group Type Conc jig ml MW kD Molar OM Protein A Load 125 O0 ProteinA Load 125 AQ 1X Kinetics Buffer Buffer C9 1X Kinetics Buffer Buffer E9 1XKinetics Buffer Buffer G9 1X Kinetics Buffer Buffer 19 1XKinetics Buffer Buffer K9 1X Kinetics Buffer Buffer M9 1X Kinetics Buffer Buffer
229. Restart Server desktop icon figure 399 Restart Server window figure 399 restarting the GxP Server module 398 Resume automation interface command 350 resuming user session 66 Reuse Buffer parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Review Experiment window 114 191 258 322 Review Experiment window figure 114 191 259 323 reviewing experiments kinetics 96 258 Run automation interface command 349 Run Experiment tab 117 Run Experiment window Octet RED RED96 and QKe figure 117 194 Run Experiment window settings 2nd Plate Name Barcode 119 196 Assay Type 119 196 Auto Increment File ID Start 120 197 Experiment Run Name 119 196 Plate Name Barcode 119 196 Quantitation Data Repository 119 196 Run Experiment window Octet RED and Octet RED96 figure 262 326 run name 264 328 run settings quantitation 384 Delayed Experiment Start 197 Start After setting 197 quantitation 96 Delayed Experiment Start 120 Start After setting 120 run settings listed quantitation 384 197 quantitation 96 120 running experiment settings 119 196 Runtime Binding Chart adding title 271 336 quantitation 384 203 quantitation 96 126 copying kinetics 384 338 kinetics 96 273 exporting to a graphic file 273 337 exporting to a graphic or data file 127 204 272 337 magnifying 271 335 quantitation 384 202 quantitation 96 125 managing Octet System Data Acquisition User Guide
230. Sample Plate Map 1 Select the samples to group right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 5 17 enter a name in the Replicate Group box and click OK Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 85 z Set Well Data Well Information 200 SmE By value 200 IgG Standard l f Dilution series Replicate Group j Sere ais 200 i perator Wel Information Sample Diluent series operand 2 Dilution orientation 833 Right Left g Down Up Figure 5 17 Add Replicate Group from the Sample Plate Map 3 Repeat the previous steps to assign new samples to the existing Replicate Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and D calculate statistics for samples that use the same Replicate Group names spacing and capitalization must be identical For example samples assigned to Group 2 and group2 are treated as two groups NOTE When performing a Multiple Analyte experiment if the same Replicate gt Group name is used with different biosensor types they will be treated as sep arate groups Statistics for these groups will be calculated separately for each biosensor type Wells in the Sample Plate Map will show colo
231. Standard 25 nja O El IgGStandard 10 Standard 10 n a F1 IgGStandard 5 Standard 5 n a Figure 5 23 Import Button in Sample Plate Table 2 Inthe Import Plate Definition window see Figure 5 24 select the plate definition csv and click Open Octet System Data Acquisition User Guide Release 7 1 page 90 Chapter 5 Quantitation Experiments Octet RED96 QK and QK if a EF Import Plate Definition gO I Forte Bio Search Data and met Organize 7 New folder E F k Favorites a Documents library E Desktop Data and methods J Downloads Name Date modified Type Arrange by Folder 7 Recent Places 4 96 standard plate csv 4 22 2011 6 34 PM _ Microsoft Excel C E Desktop 5 Libraries Documents J My Documents JL Public Documents Music 5 Pictures a Videos lt m r File name 96 standard plate csv v CSV Files csv x L 4 Figure 5 24 Import Plate Definition Window NOTE You can also create a csv file for import Figure 5 25 shows the appro priate column information layout A B E D E r N E 1 PlateWells 96 E 2 Well ID Replicate Group Group Concentration ug ml Dilution Information E 3 A1 IgG Standard 200 Standard 200 Sample Diluent 4 Bi IgG Standard 100 Standard 100 Sample Diluent 5 c1 IgG Standard 50 Standard 50 Sample Diluent 6 D1 IgG Standard 25 Standard 25 Sample Diluent EAEL IgG Standard 10 Standard 10 Sample Dilue
232. Tray Format dialog box displays see Figure 6 40 2 Select Heterogeneous and click OK Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 179 Tray Format ES Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical C Homogeneous A different sensor tray is used for each sensor type Sensors SAUSAGE Add Remove Change Move Up Move Down LK cancel Figure 6 40 Tray Format Dialog Box The Tray 1 Sensor Tray Map will be displayed by default 3 Select all columns with default biosensor assignments in the Sensor Tray Map right click and select the first biosensor type to be used see Figure 6 41 The Sensor Type column will update accordingly l Repce Tayi W Replace sensors in tray after use of 2 1 2 3 4 HE Sar auto assign Anti Human IgG Fc Anti Mouse IgG Fv Protein A Protein G Protein L SA Streptavidin Residual Protein A Anti Penta HIS Custom HODDIDIDODDDIBSEe Bers Positive Control Legend _ Unassigned sensors 583 Missing sensors Negative Control Figure 6 41 Populating the Sensor Tray Map with First Biosensor Type 4 Select the columns in the Sensor Tray Map that should contain the second biosensor type right click and select the second biosensor type see Figure 6 43 The Sensor Type column will update accordingly
233. User Guide opening online version 38 Data Acquisition icon 8 Data Analysis 21 CFR Part 11 software overview 52 Data Analysis icon 8 data column displaying acquisition 267 331 quantitation 384 199 quantitation 96 122 data display significant digits 42 data file location and name settings quantitation 384 listed 196 quantitation 96 listed 119 Data File repositories setting Data File repositories 347 data files kinetics data repository 41 quantitation data repository 41 Use extended sample types 42 Use old 5 0 file format for FRD files 42 data preferences setting 40 DataAcquisition CFR 7_0_0_x exe 366 default biosensor columns 252 316 default locations for reserved wells in a 96 well sample plate map figure 72 default server settings localhost 54 Port 2002 54 default temperature value saving 44 default temperature defining new 44 default Tray Format 101 default user group privileges 385 default user groups 388 default windows Octet System Data Acquisition software 31 Default advanced settings 121 defining custom assays quantitation 384 206 quantitation 96 129 kinetic assays 236 new assay 35 new assay figure 130 207 new default temperature 44 reagent plates quantitation 384 166 sample plates kinetics 384 278 kinetics 96 218 quantitation 384 142 quantitation 96 70 samples by entering sample information figure 284 step types 237 303 kinetics 384 305 kinetics 96 240 defining st
234. _ Threshold B O00000 gt equilibration 120 1000 Custom Loading 300 1000 IZ Loading m Assay steps designated as Threshold will terminate when either the step time elapses or the threshold termination criteria is reached F si Active Channels a ee Channel 1 Channel 9 Deon Channel 2 Channel 10 The threshold is achieved when ae ia 5 Binding ascends by threshold from step start nn ann 4 Channel 5 Channel 13 Binding descends by threshold from step start Channel 6 Channel 14 Channel 7 Channel 15 E Gradient Channel 8 Channel 16 Threshold nm min SSSSSS88 SSiSS88S88 Duration min The step is terminated when the threshold is achieved on ALL channels The threshold is a when the binding gradient stay pes t threshold fi n duration 5 the threshold is achieved on ANY ONE channel i i bel Filtering is applied before the threshold is assessed Fitter width s 10 0 Assayed reagents Unassigned reagents Figure 8 30 Setting Assay Step Threshold Parameters NOTE If thresholds are applied the step is terminated when either the step time elapses or the threshold termination criteria is reached Table 8 4 Threshold Parameters Item Description Active Channels Specifies the instrument channels that monitor the thresho
235. a delayed start time this setting shakes while waiting the plate until the experiment starts Open runtime charts Displays the Runtime Binding Chart for the current biosensor automatically during data acquisition Automatically save Saves an image jpg of the Runtime Binding Chart The runtime chart binding data frd is saved as a text file regardless of whether a chart image is created Set plate temperature Specifies a plate temperature and enters the temperature in C the dialog box If not selected the plate temperature is set to the default temperature specified in File gt Options The fac tory set default temperature is 30 C NOTE If the actual plate temperature is not equal to the set plate temperature a warning displays and the Octet System Data Acquisition software provides the option to wait until the set temperature is reached before proceeding with the run continue without waiting until the set temperature is reached or cancel the run Advanced settings are available for the Octet QK Octet RED and Octet RED96 systems The signal to noise ratio of the assay can be optimized by selecting different acquisition rates The acquisition rate refers to the number of binding signal data points reported by the Octet system per second and is reported in Hertz per second A higher acquisition rate Octet System Data Acquisition User Guide Release 7 1 Running a Quantitation Experiment page 121 ge
236. a histori cal log of all events recorded on the active GxP Server module will display To view events for a specific user account project or computer click on the User Project or Machine drop down list and select an entry user nya Project Machine any Date administrator me Project Machine Type Info 2011 EEE trator JRICHARDS User login 2011 PSmith rator JRICHARDS User logout 2911 en tor JRICHARDS User login 2011 02 07 16 20 31 Administrator JRICHARDS User login 2011 02 07 16 47 42 Administrator JRICHARDS User logout Figure B 51 Selecting Events by User Name NOTE Selections can be made in either one or all of the User Project or Machine drop down lists Octet System Data Acquisition User Guide Release 7 1 page 396 Chapter B 21 CFR Part 11 Software Administrator Options The list will then only display events for the entries selected User JBlack Mi Project Receptor Ligand scr Mi Machine ny A Date Time Login Name Project Machine Type Info 2011 02 13 20 39 33 JBlack Receptor Ligand screen JRICHARDS User login 2011 02 13 20 39 37 JBlack Receptor Ligand screen JRICHARDS User logout Figure B 52 Events Displayed for User Name In addition to the specific user project and machine selections the following list options are also available e any Displays all user project or machine events none Displays all user and machine events not associated with a s
237. a human IgG OB hlgG 5 Standard 10 n a human IgG OKI hlgG 6 Standard 5 n a human IgG OM3 hlgG 7 Standard 2 5 n a human IgG 03 higG 8 Standard 1 n a human IgG aA5 Abl g Unknown n a 2 Sample Diluent c5 Ab2 10 Unknown n a 2 Sample Diluent E5 Ab3 11 Unknown n a 2 Sample Diluent G5 Ab4 12 Unknown n a 2 Sample Diluent I5 Abs 13 Unknown n a 2 Sample Diluent K5 Ab 14 Unknown n a 2 Sample Diluent M5 Ab 15 Unknown n a 2 Sample Diluent o05 Abs 16 Unknown n a 2 Sample Diluent OA Abd 9 Unknown n a 2 Sample Diluent c Abi0 10 Unknown n a 2 Sample Diluent E Abii 11 Unknown n a 2 Sample Diluent G Abi2 12 Unknown n a 2 Sample Diluent Figure 6 22 Replicate Groups in Sample Plate Table Octet System Data Acquisition User Guide Release 7 1 page 162 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Assigning Replicate Groups in the Sample Plate Table To assign Replicate Groups in the Sample Plate Table 1 Double click the desired cell in the Replicate Group table column 2 Enter a group name see Figure 6 23 Sample Plate Table Concentration units yom nA Export Import Well Sample ID Replicate Group Type Conc jig ml Dilution Factor Information a OK3 hlgG Standard 5 n a human IgG O M3 hlgG Standard 2 5 n a human IgG 03 higG Standard 1 n a human IgG aA5 Abl Unknown n a 2 Sample Diluent c5 Ab2 Unknown n a 2 Sample Diluent E5 Ab3 Unknown n a 2 Sample Di
238. a partial plate Sensor Tray Sensor Tray A sensors in after us use Trayi 7j of 3 Tray Format Heterogeneous trays 1 Well Sensor Type Lot Number Information A1 _ ProteinA B1 Protein A C1 Protein A D1 Protein A E1 Protein A Fi Protein A G1 Protein A H1 Protein A A2 Protein A B2 Protein A Protein A Protein A Protein A Protein A A won Protein A Legend Unassigned sensors By Missing sensors si H2 Protein A enove Ca Eare Proens Ooo o oen S T Sample Plate Potent T Wi23456 101112131415 1617 18 192021222324 ProtenG O00 poten J o o Proteine ens O e Proteine T Proteine Proteine J o o Proteine Eroe CT Proteins Proteine T eea r Prot aa as A5 Protein A B5 Protein A C5 Protein A D5 Protein A r A B C D IE F G AURRA 0000000000009 VOZSrxc ramtmMooDOPY 00000000000 0000000000000 000000000000 0N 5 8 8 8 8 0000000000000 000000000000 c 8 pa H a Unassigned samples Figure 6 43 Biosensor Assignment using Heterogeneous Trays and Two Biosensor Types 6 To view or change the biosensor assignments in another tray click the Sensor Tray button and select a tray number from the drop down list The Sensor Tray Map and table for the tray selected will be shown and biosensor assignme
239. about the assay 6 Click Save The new assay appears in the directory tree of available assays see Figure 6 67 bot tom Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 207 r E Anti Penta HIS High sensitivity Edit Assay Parameters Available Assays Assay Parameters Basic Quantitation Name Standard Assay Description Basic Quantitation Standard Assay Read Only Anti Penta HIS Standard range High sensitivity Human IgG quantitation Human IgG Quantitation Immunogenicity Direct detection Murine IgG Quantitation Protein L Standard range Standard Assay Basic Quantitation with Regeneration E High sensitivity assay with regeneration E Protein L Standard range E Standard Assay Advanced Quantitation 2 Immunogencity Enzyme Linked Residual Protein A Standard Assay Single analyte ows ows ome A CA A ems Quantitation Multiple analyte Replicates Time s 120 e 1 t per sensor type Shake speed w E E Three Step Assay i New Assay Enter Assay Information Assay name Blueindicates a ForteBio buitt in assq Remove Assay description My Basic Quant Assay Enter a short description of the assay here Edit Assay Parameters Available Assays Basic Quantitation Z
240. accept this path location The Choose Start Menu Folder dialog box displays Figure B 3 i Data Acquisition 7 0 Setup Choose Start Menu Folder ae Choose a Start Menu folder for the Data Acquisition 7 0 shortcuts tee Select the Start Menu folder in which you would like to create the program s shortcuts You can also enter a name to create a new folder For teBio For teBio 2BrightSparks 7 Zip Accessories ACT by Sage Premium Administrative Tools Bonjour Print Services Corel DVD MovieFactory Lenovo Edition DivX Plus ForteBio Inc ortebio com Figure B 3 Choose Start Menu Folder Dialog Box The default Start Menu folder is ForteBio 5 Click Install The installation wizard takes a few seconds to install Figure B 4 Octet System Data Acquisition User Guide Release 7 1 page 368 Chapter B 21 CFR Part 11 Software Administrator Options i Data Acquisition 7 0 Setup al a Installing e Please wait while Data Acquisition 7 0 is being installed tee Extract AutomationClient exe Extract DataSecurity dll a Extract PEGRP32D DLL Extract DMC32 dll Extract Dmcbus32 dll Extract Dmcser32 dll Extract WAModbus dll Extract GalilController exe Extract PortAssignment exe Extract ControllerSetup exe Extract AutomationClient exe ForteBio Inc www fortebio com lt Back Next gt Cancel Figu
241. after use Tray Format Heterogeneous trays Voi 2 3 4 5 6 7 8 9 10 11 12 Well Sensor Type Lot Number Information E aApocroomgoUUL BAren gr gE Ea como oOmmOLLLILIL e anuman gre gt Se SS eee 5 A E OC epean cmmogEEgOLUL J D2 Anti Human IgG Fc HEBD E Bal tence J Legend __ Unassigned sensors RRI Missing sensors ee Ant Human 196 Fc H2 Anti Human IgG Fc Fil Fil Plate A3 Anti Human IgG Fc B3 Anti Human IgG Fc mple Plate c3 Anti Human IgG Fc 1234 011121314151617 18192021222324 D3 Anti Human IgG Fc E3 Anti Human IgG Fc F3 Anti Human IgG Fc G3 Anti Human IgG Fc H3 Anti Human IgG Fc A4 Anti Human IgG Fc B4 Anti Human IgG Fc C4 Anti Human IgG Fc Anti Human IgG Fc Anti Human IgG Fc Anti Human IgG Fc Anti Human IgG Fc Anti Human IgG Fc Anti Human IgG Fc Anti Human IgG Fc CS Anti Human IgG Fc D5 Anti Human IgG Fc at g D o o o 0 0 08080808 0000000000000 x Oo VOZErxc TOaNmMoOoODPY 00080O080808 0OO 080 080O0 8 0000000000000 0000080000808080 000008008008 O RAREST 8 oO 3 a Unassigned samples Figure 6 38 Sensor Assignment Window for Basic Quantitation Using the Multiple Analyte Option Octet System Data Acquisition User Guide Release 7 1 page 178 Chapter 6 Quantitation Experiments Octet RED384 and QK384 There are tw
242. and one punctuation character PasswordTTL Amount of time that a password 180 Minimum 0 is allowed to remain unchanged no max value UserldleMin Idle time allowed during a user 15 Minimum 0 session after which the session is no max value automatically closed Creating a New Constant 1 Right click anywhere in the Constants Tab and select New Constant from the Tab menu or double click in a blank area The New Constant dialog box will display New Constant Constant name Value Figure B 48 New Constant Dialog Box 2 Enter the Constant name and Value Please refer to Table B 3 for a list of available con stants and value ranges Octet System Data Acquisition User Guide Release 7 1 page 394 Chapter B 21 CFR Part 11 Software Administrator Options 3 Click OK to save changes and exit Viewing and Changing Constants 1 Right click on the constant and select Edit Constant from the Tab menu or double click on the constant The Edit Constant dialog box will display r Constant name UserIdleMin Value 15 Figure B 49 Edit Constant Dialog Box 2 If needed modify the constant settings For more information on available constants and their values please see Table B 3 3 Click OK to save changes and exit Deleting a Constant 1 Right click on the constant and select Delete Constant from the Tab menu 2 Click OK in the dialog box displayed Event Log The Events Tab al
243. aol human IgG Dilution series Repiicate Group Starting value l1 Series operator I se Well Information Series operand 22 Dilution orientation 833 Right 8883 Left Wel Data Sample only Down up Molecular Weight kD a Molar Concentration nM Lax L d Figure 8 10 Sample Plate Map Assigning Sample Concentrations by Value 3 Click OK The Sample Plate Table will display the entered concentration Assigning Concentrations Using a Dilution Series To assign sample concentrations using a dilution series 1 Inthe Sample Plate Map select the wells right click and select Set Well Data The Set Well Data dialog box displays see Figure 8 11 2 Select the Dilution Series option and enter the starting concentration value Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 287 AAA ASAAN FJK Sample Reference O Control Negative Control Positive Control Buffer Activation Quench Load Ww Wash Regeneration Set Well Data Clear Bata INOQOQOOOOO0O o O OOOOO POOOOOO00 Set Well Data Well Information Well Data Sample only Molecular Weight kD Molar Concentration nM Concentration ug ml Sample only By value Dilution series Starting value 40 Series operand 2 Series o
244. arameter values quantitation 384 208 quantitation 96 131 projects 391 sample data in the Sample Plate Table kinetics 384 295 kinetics 96 231 standard concentration quantitation 384 151 quantitation 96 76 step type figure 241 306 editing step types 240 305 Electrical hazard symbol 13 electrical requirements Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 emptying waste container 340 ending a user session 66 enhanced legend options in the Runtime Binding Chart 12 entering annotations Octet System Data Acquisition User Guide Release 7 1 page 14 quantitation 384 157 quantitation 96 82 biosensor information displayed figure 252 316 procedure 252 315 entering an individual standard concentration quantitation 384 151 quantitation 96 76 environmental features Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 Enzyme Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Enzyme Time and Shake speed parameter 136 213 equipment classifications Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 events list options available 396 viewing 395 Events tab figure 395 example csv plate definition file figure 235 299 example ass
245. are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE For greater clarity annotation text may be displayed as the legend of the Runtime Binding Chart during data acquisition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 183 10 Optional After an assay is completed the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container To return the biosensors to the tray click the Replace sensors in tray after use check box see Figure 6 37 Sensor Tray v Replace sensors in tray after use y 2 3 HOD Legend Unassigned sensors 683 Missing sensors remove a J rire Figure 6 45 Replace Sensors in Tray After Use Check Box NOTE Biosensors can be regenerated up to a max of 11 times per experiment Biosensor Assignment Using Homogeneous Trays Homogeneous biosensor trays contain only one biosensor type NOTE Using the Homogeneous option will necessitate switching trays dur ing the experiment 1 Click Tray Format The Tray Format dialog box displays see Figure 6
246. ase 7 1 page 21 Octet QK instrument 23 biosensor tray type 24 biosensor type 24 capabilities 23 compliance 23 dimensions 24 electrical requirements 24 environment 23 equipment classifications 23 mechanics 24 optics 24 orbital flow capacity 24 sample types 24 sample volume 24 sampling format 24 temperature range 24 throughput 24 Octet QK system specifications 23 Octet QK384 sensor offset 20 27 well volumes 20 27 Octet QK384 instrument automation 26 capabilities 25 compliance 25 dimensions 27 electrical requirements 27 environment 25 equipment classifications 25 mechanics 26 optics 26 sample types 26 sampling format 26 weight 27 Octet QK384 instrument figure 25 Octet QK384 system specifications listed table 25 Octet QKe and Octet RED Run Experiment window advanced settings listed table 266 Octet QKe instrument biosensor tray type 22 biosensor type 22 capabilities 22 compliance 21 dimensions 22 displayed figure 21 electrical requirements 22 environment 21 equipment classifications 21 mechanics 22 optics 22 orbital flow capacity 22 sample types 22 sample volume 22 sampling format 22 temperature range 22 throughput 22 weight 22 Octet QKe system specifications listed table 21 Octet RED instrument replacing fuses 341 Octet RED system warm up 30 Octet RED384 sensor offset 20 27 starting Octet System Data Acquisition User Guide Release 7 1 page 22 kinetics e
247. ase 7 1 page 226 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Annotating Wells in the Sample Plate Table To annotate an individual well in the Sample Plate Table 1 Double click the table cell for Sample ID or Well Information 2 Enter the desired information in the respective field see Figure 7 11 NOTE A series of Sample IDs may also be assembled in Excel and pasted into the Sample Plate Table Sample Plate Table Concentration units Molar concentration units my Well Sample ID Replicate Group Type Conc pg ml MW kD Molar Conc nM Information a G3 Dissociation Buffer 1X Kinetics Buffer H3 Dissociation Buffer 1X Kinetics Buffer A4 Association Sample 10 150 66 67 1X Kinetics Buffer B4 Association Sample 5 150 33 33 1X Kinetics Buffer C4 Association Sample 25 150 16 67 1X Kinetics Buffer D4 Association Sample 1 25 150 8 333 1X Kinetics Buffer E4 Association Sample 0 625 150 4 167 1X Kinetics Buffer F4 Association Reference 1X Kinetics Buffer G4 Association Reference 1X Kinetics Buffer H4 Association Reference 1X Kinetics Buffer Figure 7 11 Add Sample Annotations in the Sample Plate Table NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right cli
248. assay parameter quantitation 384 209 quantitation 96 132 Quantitation Time parameter quantitation 384 169 quantitation 96 92 quantitative experiment analyzing 68 140 216 276 setting up 68 140 216 276 Quench well type kinetics 384 281 kinetics 96 218 quenching steps 237 303 R raw reference subtracted data viewing quantitation 384 201 quantitation 96 123 read head configuration kinetics 384 278 quantitation 384 143 reagent plate defining quantitation 384 166 modifying quantitation 384 299 Octet System Data Acquisition User Guide Release 7 1 page 26 reagent plate definitions saving 301 Reagent Plate Map 166 Reagent Plate Map figure 166 300 Reagent Plate radio button 166 reagent plates loading kinetics 384 324 Received well type quantitation 384 145 quantitation 96 71 recommended sensor offset 198 330 Reference well type 218 kinetics 384 280 quantitation 384 145 quantitation 96 71 reference biosensors designating 105 110 182 187 257 258 321 designating during acquisition 268 333 reference biosensors designating during acquisition quantitation 384 201 quantitation 96 124 Reference menu 124 201 268 333 reference wells defined 81 156 designating quantitation 384 156 quantitation 96 81 reference type of well 71 145 reference subtracted data viewing kinetics 384 332 kinetics 96 268 reference subtracted data viewing quantitation 384 201 quantitation 96 123 Re
249. ate run Developers can create run save and export data Lab User run Lab Users can only run experiments Guest none Guests have no explicit privileges Figure B 41 Groups Tab When a user account is assigned to a user group the privileges defined in the group are also applied to the individual user account The following default user groups are available and the privileges assigned to each are shown Table B 2 e Administrators Can add delete and change user accounts and groups Supervisors Can review data and events Developers Can create run save and export data Lab Users Can only run experiments Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 389 e Guests Have no explicit privileges these must be assigned by the administra tor Table B 2 Default user group privileges Privilege Administrator Supervisor Developer Lab User Guest Administration PA Review v v Change vA v Plate v v Run vV v Creating a New User Group 1 Right click anywhere in the Groups Tab and select New Group from the Tab menu or double click in a blank area The New Group dialog box will display Group name Information Privileges Administration administers the user database _ Review reviews changes and events Change can change methods and configuration values Plate can change sample plate properties Run can run experime
250. ate Map 1 Select the samples you wish to group right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 7 13 enter a name in the Replicate Group box and click OK Octet System Data Acquisition User Guide Release 7 1 page 228 Chapter 7 Kinetics Experiments Octet RED96 QK and QK E Set Well Data _ ____ _ Well Information Dilution Factor Unknown only Sample ID By value 2 Dilution series Replicate Group Starting value 1 1l Series operator Well Information 1X Kinetics Buffer series operand 2 Dilution orientation 833 O Right 8883 Left 8 Down g Up Figure 7 13 Add Replicate Group from the Sample Plate Map 3 Repeat the previous steps to assign new samples to the existing Replicate Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and group samples that use the same Replicate Group names spacing and capi talization must be identical For example samples assigned to Group 2 and group2 are treated as two groups Wells in the Sample Plate Map will show color coded outlines as a visual indication of which wells are in the same group see Figure 7 14 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 229 ADOOOOOOOOOO
251. ating assay times as steps are added to the assay figure 242 307 Runtime Binding Chart kinetics 384 331 kinetics 96 267 quantitation 384 199 quantitation 96 122 Use extended sample types user option 42 Use old 5 0 file format for FRD files user option 42 user account creating new 384 deleting 386 user account passwords changing 387 user account settings changing 386 viewing 386 user data files options 41 user data options 42 user group assigning 385 creating new 389 deleting 390 privileges 385 user groups default 388 User name setting 121 199 330 user options Automation 43 kinetics data repository 41 listed table 41 quantitation data repository 41 significant digits 42 Simulation 43 temperature 42 Use extended sample types 42 Use old 5 0 file format for FRD files 42 viewing 40 Web Server 43 user password changing 65 user session changing projects during 64 starting 56 starting an administrator 378 user sessions discontinuing 66 ending 66 Login dialog box 56 resuming 66 user startup options 42 user defined default start up temperature 12 UserldleMin constant 381 user modifiable settings for an assay quantitation 384 167 quantitation 96 91 username selection figure 57 Users tab 384 using Octet System Data Acquisition User Guide Release 7 1 page 37 heterogeneous biosensor trays kinetics 384 317 kinetics 96 254 partial biosensor trays kinetics 384 320 kinetics
252. ation F 12 3 5 6 7 8 9 10 11 12 HOQQOQOQOOOOOOO Advanced Quantitation F 12 3 5 6 7 9 10 1 12 ADOOOUOOOO OO BOQQQOQOQOOOO0OO0OD COQOQOQOOOOOOOO DOQOQOOQOOOOOSOOD EOQOQOOQOQOOOO0O0OQD FOQQOQOOOCOOOO0O GOQQOOQOOOOOOOOD HOOQOOOOOOO O0OO Figure 5 2 Default Locations for Reserved Wells in a 96 Well Sample Plate Map Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 73 Selecting Wells in the Sample Plate Map There are several ways to select wells in the Sample Plate Map Click a column header or select adjacent column headers by click hold drag Figure 5 3 left To select non adjacent columns hold the Ctrl key and click the col umn header Click a row header or select adjacent row headers by click hold drag Figure 5 3 cen ter Click a well or draw a box around a group of wells Figure 5 3 right Sample Plate Semple Plate Sample Plate 96 wells Sample Piste 86 woke y y 1 2 3 4 5 6 1 8 9 1 1 12 A AO OOOO B BOQOQQQOQOOO0O0OO E cOOOQOOOOOOQOOQOQ D DOOOQOOOOOQOOOQO E EOOOQOOQOOQOQOQOOQQOQ F FOQOQOQOQOOOOOOOO GOQOQOOQOOOOOOO GOQOQOQOOOOOOCOO H I X HOQQQOQOQOQQQQQQ O Sanda _ cono _ Unassigned O Sendoa Controt_ O Unassigned O Sandd Q_ Contr C unassigned O Unknown Reference O Reserved O unon Reference O Reseved O Unknown Reerence O Reserved Figure 5 3 Selecting Wells i
253. ation 348 Octet instrument to computer 30 to a TCP IP socket connection locally using localhost 348 Connections to Clients box figure 397 constants changing 394 creating new 393 deleting 394 viewing 394 Constants tab figure 392 constants administrator listed table 393 contacting ForteBio technical support 13 Control well type 218 kinetics 384 280 quantitation 384 145 quantitation 96 71 control type of well 71 145 controls 156 defined 81 156 designating 156 quantitation 384 156 quantitation 96 81 conventions used in this guide 13 copying assay steps 243 308 Runtime Binding Chart kinetics 384 338 kinetics 96 273 quantitation 384 205 quantitation 96 128 step type kinetics 384 305 kinetics 96 240 creating csv file for import 90 assay step type figure kinetics 384 303 kinetics 96 238 different types of assay steps 237 303 new constants 393 new user account 384 new user group 389 step types 237 303 Current Binding Charts box 331 custom assays defining quantitation 384 206 quantitation 96 129 selecting quantitation 384 214 quantitation 96 137 custom biosensors 48 custom steps 237 303 D Data Acquisition 21 CFR Part 11 software overview 52 Data Acquisition desktop icon 30 Data Acquisition Software New Features 12 Data Acquisition User Guide menu 38 Octet System Data Acquisition User Guide Release 7 1 page 11 Data Acquisition User Guide opening online version 38
254. ation 384 153 quantitation 96 78 updating assay times as steps are added to the assay figure 242 307 Runtime Binding Chart kinetics 384 331 kinetics 96 267 quantitation 384 199 quantitation 96 122 Use extended sample types user option 42 Use old 5 0 file format for FRD files user option 42 user account creating new 384 deleting 386 user account passwords changing 387 user account settings changing 386 viewing 386 user data files options 41 user data options 42 user group assigning 385 creating new 389 deleting 390 privileges 385 user groups default 388 User name setting 121 199 330 user options Automation 43 kinetics data repository 41 listed table 41 quantitation data repository 41 significant digits 42 Simulation 43 temperature 42 Use extended sample types 42 Use old 5 0 file format for FRD files 42 viewing 40 Web Server 43 user password changing 65 user session changing projects during 64 starting 56 starting an administrator 378 user sessions discontinuing 66 ending 66 Login dialog box 56 resuming 66 user startup options 42 user defined default start up temperature 12 UserldleMin constant 381 user modifiable settings for an assay quantitation 384 167 quantitation 96 91 username selection figure 57 Users tab 384 using Octet System Data Acquisition User Guide Release 7 1 page 37 heterogeneous biosensor trays kinetics 384 317 kinetics 96 254 partial bios
255. ation to samples 222 285 user specified concentration to standards quantitation 384 151 quantitation 96 76 assigning molar concentration kinetics 96 221 association steps 236 302 Audit Trail described 62 illustrated figure 62 list options 64 selecting a project 63 sorting 63 viewing 62 Authentication Server dialog box 53 Auto Increment File ID 264 328 Octet System Data Acquisition User Guide Release 7 1 page 6 Auto Increment File ID Start Run Experiment window settings quantitation 384 197 quantitation 96 120 Auto Scroll to bottom check box 39 Automatically save runtime chart setting 120 197 265 329 automation for Octet QK384 26 for Octet RED384 19 Automation box 346 Automation Client example application connecting 348 automation interface commands Cleanup 350 Close 350 GetMethodInfo 349 GetRunInfo 349 Present 350 Reset 349 Resume 350 Run 349 Status 350 Stop 350 Version 349 automation interface control setup 346 automation interface design 346 automation session typical 351 Automation user option 43 AutomationAPI h header file 349 AutomationClient exe 346 baseline step 237 303 basic kinetics experiment 216 276 Basic Kinetics Experiment window figure 277 Basic Quantitation Assay Parameters listed table 92 131 169 208 Multiple Analyte quantitation 384 209 quantitation 96 132 quantitation 384 Multiple Analyte and Replicates per Sensor Type parameter
256. ator Options Figure B 57 Server Found To return to the originally configured GxP Server module settings click Default at any time RESTARTING THE GXP SERVER MODULE If the host location of the GxP Server module cannot be found during user login or if users are unable to login with valid credentials the GxP Server module may be offline and need to be restarted NOTE ForteBio recommends contacting your IT department to confirm whether or not network or firewall settings may have been changed This may also be preventing access to the GxP Server module Ifthe GxP Server module is installed on a network location Double click on the FBServer exe file in the FBServer7 folder from the installed location File Edit View Tools Help Organize 7 Include in library 7 Share with 7 Burn New folder e 0 0 4 ForteBio a Name Date modified Type Size J DataAcquisition7 3 re FBServer exe 12 3 2010 3 53 PM Application 2 966 KB gt DataAnalysis7 A FBServerConfig exe 12 3 2010 3 53 PM _ Application 7 821 KB J FBServer7 2 3 FBServerMonitor exe 12 3 2010 3 54 PM Application 6 909 KB ft ForteBio 2 10 2011 6 20 PM Internet Shortcut 1 KB Globe ico 12 1 2010 4 21 PM Icon 25 KB E uninst exe 2 10 2011 6 20 PM Application 54 KB m Figure B 58 Accessing the GxP Server on the Network Ifthe GxP Server module is installed on a local computer Double click the Restart
257. aved however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning Octet System Data Acquisition User Guide Release 7 1 page 196 Chapter 6 Quantitation Experiments Octet RED384 and QK384 M 14 47 39 Ml 14 47 39 M 14 47 40 14 47 40 14 47 40 14 47 40 14 47 41 14 47 41 14 47 41 14 47 51 14 47 51 14 47 51 14 47 52 14 47 52 14 47 53 14 47 53 14 47 53 22 Instrument Status Sensor 7 Integration Time 1 0 ms Sensor 8 Integration Time 1 0 ms Picking sensors completed location A1 Plate temperature 30 C Ready to move to sample location A1 Moving to sample location A1 Arrived at sample location A1 Waiting to start sample location A1 Processing sample location A1 Sample completed location A1 Waiting to start new step Starting new step Ready to move to sample location A2 Moving to sample location A2 Arrived at sample location A2 Waiting to start sample location A2 Processing sample location A2 sex Figure 6 59 v Auto scroll to bottom Instrument Status Log Run Experiment Window Settings The following Data File Location and Name settings are available on the Run Experiment Tab Table 6 9 Data File Location and Name Item Description Assay type The name of the selected assay Quantitation data repository The location where quan
258. ay Columns 1 and 2 were reassigned as Streptavidin according to the heterogeneous tray being used Octet System Data Acquisition User Guide Release 7 1 page 320 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Sensor Tray I Replace ser sensors in tray after use SA Streptavidin es e SA Streptavidin sa Steptavidn J Y T H1 A2 B2 C2 SA Streptavdn J D2 sa streptavdn a E2_ sa streptavin F2_ sa streptavidn Legend C Unassigned sensors R Missing sensors G2_ sa Streptavidn J 2 5A stretavam LL AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture Sample Plate C3 AHC Anti hlgG Fc Capture 123456 101112131415 1617 1819 2021222324 D3 AHC Anti hIgG Fc Capture O E3 AHC Anti hIgG Fc Capture F3 AHC Anti hIgG Fc Capture G3 AHC Anti hIgG Fc Capture H3 AHC Anti hIgG Fc Capture A4 AHC Anti hIgG Fc Capture B4 AHC Anti hIgG Fc Capture C4 AHC Anti hIgG Fc Capture AHC Anti hIgG Fc Capture E4 AHC Anti hIgG Fc Capture F4 AHC Anti hIgG Fc Capture G4 AHC Anti hIgG Fc Capture H4 AHC Anti hIgG Fc Capture A5 AHC Anti hIgG Fc Capture BS AHC Anti higG Fc Capture C5 AHC Anti hIgG Fc Capture D5 AHC Anti higG Fc Capture RR Fan Rta Fo Canteen aes rs sa Streptavidin ss C CT A B c D E F G H Remove Fill Fill Plate x 090909090900 N 9
259. ay using one partial biosensor tray and biosensors from a second tray 113 190 example experiment using two biosensor trays figure 257 321 Exit menu 34 experiment prior to running 258 322 Experiment menu described 34 figure 35 list of menu commands 35 experiment method files managing 128 274 quantitation 384 205 quantitation 96 128 saving 33 saving to new name 33 experiment method files managing 274 338 experiment methods saving manually 114 191 Experiment Run Name setting Run Experiment window settings quantitation 384 196 quantitation 96 119 experiment settings advanced settings Octet QK384 198 330 data file location and names 2nd plate name barcode 264 328 Assay Type 328 assay type 264 Auto Increment File ID Start 264 Octet System Data Acquisition User Guide Release 7 1 page 15 328 kinetics data repository 264 328 plate name barcode file prefix 264 328 run name 264 328 general information Description 121 199 331 Machine name 121 199 330 User name 121 199 330 run settings Automatically save runtime charts 120 197 265 329 Delayed experiment start 265 329 Open runtime charts automatically 120 197 265 329 Set Plate Temperature 120 197 265 329 shake sample plate while waiting 120 197 265 329 Start After 265 329 experiment settings data file location and names quantitation 384 2nd Plate Name Barcode 196 Assay Type 196 Auto Incremen
260. ber column 252 lower acquisition rate 121 198 329 M Machine drop down list 63 Machine name setting 121 199 330 magnification undoing 125 202 271 335 magnifying Runtime Binding Chart 271 335 quantitation 384 202 quantitation 96 125 Main Menu Octet System Data Acquisition software 31 main screen Octet System Data Acquisition software 31 main toolbar hiding 34 showing 34 managing experiment method files 128 274 338 quantitation 384 205 quantitation 96 128 Runtime Binding Chart kinetics 96 267 managing experiment method files 274 manually save an experiment 259 323 mechanics Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 menu bar Octet System Data Acquisition software 32 menu commands listed 33 34 35 36 method file fmf 68 140 216 276 method file fmf described 32 method files closing 33 saving 33 saving all 33 Modify Plates dialog box 166 modifying assay parameter settings quantitation 384 167 quantitation 96 91 reagent plate quantitation 384 166 299 molar concentration units 222 284 Octet System Data Acquisition User Guide Release 7 1 page 20 molar concentration assigning kinetics 96 221 molecular weight assigning kinetics 96 221 monitoring experiments remotely 45 Multiple Analyte assay parameter quantitation 384 209 quantitation 96 132 Multiple Analyte experiments
261. cally displayed when data acquisition starts see Figure 6 60 The Runtime Binding Chart window displays the current step number time remaining for the current step total elapsed experimental time and total experiment time The Runtime Binding Chart is updated at the start of each experimental step The active biosensor column is color coded A green B magenta C orange D purple E olive F black G red H blue within the Sensor Tray Map Used sensor columns that are inactive are colored black Active sample columns are colored green Each data acquisition step is represented by Sample Column X in the Current Binding Charts box To selectively display acquisition data for a particular acquisition step 1 Click the corresponding Sample Column number 2 Select a sub set of sensors for a displayed column in the Sensors to Chart box see Figure 6 60 Octet System Data Acquisition User Guide Release 7 1 page 200 Chapter 6 Quantitation Experiments Octet RED384 and QK384 WARNING Do not close the Runtime Binding Chart window until the experi ment is complete and all data is acquired If the window is closed the charts are not saved To remove the chart from view minimize the window The Octet System Data Acquisition software saves the Runtime Binding Chart as dis played at the end of the experiment For example modifying a chart by hiding the data for a particular biosensor will cause this data not to be included in
262. cate Group names spacing and capi talization must be identical For example samples assigned to Group 2 and group2 are treated as two groups Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 295 Editing the Sample Table Changing Sample Well Designations To change a well designation right click the well in the Sample Plate Table and make a new selection see Figure 8 20 SamnleP Concentration units O Rea oO Sample Molar concentration units mM Well Reference e Conc pg ml MW kD Molar o n Control ae Ag Negative Control ii ca Positive Control er E9 er G9 Buffer Br 9 Activation er K9 5 Quench i Mg er 09 Load er ANI Wash br C11 A er E11 Regeneration EF G11 Set Well Data alt ai Clear Data gt M11 Copy to Clipboard er Ol Extended Sample Types pr Urrrenrrngea ple 40 Figure 8 20 Sample Plate Table Well Designation Editing Sample Information To edit sample data in the Sample Plate Table double click a value and enter a new value see Figure 8 21 Octet System Data Acquisition User Guide Release 7 1 page 296 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Sample Plate Concentration units _ Reagent Plate Molar concentration units mM Well Sample ID Replicate Group Type Conc jig ml MW kD Molar 4 OM Protein A Load 125 07 Proteina Load
263. cation where quantitation data files frd are saved Click repository Browse to select another data location NOTE It is recommended that you save the data to the local machine first then transfer to a net work drive Experiment Run name Specifies a subdirectory name for the data files frd that are sub directory created The software generates one data file for each biosen sor Plate name barcode A user defined field where you can enter text or a barcode file prefix barcode reader required 2nd Plate name bar A user defined field where you can enter text or a barcode code barcode reader required for a second plate Octet System Data Acquisition User Guide Release 7 1 page 120 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 9 Data File Location and Name Continued Item Description Auto Increment FileID Each file is saved with a number after the plate name For Start example if the Auto Increment File ID Start number is 1 the first file name is xxx_001 frd The following Run Settings are available on the Run Experiment Tab Table 5 10 Run Settings Item Description Delayed experiment Specifies a time delay for the start of the experiment Enter the start number of seconds to wait before the experiment starts after you click Q Start after Enter the number of seconds to delay the start of the experi ment Shake sample plate If the experiment has
264. ccessing 12 temperature range Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 Temperature Setting dialog box displayed figure 43 opening 35 temperature value default saving 44 temperature startup user option 42 Templates menu 35 templates viewing kinetics 384 324 kinetics 96 260 terminating a step in the assay 271 335 testing server 397 Threshold check box 238 threshold parameters Active Channels 239 304 Filtering 239 305 Gradient 239 305 listed table 239 304 Signal Change 239 304 Threshold Parameters dialog box 304 threshold applying to assay steps 238 304 throughput Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 Tile menu 37 tiling windows vertically 37 Toolbar menu 34 toolbar Octet System Data Acquisition software 31 tooltip of well information 241 Tray Format button 106 types of wells control 71 145 reference 71 145 reserved 71 145 standard 71 145 unassigned 71 145 Unknown 71 unknown 145 U Unaligned menu 270 334 unassigned type of well 71 145 UNC folder names 347 undo magnification 125 202 271 335 Unknown well type quantitation 384 145 quantitation 96 71 unknowns assigning a dilution factor quantitation 384 153 Octet System Data Acquisition User Guide Release 7 1 page 36 quantitation 96 78 assigning serial dilution quantitation 384 153 quantitation 96 78 designating quantit
265. ccount and select Edit User from the Tab menu or double click on the user account The Edit User dialog box will display v Es Login name Full name Richard Brown Information Group Supervisor Supervisors can review data and events Privileges Administration administers the user database Review reviews changes and events Change can change methods and configuration values _ Plate can change sample plate properties _ Run can run experiments and analyses T Password does not expre Figure B 38 Edit User Dialog Box 2 If needed modify the user account settings For more details on individual settings please refer to Creating a New User Account on page 384 3 Click OK to save changes and exit Deleting a User Account To delete a user account 1 Right click on the user account and select Delete User from the Tab menu 2 Click OK in the dialog box displayed Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 387 Changing User Account Passwords To change user account passwords 1 Right click on the user account and select Set Password from the Tab menu The Change Password dialog box will display Current password New password Confirm new password Password reminder Figure B 39 Change Password Dialog Box 2 Enter the Current password for the user accou
266. change the sample plate format 1 Click the Modify button above the plate map 2 In the Modify Plates box select 96 Well or 384 Well format Sample Plate Sample Plate Sample Plate 96 wells Sample Plate 384 wells P 12345678 9101112131415161718192021222324 0000000000000000 0000000q OOO0000 OOO0O Sample Plate QOQ O96 well OOQ 384 Well FOQQQQOQOOO0OOUCD GOQQOQOQOOOOOOOO HOQOOOOOOOOOOO Figure 6 4 Changing the Sample Plate Format DOOOOO000000000 NOTE In Basic Quantitation with Regeneration and Advanced Quantitation experiments a reagent plate format option is also available Please refer to Working with a Reagent Plate on page 165 for more information Designating Samples Each well may be designated as a Standard Unknown Control or Reference A well may also remain Unassigned or be designated as Reserved by the system for Basic Quantita tion with Regeneration and Advanced Quantitation experiments Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 145 NOTE It is important to define all of the wells that will be used in the assay Only wells that are selected and defined using one of the sample types in Table 6 4 will be included in the assay Table 6 4 Types of Sample Wells Icon Description O Standard _ Contains an analyte of known concentration Data from the well is used to generate a standard curve dur
267. ck to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Replicate Groups Replicate Groups enable data to be organized into custom groups during data analysis see Figure 7 12 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 227 Index Include Color SensorLocation Sensor Type SensorInfo Replicate Group Baseline Loc lt 2 x E c SA Streptavidin 3 C3 a x ae c2 SA Streptavidin 3 c3 220 x E 2 SA Streptavidin 4 D3 23 x D2 SA Streptavidin 4 D3 24 x E2 SA Streptavidin 5 E3 25 x E2 SA Streptavidin 5 E3 2 x ae 2 SA Streptavidin 6 F3 27 x ae 2 SA Streptavidin 6 F3 2 x E c2 SA Streptavidin 6 G3 2 x E c2 SA Streptavidin 6 G3 30 x Dy 2 SA Streptavidin 6 H3 31 x 2 SA Streptavidin 6 H3 322 x E 3 SA Streptavidin 1 A3 3 x E 1 3 SA Streptavidin 1 A3 4 x He 3 SA Streptavidin 2 B3 3 x E 3 SA Streptavidin 2 B3 3 x He c SA Streptavidin 3 c3 337 x B c SA Streptavidin 3 C3 38x HM bs SA Streptavidin 4 D3 20 x EE 2 QA Gtrantavidin 4 na Ss Figure 7 12 Replicate Group Color Coding NOTE Replicate Group information can also be entered in the Octet System Data Analysis software Assigning Replicate Groups in the Sample Plate Map To assign Replicate Groups in the Sample Pl
268. clicking the Subtract Reference Biosensor check box in the chart window To view raw data remove the check mark next to this option Reference biosensors can be designated During experiment setup in the Sensor Assignment tab e During acquisition in the Runtime Binding Chart Sensors to Chart box e During analysis in the Data Selection tab Designating a Reference Biosensor During Acquisition To designate a reference biosensor during acquisition 1 In the Sensors to Chart list or the Sensor Tray right click a biosensor and select Refer ence see Figure 7 54 Current Binding Charts Sensors to Chart Kinetics Assay 1 SelectAll Kinetics Assay 2 Kinetics Assay 3 Sensor A2 iSensor B2 Sensor C2 Sensor E2 Reference PSensor F2 sensor G2 Sensor H2 Subtract reference sensors Figure 7 54 Designating a Reference Biosensor in the Runtime Binding Chart The selected biosensor will be shown with an R in the Sensors to Chart list and Sensor Tray see Figure 7 55 2 Click the Subtract reference sensors check box see Figure 7 55 Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 269 Current Binding Charts Sensors to Chart Kinetics Assay 1 SelectAll Plate Status Sensor Tray x 1 Kinetics Assay 2 Kinetics Assay 3 sensor A2 Sensor B2 Sensor C2 PBSensorD2 R sensor E2 sensor F2 sensor G2 sensor H2
269. column information layout A B E D E F G 1 PlateWells 384 2 Well ID Replicate Group Group Concentration ug ml Dilution Information 3 A1 higG 1 Standard 200 human IgG 4 C1 higG 2 Standard 100 human IgG EREL higG 3 Standard 50 human IgG 6 G1 higG 4 Standard 25 human IgG 7 E higG 5 Standard 10 human IgG 8 K1 higG 6 Standard 5 human IgG 9 M1 higG 7 Standard 25 human IgG 10 O01 higG 8 Standard 2 human IgG v u 4 gt 384 Q method export 3 1K m 2i Figure 6 28 Example Sample Plate Definition File csv WORKING WITH A REAGENT PLATE You can include an optional reagent plate in a Basic Quantitation with Regeneration or Advanced Quantitation experiment Using a reagent plate enables higher sample through put since no reagents are included in the sample plate A reagent plate can contain Regeneration and neutralization reagents for Basic Quantitation with Regeneration experiments Buffers enzyme solutions and detection reagents for Advanced Quantitation exper iments Octet System Data Acquisition User Guide Release 7 1 page 166 Chapter 6 Quantitation Experiments Octet RED384 and QK384 An experiment can include any combination of sample and reagent plate formats 96 or 384 well However a reagent plate can include only reagent wells regeneration neutral ization detection Wells for standards unknowns controls and references can not be assigned to the reagent plate NOTE
270. compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Starting an Experiment Using the Experiment Wizard To start an experiment using the Experiment Wizard 1 If the Experiment Wizard is not displayed when the software is launched click the Experiment Wizard toolbar button 4 or click Experiment gt New Experiment Wiz ard Ctrl N from the Main Menu m In the Experiment Wizard select New Quantitation Experiment see Figure 5 1 left w Select a type of quantitation experiment see Table 5 2 for options Table 5 2 Quantitation Experiment Selection Quantitation Experiment Description Basic Quantitation A standard quantitation assay Basic Quantitation with A standard quantitation assay that enables regeneration of Regeneration biosensors Octet System Data Acquisition User Guide Release 7 1 page 70 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 2 Quantitation Experiment Selection Quantitation Experiment Description Advanced Quantitation A standard two or three step quantitation assay that enables signal amplification for higher detection sensitiv ity iy Basic Quantitation Experiment cole Plate Definition Sensor Assignment Review Experment Run Experiment Inthis step all the information about the sample plate and its wells will be entered First check the assay settings Then h
271. control characters Insert Unicode control character Open IME Reconversion Figure 8 32 Editing a Step Value left or Step Type right Building an Assay After creating the different step types that the assay will use step types are assigned to col umns in the Sample Plate or Reagent Plate maps To build an assay 1 Select a step type in the Step Data List 2 Inthe Sample Plate or Reagent Plate Map double click the column that is associated with the selected step type For information about sample or reagent plate wells mouse over a well to view a tool tip see Figure 8 33 Sample Plate 384 wells Pa 7 5 2 7 Z 2 E e eieaa Assayed samples O Unassigned samples Figure 8 33 Tool Tip of Well Information The selected wells are marked with hatching for example Z and the step appears in the Assay Steps List see Figure 8 34 with an associated Assay Time Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 307 NOTE In the Assay Steps List Plate 1 is the Sample Plate and Plate 2 is the Reagent Plate Sample Plate 384 wells Step Data List JP 1234567 8 9 101112131415161718192021222324 Add aa D A AWODOODOGD 000000000000000 Jl Jl B Name Time Shake speed Type Threshold c equilibration 120 1000 32 Custom m D Loading 300 1000 L Loading Vv Baseline 300 1000 ke Baseline m G Association 300 1000 Y Associatio
272. cquisition 3 Optional Double click in any cell in the Lot Number column to enter the biosensor lot number All wells in the Lot Number column will automatically populate with the lot number entered 4 Optional Double click in a cell in the Information column to enter biosensor informa tion for a particular cell NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu Octet System Data Acquisition User Guide Release 7 1 page 176 Chapter 6 Quantitation Experiments Octet RED384 and QK384 NOTE For greater clarity annotation text may be displayed as the legend of the Runtime Binding Chart during data acquisition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend 5 Optional After an assay is completed the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container To return the biosensors to the tray click the Replace sensors in tray after use check box see Figure 6 37 Sensor Tray v Replace sensors in tray after use Legend Unassigned sensors 683
273. cs 384 305 kinetics 96 240 defining step types 236 Delayed experiment start setting 265 329 Delayed Experiment Start setting quantitation 384 197 quantitation 96 120 deleting constants 394 factory loaded biosensor types 49 projects 392 step types 240 305 Octet System Data Acquisition User Guide Release 7 1 page 12 user account 386 user group 390 Description setting 121 199 331 designating controls quantitation 384 156 quantitation 96 81 controls figure 81 156 reference biosensor during acquisition 268 333 reference biosensors 105 110 182 187 257 321 reference biosensors during acquisition quantitation 384 201 quantitation 96 124 reference wells quantitation 384 156 quantitation 96 81 reference wells figure 81 156 samples kinetics experiments 218 unknowns quantitation 384 153 quantitation 96 78 well type kinetics 384 282 well types kinetics experiments 282 designating reference biosensors 258 designating standards quantitation 384 148 quantitation 96 73 designating well types kinetics 96 219 Detection 95 136 172 213 Detection reserved well requirements quantitation 384 146 quantitation 96 72 Detection Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Detection Time and Shake speed parameter 136 213 determining the GxP Server module host location 52 developing the automation client 347 dialog boxes Options
274. ctet384 Systems with an Automation Interface OVERVIEW The Octet Data Acquisition software provides support for an automation interface using a COM port RS 232 or a Transmission Control Protocol Internet Protocol TCP IP socket port An example application for testing the automation interface called AutomationCli ent exe is included in the applications and Dynamic Link Libraries DLLs installed with the Octet Data Acquisition software The file is located in the C Program Files ForteBio DataAc quisition directory NOTES The automation interface can be used with Octet384 systems only The examples that follow are illustrated using a TCP IP connection but the serial port connection behaves identically DESIGN OF THE AUTOMATION INTERFACE The automation interface is designed to be as universal as possible making no assump tions about the communication medium or the language of the client application connect ing to the Octet System Data Acquisition software The following guidelines apply All commands and responses are ASCII strings one per line All lines are terminated with both carriage return and line feed characters r n Each command starts with the name of the command and may then be followed by required and optional parameters Each parameter starts with a switch definition ala dos unix command line followed by the parameter itself which allows parameters to be sent in any order The
275. custom assay when you define a sample plate To select a custom assay 1 Inthe Plate Definition tab click Modify in the Assay Settings box The Edit Assay Parameters dialog box displays see Figure 5 66 Plate Definition Sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and right click to enter modify well data Assay Settings Sample Plate Table Assay Basic Quantitation Concentration units uomi Z Export Import Eaa Well Sample ID Replicate Group Type Conc pg ml Dilution Factor Information Quantitation o i mo uii Assay Paranteters Available Assay Parameters a Quantitation i Single analyte Multiple analyte Anti Penta HIS Hi siti Replicates per sensor type Sample Plate B PAS pietas wed i i l i Sample Plate 96 wells E High sensitivity Human IgG quantitation YEE EFT H A O O O O O O O O E Murine IgG Quantitation ar 9 z Sake E My Basic Quant Assay uantitation jea ica 200000000 DOOOQOQOQOQOQOQO EOOQOOQOQOOQOOQQOQ FOQOOOOO00O0 GOOOO0OO0O0O0 HOOOOOOOO lO Seman Sonel Q Blueindicates a built in assa _ Unknown Q Reference if Figure 5 66 Selecting a C
276. d To start an experiment from the Experiment Wizard 1 If the Experiment Wizard is not displayed when the software is launched click the Experiment Wizard toolbar button 4 or click Experiment gt New Experiment Wiz ard Ctrl N from the Main Menu In the Experiment Wizard click New Kinetics Experiment see Figure 8 1 left Click the arrow button The Basic Kinetics Experiment window displays Figure 8 1 right Octet System Data Acquisition User Guide Release 7 1 page 278 Chapter 8 Kinetics Experiments Octet RED384 and QK384 iy Basic Kinetics Experiment snag ex O Pte Defniton Assay Defnition Sensor Assignment Review Experment Run Experiment In this step all the information about he sample plate and its wells will be entered Highlight one or more wells on the semple plata and rightclick 10 enterimactty well data l Read Head Read Head Setting Eremi Bie O sanplePite Sample Plate 384 wells Reagent Plate uri pes Sere J loltia 1a i4sisy 1ee202 1222024 Well Sample ID Replicate Group Type Cone ug ml MW EE anc nM I BOOO 000000000 000000000009 cOO0 000000000 000000000009 DOOOOOOOVONOONOOODGOOO00NG EQOOO 000000000 00 0G00000009 FOQ00000000 0000000000000 SOOO OOOOCOOOCO OO DAD 0OOOOOG HOOD OOOOOO OOO 00000000000 1OOOOOO0OD ODN OO O00 000000 JO OOQOQOOOOQQ0Q00Q0000000009 KOOQQQQQQQQQQQQQQQOQQQQQQQ L OQOQQQQQQ0Q0QQ00000000 M
277. d QO Control O Unassigned Unknown i Reference Reserved Figure 6 16 Designate Controls or Reference Wells NOTE Shift clicking in the Sample Plate Map mimics the head of the instru ment during the selection Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 157 To remove a well designation select the well s and click Unassigned Or right click the well s and select Clear Data Annotating Samples You can enter annotations notes for multiple samples in the Sample Plate Map or enter information for an individual sample in the Sample Plate Table For greater clarity annota tion text may be displayed as the legend of the Runtime Binding Chart during data acqui sition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend Annotating Wells in the Sample Plate Map To annotate one or more wells 1 Inthe Sample Plate Map select the samples to annotate right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 6 17 enter Sample ID and or Well Infor mation and click OK Sample Plate Sample Plate 384 wells P1234567 8 9 1011121314151617 18192021 222324 ANOO C245 4545450808005 00000 BIOOC Standard O0000 poe Unknown 80000 i mod O enn Set W
278. d O Standard Conor O Unassigned O Standard contor C Unassignea Unknown Refrence O Reserved Unknown Reference O Reserved Unknown Refrence O Reserved Figure 6 6 Selecting Wells in the Sample Plate Map NOTE Shift clicking in the Sample Plate Map mimics the head of the instru ment during the selection Designating Standards To designate standards 1 In the Sample Plate Map select the wells to define as standards 2 Click the Standard button below the Sample Plate Map see Figure 6 7 or right click and select Standard The standards are marked in the plate map and the Sample Plate Table is updated 3 Select the concentration units for the standards using the Concentration Units drop down list above the Sample Plate Table Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 149 Concentration units a Basic Quantitation Experiment 384 Q method 1 fmf x Plate Definition LQ Sensor Assignment Review Experiment Run Experiment Inthis step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and rightclick to enfer madity well data Read Head Channels 16 Channels Sample Plate Table Concentration units ugni 7 _ Export impots Assay Settings j i i Well Sample ID Replicate Gr
279. d figure 278 well volumes 20 27 Octet RED384 instrument automation 19 capabilities 18 compliance 18 dimensions 20 electrical requirements 20 environment 18 equipment classifications 18 mechanics 19 optics 19 sample types 19 sampling format 19 weight 20 Octet RED384 instrument figure 18 Octet RED384 stage platform figure 193 Octet RED96 instrument biosensor tray type 17 19 26 biosensor type 17 19 26 capabilities 17 compliance 16 dimensions 17 electrical requirements 17 environment 16 equipment classifications 16 mechanics 17 optics 17 orbital flow capacity 17 20 27 sample types 17 sampling format 17 sampling volume 17 temperature range 17 throughput 17 19 26 weight 17 Octet RED96 instrument figure 16 Octet RED96 system specifications displayed figure 18 listed table 16 18 25 Octet system biosensor stage left and sample stage right figure 325 Octet System Data Acquisition software Main Menu 31 main toolbar 32 new features 12 starting 30 toolbar 31 Octet System Data Acquisition software Main Screen 31 Octet System Data Acquisition analysis options viewing 40 Octet system described 8 Offline parameter 136 213 Advanced Quantitation quantitation 384 172 quantitation 96 95 Offset steps option 244 309 Offset steps check box 243 Open Experiment menu 268 332 Open Experiment menu 33 Open Method File menu 33 Open runtime charts automatically sett
280. d range pi 384 wells High sensitivity Human IgG quantitation Human IgG Quantitation vi 23456 7 8 9 101112131415 Immunogenicity Direct detection AI OOOCOOOCO0O0000O0 Murine IgG Quantitation bab Time F Shake e 2099999999999999 m oe Protein L Standard range 2899899399999999 L Samana F O00000 0000000 cOOOO0O0OO0O00000000Q HOOOQOOOOOO0000000 OOOOOOOOOOO00ONOO JIOOOOOOOOONOO0O0O0O KOQOOQOOOQOOO0000000 ILIOOOOOOOOOOOONOO MOQOOQOOOQCO000000O INOOOOQOOOOOO0000O loleloleleleleleleleleleleye POOOOOOOOO000000 O Standard Sentral Blueindicates a buitt in assay Unknown IC Reference Figure 6 71 Selecting a Custom Assay 2 Select the custom assay from the directory tree and click OK Octet System Data Acquisition User Guide Release 7 1 page 215 CHAPTER 7 Kinetics Experiments Octet RED96 QKS and QK I laiecolo LEKE tolp re E E E ceadewpnvamad sevenee tev eenned ects 216 Starting a Basic Kinetics Experiment 0 cece eee cece cence nent nen eee eens 217 Defining the Sample Plate cece cece een n ene nee e nee Er EEE eaS 218 Managing Sample Plate Definitions cc cece cece cece cece cece en ee ene enenens 232 Defininigia Kinetic Assay sc 000 5csensensatemerseseuiteens ee e ea eatedeadameeenae es 236 Assigning Biosensors to Samples cc cece cence cece cence een ee eee eneeeeneens 249 Reviewing Experiments ccc ccc cece c cece eee eee ee
281. d well requirements quantitation 384 146 quantitation 96 72 Regeneration well type kinetics 384 281 kinetics 96 218 Regeneration Cycles parameter Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 Regeneration cycles parameter Advanced Quantitation 137 214 quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration 134 211 Regeneration Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Regeneration Time and Shake speed parameter 133 136 210 213 remote view of experiment via web browser figure 47 Octet System Data Acquisition User Guide Release 7 1 page 27 removing assay from the quantitation application 35 assay steps 247 311 biosensor type 49 side panel of Octet instrument 343 step alignment of data 270 334 well designation 282 well designations controls or reference wells 81 157 quantitation 384 149 153 quantitation 96 74 78 reagent plates quantitation 384 167 reordering assay steps 247 311 Replace sensors in tray after use check box 176 replacing biosensors in the biosensor tray 251 315 fuses for Octet RED instrument 341 for QKe instrument 341 replicate assay steps 244 309 replicate assay adding to a plate 247 312 Replicate Group color coding figure 227 290 Replicate Groups assigning in
282. dant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types 3 Repeat the previous steps to assign new samples to the existing Replicate Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and calculate statistics for samples that use the same Replicate Group names spacing and capitalization must be identical For example samples assigned to Group 2 and group2 are treated as two groups Octet System Data Acquisition User Guide Release 7 1 page 88 Chapter 5 Quantitation Experiments Octet RED96 QK and QK NOTE When performing a Multiple Analyte experiment if the same Replicate Group name is used with different biosensor types they will be treated as sep arate groups Statistics for these groups will be calculated separately for each biosensor type MANAGING SAMPLE PLATE DEFINITIONS NOTE After you define a sample plate you can export and save the plate defi nition for future use Exporting a Plate Definition To export a plate definition 1 Inthe Sample Plate Table see Figure 5 21 click Export Sample Plate Table Concentration units ug mi z Export Import Well Sample ID Replicate Group Type Conc ug ml Dilution Factor O Al
283. data display 42 user option 42 simulation user option 43 Single Analyte assay parameter quantitation 384 208 quantitation 96 131 single analyte experiment assigning biosensors quantitation 384 173 quantitation 96 96 Single Analyte parameter Advanced Quantitation quantitation 384 171 quantitation 96 94 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 133 quantitation 384 169 quantitation 96 92 Skip Step menu 35 specifying number of significant digits for the values of Molecular Weight Concentration and Dilution used during data analysis 42 Standard well type quantitation 384 145 quantitation 96 71 Standard button 73 148 standard concentration entering quantitation 384 151 quantitation 96 76 standard type of well 71 145 standards designating quantitation 384 148 quantitation 96 73 Start After setting kinetics 384 329 kinetics 96 265 quantitation 384 197 quantitation 96 120 starting administrator user session 378 an experiment 261 325 quantitation 384 194 quantitation 96 117 basic kinetics experiment 384 277 96 217 experiment from the Experiment wizard 141 kinetics experiment with the Experiment wizard figure Octet RED384 278 Octet System Data Acquisition User Guide Release 7 1 page 34 new assay 244 309 Octet System Data Acquisition software 30 quantitation experiment 69 141 user session 56 starting concentration value 76 151 222 285
284. dilution factor in the sample table quantitation 384 155 quantitation 96 80 parameter values quantitation 384 208 quantitation 96 131 projects 391 sample data in the Sample Plate Table kinetics 384 295 kinetics 96 231 standard concentration quantitation 384 151 quantitation 96 76 step type figure 241 306 editing step types 240 305 Electrical hazard symbol 13 electrical requirements Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 emptying waste container 340 ending a user session 66 enhanced legend options in the Runtime Binding Chart 12 entering annotations Octet System Data Acquisition User Guide Release 7 1 page 14 quantitation 384 157 quantitation 96 82 biosensor information displayed figure 252 316 procedure 252 315 entering an individual standard concentration quantitation 384 151 quantitation 96 76 environmental features Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 Enzyme Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Enzyme Time and Shake speed parameter 136 213 equipment classifications Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 events list options available 396 viewing 395 Events tab fi
285. driver gently pop the fuse drawer out 2 Remove the expired fuse and place a new one in the holder Octet System Data Acquisition User Guide Release 7 1 page 342 Chapter 9 Maintenance WARNING Only use 5 amp slow blow fuses 3 Reinstall the fuse drawer OCTET RED384 AND OCTET QK384 SYSTEMS Cleaning the Octet Instrument NOTE If you use the Octet instrument regularly clean the interior horizontal surfaces daily with a Kimwipe moistened with a 30 60 isopropyl alcohol solution Otherwise clean once a week or as needed To clean the Octet instrument 1 Present the sample plate stage Figure 9 4 Turn off the power to the instrument Open the system door Wipe the biosensor and sample platform wo fk WN Allow the surfaces to dry for at least one minute with the door open Position for well A1 Biosensor tray and rehydration plate Sample plate stage Reagent plate stage Figure 9 4 Octet RED384 and QK384 Stage Platform Octet System Data Acquisition User Guide Release 7 1 Octet RED384 and Octet QK384 Systems page 343 Cleaning the Biosensor Pickup Tips The biosensor pickup tips hold the biosensors during an assay NOTE The biosensor pickup tips should be cleaned weekly or as needed To clean the biosensor pickup tips 1 Present the sample plate stage 2 Turn off the power to the instrument 3 Remove the side panel of the instrument Figure 9 5 Bio
286. e else if csStatus AUT_RUNNING FElLurn True else if csStatus AUT WAITING return true else if csStatus AUT _LOADSENSORS return true Octet System Data Acquisition User Guide Release 7 1 page 356 Chapter A Using Octet384 Systems with an Automation Interface else if csStatus AUT BUSY else if csStatus AUT ERROR return false TRACE1 Timeout waiting for not busy after d ms n Timer GetElapsed return false Automation API H kkkxkxkxk xkxkxkxkxkxkxkkkxkkxkkxkxkkkxkxkkkkxkkkkkkkkxkkkkkkxkkkkxkxkkkkkkkkkkkkkkkkkkkkkkxk KK Copyright c 2011 ForteBio All rights reserved KKK KK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KK KKK KK KKK KKK KK KKKK KKK KK KKKKK KK HEADER AutomationAPI h PURPOSE Defines the commands supported by the automation API AUTHOR BHI Nov 2008 ifndef INC_ACQUISITION AUTOMATIONAPI H define INC_ACQUISITION AUTOMATIONAPIT H NOTES Do not position the Octet instrument such that it is difficult to disconnect the power The automation interface is string based Commands and responses are strings one per line Bach command starts with the name of the command and may then be followed by required and optional parameters Each parameter starts with a switch definition a la dos unix com mand line followed by the parameter itself This allows parameters to
287. e Instrument Status window Stop Shaker N A Stops the sample plate shaker Present Stage a Presents the instrument stage that houses the biosensor tray sample and reagent plates Octet RED384 and Octet QK384 only Security Menu The Security menu is only available in the 21 CFR Part 11 version of the Data Acquisition software For complete details on menu options please refer to Compliance Features on page 59 Octet System Data Acquisition User Guide Release 7 1 Software Overview page 37 Window Help Verify Document View Audit Trail Change Project Change Password Server Administration Lock Application Logoff Figure 3 8 Security Menu Window Menu The Window menu provides display options for the open windows in the Main Screen All open windows are listed at the bottom of the menu and a check mark indicates the win dow that is currently active To view another window select it from the list Help New Window Cascade Tile Arrange Icons 1 Experiment Wizard 2 Instrument Status 3 Basic Quantitation Experiment Example Quantitation Method file fmf 4 Basic Kinetics Experiment BH081908 4 ADAM titration_LABUSER081908_ExpMethod fmf v 5 Basic Quantitation Experiment LABUSER090811_ExpMethod fmf Open Windows Figure 3 9 Window Menu Table 3 5 Window Menu Commands New Window Opens a new Runtime Binding Chart window Cascade Organize
288. e 30 Sample Plate and Reagent Plate Layouts for an Advanced Quantitation Experiment 16 Channel Read Head figure 167 Sample Plate File csv example figure 90 165 sample plate format changing kinetics 384 280 quantitation 384 144 Sample Plate Map Setting a Dilution Series figure 75 150 223 286 sample plate shaker stopper 36 Sample Plate Table Shortcut Menu of Edit Commands figure 77 80 152 155 231 232 295 296 sample plate temperature recorded in log file 12 sample plates adding assays 248 313 assigning biosensors to samples 249 313 assigning step types to 242 307 defining kinetics 96 218 quantitation 384 142 quantitation 96 70 defining kinetics 384 278 importing definitions kinetics 384 298 kinetics 96 234 sample step types for kinetic assays listed table 236 Sample steps only option 244 309 Sample steps will be adjusted by vertically by one row option 244 309 Sample steps will be adjusted by X columns option kinetics 384 309 kinetics 96 244 Sample Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 sample types Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 sample volume Octet QK instrument 24 Octet QKe instrument 22 samples changing biosensor type 320 designating kinetics experiments 218 specifying analyte concentration 22
289. e Layouts for an Advanced Quantitation Experiment 16 Channel Read Head figure 167 Sample Plate File csv example figure 90 165 sample plate format changing kinetics 384 280 quantitation 384 144 Sample Plate Map Setting a Dilution Series figure 75 150 223 286 sample plate shaker stopper 36 Sample Plate Table Shortcut Menu of Edit Commands figure 77 80 152 155 231 232 295 296 sample plate temperature recorded in log file 12 sample plates adding assays 248 313 assigning biosensors to samples 249 313 assigning step types to 242 307 defining kinetics 96 218 quantitation 384 142 quantitation 96 70 defining kinetics 384 278 importing definitions kinetics 384 298 kinetics 96 234 sample step types for kinetic assays listed table 236 Sample steps only option 244 309 Sample steps will be adjusted by vertically by one row option 244 309 Sample steps will be adjusted by X columns option kinetics 384 309 kinetics 96 244 Sample Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 sample types Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 sample volume Octet QK instrument 24 Octet QKe instrument 22 samples changing biosensor type 320 designating kinetics experiments 218 specifying analyte concentration 221 283 specifying concentration unit
290. e allows the software enough time to perform more averages of the collected data Typically more averaging leads to reduced noise and thus better signal to noise ratios Therefore the frequency setting should be determined based on consider ation of the binding rate the amount of signal generated in your assay and some experi mentation with the settings Octet System Data Acquisition User Guide Release 7 1 page 330 Chapter 8 Kinetics Experiments Octet RED384 and QK384 The following Advanced Settings are available for the Octet384 system Table 8 8 Advanced Settings Octet RED384 Item Description Acquisition rate High sensitivity kinetics 2 0 Hz averaging by 50 The aver age of 50 data frames is reported as one data point Two data points are reported per second e Standard kinetics 5 0 Hz averaging by 20 The average of 50 data frames is reported as one data point Five data points are reported per second e Fast kinetics 10 0 Hz averaging by 5 The average of 5 data frames is reported as one data point Ten data points are reported per second Sensor off set Recommended sensor offset Large molecule kinetics 4 mm mm Default Sets the acquisition speed and sensor offset at the default settings The following Advanced Settings are available for the OctetQK384 system Table 8 9 Advanced Settings Octet QK384 Item Description Acquisition rate High sensitivity kinetics 0 3 Hz averag
291. e n ene teen eeeneeneeees 258 Saving ExperiMents 0 cece ccc e eee cence eee e eee eens ene e eee eeeeneees 259 Running a Kinetics Experiment 0 cece cece eee ence e nee eee eee ennenee 260 Managing the Runtime Binding Chart cece cece e cence ene eee ee nn eee 267 Managing Experiment Method Files 0 ccc cece cece cence ence cence ene eneneees 274 Octet System Data Acquisition User Guide Release 7 1 Chapter 7 Kinetics Experiments Octet RED96 QK and QK page 216 INTRODUCTION A basic kinetics experiment enables you to determine the association and dissociation rate of a molecular interaction After starting the Octet system hardware and the Octet System Data Acquisition software follow the steps in Table 7 1 to set up and analyze a quantita tion experiment Table 7 1 Setting Up and Analyzing a Kinetic Experiment Software Data 1 Acquisition Step Select a kinetics experiment in the Experiment Wizard or open a method file fmf See Starting a Basic Kinetics Experiment on page 217 Define a sample plate or import a sample plate definition Defining the Sample Plate on page 218 Specify assay steps Defining a Kinetic Assay on page 236 Assign biosensors to samples Assigning Biosensors to Samples on page 249 Run the experiment Running a Kinetics Experi ment on page 260 Data Analysis bet 7
292. e plate format 96 or 384 wells and the Octet instrument read head configura tion 8 or 16 channels Reserved samples cannot be removed from the sample plate but you can change their col umn location To change the location of a reserved column or right click a col umn header in the Sample Plate Map and select Regeneration Neutralization or Detection Table 6 5 Reserved Well Requirements Reserved Well Must Contain Regeneration Regeneration buffer that is used to remove analyte from the bio sensor typically low pH high pH or high ionic strength Neutralization Neutralization buffer that is used to neutralize the biosensor after the regeneration step Detection Secondary antibody or precipitating substrate that is used with an enzyme antibody conjugate to amplify the analyte signal Sample concentrations are computed using the binding data from the detection wells Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 147 Basic Quantitation with Regeneration Advanced Quantitation Vietegsas e 7TfTs9m0u 2 WM 1 2 3 4 5 6 7 8 9 0 1 12 16 Channel Read Head 8 Channel Read Head 16 Channel Read Head 8 Channel Read Head Figure 6 5 Default Locations for Reserved Wells in tom 6 well top and 384 well Sample Plate Maps bot Octet System Data Acquisition User Guide Release 7 1 page 148 Chapter 6 Qua
293. e reader required prefix 2nd Plate A user defined field where you can enter text or a barcode barcode name barcode reader required for a second plate This field is also used to generate the path of the saved directory Auto Incre Each file is saved with a number after the plate name For example if ment File ID the Auto Increment File ID Start number is 1 the first file name is Start xxx_001 frd Octet System Data Acquisition User Guide Release 7 1 Running a Kinetics Experiment page 265 The following Run Settings are available on the Run Experiment Tab Table 7 7 Run Settings Item Description Delayed experi Specifies a time delay for the start of the experiment Enter the num ment start ber of seconds to wait before the experiment starts after you click Q Start after Enter the number of seconds to delay the start of the experiment Shake sample If the experiment has a delayed start time this setting shakes the plate while plate until the experiment starts waiting Open runtime Displays the Runtime Binding Chart for the current biosensor dur charts auto ing data acquisition matically Automatically Saves an image jpg of the Runtime Binding Chart The binding save runtime data frd is saved as a text file regardless of whether a chart image is chart created Set plate tem Specifies a plate temperature and enters the temperature in the dia perature C log box If not selected t
294. e sample plate while waiting Set plate temperature C 30 Advanced Settings Acquisition rate Standard kinetics 5 0 Hz averaging by 20 x Default Sensor offset mm distance to sensor tip from bottom of well Warming changing these settings could affect assay signal to noise Ifyou are unsure of how to use these settings please consultthe Data Acquisition User Guide General Information Username Owner Machine name JRICHARDS Description Figure 8 55 Run Experiment Tab Octet RED384 2 Confirm the default settings or enter new settings See Run Experiment Window Set tings on page 328 for more information on experimental settings NOTE If you delay the experiment start you have the option to shake the plate until the experiment starts 3 To start the experiment click If you specified a delayed experiment start a message box displays the remaining time until the experiment starts If you select the Open runtime charts automatically option the Runtime Binding Chart window displays the binding data in real time as well as the experiment prog ress Figure 8 56 NOTE For more details about the Runtime Binding Chart see Managing the Runtime Binding Chart on page 331 Octet System Data Acquisition User Guide Release 7 1 Running a Kinetics Experiment page 327 Lx C Users Owner Documents Contracting Forte Bio User_Guides Data and methods 384 04 27 11 3
295. ease 7 1 page 4 quantitation 384 209 quantitation 96 132 Quantitation Time quantitation 384 209 quantitation 96 132 Single Analyte quantitation 384 208 quantitation 96 131 Assay Parameters Advanced Quantitation Standard Assay figure 94 135 171 212 Assay Parameters Basic Quantitation Assay figure 92 131 169 208 Assay Parameters Basic Quantitation with Regeneration figure 93 133 170 210 Assay Settings box 91 Assay Step Definition dialog box 303 assay step name changing figure 247 311 assay steps adding 243 308 copying 243 308 inserting 245 310 removing 247 311 reordering 247 311 assay times updating figure 242 307 Assay Type setting Run Experiment window settings kinetics 384 328 kinetics 96 264 quantitation 384 196 quantitation 96 119 assays adding steps 245 310 adding to sample plates 248 313 assigning biosensors to samples 249 313 automatic addition of sensor tray maps 256 320 building 241 changing biosensor locations 252 257 changing biosensor type 320 copying steps between 243 308 editing 246 311 example using one partial biosensor try and biosensors from a second tray quantitation 384 190 quantitation 96 113 removing steps 247 311 reordering steps 247 311 replicating steps 244 309 starting new 244 309 assigning account details 385 biosensors in Multiple Analyte experiments quantitation 384 177 quantitation 96 99 biosensors in s
296. ect the Start Menu folder in which you would like to create the program s shortcuts You can also enter a name to create a new folder For teBio 2BrightSparks 7 Zip Accessories ACT by Sage Premium Administrative Tools Bonjour Print Services Corel DVD MovieFactory Lenovo Edition DivX Plus Dropbox FileZilla FTP Client FileZilla Server ForteBio ForteBio Inc www fortebio com Figure B 13 Choose Start Menu Folder Dialog Box The default Start Menu folder is ForteBio 6 Click Install The installation wizard takes a few seconds to install Figure B 14 33 ForteBio GxP Server 7 0 Setup Se Installing Please wait while ForteBio GxP Server 7 0 is being installed Execute C Program Files ForteBio 7 CFR FBServer7 FBServer exe 2 s Create shortcut C Users wms AppData Roaming Microsoft Windows Start Menu Pr Create shortcut C Users wms AppData Roaming Microsoft Windows Start MenulPr Create shortcut C Users wms Desktop ForteBio GxP Server lnk Create shortcut C Users wms AppData Roaming Microsoft Windows Start Menu Pr Create shortcut C Users wms Desktop Restart Server nk Output folder C Program Files ForteBio 7 CFR FBServer7 Create shortcut C Users wms AppData Roaming Microsoft Windows Start MenuPr S Created uninstaller C Program Files ForteBio 7 CFR FBServer 7 uninst exe a Execute C Program Files ForteBio 7 CFR FBServer7 FBServer exe S
297. ed a ma Quantitation 120 400 os ewe por pr g m re oes ee ou oes ee ee w a owe fons om pn Blue indicates a ForteBio built in assay and cannot be modified or deleted oie remove L d Figure 5 64 Assay Parameters Basic Quantitation with Regeneration Table 5 16 Assay Parameters Basic Quantitation with Regeneration Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte For multi analyte experiments using multiple biosensor types per and Replicates per sample well and the number of replicate assays in each well per sensor type biosensor type Quantitation The duration of data acquisition in seconds while the biosensor is Time s and Shake incubated in sample and the sample platform orbital shaking speed rpm speed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incubated in regeneration buffer to speed rpm remove bound analyte Octet System Data Acquisition User Guide Release 7 1 page 134 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 16 Assay Parameters Basic Quantitation with Regeneration Parameter Description Neutralizati
298. ed in the Run Experiment window the Runtime Binding Charts are automatically displayed when data acquisition starts see Figure 8 58 The Runtime Binding Chart window displays the assay step status experiment progress and the elapsed experiment time The Runtime Binding Chart is updated at the start of each experimental step The active biosensor column is color coded A green B magenta C orange D purple E olive F black G red H blue within the Sensor Tray Map Used sensor columns that are inactive are colored black Active sample columns are colored green Each assay in the experiment is represented by Assay X in the Current Binding Charts box To selectively display data for particular assay 1 Click the corresponding Assay number 2 Select a subset of sensors for a displayed column under Sensors to Chart box see Figure 8 58 WARNING Do not close the Runtime Binding Chart window until the experi amp ment is complete and all data is acquired If the window is closed the charts are not saved To remove the chart from view minimize the window The Octet System Data Acquisition software saves the Runtime Binding Chart as dis played at the end of the experiment For example modifying a chart by hiding the data for a particular biosensor will cause this data not to be included in the bitmap image generated at the end of the run Octet System Data Acquisition User Guide Release 7 1 page 332 Chapter 8 Kinetics Expe
299. ed will continue to run To lock the application 1 Click Security gt Lock Application The software will be placed in locked mode immediately and the Application Locked dialog box will display Octet System Data Acquisition User Guide Release 7 1 page 66 Chapter 4 21 CFR Part 11 Compliance fort sio a JBlack John Black Figure 4 24 Application Locked Dialog Box 2 The application will remain locked until it is unlocked or the active user logs off Unlock To resume the user session enter your password and click Unlock Log off To discontinue the user session click Logoff Ending a User Session To end a user session 1 Click Security gt Logoff 2 Inthe displayed dialog box click OK Octet System Data Acquisition User Guide Release 7 1 page 67 Quantitation Experiments Octet RED96 OKS and QK INTPOGUCHON u eE E E E E E edEM ane ehenw ed aoe 68 Starting a Quantitation Experiment ssssssssssesessesssresrrrsrressrrerrrssrre 69 Defining the Sample Plate 0 cc cece cece cence ence d ran n nen E neeeees 70 Managing Sample Plate Definitions cece cece cece cence eee ene n ene eeeaeees 88 Managing Assay Parameter Settings cece eee eee centre ne eee n en eeeeneeeee 91 Assigning Biosensors to Samples cece cece cence ence ence nee en eee eneeneaenes 96 Reviewing Experiments ccc ccc c eee cee n een ene e ene ennenneene
300. eee eee ee eee eee e eee e eens 206 Chapter 6 Quantitation Experiments Octet RED384 and QK384 page 140 INTRODUCTION A quantitation experiment enables you to determine analyte concentration within a sam ple using a reference set of standards After starting the Octet system hardware and the Octet System Data Acquisition software follow the steps in Table 6 1 to set up and analyze a quantitation experiment Table 6 1 Setting Up and Analyzing a Quantitative Experiment Software Data 1 Acquisition izles Step Select a quantitation experiment in the Experiment Wizard or open a method file fmf See Starting a Quantitation Experiment on page 141 Define a sample plate or import a sample plate definition Defining the Sample Plate on page 142 Define a or import a reagent plate optional for a Basic Quantitation with Regeneration experiment or an Advanced Quantitation experiment Confirm or edit the assay settings Working with a Reagent Plate on page 165 Modifying Assay Parame ter Settings on page 167 Assign biosensors to samples Assigning Biosensors to Samples on page 173 Run the experiment Running a Quantitation Experiment on page 193 Data Analysis et 8 N Analyze the binding data Generate a report Octet System Data Analysis Software User Guide Octet System Data Acquisition User Guide Release 7 1
301. eees 114 Saving ExperiMents 0 ccc cece cece ence eee n eee ence este cent eee e a a 114 Running a Quantitation Experiment cece eee een n eee e nee eenes 116 Managing Runtime Binding Charts 0 0 cece cece cee n ence eee n cence enn eneneeans 122 Managing Experiment Method Files ccc c cece ence e teen cence ena eeneeas 128 Custom Quantitation Assays 1 0 0 ccc cece eee e eee eee eee e eee e eee ees 129 page 68 Chapter 5 Quantitation Experiments Octet RED96 QK and QK INTRODUCTION A quantitation experiment enables you to determine analyte concentration within a sam ple using a reference set of standards After starting the Octet system hardware and the Octet System Data Acquisition software follow the steps in Table 5 1 to set up and analyze a quantitation experiment Table 5 1 Setting Up and Analyzing a Quantitative Experiment Software Step See Data 1 Selecta quantitation experimentin Starting a Quantitation Acquisition the Experiment wizard or opena Experiment on page 69 Es method file fmf 2 Define a sample plate or import a Defining the Sample Plate sample plate definition on page 70 3 Confirm or edit the assay settings Managing Assay Parameter Settings on page 91 4 Assign biosensors to samples Assigning Biosensors to Samples on page 96 5 Run the experiment Running a Quantitation Experiment on page 116 Data
302. egenerated state The sample plate temperature is recorded in the Instru ment Status window at the beginning of the experiment as well as when each set of sensors is picked up by the manifold Enhanced legend options in the Runtime Binding Chart The biosensor legend displayed in the Runtime Binding Chart provides four options for enhanced monitoring Sensor Location Sample ID Sensor Information and Con centration Dilution Multiple Runtime Binding Charts During data acquisition multiple Runtime Binding Charts may be opened allowing the comparison of different channel settings Octet System Data Acquisition User Guide Release 7 1 Conventions and Symbols Used in This Guide page 13 CONVENTIONS AND SYMBOLS USED IN THIS GUIDE NOTE A note presents pertinent details on a topic For example general infor mation about tips or alternate options IMPORTANT An important message for instances where the assay or proce dure will not work if not properly followed D WARNING A warning informs the user that specific actions could cause irre versible consequences or damage Table 9 Octet Instrument Labels Symbol Definition A Electrical hazard AN Heat hot E tse FORTEBIO TECHNICAL SUPPORT You can contact ForteBio technical support at any of the locations listed in Table 10 Table 10 ForteBio Technical Support Main Office European Office Asia Office ForteBio Inc
303. elease 7 1 page 218 Chapter 7 Kinetics Experiments Octet RED96 QK and QK DEFINING THE SAMPLE PLATE The steps to define a sample plate include Step See Page 4 Designate the samples 218 5 Save the sample plate definition optional 232 Designating Samples NOTE It is important to define all of the wells that will be used in the assay Only wells that are selected and defined using one of the sample types in Table 7 2 will be included in the assay Table 7 2 displays the well types that can be assigned to a plate map Table 7 2 Types of Sample Wells Icon Description OSample Any type of sample For example an analyte Reference Reference sample For example a buffer only control biosensor that is used to correct for system drift controls A control sample either positive or negative of known analyte compo sition Positive Control A control sample that contains analyte of known concentration Negative Control A control sample known not to contain analyte Buffer Any type of buffer For example the buffer in a baseline association or dissociation step Activation Activation reagent Makes the biosensor competent for binding Quench Quenching reagent Blocks unreacted immobilization sites on the bio sensor surface Load Ligand to be immobilized loaded on the biosensor surface Wash Wash buffer Regeneration Regeneration reagents dissociate
304. ell Data clood Reference HOO n Well Infi j T Concentration ug ml Standard only Bod Clear Data samata 2 By value higG a 5 kBod Copy to Clipboard Dilution series MOOG Extended Sample Types RESTON Starting value NOQOUDUDUUUUUDUU0UU 2190908080808 08O werintormaton a eia x human Iga este pes Dilution orientation 28388 OR 8888 Oef Down g Up L Figure 6 17 Adding Sample Annotations from the Sample Plate Map Annotating Wells in the Sample Plate Table To annotate an individual well in the Sample Plate Table 1 Double click the table cell for Sample ID or Well Information 2 Enter the desired information in the respective field see Figure 6 18 Octet System Data Acquisition User Guide Release 7 1 page 158 Chapter 6 Quantitation Experiments Octet RED384 and QK384 NOTE A series of Sample IDs may also be assembled in Excel and pasted into the Sample Plate Table Sample Plate Table Concentration units yoy x Export Import Well Sample ID Replicate Group Type Conc ug ml Dilution Factor Information OA higG Standard 200 n a human IgG ci Standard 100 n a Ob Standard 50 n a ci Standard 25 n a on Standard 10 n a OKI Standard 5 n a Figure 6 18 Adding Sample Annotations in the Sample Plate Table NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v U
305. ems with an Automation Interface Octet System Data Acquisition User Guide Release 7 1 page 365 APPENDIX B 21 CFR Part 11 Software Administrator Options Installing the Data Acquisition 7 0 21 CFR Part 11 Software 0c cece eee eee e ee 366 Installing the Data Analysis 7 0 21 CFR Part 11 Software cece eee ee cree eee es 369 Installing the ForteBio GxP Server Module cece ccc c eee n ence nen eeeeaeaee 371 Administrator Account Setup cece cece eet n ence nen e cent eens teense nee eens 374 Starting an Administrator User Session ccc cece eee eee e eee eee n eee ee eens 378 Accessing Administrator Options ccc cece ence cece ence nee en cent nent eneees 381 Accessing the GxP Server Module Directly 0 cece eee e cece cece een ee ence eee 396 Restarting the GxP Server Module ccc cece cece cence nen e eee e eee eneeeeeeeee 398 Octet System Data Acquisition User Guide Release 7 1 page 366 Chapter B 21 CFR Part 11 Software Administrator Options INSTALLING THE DATA ACQUISITION 7 0 21 CFR PART 11 SOFTWARE To install the Data Acquisition 7 0 21 CFR Part 11 software 1 Insert the software V7 0 CFR CD 7 00 35 7 0 0 9 into your CD drive e If the Autoplay dialog box displays choose to open the CD to view files e If the Autoplay dialog box does not display navigate to the CD using Windows Explorer Optical drives are typically found under the D
306. en DE spse E en Fb cement GG amn HE F4 Figure 8 61 Data Inverted Using Flip Data Function Aligning Data by a Selected Step To align the binding data to the beginning of a user selected step in the Runtime Binding Chart see Figure 8 62 right click a step and select Align to Step lt number gt To remove the step alignment right click the step and select Unaligned Align to Step 4 Association Unaligned oe Properties g2 Export Data E 315 Undo Zoom z Fullscale a 10 Autoscale 0 5 00 05 I 10 1 1 1 i CONT ere 0 200 400 600 800 1000 1200 1400 1600 Time sec Sensor A6 Sensor B6 Sensor C6 Sensor D6 Sensor E6 Figure 8 62 Runtime Binding Chart Aligning the Data to a User Selected Step Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 335 Extending or Skipping an Assay Step During acquisition the duration of the active step may be extended You can also terminate the active step and begin the next step in the assay NOTE If the step you want to extend or terminate includes biosensors used in Parallel Reference Double Reference or Average Reference subtraction meth ods the data will not be analyzed To extend the duration of the active step 1 Inthe chart window click the Extend Current Step button 2 Inthe Extend Current Step dialog box see Figure 8
307. en the runtime view optional u Use the state of the sensor tray as it was left after last run Response OK r n Error not ready r n Error bad method r n Error bad barcode r n const char AUT_CMD_GETRUNINFO GetRuninfo Returns information about an experiment that is currently running Args none Response OK n Experiment 1 p fbdata Quantitation Experiment 1 r n Error lt reason gt r n Response params n lt experiment name gt Name of the experiment folder name in repos itory e g n Experiment 1 p lt experiment path gt Full path to experiment folder in repository e g p fbdata Quantitation Experiment 1 const char AUT CMD STOP Stop Stops a running experiment Args none Response II OK r n if Error lt reason gt r n const char AUT CMD SETVALUE SetValue Sets a value Octet System Data Acquisition User Guide Release 7 1 page 360 Chapter A Using Octet384 Systems with an Automation Interface Args t lt temp gt Sets heater target temperature DegC Response OK r n Error lt reason gt r n const char AUT CMD STATUS Status Returns status OK ready Busy running Error Experiment was termi nated by an error Busy is followed by descriptive information on the progress of the o experiment complete Args none Response OK r
308. ence Wi n Concentration ug ml Standard only l Sample ID Set Well Data ms By values J Clear Data T Dilution series te Group s A r Copy to Clipboard Seoti 7 M Extended Sample Types Series operator X N ehi Well Information EI 3 oOO0O0OO0000000000q Series operand 2 lJ01010101010101010101010101016 E lution orientation 2833 Right 88383 OLeft B Down g up Gao aca L Figure 6 8 Sample Plate Map Setting a Dilution Series 2 Select the Dilution Series option and enter the starting concentration value 3 Select a series operator enter an operand and select the appropriate dilution orienta tion see Figure 6 10 Highest Concentration Lowest Concentration Figure 6 9 Concentration Representation in Dilution Series 4 Click OK The Sample Plate Table will display the standard concentrations entered Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 151 Assigning a User Specified Concentration to Standards To assign a user specified concentration to standards 1 Inthe Sample Plate Map select the standard wells right click and select Set Well Data The Set Well Data dialog box displays see Figure 6 10 Sample Plate Sample Plate 384 wells y 123456 1e 8 9 1011 BRAS OOO S50 aO s0010 Sane Basses O16 Unknown e838 EIOO Control SS xX B Ba Reference set Well Data x
309. end of the Runtime Binding Chart during data acqui sition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend Annotating Wells in the Sample Plate Map To annotate one or more wells 1 Inthe Sample Plate Map select the samples to annotate right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 7 10 enter the Sample ID and or Well Information and click OK Sample Plate 1 4 io 11 1 4 5 6 7 8 9 666 B Reference Control i Negative Control Positive Control E Buffer F Activation G H O N D Oo Quench Load Ww Wash Unassigned ml Regeneration Set Well Data Clear Data Copy to Clipboard Exter ES Set Well Data Well Information Concentration ug ml Sample only i Sample ID By value Association Diution series Replicate Group Starting value i Series operator y Well Information z 1X Kinetics Buffer mae e eE fl Z Dilution orientation 333 Right 888 Left well Data Sample only Down Up Molecular Weight kD 150 Molar Concentration nM cna L 4 Figure 7 10 Add Sample Annotations from the Sample Plate Map Octet System Data Acquisition User Guide Rele
310. ensor Tray Type 8x 12 format 96 biosensor tip tray green color Optics and e 8 channel biosensor manifold Mechanics e Optical interferometer e One spectrometer shared by eight biosensors Throughput e Up to 8 biosensors in parallel maximum of 96 tests unat tended One 96 well plate and one biosensor tray at once Orbital Flow Static or 100 1 500 rpm Capacity Temperature Range Ambient 4 C 40 C 1 C increments Dimensions 18 6 H x 17 W x 20 8 D 47 cm Hx 43 cm W x 53 cm D Weight 50 Ib 23 kg Electrical e Mains AC 100 240 V 5 0 2 0 A 50 60 Hz single phase Requirements e Power consumption 120 W 240 W peak Octet System Data Acquisition User Guide Release 7 1 Octet QK384 System Specifications page 25 OCTET QK384 SYSTEM SPECIFICATIONS Automatic Sliding Door fort Ort sio Biosensor tray amp rehydration plate Sample plate stage Biosensor chute to waste Reagent plate stage Figure 2 5 Octet QK384 Instrument Door Closed Left or Open Right Table 2 6 Octet QK384 System Specifications Item Description Equipment Classifications Product Classification Class 1 Detachable power cord Installation Overvoltage Category Category II Pollution Degree Degree 2 EMC Classification Group I Class A ISM Equipment EN55011 emissions EN61326 immunity Environmental Storage Temperature 20 to 70 C Optimum Operating Tempe
311. ensor trays kinetics 384 320 kinetics 96 256 quantitation 96 112 V Verify Digital Signature dialog box figure 60 verifying digital signatures 60 Version automation interface command 349 View menu described 34 figure 34 list of menu commands 34 viewing analysis options 40 Audit Trail 62 available types of biosensors 48 constants 394 events 395 events for a specific project or computer 63 group settings 390 inverted data displayed in the Runtime Binding Chart 269 334 multiple Runtime Binding Charts kinetics 384 336 kinetics 96 272 quantitation 384 204 quantitation 96 127 project settings 391 raw reference subtracted data quantitation 384 201 quantitation 96 123 reference subtracted data kinetics 384 332 kinetics 96 268 quantitation 384 201 quantitation 96 123 templates 260 324 user account settings 386 user options 40 user modifiable settings for an assay quantitation 384 167 quantitation 96 91 W warm up time 30 Wash well type kinetics 384 281 kinetics 96 218 waste container emptying 340 for the Octet instrument figure 341 web browser opening 38 remote view of experiment 47 Web Server check box 45 URL figure 46 user option 43 Octet System Data Acquisition User Guide Release 7 1 page 38 weight Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 well designations changing ki
312. ensor type 24 capabilities 23 compliance 23 dimensions 24 electrical requirements 24 environment 23 equipment classifications 23 mechanics 24 optics 24 orbital flow capacity 24 sample types 24 sample volume 24 sampling format 24 temperature range 24 throughput 24 Octet QK system specifications 23 Octet QK384 sensor offset 20 27 well volumes 20 27 Octet QK384 instrument automation 26 capabilities 25 compliance 25 dimensions 27 electrical requirements 27 environment 25 equipment classifications 25 mechanics 26 optics 26 sample types 26 sampling format 26 weight 27 Octet QK384 instrument figure 25 Octet QK384 system specifications listed table 25 Octet QKe and Octet RED Run Experiment window advanced settings listed table 266 Octet QKe instrument biosensor tray type 22 biosensor type 22 capabilities 22 compliance 21 dimensions 22 displayed figure 21 electrical requirements 22 environment 21 equipment classifications 21 mechanics 22 optics 22 orbital flow capacity 22 sample types 22 sample volume 22 sampling format 22 temperature range 22 throughput 22 weight 22 Octet QKe system specifications listed table 21 Octet RED instrument replacing fuses 341 Octet RED system warm up 30 Octet RED384 sensor offset 20 27 starting Octet System Data Acquisition User Guide Release 7 1 page 22 kinetics experiment with the Exper iment wizard figure 278 well volumes 20 27
313. enta HIS Custom Figure 3 21 Adding a Biosensor Type Removing a Biosensor Type To remove a biosensor type select the biosensor name in the Quantitation Sensors or Kinetic Sensors box and click Delete Factory loaded biosensor types cannot be deleted Only the biosensor types that users add to the system can be deleted Octet System Data Acquisition User Guide Release 7 1 page 50 Chapter 3 Getting Started Octet System Data Acquisition User Guide Release 7 1 page 51 CHAPTER 4 21 CFR Part 11 Compliance 21 CFR Part 11 Software s cccscsercedwetedecadeerasadso Paha ty eden EEEE Ea EERE 52 ForteBio GXP Server Module 0 6c c cece ee cece ec ene NEE EEE sb ewececbece seen 52 Selecting a Server Location s oserrisvi dints tidas ts nce td ene ene eens e eee ee een eneenee 52 Starting a User S SSION s 085 cocks neater eabacs seaue erasers E berate Me E TEE 56 Compliance Features 0 0 cece cece cence nee ene n eee eens ESRA PERSSE RESES AER 59 page 52 Chapter 4 21 CFR Part 11 Compliance 21 CFR PART 11 SOFTWARE The Data Acquisition and Data Analysis software for Octet systems is available in an optional 21 CFR Part 11 version that enables users in GMP and GLP laboratories to comply with 21 CFR Part 11 regulations This version of the software includes features such as user account management audit trails and electronic signatures In addition the 21 CFR Part 1
314. ep is lost The data acquired in previous steps is saved however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning Octet System Data Acquisition User Guide Release 7 1 Running a Quantitation Experiment page 119 22 Instrument Status cl E Ea Hl 14 47 39 Sensor 7 Integration Time 1 0 ms a H 14 47 39 Sensor 8 Integration Time 1 0 ms Hl 14 47 40 Picking sensors completed location A1 14 47 40 Plate temperature 30 C 14 47 40 Ready to move to sample location A1 14 47 40 Moving to sample location A1 14 47 41 Arrived at sample location A1 14 47 41 Waiting to start sample location A1 14 47 41 Processing sample location A1 14 47 51 Sample completed location A1 a 14 47 51 Waiting to start new step 14 47 51 Starting new step 14 47 52 Ready to move to sample location A2 14 47 52 Moving to sample location A2 14 47 53 Arrived at sample location A2 14 47 53 Waiting to start sample location A2 I 14 47 53 Processing sample location A2 in I gt V Auto scroll to bottom Save to File Figure 5 54 Instrument Status Log Run Experiment Window Settings The following Data File Location and Name settings are available on the Run Experiment Tab Table 5 9 Data File Location and Name Item Description Assay type The name of the selected assay Quantitation data The lo
315. ep types 236 Delayed experiment start setting 265 329 Delayed Experiment Start setting quantitation 384 197 quantitation 96 120 deleting constants 394 factory loaded biosensor types 49 projects 392 step types 240 305 Octet System Data Acquisition User Guide Release 7 1 page 12 user account 386 user group 390 Description setting 121 199 331 designating controls quantitation 384 156 quantitation 96 81 controls figure 81 156 reference biosensor during acquisition 268 333 reference biosensors 105 110 182 187 257 321 reference biosensors during acquisition quantitation 384 201 quantitation 96 124 reference wells quantitation 384 156 quantitation 96 81 reference wells figure 81 156 samples kinetics experiments 218 unknowns quantitation 384 153 quantitation 96 78 well type kinetics 384 282 well types kinetics experiments 282 designating reference biosensors 258 designating standards quantitation 384 148 quantitation 96 73 designating well types kinetics 96 219 Detection 95 136 172 213 Detection reserved well requirements quantitation 384 146 quantitation 96 72 Detection Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Detection Time and Shake speed parameter 136 213 determining the GxP Server module host location 52 developing the automation client 347 dialog boxes Options 41 setting default temperature 44 Temp
316. eplicate Group color coding figure 227 290 Replicate Groups assigning in the Sample Plate Table quantitation 384 162 quantitation 96 87 defined 226 quantitation 384 159 quantitation 96 84 displayed in Sample Plate Map quantitation 384 figure 161 quantitation 96 figure 86 displayed in Sample Plate Table quantitation 384 figure 161 quantitation 96 figure 86 Replicate Groups displayed in Sample Plate Map figure 229 Replicate Groups in Sample Plate Table figure 229 replicate steps All steps option 244 309 Append as new assay option 244 309 Append to current assay option 244 309 Offset steps option 244 309 options table 244 309 Sample steps only option 244 309 Sample steps will be adjusted by vertically by one row option 244 309 Sample steps will be adjusted by X column option 244 309 Replicate Steps dialog box figure 243 requirements for reserved wells 72 reserved column changing location quantitation 384 146 quantitation 96 72 Reserved Well requirements 72 146 reserved well requirements 72 Detection quantitation 384 146 quantitation 96 72 Octet System Data Acquisition User Guide Release 7 1 page 28 Neutralization quantitation 384 146 quantitation 96 72 Regeneration quantitation 384 146 quantitation 96 72 reserved wells 72 reserved type of well 71 145 Reset automation interface command 349 Reset menu 36 resetting Octet instrument 36
317. erature Setting 43 digital signatures verifying 60 dilution factor assigning to selected wells quantitation 384 154 quantitation 96 79 dilution factor assigning to unknowns quantitation 384 153 quantitation 96 78 dilution factor editing in sample table quantitation 384 155 quantitation 96 80 dilution series assigning sample concentrations kinetics 384 286 kinetics 96 223 assigning standard concentrations quantitation 384 149 quantitation 96 74 Octet System Data Acquisition User Guide Release 7 1 page 13 Dilution Series option 75 223 dimensions Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 discontinuing user session 66 displaying acquisition for a data column 267 331 quantitation 384 199 quantitation 96 122 GxP Server location figure 377 Instrument Status window 34 license information 38 Octet System Data Acquisition software properties 38 step types figure 305 dissociation steps 236 302 E Edit Assay Parameters dialog box figure 129 206 Edit Assay Parameters dialog box opening 35 Edit Assay Parameters menu 35 edit commands 226 Edit Constant dialog box figure 394 Edit Project dialog box figure 392 Edit Sensor Types menu 35 editing assay parameter values quantitation 384 208 quantitation 96 131 assays 35 246 311 biosensor information figure 252 316 dilution factor in the sample table qua
318. eriment gt Edit Assay Parameters The Edit Assay Parameters dialog box appears see Figure 6 66 r 7 Edit Assay Parameters A Available Assays Assay Parameters E Basic Quantitation Name Standard Assay Anti Penta HIS High sensitivity Anti Penta HIS Standard range High sensitivity Human IgG quantitation Human IgG Quantitation Immunogenicity Direct detection Murine IgG Quantitation Protein L Standard range Standard Assay Basic Quantitation with Regeneration Time s Shake speed High sensitivity assay with regeneration Quantitation 120 400 Protein L Standard range Standard Assay vanced Quantitation E Immunogencity Enzyme Linked Residual Protein A Standard Assay Three Step Assay Description Basic Quantitation Standard Assay Read Only Single analyte Multiple analyte Replicates per sensor type 1 wr frm CA fw CA CA ow z E Ca m Pe be oo fom Blueindicates a ForteBio built in assay and cannot be modified or deleted L d Figure 6 66 Edit Assay Parameters Dialog Box 2 Inthe directory tree of assays select the type of standard assay to modify For example to define a new basic quantitation assay in the Basic Quantitation folder select Stan dard Assay 3 Click Duplicate 4 Inthe New Assay dialog box see Figure 6 67 top enter an Assay name 5 Optional In the Assay Description enter information
319. erties dialog box select Fullscale or Autoscale Adding a Runtime Binding Chart Title To add a Runtime Binding Chart title 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box enter a graph title or subtitle Selecting a Runtime Binding Chart Legend To select a Runtime Binding Chart legend 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box see Figure 5 59 select one of the fol lowing legends Sensor Location Sample ID Sensor Information e Concentration Dilution Runtime Graph Properties 2x Title Subtitle Legend Sensor Location Sensor Information Sample ID Concentration Dilution Figure 5 59 Selecting a Runtime Binding Chart Legend L NOTE Text for Sample ID Sensor Information or Concentration Dilution is taken from the Plate Definition and Sensor Assignment tabs and must be entered before the experiment is started 3 Click OK Octet System Data Acquisition User Guide Release 7 1 Managing Runtime Binding Charts page 127 Viewing Multiple Runtime Binding Charts To view multiple Runtime Binding Charts click Window gt New Window Exporting or Printing the Runtime Binding Chart To export the Runtime Binding Chart as a graphic or data file 1 Right click the chart and select Export Data 2 Inthe Exporting dialog box see Figure 5 60 select the export options and cl
320. es generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software cannot be opened and a message indicating this will be presented Octet System Data Acquisition User Guide Release 7 1 page 60 Chapter 4 21 CFR Part 11 Compliance Verifying Digital Signatures The electronic signature of method fmf and data frd files can be verified to ensure they were generated using 21 CFR Part 11 compliant software To verify digital signatures 1 Click Security gt Verify Document The Verify Digital Signature dialog box will display fe Verify Digital Si Figure 4 14 Verify Digital Signature Dialog Box 2 Click to browse for the desired fmf or frd file NOTE When verifying digital signatures both method fmf and data frd files can be selected in the Data Acquisition and Data Analysis software Octet System Data Acquisition User Guide Release 7 1 Compliance Features page 61 in Jy Forte Bio i example files Quantitation X l Search Quantitation Pp i Organize 7 New folder X Favorites Documents library EE Desktop Quantitation J Downloads gt Recent Places Arrange by Folder 7 Name Date modified Type LABUSERO90811_072 frd 2 14 2011 12 08 PM FRD File GB Libraries F LABUSER090811_071 frd 2 14 2011 12 08 PM FRD File DE LABUSER090811_070 frd 2 14 2011 12 08 PM_FRD File BMus LABUSER090811_0
321. eter 169 Single Analyte parameter 169 quantitation 96 Multiple Analyte and Replicates per Sensor Type parameter 92 Quantitation Shake Speed param eter 92 Quantitation Time parameter 92 Single Analyte parameter 92 Quantitation Shake Speed quantitation 384 209 quantitation 96 132 Quantitation Time quantitation 384 209 quantitation 96 132 Single Analyte quantitation 384 208 quantitation 96 131 Octet System Data Acquisition User Guide Release 7 1 page 7 basic quantitation assay parameters listed table quantitation 384 208 quantitation 96 131 Basic Quantitation with Regeneration shortcut menu option 166 Basic Quantitation with Regeneration assay parameter 133 210 Basic Quantitation with Regeneration assay parameters Neutralization Time and Shake speed 134 211 Post condition sensors 134 211 Pre condition sensors 134 211 quantitation 384 170 Multiple Analyte parameter 170 Neutralization Time and Shake Speed parameter 170 Post condition sensors parameter 171 Precondition sensors parameter 171 Regeneration Cycles parameter 171 Regeneration Time and Shake Speed parameter 170 Single Analyte parameter 170 quantitation 96 93 Multiple Analyte parameter 93 Neutralization Time and Shake Speed parameter 93 Post condition sensors parameter 94 Precondition sensors parameter 94 Quantitation Time and Shake speed 93 Regeneration Cycles parameter 94 Regeneration Time
322. eters ES Available Assays Assay Parameters amp Basic Quantitation Name Standard Assay E Anti Penta HIS High sensitivity Anti Penta HIS Standard range High sensitivity Human IgG quantitation Single analyte Multiple analyte Human IgG Quantitation i Replicates per sensor type L E Immunogenicity Direct detection Murine IgG Quantitation Protein L Standard range Standard Assay Basic Quantitation with Regeneration Time s Shake speed E High sensitivity assay with regeneration Quantitation io 400 SS E Protein L Standard range Za E Standard Assay Advanced Quantitation Immunogencity Enzyme Linked Residual Protein A Standard Assay E Three Step Assay Description Basic Quantitation Standard Assay Read Only ows ow ome CA CA owe ems r New Assay Enter Assay Information My Basic Quant Assay Assay name Blueindicates a ForteBio buitt in assq Remove Assay description Enter a short description of the assay here F D Edit Assay Parameters Available Assays Assay Parameters Basic Quantitation Name My Basic Quant Assay Z Anti Penta HIS High sensitivity Anti Penta HIS Standard range f p is per tell ge quantitation Single analyte Multiple analyte uman IgG Quan n Replicates per s E Immunogenicity Direct detecti
323. ethod file opening function 33 Experiment type for the Octet RED384 142 for the Octet RED96 70 in the Experiment Wizard 70 from a set of predefined ForteBio quantitation or kinetics method templates 35 molar concentration units 222 284 molar concentration units in the Plate Definition window figure 222 285 non adjacent steps to add and copy 243 308 project in the Audit Trail 63 Runtime Binding Chart legend kinetics 384 336 kinetics 96 271 quantitation 384 203 quantitation 96 126 server location 53 wells in the Sample Plate Map kinetics 384 282 Octet System Data Acquisition User Guide Release 7 1 page 32 kinetics 96 219 quantitation 384 148 quantitation 96 73 wells in the Sample Plate Map kinetics 384 281 selecting the Web Server in the Options dialog box figure 45 selectively display the acquisition for a data column 267 331 quantitation 384 199 quantitation 96 122 Send Commands Command Field figure 349 Sensor Assignment tab 48 96 100 173 177 303 Sensor Assignment window 96 100 173 177 303 displayed figure 250 314 Sensor Assignment Window for Basic Quantitation without Regeneration figure 97 100 174 177 sensor offset 198 330 Octet QK384 20 27 Octet RED384 20 27 Sensor offset Octet QKe advanced settings 121 Sensor Tray map color codes 122 199 267 331 sensor tray maps 256 automatically adding 256 320 changing biosensor locations 25
324. etics Buffer Buffer C9 1X Kinetics Buffer Buffer E9 1XKinetics Buffer Buffer G9 1X Kinetics Buffer Buffer 19 1X Kinetics Buffer Buffer K9 1X Kinetics Buffer Buffer M9 1X Kinetics Buffer Buffer 09 1XKinetics Buffer Buffer A11 1X Kinetics Buffer Buffer C11 1X Kinetics Buffer Buffer E11 1X Kinetics Buffer Buffer G11 1X Kinetics Buffer Buffer 11 1X Kinetics Buffer Buffer K11 1X Kinetics Buffer Buffer M11 1X Kinetics Buffer Buffer O11 1X Kinetics Buffer Buffer A13 human IgG Group 1 Sample 40 C13 human IgG Group 2 Sample 20 E13 human IgG Group 3 Sample 10 Figure 8 19 Add Replicate Group from the Sample Plate Table Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sample Plate Table To view edit com mands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types 3 Repeat the previous steps to assign new samples to the existing Replicate Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and group samples that use the same Repli
325. f data acquisition in seconds while the biosensor is Shake speed rpm incubated in sample and the sample platform orbital shaking speed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Buffer Time s and The duration of biosensor incubation in the first buffer in seconds Shake speed rpm and the sample platform orbital shaking speed rotations per minute Enzyme Time s The duration of biosensor incubation in seconds in the enzyme and Shake speed solution and the sample platform orbital shaking speed rotations rpm per minute 2nd Buffer Time s The duration of biosensor incubation in seconds in the second and Shake speed buffer solution and the sample platform orbital shaking speed rpm rotations per minute Detection Time s amp The duration of data acquisition during the detection step in sec Shake speed rpm onds in an advanced quantitation assay NOTE A subset of data points may be selected for processing during data analysis Offline Choose this option to incubate sample with biosensors outside the Octet system Offline incubation is best performed on the ForteBio Sidekick biosensor immobilization station Reuse Buffer Allows buffer wells to be reused If unselected the number of buf fer columns must equal the number of sample columns If selected the number of buffer columns may be less than the number of sample columns as
326. fied concentration to standards quantitation 384 151 quantitation 96 76 assigning molar concentration kinetics 96 221 association steps 236 302 Audit Trail described 62 illustrated figure 62 list options 64 selecting a project 63 sorting 63 viewing 62 Authentication Server dialog box 53 Auto Increment File ID 264 328 Octet System Data Acquisition User Guide Release 7 1 page 6 Auto Increment File ID Start Run Experiment window settings quantitation 384 197 quantitation 96 120 Auto Scroll to bottom check box 39 Automatically save runtime chart setting 120 197 265 329 automation for Octet QK384 26 for Octet RED384 19 Automation box 346 Automation Client example application connecting 348 automation interface commands Cleanup 350 Close 350 GetMethodInfo 349 GetRunInfo 349 Present 350 Reset 349 Resume 350 Run 349 Status 350 Stop 350 Version 349 automation interface control setup 346 automation interface design 346 automation session typical 351 Automation user option 43 AutomationAPI h header file 349 AutomationClient exe 346 baseline step 237 303 basic kinetics experiment 216 276 Basic Kinetics Experiment window figure 277 Basic Quantitation Assay Parameters listed table 92 131 169 208 Multiple Analyte quantitation 384 209 quantitation 96 132 quantitation 384 Multiple Analyte and Replicates per Sensor Type parameter 169 Quantitation Shake Speed param
327. fore the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend Octet System Data Acquisition User Guide Release 7 1 page 188 Chapter 6 Quantitation Experiments Octet RED384 and QK384 10 Optional After an assay is completed the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container To return the biosensors to the tray click the Replace sensors in tray after use check box see Figure 6 37 Sensor Tray v Replace sensors in tray after use EWOUUOOU a Em EE g mm EE HOD Legend Unassigned sensors 683 Missing sensors Remove Fill Fill Plate Figure 6 51 Replace Sensors in Tray After Use Check Box NOTE Biosensors can be regenerated up to a max of 11 times per experiment Biosensor Regeneration For Basic Quantitation with Regeneration experiments only the Sensor Assignment tab includes the Regenerations parameter which specifies the maximum number of regenera tion cycles for each column of biosensors The specified number of regeneration cycles determines the minimum number of cycles required for each column of sensors This calcu lation may result in non equal regeneration cycles for columns of biosensors The fractional use of the regeneration and neutralization wells by each column of sensors is represented by a pie c
328. fresh settings 45 Regeneration reserved well requirements quantitation 384 146 quantitation 96 72 Regeneration well type kinetics 384 281 kinetics 96 218 Regeneration Cycles parameter Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 Regeneration cycles parameter Advanced Quantitation 137 214 quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration 134 211 Regeneration Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Regeneration Time and Shake speed parameter 133 136 210 213 remote view of experiment via web browser figure 47 Octet System Data Acquisition User Guide Release 7 1 page 27 removing assay from the quantitation application 35 assay steps 247 311 biosensor type 49 side panel of Octet instrument 343 step alignment of data 270 334 well designation 282 well designations controls or reference wells 81 157 quantitation 384 149 153 quantitation 96 74 78 reagent plates quantitation 384 167 reordering assay steps 247 311 Replace sensors in tray after use check box 176 replacing biosensors in the biosensor tray 251 315 fuses for Octet RED instrument 341 for QKe instrument 341 replicate assay steps 244 309 replicate assay adding to a plate 247 312 Replicate Group color coding figure 227
329. g in the Assay Definition window 258 322 biosensor type changing in the Sensor Assignment window 254 318 biosensor types changing 246 311 biosensors assigning quantitation 384 173 quantitation 96 96 assigning to samples 249 313 automatically adding experiment tray maps 256 320 changing locations kinetics 96 252 changing type 320 designating reference 105 110 182 187 257 321 entering information 252 315 preparing 68 removing from sensor tray maps 253 317 replaying in the biosensor tray 251 315 viewing available 48 biosensors reference designating 258 browser window functions 47 Buffer well type kinetics 384 280 kinetics 96 218 Buffer Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Buffer Time and Shake speed parameter 135 212 building assays 241 By value option 76 151 222 285 C capabilities Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 22 Octet RED384 instrument 18 Octet RED96 instrument 17 Octet System Data Acquisition User Guide Release 7 1 page 9 cascade arrangement organizing windows 37 Cascade menu 37 Change Password dialog box figure 387 Change Projects menu 64 changing administrator password 387 assay step name figure 247 311 biosensor Location Method 1 253 316 biosensor location Method 2 254 317 biosensor type figure 247 311 biosensor type in the Assay Defini
330. g point to create your own step types Table 7 3 Sample Step Types for Kinetic Assays Step Type Step Description Association Calculates the kops Select this step type when binding the second pro tein of interest analyte to the biosensor This step should be performed at 1 000 rpm Dissociation Calculates the kg Select this step type when monitoring the dissociation of the protein complex This step should be performed at 1 000 rpm Baseline Can be used to align the data Select this step type when establishing the biosensor baseline in the presence of buffer This step can be performed with no flow 0 rpm However if the baseline step directly precedes an association step perform the baseline step at 1 000 rpm IMPORTANT An assay must include a baseline step fol lowed by a set of association dissociation steps to be ana lyzed The Octet System Data Analysis software recognizes the baseline association dissociation step series during processing Data cannot be processed if this sequence is not included in the assay setup Loading Not used in data analysis Select this step type when binding the first protein of interest ligand to the biosensor NOTE This step may be performed offline outside the Octet instrument Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 237 Table 7 3 Sample Step Types for Kinetic Assays Continued Step Type Step Description
331. g the Experiment SEND Version r n RECV 6 1 0 30 Pegasys 1 0 SEND Status r n RECV OK Getting Information about the Experiment SEND Version r n RECV 6 1 0 30 Pegasys 1 0 SEND Status r n RECV OK Monitoring the Experiment bool bBusy true while bBusy Send Status r n response Recv if response OK Octet System Data Acquisition User Guide Release 7 1 page 352 Chapter A Using Octet384 Systems with an Automation Interface bBusy false else Sleep 1000 sleep for a second SEND Status r n RECV Running 5 SEND Status r n RECV Running 25 SEND Status r n RECV Running 45 SEND Status r n RECV Running 75 SEND Status r n RECV Running 95 SEND Status r n RECV OK Stopping the Experiment and Presenting the Plate for Unloading Both the Stop and the Present commands are asynchronous they initially return OK to indicate that the command was accepted and started OK but status must be polled until OK is returned to indicate completion SEND RECV SEND RECV SEND RECV SEND RECV SEND RECV Stop r n OK Status r n Busy Status r n Busy Status r n OK Present r n OK Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 353 SEND Status r n RECV Busy SEND Status r n RECV Busy SEND Status r n RECV OK Advanced Automation Session If an experiment is sufficiently complex
332. gG biosensor_8CH_96W fmf Anti mlgG biosensor_16CH_96W fmf Anti mIgG biosensor_8CH_96W fmf Anti Penta HIS Dilution Factor Scouting_96W fmf Anti Penta HIS Spike Recovery Assay_96W fmf DirectDetectionimmunogenicity_16CH_96W fmf DirectDetectionImmunogenicity_8CH_96W fmf Protein A biosensor_16CH_96W fmf Protein A biosensor_8CH_96W fmf Protein A or G biosensor_16CH_96W fmf Protein A or G biosensor_8CH_96W fmf Protein L biosensor_16CH_96W fmf Protein L biosensor_8CH_96W fmf Templates Skip Step Stop Figure 5 50 Experiments in the Template Folder Octet System Data Acquisition User Guide Release 7 1 page 116 Chapter 5 Quantitation Experiments Octet RED96 QK and QK RUNNING A QUANTITATION EXPERIMENT IMPORTANT Before starting an experiment ensure that the biosensors are properly rehydrated For details on how to prepare the biosensors see the appropriate biosensor product insert Loading the Biosensor Tray and Sample Plate To load the biosensor tray and sample plate 1 Open the Octet instrument door lift the handle up 2 Place the biosensor tray on the biosensor stage left side so that well A1 is located at the upper right corner see Figure 5 51 3 Place the sample plate on the sample stage right side so that well A1 is located at the upper right corner see Figure 5 51 bib bbb g 3 Well A1 Position Biosensor tray Sample plate Figure 5 51 Biosensor Stage left
333. gnating Samples Each well may be designated as a Standard Unknown Control or Reference A well may also remain Unassigned or be designated as Reserved by the system for Basic Quantita tion with Regeneration and Advanced Quantitation experiments NOTE It is important to define all of the wells that will be used in the assay Only wells that are selected and defined using one of the sample types in Table 5 4 will be included in the assay Table 5 4 Types of Sample Wells Icon Description O Standard Unknown Contains an analyte of known concentration Data from the well is used to generate a standard curve during analysis Contains an analyte of unknown concentration The concentration of the analyte is calculated from the well data and the standard curve 2 Control A control sample either positive or negative of known analyte com position Data from the well is not used to generate a standard curve during analysis Positive Control A control sample that contains analyte of known concentration e Negative Control A control sample known not to contain analyte Reference Provides a baseline signal which serves as a reference signal for Unknowns Controls and Standards The reference signal can be subtracted during data acquisition in the Runtime Binding Chart and during data analysis Q Unassigned Not used during the experiment O Reserved Used by the system during Basic Q
334. gure 395 example csv plate definition file figure 235 299 example assay using one partial biosensor tray and biosensors from a second tray 113 190 example experiment using two biosensor trays figure 257 321 Exit menu 34 experiment prior to running 258 322 Experiment menu described 34 figure 35 list of menu commands 35 experiment method files managing 128 274 quantitation 384 205 quantitation 96 128 saving 33 saving to new name 33 experiment method files managing 274 338 experiment methods saving manually 114 191 Experiment Run Name setting Run Experiment window settings quantitation 384 196 quantitation 96 119 experiment settings advanced settings Octet QK384 198 330 data file location and names 2nd plate name barcode 264 328 Assay Type 328 assay type 264 Auto Increment File ID Start 264 Octet System Data Acquisition User Guide Release 7 1 page 15 328 kinetics data repository 264 328 plate name barcode file prefix 264 328 run name 264 328 general information Description 121 199 331 Machine name 121 199 330 User name 121 199 330 run settings Automatically save runtime charts 120 197 265 329 Delayed experiment start 265 329 Open runtime charts automatically 120 197 265 329 Set Plate Temperature 120 197 265 329 shake sample plate while waiting 120 197 265 329 Start After 265 329 experiment settings data file location and name
335. h sensitivity Human IgG quantitation Human IgG Quantitation Immunogenicity Direct detection Murine IgG Quantitation Protein L Standard range Standard Assay Basic Quantitation with Regeneration Time s Shake speed High sensitivity assay with regeneration Quantitation 120 400 Protein L Standard range Standard Assay vanced Quantitation E Immunogencity Enzyme Linked Residual Protein A Standard Assay Three Step Assay Description Basic Quantitation Standard Assay Read Only Single analyte Multiple analyte Replicates per sensor type 1 wr frm CA fw CA CA ow z E Ca m Pe be oo fom Blueindicates a ForteBio built in assay and cannot be modified or deleted L d Figure 5 61 Edit Assay Parameters Dialog Box 2 Inthe directory tree of assays select the type of standard assay to modify For example to define a new basic quantitation assay in the Basic Quantitation folder select Stan dard Assay 3 Click Duplicate 4 Inthe New Assay dialog box see Figure 5 62 top enter an Assay name 5 Optional In the Assay Description enter information about the assay 6 Click Save The new assay appears in the directory tree of available assays see Figure 5 62 bot tom Octet System Data Acquisition User Guide Release 7 1 page 130 Chapter 5 Quantitation Experiments Octet RED96 QK and QK f Edit Assay Param
336. hake Speed pa rameter 172 Detection Time and Shake Speed parameter 172 Enzyme Time and Shake Speed pa rameter 172 Multiple Analyte parameter 171 Neutralization Time and Shake Speed parameter 172 Offline parameter 172 Post condition sensors parameter 173 Pre condition sensors parameter 173 Regeneration cycles parameter 173 Regeneration Time and Shake Speed parameter 172 Reuse Buffer parameter 172 Sample Time and Shake Speed pa rameter 172 Single Analyte parameter 171 quantitation 96 94 2nd Time and Shake Speed param eter 95 Buffer Time and Shake Speed pa rameter 95 Detection Time and Shake Speed parameter 95 Enzyme Time and Shake Speed pa rameter 95 Multiple Analyte parameter 94 133 Neutralization Time and Shake Speed parameter 95 Offline parameter 95 Post condition sensors parameter 96 Pre condition sensors parameter 96 Regeneration cycles parameter 96 Regeneration Time and Shake Speed parameter 95 Reuse Buffer parameter 95 Sample Time and Shake Speed pa rameter 95 Single Analyte parameter 94 Octet System Data Acquisition User Guide Release 7 1 page 3 Regeneration cycles 137 214 Regeneration Time and Shake speed 136 213 Sample Time and Shake speed 212 Advanced Quantitation Quantitation 384 Experiment 142 advanced run experiment settings 120 197 329 advanced settings Acquisition rate Octet QKe 121 Acquisition rate Octet RED 12
337. han one type of biosensor the software automatically creates a separate sensor tray for each type of biosensor If the different types of biosensors are in the same tray change the biosensor type as appropriate The biosensor types shown in the Sensor Type table column are those designated during the kinetics assay definition In the example shown in Figure 8 41 the experiment includes two assays in the same wells The use of those wells by two different biosensors is indicated by the pie chart colors NOTE The Sensor Type for the assay must be selected or changed from the Assay Steps List in the Assay Definition Tab Changing the Sensor Type from the Sensor Assignment Tab will not update the assay Octet System Data Acquisition User Guide Release 7 1 page 314 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Piate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment f In this step sensors are assigned to samples If you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial tray Right click to assign a sensor type to selected sensors Sensor Tray Replace sensors in tray after use y e Lot Number Information Fc Capture TOT Cd IgG Fc Capture C1 AHC Anti hIgG Fc Capture D1 AHC Anti hIgG Fc Capture E
338. hart Figure 6 52 Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 189 Plate Definition Sensor Assignment Review Experiment Run Experiment In this step sensors are assigned to samples Regenerations od Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Times sensors will be reused Only the first sensor tray can be a partial plate 2 E Sensor Tray 7 Replace sensors in tray after use P i 2 3 4 5 6 7 8 9 0 1 12 y S ype N Ini al A B1 Protein A B C1 Protein A D1 ProteinA Cc E1 Protein A D z 5 F1 Protein A G1 Protein A E 2 2 H1 Protein A A2 Protein A F 2 2 B2 Protein A C2 ProteinA G Ea Ea D2 Protein A H el E E2 Protein A F2 Protein A i j G2 Protein A Legend Unassigned sensors Ba Missing sensors Fol Poena Remove l Fil Fill Plate A3 Protein A B3 Protein A Sample Plate c3 Protein A W123 45 6 7 8 9101112131415161718192021222324 D3 Protein A agosogogotogeoeoonoS aoa aims B cO O 000 0000 000 O 2 D C 0CO0O0O0O08D e i EO00000000500000 Poe Protein A FO C COCO0 0O08C e AA Protein A 6GO0O0O09000000090 B4 Protein A H C OCO0O0O0O080 e C4 Protein A poscgoguscejgogcoooo ges eames J KO O000 000 600 O E oA L C 0O0O0O0O080e a M C C C 0OCO0eC e ae Proten A NOOO00
339. he Login box NOTE Once the GxP Server module host location is selected this location will be used as the default selection for the administrator account It does not need to be re selected each time a new session is initiated Octet System Data Acquisition User Guide Release 7 1 Administrator Account Setup page 377 Figure B 21 Login Dialog Box DisplayingGxP Server Location 3 From the User drop down list select Administrator 4 Leave the Password blank and the Project set to none and click OK fort sio Server localhost 20002 User Administrator Password Project none Figure B 22 Administrator User Selection The Change Password dialog box will display Figure B 23 Octet System Data Acquisition User Guide Release 7 1 page 378 Chapter B 21 CFR Part 11 Software Administrator Options The password has not been set for this user New password eecccccece Confirm new password ecccccocee Password reminder Default Figure B 23 Change Password Dialog Box 5 Enter a New password and Password reminder optional and click OK The Data Acquisition or Data Analysis software will now launch and initiate an adminis trator user session which will allow access to administration options STARTING AN ADMINISTRATOR USER SESSION Administrators initiate new user sessions the same way non administrative users do To start an administrato
340. he app being automated the hardware plat form it controls and the API version Args none Response App product version e g 6 0 0 120 Pegasys 1 0 r n const char AUT CMD RESET Reset Stops any running experiment and resets the instrument Args none Response IA OK r n Error lt reason gt r n const char AUT CMD GETMETHODINFO GetMethodInfo Returns info about a method file Args m lt path gt Method file name required Response OK r lt bool gt t lt int gt s lt name gt r n e g OK p96 0 t2 s SA Streptavidin r n Response params p lt int gt lt int gt Sizes of the plates in use e g p384 96 t lt int gt Number of sensor trays required 0 5 e g t2 s lt name gt Name of first sensor in the tray e g s SA Streptavidin Error load method r n Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 359 Error bad method r n const char AUT CMD RUN Run Runs an experiment Args m lt path gt Method file name required p lt path gt Plate file to update sample plate in method set tings optional b lt barcode gt Sample plate bar code optional Be 1 lt barcode gt Sample plate bar code optional 2 lt barcode gt Reagent plate bar code optional 1 lt lotnumber gt Sensor tray lot number optional s Silent does not op
341. he dilution factors entered Octet System Data Acquisition User Guide Release 7 1 page 80 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Editing a Dilution Factor in the Sample Plate Table To edit a dilution factor in the Sample Plate Table 1 Inthe Set Well Data dialog box see Figure 5 10 double click a cell in the Dilution Factor column for the desired unknown 2 Enter the new value the default dilution factor is 1 Sample Plate Table Concentration units ug ml M Export Import Well Sample ID Replicate Group Type Conc ig ml Dilution Factor Informe G2 Standard 5 n a H2 Standard 2 5 n a Oa3 Standard 1 n a B3 Standard 200 n a c3 Standard 100 n a D3 Standard 50 n a OE3 Standard 25 n a F3 Standard 10 n a O G3 Standard 5 n a H3 Standard 2 5 n a Ss O A4 Unknown n a B4 Unknown n a 2 Undo Oc4 Unknown n a 2 D4 Unknown n a 2 Cut E14 Unknown n a 2 Copy F4 Unknown n a 2 Paste G4 Unknown n a 2 Delete H4 Unknown n a 2 OAS Unknown n a 2 Select All 5s Chlain Ue 2 Right to left Reading order cs Unknown n a 2 i D5 Uuand 2 Show Unicode control characters OES Unknown n a 2 Insert Unicode control character Fs Unknown n a 2 Open IME G5 Unknown n a 2 GH Uine ro 2 Reconversion Figure 5 12 Sample Plate Table Shortcut Menu of Edit Commands NOTE Edit commands Cut Copy
342. he plate temperature is set to the default temperature specified in File gt Options The factory set default tem perature is 30 C NOTE If the actual plate temperature is not equal to the set plate temperature a warning displays and the Octet System Data Acquisition software provides the option to wait until the set temperature is reached before proceeding with the run continue without wait ing until the set temperature is reached or cancel the run Advanced settings are available for the Octet QK Octet RED and Octet RED96 systems The signal to noise ratio of the assay can be optimized by selecting different acquisition rates The acquisition rate refers to the number of binding signal data points reported by the Octet system per minute and is reported in Hertz per second A higher acquisition rate generates more data points per second and monitors faster binding events better than a slower acquisition rate A lower acquisition rate allows the software enough time to per form more averages of the collected data Typically more averaging leads to reduced noise Octet System Data Acquisition User Guide Release 7 1 page 266 Chapter 7 Kinetics Experiments Octet RED96 QK and QK and thus better signal to noise ratios The choice of a setting should be determined based upon consideration of the binding rate and the amount of signal generated in your assay and some experimentation with the settings Table 7 8
343. he sample plate and right click to enter modify well data Read Head 8Channels 16 Channels Modify Plates Sample Plate Concentration units Sample Plate 384 wells Reagent Plate Molar concentration units W123 4 5 6 78 9 101112131415 161718192021 222324 Sample ID Replicate Group Type Conc jig ml MW kD 4 wOZErAcC TOmMmMIODyYS O Unassigned Import J Export J Remove Reagent Plate 384 wells Set Well Data Clear Data Copy to Clipboard OQ V Extended Sample Types O Unassigned ba uv Figure 8 28 Defining Wells in the Reagent Plate 7 Optional Enter well data or reagent information in the Reagent Plate Table To remove well designations select the column s and click Remove or right click and choose Clear Data Saving a Reagent Plate Definition Exporting and saving reagent plate definition is done in the same manner as you would for sample plates For details Managing Sample Plate Definitions on page 296 Octet System Data Acquisition User Guide Release 7 1 page 302 Chapter 8 Kinetics Experiments Octet RED384 and QK384 DEFINING A KINETIC ASSAY After the sample plate is defined the assay must be defined The steps to define a kinetic assay include Step See Page 1 Define the step types 302 2 Build the assay by assigning a step type to a column s in the 306 sample plate 3
344. hows the appro priate column information layout Octet System Data Acquisition User Guide Release 7 1 Managing Sample Plate Definitions page 235 A B D E F G H E 1 PlateWells 96 2 Well ID Replicate Group Group Concentration ug ml Molecular Weight kD Molar Concentration M Information a 3 A1 Kinetics Buffer Buffer 1X Kinetics Buffer 4 B1 Kinetics Buffer Buffer 1X Kinetics Buffer fe Kinetics Buffer Buffer 1X Kinetics Buffer 6 D1 Kinetics Buffer Buffer 1X Kinetics Buffer BREL Kinetics Buffer Buffer 1X Kinetics Buffer 8 F1 Kinetics Buffer Buffer 1X Kinetics Buffer 9 G1 Kinetics Buffer Buffer 1X Kinetics Buffer 10 H1 Kinetics Buffer Buffer 1X Kinetics Buffer 11 A2 Loading Load 12 5 ug ml ProA 12 B2 Loading Load 12 5 ug ml ProA M 4 gt 96 standard plate I 7 maL u ni all Figure 7 23 Example Plate Definition File csv Octet System Data Acquisition User Guide Release 7 1 page 236 Chapter 7 Kinetics Experiments Octet RED96 QK and QK DEFINING A KINETIC ASSAY After the sample plate is defined the assay must be defined The steps to define a kinetic assay include Step See Page 1 Define the step types 236 2 Build the assay by assigning a step type to a column s in the 241 sample plate 3 Save the sample plate definition optional 232 Defining Step Types Table 7 3 lists the example step types to define a kinetic assay Use these examples as a startin
345. icate Group names spacing and capitalization must be identical For example samples assigned to Group 2 and group2 are treated as two groups NOTE When performing a Multiple Analyte experiment if the same Replicate gt Group name is used with different biosensor types they will be treated as sep arate groups Statistics for these groups will be calculated separately for each biosensor type Wells in the Sample Plate Map will show color coded outlines as a visual indication of which wells are in the same group see Figure 6 21 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 161 Sample Plate Sample Plate 384 wells Figure 6 21 Replicate Groups Displayed in Sample Plate Map The Sample Plate Table will update with the Replicate Group names entered see Figure 6 22 Sample Plate Table Concentration units pg ml fA Well Sample ID Replicate Group Type Conc ug ml Dilution Factor Information a hlgG 1 Standard 200 n a human IgG p C1 hlgG 2 Standard 100 n a human IqG OE higG 3 Standard 50 n a human IqG GI higG 4 Standard 25 n a human IgG on hlgG 5 Standard 10 n a human IgG OKI hlgG 6 Standard 5 n a human IqG MI hgG 7 Standard 2 5 n a human IgG 0001 hlgG 8 Standard 1 n a human IqG A3 hlgG 1 Standard 200 n a human IgG C3 hlgG 2 Standard 100 n a human IqG E OE higG 3 Standard 50 n a human IgG OGI higG 4 Standard 25 n
346. ick Export F Exporting Export eEMF wmF sBMP vPG PNG Text Data Export Destination ClipBoard File Browse Printer Export Size Inches Points Millimeters Width 152 400 101 600 Millimeters Large Font Figure 5 60 Exporting Dialog Box Table 5 13 Runtime Binding Chart Export Options Task Export Option Export Result Destination Text EMF WMF Data BMP JPG or PNG Save the vV Click File gt Creates a tab delimited text binding Browse to file of the numerical raw data data select a folder from each biosensor Open and enter a file the file with a text editor name such as Notepad Export the v Click File gt Creates a graphic image Runtime Browse to Binding select a folder Chart toa and enter a file graphic file name Octet System Data Acquisition User Guide Release 7 1 page 128 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 13 Runtime Binding Chart Export Options Continued Task Export Option Export Result Destination Copy the vV Clipboard Copies the chart to the sys Runtime tem clipboard Binding Chart Print the v Printer Opens the Print dialog box Runtime Binding Chart MANAGING EXPERIMENT METHOD FILES After you run an experiment the Octet System Data Acquisition software automatically saves the method file fmf which includes the sample plate definition biosensor assign me
347. ighlight ane or mare wells on the sample plate and right click to enter madifywell data Assay Settings Sample Plate Table Assay Basc Quanatn Mealy Corcentationunis pa 7 Standard Assay Singk analyte Time 5 Shake speed Quantitation 120 200 Well Sample ID Replicate Group Type Conc 1g m Dilution Factor Information Sample Piate Sample Plate 96 wells I Experiment Wizard ies Pai 2 3 4 5 67 8 9 0 1 Choose an option to start a New Quantitation Experiment Bast cumtaton OQQOQOOOOOOOOO Basic Quantitation wth Regeneration Advanced Quanttation OOOOOO r G OOCOO co Ne ia HOOCOCO00O Basic Kinetics O Standard Contiot__ Unassigned _ O Unknown _ Reference Reserves moguwp O O Q O Q Q O O O O O O OO OQO Figure 5 1 Selecting an Experiment Type in the Experiment Wizard for Octet RED96 4 Click the 5 arrow The Experiment dialog box displays Figure 5 1 right DEFINING THE SAMPLE PLATE Table 5 3 lists the steps to define a sample plate Table 5 3 Defining a Sample Plate Step See Page 1 Designate the samples 70 2 Annotate the samples optional 82 3 Save the sample plate definition optional 88 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 71 Desi
348. igure 4 12 Status Bar NOTES Software operation may be restricted based on your user privileges For more information on user privileges please contact your administrator User sessions are automatically locked after a period of inactivity which is set by the administrator The Login dialog box will display and a message indicat ing the session has been locked will be shown You can choose to log back into the session or log off at this time User sessions will not be locked during exper imental data acquisition Octet System Data Acquisition User Guide Release 7 1 Compliance Features page 59 COMPLIANCE FEATURES The 21 CFR Part 11 compliant features provided in the 21 CFR Part 11 versions of the Data Acquisition and Data Analysis software can be accessed by clicking the Security menu from the software s Main Menu Window Help Verify Document View Audit Trail Change Project r Change Password Server Administration Lock Application Logoff Figure 4 13 Security Menu NOTES The Server Administration menu option in the Security menu can be accessed only if you have administrator or review privileges Security menu options in the Data Acquisition and Data Analysis software applications are identical Experiment and Method File Compliance When using the 21 CFR Part 11 version of the Octet System Data Acquisition software only 21 CFR Part 11 compliant experiments and method fil
349. ile waiting Advanced Settings v Open runtime charts automatically W Automatically save runtime chart 7 Set plate temperature C Acquisition rate Standard quantitation 5 0 Hz averaging by 20 gt Default General Information Username Owner Description Machine name Warming changing these settings could affect assay signalto noise Ifyou are unsure of how to use these settings please consult the Data Acquisition User Guide JRICHARDS Figure 5 52 Run Experiment Window Octet RED96 2 Confirm the defaults or enter new settings See Run Experiment Window Settings on page 119 for more information on experimental settings gt NOTE If you delay the experiment start you have the option to shake the plate until the experiment starts 3 To start the experiment click If you specified a delayed experiment start a message box displays the remaining time until the experiment starts If you selected the Open runtime charts automatically option the Runtime Binding Chart window displays the binding data in real time and the experiment progress see Figure 5 53 Octet System Data Acquisition User Guide Release 7 1 page 118 Chapter 5 Quantitation Experiments Octet RED96 QK and QK NOTE For more details about the Runtime Binding Chart see Managing Runtime Binding Charts on page 122
350. ime and Shake speed 93 Regeneration Cycles parameter 94 Regeneration Time and Shake Speed parameter 93 Single Analyte parameter 93 133 Quantitation Time and Shake speed 133 170 210 Regeneration cycles 134 211 Regeneration Time and Shake speed 133 210 Basic Quantitation with Regeneration Quantitation Experiment 69 141 Basic Quantitation Quantitation Experiment 69 141 beginning an experiment 216 276 beginning the next step in the assay 271 335 binding data aligning kinetics 384 334 kinetics 96 270 exporting quantitation 384 204 quantitation 96 127 saving kinetics 384 337 kinetics 96 273 quantitation 384 204 quantitation 96 127 biosensor column active 122 199 267 331 biosensor columns default 252 316 biosensor pickup tips cleaning 343 biosensor regeneration described quantitation 384 188 Octet System Data Acquisition User Guide Release 7 1 page 8 quantitation 96 111 biosensor stage left and sample stage right figure 116 261 biosensor tray loading kinetics 384 324 kinetics 96 260 replacing biosensors 251 315 biosensor tray type 17 19 26 Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 biosensor tray loading quantitation 384 193 quantitation 96 116 biosensor type adding 49 changing figure 247 311 Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 removing 49 biosensor type changin
351. iment 1 Click Save Method File 5 or on the main menu click File gt Save Method File If there is more than one open experiment and you want to save all of them click Save All Methods Files 2 Inthe Save dialog box enter a name and location for the file and click Save Octet System Data Acquisition User Guide Release 7 1 page 324 Chapter 8 Kinetics Experiments Octet RED384 and QK384 NOTE If you edit a saved experiment and want to save it without overwriting the original file click File gt Save Method File As and enter a new name for the experiment Saving an Experiment to the Template Folder If you save an experiment to the factory installed Template folder the experiment will be available for selection To view templates select Experiment gt Templates gt Kinetics gt Experiment Name see Figure 8 53 Follow the steps above to save an experiment to the Template folder located at C Program Files ForteBio DataAcquisition TemplateFiles IMPORTANT Do not change the location of the Template folder If the Tem plate folder is moved from the factory set location the software may not func tion properly Experiment Instrument Window Help V New Experiment Wizard Ctrl N Edit Assay Parameters Edit Sensor Types Set Plate Temperature Biomolecule kinetics AHC biosensor Kinetic Characterization_16CH_96W fmf Biomolecule kinetics AMC biosensor Kinetic Cha
352. iment method 1 Click the Save Method File button 5 or on the main menu click File gt Save Method File To save more than one open experiment click the Save All Methods Files button Ba 2 Inthe Save dialog box enter a name and location for the file and click Save Octet System Data Acquisition User Guide Release 7 1 Saving Experiments page 115 NOTE If you edit a saved experiment and want to save it without overwriting the original file select File gt Save Method File As and enter a new name for the experiment Saving an Experiment to the Template Folder If you save an experiment to the factory installed Template folder the experiment will be available on the menu bar To view templates click Experiment gt Templates gt Quantita tion gt Experiment Name see Figure 5 50 Follow the steps above to save an experiment to the Template folder located at C Program Files ForteBio DataAcquisition TemplateFiles 1 IMPORTANT Do not change the location of the Template folder If the Tem plate folder is not at the factory set location the software may not function properly Experiment Instrument Window Help V New Experiment Wizard Ctrl N Edit Assay Parameters Edit Sensor Types Set Plate Temperature Kinetics U Quantitation gt Advanced Quantitation Basic Quantitation Anti higG biosensor_16CH_96W fmf Basic Quantitation with Regeneration Anti hI
353. iments 43 Defining a New Default Sample Plate Temperature cece cece eee e ee 44 Monitoring Experiments Remotely 45 Managing Biosensor Types 48 Viewing Available Biosensor Types 48 Adding a Biosensor Type 49 Removing a Biosensor Type 49 Chapter 4 21 CFR Part 11 Compliance 51 21 CFR Part 11 Software 0 000 52 ForteBio GxP Server Module 52 Selecting a Server Location 52 Starting a User Session 0004 56 Compliance Features c0cceeeees 59 Experiment and Method File Compliance 59 Verifying Digital Signatures 60 Viewing the Audit Trail 62 Changing Projects During a User Session 64 Changing the User Password 65 Locking the Application 65 Ending a User Session 66 Octet System Data Acquisition User Guide Release 7 1 page 2 Chapter 5 Quantitation Experiments Octet RED96 QK and QK 67 INtFOGUCTION 0 6 cc ccc cece eee e ee ne ees 68 Starting a Quantitation Experiment 69 Starting an Experiment Using the Experiment Wizard 00065 69 Defining the Sample Plate 70 Designating Samples 4 71 Selecting Wells in the Sample Plate Map 73 Designating Standards 73 Designating Unknowns 78 Designating Controls or Reference Wells 81
354. in the Sensor Assignment window 254 318 constants 394 group settings 390 project settings 391 projects during a user session 64 sample plate format kinetics 384 280 quantitation 384 144 sample plate format figure 144 280 user account passwords 387 user account settings 386 user password 65 well designations kinetics 384 295 kinetics 96 231 changing location of a reserved column quantitation 384 146 quantitation 96 72 changing projects figure 64 Choose Install Location dialog box figure 367 369 Choose Start Menu Folder dialog box figure 367 370 373 cleaning biosensor pickup tips 343 cleaning Octet instrument 340 342 Cleanup automation interface command 350 Close automation interface command 350 Close Method File menu 33 closing active method file 33 application 34 color codes 122 199 267 331 color coded wells displaying how biosensors interrogate a 384 well plate 8 channel or 16 channel read head 143 279 a 96 well plate 8 channel or 16 channel read head 143 279 compliance Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 compliant features 21 CFR Part 11 59 Conc column 76 151 concentration representation in dilution series figure 224 Concentration Units drop down list 73 Connect as IP address changing 45 Octet System Data Acquisition User Guide Release 7 1 page 10 connec
355. in the Template Folder RUNNING A KINETICS EXPERIMENT D IMPORTANT Before starting an experiment ensure that the biosensors are properly rehydrated For details on how to prepare biosensors see the appro priate biosensor product insert Loading the Biosensor Tray and Sample Plate To load the biosensor tray and sample plate 1 Open the Octet instrument door lift the handle up 2 Place the biosensor tray on the biosensor stage left side so that well A1 is located at the upper right corner see Figure 7 49 3 Place the sample plate on the sample stage right side so that well A1 is located at the upper right corner see Figure 7 49 Octet System Data Acquisition User Guide Release 7 1 Running a Kinetics Experiment page 261 Well A1 Position Biosensor tray Sample plate Figure 7 49 Biosensor Stage left and Sample Stage right T IMPORTANT Make sure that the bottom of the sample plate and biosensor tray are flat on the stages 4 Close the Octet instrument door 5 Allow the plate to equilibrate The time required for temperature equilibration depends on the temperature that your application requires and the initial temperature of the sample plate For specific biosen sor rehydration times see the appropriate biosensor product insert Starting the Experiment To start the experiment 1 Click the Run Experiment tab or click the arrow to access the Run Experiment window see Figure 7 5
356. inetics 384 297 kinetics 96 233 quantitation 384 163 quantitation 96 88 importing quantitation 384 164 quantitation 96 89 Plate Definition window Designate Unknown Wells figure 78 153 Designating Standards figure 74 149 Export button figure 233 234 Import button figure 234 Octet System Data Acquisition User Guide Release 7 1 page 24 kinetics experiments 282 selecting concentration units figure 222 285 molar concentration units figure 222 285 plate definitions importing kinetics 384 298 kinetics 96 234 plate name barcode file prefix 264 328 Plate Name Barcode setting Run Experiment window settings quantitation 384 196 quantitation 96 119 plate temperature range 43 plate temperature setting 43 Port 2002 default server settings 54 Positive control 218 Positive Control well type kinetics 384 280 quantitation 384 145 quantitation 96 71 post condition biosensors 12 Post condition sensors parameter 134 211 Advanced Quantitation quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 Pre condition sensors parameter Advanced Quantitation 136 213 quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration 134 211 Precondition sensors parameter Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 preparing biosensors 68 preparing samples for quantitation or kinetic
357. ing 120 197 265 329 Open runtime charts automatically check box 267 Octet System Data Acquisition User Guide Release 7 1 page 23 Open runtime charts automatically option 326 Open Windows menu 37 opening dialog box to select an experiment method file 33 Edit Assay Parameters dialog box 35 Experiment Wizard 35 online Data Acquisition User Guide 38 Runtime Binding Chart 268 332 quantitation 384 200 quantitation 96 123 Sensor Types dialog box 35 Temperature Setting dialog box 35 web browser 38 optics Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 Options dialog box displayed figure 41 setting FRD file format to the earlier 5 0 for mat 34 significant digits 34 viewing analysis options 41 Options dialog box figure 41 Options dialog box Automation Interface selection figure 347 Options menu 34 orbital flow capacity Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 20 27 organizing windows in a cascade arrangement 37 P panel Octet instrument removing 343 parameter settings assay modifying quantitation 384 167 quantitation 96 91 parameter values editing quantitation 384 208 quantitation 96 131 partial biosensor trays using 256 kinetics 384 320 password reminder user and administrator figure 57 plate definition exporting kinetics 384 297 kinetics 96 233 quanti
358. ing Chart 331 Opening the Runtime Binding Chart 332 Viewing Reference Subtracted Data 332 Viewing Inverted Data 334 Aligning Data by a Selected Step 334 Extending or Skipping an Assay Step335 Magnifying the Runtime Binding Chart 335 Scaling a Runtime Binding Chart 335 Adding a Runtime Binding Chart Title336 Selecting a Runtime Binding Chart Legend 336 Viewing Multiple Runtime Binding Charts 336 Exporting or Printing the Runtime Binding Managing Experiment Method Files 338 Octet System Data Acquisition User Guide Release 7 1 page 6 Chapter 9 Maintenance eeeeeeee 339 Octet RED96 and Octet QK Systems 340 Cleaning the Octet Instrument 340 Emptying the Waste Container 340 Replacing Fuses Octet RED96 and Octet QK Systems Only 00ceeeees 341 Octet RED384 and Octet QK384 Systems342 Cleaning the Octet Instrument 342 Cleaning the Biosensor Pickup Tips 343 Replacing FUSCS 0cceeeeues 343 Appendix A Using Octet384 Systems with an Automation Interface 345 OVEIVICW 0 eee cece ence eee e eee ses 346 Design of the Automation Interface 346 Automation Interface Control Setup 346 Automation Client Example Application 348 Automation Commands 349 Typical Automation Session 351 Advanced Automation Session 353 Automation API H 0e econ 356 Analysis Automation API 361
359. ing analysis Unknown Contains an analyte of unknown concentration The concentration of the analyte is calculated from the well data and the standard curve O como A control sample either positive or negative of known analyte com position Data from the well is not used to generate a standard curve during analysis e Positive Control A control sample that contains analyte of known concentration Negative Control A control sample known not to contain analyte Provides a baseline signal which serves as a reference signal for Unknowns Controls and Standards The reference signal can be subtracted during data acquisition in the Runtime Binding Chart and during data analysis Not used during the experiment Reserved Used by the system during Basic Quantitation with Regeneration experiments and Advanced Quantitation multi step experiments for Regeneration R Neutralization N or Detection D Reserved wells are not available for use as Standards Unknowns Controls or References Octet System Data Acquisition User Guide Release 7 1 page 146 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Reserved Wells In a Basic Quantitation with Regeneration or an Advanced Quantitation experiment the Sample Plate Map includes gray wells These wells are reserved by the system and specify the location of particular sample types The default location of the reserved wells depends on the sampl
360. ing by 40 The average of 40 data frames is reported as one data point One data point is reported every 3 3 seconds Standard kinetics 0 6 Hz averaging by 5 The average of 5 data frames is reported as one data point One data point is reported every 1 6 seconds Sensor off set Recommended sensor offset Large molecule kinetics 4 mm mm Default Sets the acquisition speed and sensor offset at the default settings The following General Settings are available on the Run Experiment Tab Table 8 10 General Settings Item Description Machine name The computer name that controls the Octet instrument and acquires the data User name The user logon name Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 331 Table 8 10 General Settings Continued Item Description Description A user specified description of the assay or assay purpose The description is saved with the method file fmf Stopping an Experiment To stop an experiment in progress click x or click Experiment gt Stop The experiment is aborted The data for the active biosensor is lost the biosensor is ejected into the waste tray and the event is recorded in the experimental log NOTE After the experiment is run the software automatically saves the exper iment method fmf MANAGING THE RUNTIME BINDING CHART If the Open runtime charts automatically check box is select
361. ingle analyte experiments quantitation 384 173 quantitation 96 96 biosensors to samples 249 quantitation 384 173 quantitation 96 96 dilution factor to selected wells quantitation 384 154 quantitation 96 79 Octet System Data Acquisition User Guide Release 7 1 page 5 dilution factor to unknowns quantitation 384 153 quantitation 96 78 heterogeneous biosensor trays quantitation 96 101 heterogenous biosensor trays quantitation 384 178 homogenous biosensor trays quantitation 384 183 quantitation 96 106 molecular weight kinetics 96 221 molecular weight and molar concentration kinetics 283 privileges 385 Replicate Groups in the Sample Plate Map kinetics 384 290 kinetics 96 227 quantitation 384 159 quantitation 96 84 Replicate Groups in the Sample Plate Table kinetics 384 293 kinetics 96 229 quantitation 384 162 quantitation 96 87 sample concentrations by value kinetics 96 figure 223 sample concentrations using dilution series kinetics 384 286 kinetics 96 223 kinetics 96 figure 224 serial dilution to selected wells quantitation 384 154 quantitation 96 79 serial dilution to unknowns quantitation 384 153 quantitation 96 78 standard concentration quantitation 384 figure 151 quantitation 96 figure 76 standard concentrations using a dilution series quantitation 384 149 quantitation 96 74 step types in the sample plate figure 242 307 user group 385 user specified concentr
362. ings Octet QK384 Kinetics 330 Octet QK384 Quantitation 198 Octet QKe 121 Octet RED 121 Activation well type 218 kinetics 384 281 activation steps 237 303 active biosensor column 122 199 267 331 Active Channels threshold parameter 239 304 active method file closing 33 active steps extending duration 270 335 Add Sensor dialog box figure 49 Adding 49 adding biosensor type 49 replicate assay to a plate 247 312 Replicate Groups from the Sample Plate Map kinetics 384 291 kinetics 96 228 quantitation 384 figure 160 quantitation 96 figure 85 Runtime Binding Chart title 271 336 quantitation 384 203 quantitation 96 126 Octet System Data Acquisition User Guide Release 7 1 page 2 sample annotations from the Sample Plate Map kinetics 96 figure 225 adjacent steps selecting 243 308 administrator account setting up 374 administrator constants listed table 393 administrator password changing 387 administrator user session starting 378 administrator username selection figure 379 Advanced Quantitation shortcut menu option 166 Advanced Quantitation assay parameters 94 135 171 212 2nd Buffer Time and Shake speed 136 213 Buffer Time and Shake speed 135 212 Detection Time and Shake speed 136 213 Enzyme Time and Shake speed 136 213 Offline 136 213 Pre condition sensors 136 213 quantitation 384 2nd Time and Shake Speed param eter 172 Buffer Time and S
363. ings or enter new settings See Run Experiment Window Set tings on page 264 for more information on experimental settings NOTE If you delay the experiment start you have the option to shake the plate until the experiment starts 3 To start the experiment click If you specified a delayed experiment start a message box displays the remaining time until the experiment starts If you select the Open runtime charts automatically option the Runtime Binding Chart window displays the binding data in real time as well as the experiment prog ress Figure 7 51 NOTE For more details about the Runtime Binding Chart see Managing the Runtime Binding Chart on page 267 Octet System Data Acquisition User Guide Release 7 1 Running a Kinetics Experiment page 263 L x C Users Owner Documents Contracting Forte Bio User_Guides Data and methods Kinetics 96 data hIgG Prod Kinetics Kinetics Runtime Binding Chart Seon x Current Binding Charts Sensors to Chart Plate Status Plate Legend Sensor Tray Sample Piste Kinetics Assay 2 F 1234567 8 9 101112 y 5 67 8 9101112 Selected Kinetics Assay 3 AEE A O Processing B B Processed c c O Reserved D D DataEror z g Si Fail F F O Sensor Fail G G z H H Subtract reference sensors Assay Step Status Experiment Progress Step 17 of17 Step details Assay 3 of 3 Elapsedtime Total exp time nt St 10s 10s ba Eoulibraon 52
364. io 6 Click Install The installation wizard takes a few seconds to install Figure B 9 i Data Analysis 7 0 Setup Lo Installing e Please wait while Data Analysis 7 0 is being installed vo Execute msiexec f Program Fies ForteBio 7DataAnalysis7_0_0_29 Prerequisites VC90 Output folder C Program Files ForteBio 7 DataAnalysis7_0_0_29 Prerequisites Extract WindowsInstaller KB893803 v2 x86 exe Extract VC9O0Runtime msi Extract NetFx20SP2_x86 exe 100 MSI 5 0 already installed NET Framework 2 0 SP2 already installed Execute msiexec i C Program Files ForteBio 7 DataAnalysis7_0_0_29 Prerequisi ForteBio Inc www Fortebio com lt Back Next gt Cancel Figure B 9 Installation Progress Octet System Data Acquisition User Guide Release 7 1 Installing the ForteBio GxP Server Module page 371 The installation wizard displays the Completing the Data Analysis 7 0 Setup Wizard dia log box Figure B 10 i Data Analysis 7 0 Setup Lo Completing the Data Analysis 7 0 Setup Wizard Data Analysis 7 0 has been installed on your computer Click Finish to dose this wizard Figure B 10 Completing the Data Analysis 7 0 Setup 7 Click Finish to complete the installation INSTALLING THE FORTEBIO GXP SERVER MODULE The ForteBio GxP Server module can be installed and run from the following locations Alocal host computer where the
365. ion user option 43 Single Analyte assay parameter quantitation 384 208 quantitation 96 131 single analyte experiment assigning biosensors quantitation 384 173 quantitation 96 96 Single Analyte parameter Advanced Quantitation quantitation 384 171 quantitation 96 94 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 133 quantitation 384 169 quantitation 96 92 Skip Step menu 35 specifying number of significant digits for the values of Molecular Weight Concentration and Dilution used during data analysis 42 Standard well type quantitation 384 145 quantitation 96 71 Standard button 73 148 standard concentration entering quantitation 384 151 quantitation 96 76 standard type of well 71 145 standards designating quantitation 384 148 quantitation 96 73 Start After setting kinetics 384 329 kinetics 96 265 quantitation 384 197 quantitation 96 120 starting administrator user session 378 an experiment 261 325 quantitation 384 194 quantitation 96 117 basic kinetics experiment 384 277 96 217 experiment from the Experiment wizard 141 kinetics experiment with the Experiment wizard figure Octet RED384 278 Octet System Data Acquisition User Guide Release 7 1 page 34 new assay 244 309 Octet System Data Acquisition software 30 quantitation experiment 69 141 user session 56 starting concentration value 76 151 222 285 startup temperature user option 42
366. ion 96 132 Multiple Analyte experiments assigning biosensors quantitation 384 177 quantitation 96 99 used with Replicate Groups quantitation 384 163 quantitation 96 88 Multiple Analyte parameter Advanced Quantitation quantitation 384 171 quantitation 96 94 133 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 multiple runtime binding charts 12 N Negative Control well type kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 Neutralization reserved well requirements quantitation 384 146 quantitation 96 72 Neutralization Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Neutralization Time and Shake speed parameter 134 211 Neutralization Time s and Shake speed 136 213 New Experiment Wizard menu 217 277 New Experiment Wizard menu 35 new features Octet System Data Acquisition software 12 New Group dialog box figure 389 New Kinetics Experiment menu 217 277 New Quantitation Experiment 69 141 New Window menu 37 non adjacent steps selecting 243 308 O Octet instrument cleaning 340 342 resetting 36 Octet instrument labels 13 Octet instrument power supply back panel 341 344 Octet instrument to computer connecting 30 Octet instrument side panel removed 343 Octet System Data Acquisition User Guide Rele
367. ion Time quantitation 384 209 quantitation 96 132 Single Analyte quantitation 384 208 quantitation 96 131 Assay Parameters Advanced Quantitation Standard Assay figure 94 135 171 212 Assay Parameters Basic Quantitation Assay figure 92 131 169 208 Assay Parameters Basic Quantitation with Regeneration figure 93 133 170 210 Assay Settings box 91 Assay Step Definition dialog box 303 assay step name changing figure 247 311 assay steps adding 243 308 copying 243 308 inserting 245 310 removing 247 311 reordering 247 311 assay times updating figure 242 307 Assay Type setting Run Experiment window settings kinetics 384 328 kinetics 96 264 quantitation 384 196 quantitation 96 119 assays adding steps 245 310 adding to sample plates 248 313 assigning biosensors to samples 249 313 automatic addition of sensor tray maps 256 320 building 241 changing biosensor locations 252 257 changing biosensor type 320 copying steps between 243 308 editing 246 311 example using one partial biosensor try and biosensors from a second tray quantitation 384 190 quantitation 96 113 removing steps 247 311 reordering steps 247 311 replicating steps 244 309 starting new 244 309 assigning account details 385 biosensors in Multiple Analyte experiments quantitation 384 177 quantitation 96 99 biosensors in single analyte experiments quantitation 384 173 quantitation 96 96 biosenso
368. ion can be useful in developing the automation cli ent on the same computer that runs the Octet System Data Acquisition soft ware NOTE ForteBio recommends that the Data File repositories be set using shared folders addressed by UNC folder names so that the internal path used by the Data Acquisition application corresponds to the external path used to access retrieve the data files recorded during the experiment Alternatively the path returned by the GetRunInfo command to access the data files from another computer on the LAN Octet System Data Acquisition User Guide Release 7 1 page 348 Chapter A Using Octet384 Systems with an Automation Interface Automation Client Example Application The Automation Client example application can connect to the Octet System Data Acqui sition software via serial port RS 232 port or TCP IP socket To connect the Automation Client example application 1 In the Octet System Data Acquisition software go to File gt Options see Figure A 1 2 Inthe Automation box select the communication port to be used either TCP IP or RS232 see Figure A 1 3 Launch AutomationClient exe located in the C Program Files ForteBio DataAcquisi tion directory to display the Automation Client dialog box Figure A 2 r D Automation Client S Application TCP IP Data Acquisition Machine Port 20000 e Data Analysis O Sidekick RS232 Testing
369. iosensor Assignment Using Heterogeneous Biosensor Trays The default Tray Format is Heterogeneous Heterogeneous biosensor trays contain a mix ture of biosensor types NOTE When using this Heterogeneous option the order of biosensor types in each tray must be identical 1 If Heterogeneous Trays is not displayed next to the Tray Format button click the but ton The Tray Format dialog box displays see Figure 5 35 2 Select Heterogeneous and click OK Octet System Data Acquisition User Guide Release 7 1 page 102 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Tray Format ES Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical C Homogeneous A different sensor tray is used for each sensor type Sensors SAUSAGE Add Remove Change Move Up Move Down Figure 5 35 Tray Format Dialog Box The Tray 1 Sensor Tray Map will be displayed by default 3 Select all columns with default biosensor assignments in the Sensor Tray Map right click and select the first biosensor type to be used see Figure 5 36 The Sensor Type column will update accordingly Sensor Tray Sensor Tray v Replace sensors in tray after use ial of 2 Well Sensor Type auto assign Anti Human IgG Fc Anti Mouse IgG Fv Protein A Protein G Protein L SA Streptavidin Residual Protein A Anti Penta HIS Custom
370. isplay reference subtracted data during acquisition in the chart by clicking the Subtract reference sensors check box in the chart window To view raw data remove the check mark next to this option Reference biosensors can be designated e During experiment setup in the Sensor Assignment tab e During acquisition in the Runtime Binding Chart Sensors to Chart box e During analysis in the Data Selection tab Designating a Reference Biosensor During Acquisition To designate a reference biosensor during acquisition 1 In the Sensors to Chart list or the Sensor Tray right click a biosensor and select Refer ence see Figure 6 61 Current Binding Charts Sensors to Chart Sample Column 1 SelectAll ald ape Sensor at Sensor A2 Sample Column 9 Is BI lis D Sample Column 13 ensor ensor Sensor C1 BsSensor c2 Sancor N Sensor Ej Site Sensor F1 Sensor F2 sensor G1 iSensor G2 sensor H1 Sensor H2 Subtract reference sensors Figure 6 61 Designating a Reference Biosensor in the Runtime Binding Chart The selected biosensor will be shown with an R in the Sensors to Chart list and Sensor Tray see Figure 6 64 2 Click the Subtract reference sensors check box see Figure 6 64 Current Binding Charts Sensors to Chart Plate Status Sample Column 1 SelectAll Sensor Tray lle at i Sensor Al Sensor A2 A SS 8 10 11 12 Sample Column 13 Sensor s1 Sensor B2 B Sensor cl sensor c2 Sensor D1 R Sens
371. istory Bookmarks Tools Help Qs CS 4 EY http betat eoso EF ForteBio DataAcquisition Ea Octet Data Acquisition BETA1 page refresh 10s Quantitation Remote Monitoring Quant Running Log File _ a 57 Step 1 of 1 aaa 57 4 o o Stop the experiment Kinetics Data Repository Quantitation Data Repository ForteBio DataAcquisition Mozilla Firefox File Edit View History Bookmarks Tools Help CTF X A EH http beta1 8080 Octet Data Acquisition BETA1 page refresh 10s Kinetics 05 17 2011 RMK Running Log File _ aay 68 Assay 1 of 1 n 68 Step 6 of 6 jez 26 4 4 0 1 Stop the experiment Skip to the next step Kinetics Data Repository Quantitation Data Repository Figure 3 19 View of Quantitation Experiment top and Kinetics Experiment bottom via Web Browser In the browser window you can e Click the experiment name to view experiment details e Click Log File to display a log of current instrument activity e Click Kinetics Data Repository or Quantitation Data Repository to open and view previously run experiments Octet System Data Acquisition User Guide Release 7 1 page 48 Chapter 3 Getting Started MANAGING BIOSENSOR TYPES The Octet System Data Acquisition software includes a factory set list of the types of bio sensors available for quantitation or kine
372. itation 384 201 quantitation 96 123 Refresh settings 45 Regeneration reserved well requirements quantitation 384 146 quantitation 96 72 Regeneration well type kinetics 384 281 kinetics 96 218 Regeneration Cycles parameter Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 Regeneration cycles parameter Advanced Quantitation 137 214 quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration 134 211 Regeneration Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Regeneration Time and Shake speed parameter 133 136 210 213 remote view of experiment via web browser figure 47 Octet System Data Acquisition User Guide Release 7 1 page 27 removing assay from the quantitation application 35 assay steps 247 311 biosensor type 49 side panel of Octet instrument 343 step alignment of data 270 334 well designation 282 well designations controls or reference wells 81 157 quantitation 384 149 153 quantitation 96 74 78 reagent plates quantitation 384 167 reordering assay steps 247 311 Replace sensors in tray after use check box 176 replacing biosensors in the biosensor tray 251 315 fuses for Octet RED instrument 341 for QKe instrument 341 replicate assay steps 244 309 replicate assay adding to a plate 247 312 R
373. ition Window Importing a Plate Definition To import a plate definition 1 Inthe Sample Plate Table see Figure 6 26 click Import Sample Plate Table Concentration units pg ml v Export Import Well Sample ID Replicate Group Type Conc ig ml Dilution Factor Information a OA hgG 1 Standard 200 n a human IgG OCI hgG 2 Standard 100 n a human IgG OEI hgG 3 Standard 50 n a human IgG OGI higG 4 Standard 25 n a human IgG on higG 5 Standard 10 n a human IgG OKI hgG 6 Standard 5 n a human IqG Figure 6 26 Import Button in Sample Plate Table 2 Inthe Import Plate Definition window see Figure 6 28 select the plate definition csv and click Open Octet System Data Acquisition User Guide Release 7 1 e e Working with a Reagent Plate page 165 r EF Import Plate Definition Ol ke Forte Bio Search Data and met P Organize New folder z Of 0 a Favorites a Documents library T Folder E Desktop Data and methods Se Downloads Name Date modified Type Recent Places a 384 standard plate csv 4 22 2011 6 41PM __ Microsoft Excel C E Desktop t Libraries Documents J My Documents J Public Documents Music 5 Pictures a Videos ul m r File name 384 standard plate csv v CSV Files csv z L Figure 6 27 Import Plate Definition Window gt NOTE You can also create a csv file for import Figure 6 28 shows the appro priate
374. ition during the detection step in sec Shake speed rpm onds in an advanced quantitation assay NOTE A subset of data points may be selected for processing during data analysis Offline Choose this option to incubate sample with biosensors outside the Octet system Offline incubation is best performed on the ForteBio Sidekick biosensor immobilization station Reuse Buffer Allows buffer wells to be reused If unselected the number of buf fer columns must equal the number of sample columns If selected the number of buffer columns may be less than the number of sample columns as the buffer columns are reused Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incubated in regeneration buffer to speed rpm remove bound analyte Neutralization The duration time and shaking speed of the neutralization step Time s and Shake where the biosensor is incubated in neutralization buffer after the speed rpm regeneration step Octet System Data Acquisition User Guide Release 7 1 page 96 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 8 Advanced Quantitation Assay Parameters Continued Parameter Description Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For
375. ity annotation text may be displayed as the legend of the Runtime Binding Chart during data acquisition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend 10 Optional After an assay is completed the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container To return the biosensors to the tray click the Replace sensors in tray after use check box see Figure 5 46 Sensor Tray v Replace sensors in tray after use HOOeoeeoo Legend Unassigned sensors 683 Missing sensors Remove Fill Fill Plate Figure 5 46 Replace Sensors in Tray After Use Check Box NOTE Biosensors can be regenerated up to a max of 11 times per experiment Biosensor Regeneration For Basic Quantitation with Regeneration experiments only the Sensor Assignment tab includes the Regenerations parameter which specifies the maximum number of regenera tion cycles for each column of biosensors The specified number of regeneration cycles determines the minimum number of cycles required for each column of sensors This calcu lation may result in non equal regeneration cycles for columns of biosensors The fractional use of the regeneration and neutralization wells by each column of sensors is represented by a pie chart Figure 5
376. l Sample ID Replicate Group Type Conc ug ml Dilution Factor Information Time s Shake speed Quantitation 120 200 if al Assay Parameters m x Sample Plate Abbe Assays Assay Parameters Sample Plate 96 wells BF Bas guaniin wah Regencalion Single analyte Multiple analyte E High sensitivity assay with regeneration on erica creer J F 1i 2 3 4 5 6 7 8 91 E Protein L Standard range ADOOOOOOOOq m Quantitation 120 a 400 B O O O O O O O O O q Regeneration 5 2 400 es cOOCOOOOOO Newelteton 5O O m DOOQCOOOOOOKd Mire cordon coon EA e EOOOOQOQOQOQ0Q00q ae FOOQO00O0007 GOOO HOOOOOQOOOQOOQOQO O Standard Contor O Unassig O Unknown e Reference Reserva Biueindicates a built in assay E Figure 5 26 Modifying Assay Parameters Octet System Data Acquisition User Guide Release 7 1 page 92 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Basic Quantitation Assay Parameters y Assay Parameters Available Assays Assay Parameters amp Basic Quantitation Single analyte Multiple analyte IE Anti Penta HIS High sensitivity Replicates per sensortype 1 E Anti Penta HIS Standard range E High sensitivity Human IgG quantitation 2 Human IgG Quantitation IE Immunogenicity Direct detection 2 Murine IgG Quantitation E Protein L Standard range Bj Standard Assay
377. l Culture screen 2011 02 BESSE e EEE Machine JRICHARDS Machine JRICHARDS JRICHARDS 2011 02 14 13 42 07 Antigen Antibody screen JRICHARDS 2011 02 14 13 42 45 Antigen Antibody screen JRICHARDS Figure 4 20 Selecting a Project in the Audit Trail Action User login User login User logout User login Description drop down lists NOTE Selections can be made in either one or both of the Project or Machine Octet System Data Acquisition User Guide Release 7 1 page 64 Chapter 4 21 cFR Part 11 Compliance The list with then only display events for the entries selected i Audit Trail b El ee Project Receptor Ligand screen nA Machine JRICHARDS n Mi Date Time Project Machine Action Description 2011 02 13 20 39 33 Receptor Ligand screen JRICHARDS User login 2011 02 13 20 39 37 Receptor Ligand screen JRICHARDS User logout Figure 4 21 Project Based Audit Trail Events In addition to the specific project and machine selections the following list options are also available e any Displays all project and or machine events for the user account none Displays all project or machine events not associated with a specific project Project list only Changing Projects During a User Session During an active session users can switch to another project in the Data Acquisition or Data Analysis software without having to log out
378. l to display a shortcut menu of editing commands see Figure 7 27 left NOTE Keyboard commands can also be used Ctrl x cut Ctrl c copy Ctrl v paste Ctrl z undo 2 Click the cell in the step s Type column then select another name from the drop down list see Figure 7 27 right Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 241 Step Data List Step Data List Ada Copy _ l Remove l Threshold Params Add l Copy l Remove l Threshold Params _ Name Time Shake speed Type Threshold Name Time Shake speed Type Threshold Equilibration 10 1000 F Custom m Equilibration 10 1000 Association Oo ProA Immobilization 120 1200 IZ Loading im ProA Immobilization 120 1200 piesodeten Go gt Baseline L Raceline i Baseline 600 1200 H E r Association 300 Undo Association 300 1000 K Activation D Dissociation 600 Cut Dissociation 600 1000 K Quenching m Regeneration 900 n Regeneration 300 1000 Custom D Neutralization 10 Copy Neutralization 10 1000 gor m Equilibration2 10 Paste Equilibration2 10 1000 3 Custom o Assay Steps List Delete Move Up Select All Assay Sample Step Nam Right to left Reading order Show Unicode control characters Insert Unicode control character Open IME Reconversion Figure 7 27 Editing a Step Value left or Step Type right Building an Assay After creating the different step types that the assay will u
379. ld criteria for the assay step Select an option for terminating the step e The threshold is achieved on ALL channels e The threshold is achieved on ANY ONE channel Signal Change The threshold is a user specified amount of ascending or descend ing signal change nm Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 305 Table 8 4 Threshold Parameters Continued Item Description Gradient The threshold is a binding gradient nm min for a user specified time min Filtering The amount of data seconds to average when computing the sig nal change or gradient threshold 4 Click OK to save the newly defined step The new step type appears in the Step Data List 5 Repeat the previous steps for each step type to create until all the desired steps are added see Figure 8 31 Step Data List Copy Remove Threshold Params Name Time Shake speed Type Threshold equilibration 120 1000 32 Custom 0O Loading 300 1000 L Loading Iv Baseline 300 1000 bk Baseline r Association 300 1000 Association Tr Dissociation 600 1000 K Dissociation E Regeneration 20 1000 3 Custom O Neutralization 20 1000 3 Custom E Figure 8 31 Step Data List Displaying Step Types 6 To delete a step type from the list click the corresponding row in the Step Data List and click Remove or press the Delete key Copying and Editing Step Types To define a step type by copying an existing
380. le Calumn 3 A Processing Sample Column 4 B Sample Column Processed Semple Column 6 Sensor D3 4 O Reserved Sample Column 7 Sensor E3 Semple Column 8 bow 3 E Wee Bencorca F Sensor Fail sensor H3 61 O00000 cates Subtract reference sensors H Experiment Progress Step 8 of 8 120s 120s Elapsed exp time 0 21 55 Total experimenttime 0 21 55 Flip Data 40 36 3 0 E2 E B 52 S ja 1 1 0 05 00 0 10 20 30 40 50 60 70 80 90 100 110 120 Time sec Sensor A4 Sensor B4 Sensor C4 Figure 5 55 Runtime Binding Chart Window Opening a Runtime Binding Chart After an experiment is run you can open and review the Runtime Binding Chart at any time 1 Click File gt Open Experiment 2 Inthe dialog box that appears select an experiment folder and click Select Viewing Reference Subtracted Data If the experiment includes reference biosensors you can display reference subtracted data during acquisition in the chart by clicking the Subtract reference sensors check box in the chart window To view raw data remove the check mark next to this option Reference biosensors can be designated e During experiment setup in the Sensor Assignment tab e During acquisition in the Runtime Binding Chart Sensors to Chart box e During analysis in the Data Selection tab Octet System Data Acquisition User Guide Release 7 1 page 124 Chapter 5 Quantitation Experiments Octet RED96 QK and QK
381. lease 7 1 Selecting a Server Location page 53 To select a server location 1 Launch the Data Acquisition or Data Analysis software by double clicking on the desk top icon ee Data Data Analysis Acquisition 7 0 CFR11 7 0 CFR11 Figure 4 1 Login Box The Login dialog box will display a as fort sio Server User Password Project none Figure 4 2 Login Dialog Box 2 Selecta Server location by clicking on Browse The Authentication Server dialog box will display Octet System Data Acquisition User Guide Release 7 1 page 54 Chapter 4 21 CFR Part 11 Compliance ro Connection to server Server address localhost v Localhost 20002 Figure 4 3 Authentication Server Dialog Box Click Default to recall the default server settings of localhost and Port 2002 e Localhost lf the local computer is to be used as the GxP Server module host select the Localhost check box Change the Port number if needed Remote host on same subnet lf the GxP Server module is hosted on the same subnet deselect the Localhost check box and click Find A list of potential GxP Server module addresses will be listed Choose the desired location from the list and click OK Choose Server Address s More than one server was found Please choose one 192 168 1 78 JRICHARDS 192 168 1 78 JRICHARDS Figure
382. lease 7 1 page 272 Chapter 7 Kinetics Experiments Octet RED96 QK and QK z Runtime Graph Properties Es Title Subtitle Legend Sensor Location Sensor Information Sample ID Concentration Dilution Figure 7 59 Selecting a Runtime Binding Chart Legend NOTE Text for Sample ID Sensor Information or Concentration Dilution is taken from the Plate Definition and Sensor Assignment tabs and must be entered before the experiment is started 3 Click OK Viewing Multiple Runtime Binding Charts To view multiple Runtime Binding Charts click Window gt New Window Exporting or Printing the Runtime Binding Chart To export the Runtime Binding Chart as a graphic or data file 1 Right click the chart and select Export Data 2 Inthe Exporting dialog box see Figure 7 60 select the export options and click Export Octet System Data Acquisition User Guide Release 7 1 Managing the Runtime Binding Chart page 273 E Exporting Export EMF O WmMF Export Destination ClipBoard OFile Printer Export Size Width 152400 Bmp uPG Browse Millimeters Inches 101 600 Large Font Figure 7 60 Exporting Dialog Box OPNG Points Millimeters Table 7 9 Runtime Binding Chart Export Options Text Data Export Task Export Option Export Result Destination Text EMF WMF Data BMP
383. lick Save to accept the new parameter values The new assay is added to the system NOTE Not all parameters are available for all of the assays Basic Quantitation Assay Parameters E x Edit Assay Parameters Available Assays Assay Parameters E Basic Quantitation Name My Basic Quant Assay oN E Anti Penta HIS High sensitivity 2 Anti Penta HIS Standard range E High sensitivity Human IgG quantitation Single analyte Multiple analyte Human IgG Quantitation Pe Immunogenicity Direct detection Murine IgG Quantitation Protein L Standard range Standard Assay mG o oge amp Basic Quantitation with Regeneration Quantitation 120 400 Z High sensitivity assay with regeneration i E Protein L Standard range E Standard Assay 2 My Basic Quant with Regen Assay amp Advanced Quantitation B B E Description Enter a short description of the assay here plicates per sensor type f1 E Immunogencity Enzyme Linked Residual Protein A Standard Assay Three Step Assay Blue indicates a ForteBio built in assay and cannot be modified or deleted Duplicate Remove Cancel L d Figure 6 68 Assay Parameters Basic Quantitation Assay Table 6 16 Basic Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Octet System
384. lick in a cell in the Information column to enter biosensor informa tion for a particular cell NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE For greater clarity annotation text may be displayed as the legend of the Runtime Binding Chart during data acquisition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend Octet System Data Acquisition User Guide Release 7 1 page 106 Chapter 5 Quantitation Experiments Octet RED96 QK and QK 10 Optional After an assay is completed the biosensors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate waste container To return the biosensors to the tray click the Replace sensors in tray after use check box see Figure 5 40 Sensor Tray M Replace sensors in tray after use HII SS Legend Unassigned sensors RRA Missing sensors geno a Figure 5 40 Replace Sensors in Tray After Use Check Box NOTE Biosensors can be regenerated up to a max of 11 times per experiment Biosensor Assignment Using Homogeneous Trays H
385. location A2 14 47 53 Processing sample location A2 LJ T gt v Auto scroll to bottom Figure 7 52 Instrument Status Log Octet System Data Acquisition User Guide Release 7 1 page 264 Chapter 7 Kinetics Experiments Octet RED96 QK and QK WARNING Do not open the Octet instrument door when an experiment is in progress If the door is opened the data from the active biosensors is lost The data already acquired is saved however the assay is aborted and cannot be restarted without ejecting the biosensors and starting from the beginning Run Experiment Window Settings The following Data File Location and Name settings are available on the Run Experiment Tab Table 7 6 Data File Location and Name Item Description Assay type The name of the selected assay Kinetics data The location where the subdirectory will be created The subdirectory repository contains the data frd files Click Browse to select another data loca tion NOTE It is recommended that you save the data to the local machine first then transfer to a network drive Experiment Specifies a subdirectory name for the data files frd The software Run Name generates one data file for each biosensor that includes the data from sub directory all steps the biosensor performs Plate name A user defined field where you can enter text or a barcode barcode barcode fil
386. lows administrators to view all the user system and software event infor mation recorded by the GxP Server module Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 395 C a ForteBio GxP Server Admininstration users Groups Projects Constants User Project Machine any z Date Time Login Name Project Machine Type Info a 2011 02 13 14 36 13 Administrator JRICHARDS User changed PSmith 2011 02 13 14 36 52 Administrator JRICHARDS User added JBlack 2011 02 13 14 36 52 Administrator JRICHARDS User changed JBlack 2011 02 13 14 37 50 Administrator JRICHARDS User added RBrown 2011 02 13 14 37 50 Administrator JRICHARDS User changed RBrown 2011 02 13 14 38 59 Administrator JRICHARDS User added GMoreno 2011 02 13 14 38 59 Administrator JRICHARDS User changed GMoreno 2011 02 13 14 45 12 Administrator JRICHARDS User changed GMoreno 2011 02 13 15 21 12 Administrator JRICHARDS User login 2011 02 13 15 24 56 Administrator JRICHARDS User deleted GMoreno 2011 02 13 15 37 38 Administrator JRICHARDS Password changed RBrown 2011 02 13 15 37 55 Administrator JRICHARDS Password changed RBrown 2011 02 13 15 41 32 Administrator JRICHARDS User logout 2011 02 13 15 41 47 JBlack JRICHARDS User login 2011 02 13 15 42 07 JBlack JRICHARDS User logout Figure B 50 Events Tab Events are tracked for individual user accounts projects and machines By default
387. ltiple biosensor types per and Replicates per sample well and the number of replicate assays in each well per sensor type biosensor type SampleTime s and The duration of data acquisition in seconds while the biosensor is Shake speed rpm incubated in sample and the sample platform orbital shaking speed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Buffer Time s and The duration of biosensor incubation in the first buffer in seconds Shake speed rpm and the sample platform orbital shaking speed rotations per minute Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 213 Table 6 18 Advanced Quantitation Assay Parameters Enzyme Time s The duration of biosensor incubation in seconds in the enzyme and Shake speed solution and the sample platform orbital shaking speed rotations rpm per minute 2nd Buffer Time s The duration of biosensor incubation in seconds in the second and Shake speed buffer solution and the sample platform orbital shaking speed rpm rotations per minute Detection Time s amp The duration of data acquisition during the detection step in sec Shake speed rpm onds in an advanced quantitation assay NOTE A subset of data points may be selected for processing during data analysis Offline Choose this option to incubate sample with biosensors outside the Octet system
388. luent G5 Ab4 Unknown n a 2 Sample Diluent Figure 6 23 Add Replicate Group from the Sample Plate Table NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types 3 Repeat the previous steps to assign new samples to the existing Replicate Group or to designate another set of samples to a new Replicate Group Multiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software will only recognize and D calculate statistics for samples that use the same Replicate Group names spacing and capitalization must be identical For example samples assigned to Group 2 and group2 are treated as two groups Octet System Data Acquisition User Guide Release 7 1 Managing Sample Plate Definitions page 163 NOTE When performing a Multiple Analyte experiment if the same Replicate Group name is used with different biosensor types they will be treated as sep arate groups Statistics for these groups will be calculated separately for each biosensor type MANAGIN
389. m Data Acquisition User Guide Release 7 1 page 104 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Pate Definition Sensor Assignment Review Experiment Q Run Experiment In this step sensors are assigned to samples If you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate Sensor Tray Sensor Tray W Replace sensors in tray after use of 3 Heterogeneous trays 10 11 12 Well Sensor Type Lot Number Information Protein A a B1 Protein A C1 Protein A D1 Protein A E1 Protein A F1 Protein A G1 Protein A H1 Protein A E HOCDoCCSoEo B2 Protein A D2 Protein A Legend _ Unassigned sensors RRA Missing sensors Remove Fill Fill Plate Protein G 9 10 11 12 orare Tornale 6000600 06000600 A B Cc ro odee 4 F G Protein G Protein G Protein G Protein G Protein G Potene o Poen O S a roen OO o o en O S en O S en O S en O en O S en O S en t S en O S oen o en O S en O S en o OOOGOGOO OOOOOGOO OOGOOGOO H A5 Protein A BS Protein A Legend Unassigned samples Poten A a Figure 5 38 Biosensor Assignment using Heterogeneous Trays and Two Biosensor Types 6 To view or change the biosensor assignments in another tray click the Sensor
390. man IgG Fc Legend _ Unassigned sensors R3 Missing sensors L p L 7 LI F A2 Anti Human IgG Fc B2 Anti Human IgG Fc C2 Anti Human IgG Fc D2 Anti Human IgG Fc PII TLL E2 Anti Human IgG Fc l F2 Anti Human IgG Fc G2 Anti Human IgG Fc H2 Anti Human IgG Fc Remove Fill Fill Plate A3 Anti Human IgG Fc B3 Anti Human IgG Fc H L L m L Z LI Z Figure 6 53 Example Assay Using One Partial Biosensor Tray and Biosensors from a Second Tray To restore biosensors that have been removed select the columns to restore and click Fill To restore all sensors on the plate click Fill Plate NOTE If multiple biosensor trays are used only the first biosensor tray can be a partial tray During the experiment the software prompts you to insert the appropriate tray in the Octet instrument Octet System Data Acquisition User Guide Release 7 1 Reviewing Experiments page 191 REVIEWING EXPERIMENTS Before running an experiment you can review the sample plate layout and the biosensors assigned to each assay in the experiment In the Review Experiment window move the slider left or right to highlight the biosensors and samples in an assay or click the gt arrows to select an assay Slider Plate Definition sensor Assigfment Review Ex
391. mation interface command 349 GetRunInfo automation interface command 349 GetRunInfo command 347 Gradient threshold parameter 239 305 group administration 388 group settings changing 390 viewing 390 Groups tab figure 388 GxP Server Address search results figure 54 GxP Server Configuration window figure 397 GxP Server module accessing directly 396 restarting 398 H Heat hot symbol 13 Help menu described 38 figure 38 list of menu commands 38 heterogeneous biosensor trays assigning biosensors quantitation 384 178 quantitation 96 101 using kinetics 384 317 kinetics 96 254 hiding main toolbar 34 status bar 34 higher acquisition rate 120 197 329 Homogeneous biosensor trays assigning biosensors quantitation 384 183 quantitation 96 106 icons Data Acquisition 8 Data Analysis 8 Import button 89 Import button figure 234 Import Plate Definition window quantitation 384 164 quantitation 96 89 Import Plate Definition window figure 234 importing plate definitions kinetics 384 298 kinetics 96 234 Octet System Data Acquisition User Guide Release 7 1 page 18 importing plate definition quantitation 384 164 quantitation 96 89 inserting assay steps 245 310 installing Data Acquisition 7 0 CFR Part 11 software 366 Data Analysis 7 0 CFR Part 11 software 369 ForteBio GxP Server 372 ForteBio GxP Server module 371 Instrument menu described 36 figure 36 list of menu commands
392. ment 17 well designations changing kinetics 384 295 kinetics 96 231 defined 144 removing quantitation 384 149 153 quantitation 96 74 78 reagent plates quantitation 384 167 removing controls or reference wells quantitation 384 157 quantitation 96 81 well information tooltip 241 well types Activation kinetics 384 281 kinetics 96 218 Buffer kinetics 384 280 kinetics 96 218 Control kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 designating kinetics 384 282 kinetics 96 219 designating kinetics experiments 282 for kinetics experiments 220 282 Load kinetics 384 281 kinetics 96 218 Negative Control kinetics 384 280 quantitation 384 145 quantitation 96 71 Positive Control kinetics 384 280 quantitation 384 145 quantitation 96 71 Quench kinetics 384 281 kinetics 96 218 Received quantitation 384 145 quantitation 96 71 Reference kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 Regeneration kinetics 384 281 kinetics 96 218 removing designated type 220 Sample kinetics 384 280 Octet System Data Acquisition User Guide Release 7 1 page 39 kinetics 96 218 Standard quantitation 384 145 quantitation 96 71 Unknown quantitation 384 145 quantitation 96 71 Wash kinetics 384 281 kinetics 96 218 well volumes Octet QK384 20 27 Octet RED384 20 27 wells annotating 82 225 288 annotating individual kinetics 384 289 kinetics 96 226
393. ment and Assay Time Updates as Steps Are Added to the Assay Octet System Data Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 243 IMPORTANT If you intend to analyze the data from a sample using the Inter step correction feature in the Octet System Data Acquisition software the assay must use the same well to perform baseline and dissociation for the sample Replicating Steps within an Assay To copy steps and add them to an assay 1 Inthe Assay Steps List select the step s to copy and click Replicate for example in Figure 7 31 step rows 1 4 are selected To select adjacent steps press and hold the Shift key while you click the first and last step in the selection To select non adjacent steps press and hold the Ctrl key while you click the desired steps 2 Inthe Replicate Steps dialog box see Figure 7 31 click the Append to current assay option 3 Click the Offset steps check box and set the options as appropriate For more details on offset options see Table 7 5 Assay Steps List Move Up Mave Down _ Remove m Be fme Assay Sample Step Name Step Type Sensor Type Assay Time 1 Equlibration v 3 Custom SA Streptavidin PIIRTEEN ProA Immobilization A Loading SA Streptavidin a ee MAeosee sanaa E aate Steps Replication Type Add as a new assay Append to current assay E offset steps Sample steps only
394. menu 36 Print menu 33 Print Preview menu 33 print preview window 33 Print Setup dialog box 33 Print Setup menu 33 printing files 33 Runtime Binding Chart 128 205 273 338 prior to running an experiment 258 322 privileges assigning 385 project administration 390 Project drop down list 63 project selection figure 58 project settings changing 391 viewing 391 project based Audit Trail events figure 64 Octet System Data Acquisition User Guide Release 7 1 page 25 projects changing figure 64 deleting 392 editing 391 Projects tab 391 projects changing during a user session 64 properties for Octet System software displaying 38 Q QKe instrument replacing fuses 341 quantitation 384 144 Quantitation Data Repository setting Run Experiment window settings quantitation 384 196 quantitation 96 119 quantitation data repository user option 41 Quantitation Experiment Advanced Quantitation quantitation 384 142 Basic Quantitation 384 141 Basic Quantitation 96 69 Basic Quantitation with Regeneration 69 141 quantitation experiment defined 68 140 starting 69 141 Quantitation Shake Speed assay parameter quantitation 384 209 quantitation 96 132 Quantitation Shake Speed parameter quantitation 384 169 quantitation 96 92 Quantitation Time and Shake speed parameter 133 170 210 Basic Quantitation with Regeneration quantitation 96 93 Quantitation Time assay parameter quantitation 384 209
395. minutes for a plate at ambient 4 C NOTE If the Octet System Data Acquisition software is closed the plate tem perature will reset to the default startup value specified in the Options dialog box when the software is relaunched Defining a New Default Sample Plate Temperature To define a new default temperature that will be used at startup and as the default plate temperature for all experiments 1 From the Main Menu click File gt Options 2 Inthe Options dialog box Figure 3 16 select a new temperature in the Startup box and click OK The plate temperature will then adjust to the new value and this setting will be used as the new default startup temperature whenever the software is launched r Options Data Files Quantitation data repository _C Temp asi Kinetics data repository C Temp F Use old 5 0 file format for FRD files Use extended sample types Startup Simulation Temperature If no instrument is connected the appiication is configured using the properties of the selected instrument eer D Octet QK Octet RED384 Significant digits 4 z Q z Octet RED O Octet QK384 Octet RED96 Octet QKe Figure 3 16 Setting the Default Startup Temperature in the Options Dialog Box 3 Allow sufficient time for the sample plate to equilibrate to the new temperature before beginning an experiment approximately 5 minutes for a plate at room temperature or 15 minutes for a
396. n Waiting r n Busy r n Running nn r n LoadSensors r n Error lt reason gt r n const char AUT CMD PRESENT Present Pegasys only Open the door and move the stage to the presentation position Args none Response OK r n Error lt reason gt r n N B Poll status waiting for Waiting condition to reappear const char AUT CMD RESUME Resume Indicates that the Waiting condition has been resolved new sensor tray installed Continues the experiment Args none Response OK r n Error lt reason gt r n Status will indicate busy until door is closed then will return to Running state const char AUT CMD CLOSE Close Closes the stage if it is open Args none Response Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 361 OK r n Error lt reason gt r n Status will indicate busy until door is closed eonst char AUT_CMD_CLEANUP Cleanup Closes open MDI windows Only valid when not busy Args none Response OK r n Error busy r n endif INC ACQUISITION AUTOMATIONAPI H Analysis Automation API KKK KK KKK KKK KKK KK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KK KKK KKK KK KKKEKKKKKKKKKEKK KK Copyright c 2011 ForteBio All rights reserved KKK KKK KKK KK KKK KKK KKK KKK KKK KK
397. n Temperature 30 E ec If no instrument is connected the application is configured using the properties of the selected instrument Daia opone octet Octet RED384 Significant digits 4 a octetRED Octet QK384 Octet RED96 Octet QkKe Web Server Port soso 10 1 1 193 Refresh s 10 z 192 168 1 78 Automation TCP IP Port 20000 Localhost T Serial RS232 Port cancel L Figure 3 14 Options Dialog Box Table 3 7 User Options Item Description Data Files Quantitation data repository Kinetics data repository The default location where quantitation data files frd are saved Click Browse to select a different folder NOTE ForteBio recommends that the data be saved to the local machine first then transferred to a network drive if needed The default location where kinetics data files frd are saved Click Browse to select a different folder NOTE ForteBio recommends that the data be saved to the local machine first then transferred to a network drive if needed Octet System Data Acquisition User Guide Release 7 1 page 42 Chapter 3 Getting Started Table 3 7 User Options Continued Item Description Use old 5 0 file format for FRD files Select this option to save data in the earlier Octet RED soft ware 5 0 format NOTE Saving data in the old file format produces larger files and may result i
398. n m H Dissociation 600 1000 K Dissociation E gt Regeneration 20 1000 Custom m z Neutralization 600 1000 amp Custom Oo L Ke Assay Steps List o New Assay Move Up Move Down Remove Replicate aon p Assay Sample Plate Step Name Step Type Sensor Type Assay Time A Assayed samples Reagent Plate 384 wells Assayed reagents stetstetetets OO Se 290000000000000 O00000 000000 O Unassigned reagents Regeneration Custom SA Streptavidin 0 00 40 New Assay Step Figure 8 34 Assigning a Step Type to a Column in the Sample Plate 3 Repeat the previous steps to define each step in the assay As each step is added the total Experiment and Assay Time update see Figure 8 35 Assay Steps List wave Up ior Total Experiment Assay Sample Plate Step Name Step Type Sensor Type Assay Time 1 Al 1 equilibration 3 Custom AHC Anti hlgG Fe Capture 1 A5 1 Loading L Loading AHC Anti hlgG Fe Capture 1 Ag 1 Baseline b Baseline AHC Anti hlgG Fc Capture 1 Al3 1 Association KC Association AHC Anti hlgG Fc Capture 1 Ag 1 Dissociation K Dissociation AHC Anti hlgG Fc Capture 1 Al 2 Regeneration 2 Custom AHC Anti hlgG Fe Capture 1 AS 2 Neutralization 4 Custom AHC Anti hlgG Fe Capture 0 29 00 Total Assay Time Figure 8 35 Experiment and Assay Time Updates as Steps Are Added to the Assay Octet System Data Acquisition User Guide Release 7 1 page 308 Chap
399. n slower data analysis Use extended sample types Select this option to extend the sample types available in the right click menu of the Sample Plate Map and Sam ple Plate Table to include negative and positive controls Startup Temperature User defined default startup plate temperature This tem perature is used as the default setting for all experiments NOTE To change the default setting the software must be restarted after entering the new value This changes the startup plate temperature only not the current plate temperature Data Options Significant digits Specifies the number of significant digits for the values of Molecular Weight Concentration and Dilution used during data analysis NOTE Six decimal places are recommended for the Protein A assay Octet System Data Acquisition User Guide Release 7 1 Setting the Plate Temperature page 43 Table 3 7 User Options Continued Item Description Simulation If the workstation is not connected to an instrument this option enables users to create and save an experiment to a method file fmf using the properties of the selected instrument type Web Server Selecting this option enables remote monitoring of the experiment using a web browser See Monitoring Experi ments Remotely on page 45 for more information Automation Allows users to select the appropriate connection for auto mation interfaces
400. n igG Sample 10 150 66 67 G13 human IgG Sample 5 150 33 33 113 human lgG Sample 25 150 16 67 K13 hurnan IgG Sample 1 25 150 8 333 M13 human IgG Sample 0 625 150 4 167 013 1XKinetics Buffer Reference Figure 8 9 Entering Molecular Weight and Molar Concentration from the Plate Table Assigning User Specified Sample Concentrations To assign sample concentrations using a dilution series 1 Inthe Sample Plate Map select the desired wells right click and select Set Well Data The Set Well Data dialog box displays see Figure 8 10 2 Select the By value option and enter the starting concentration value Octet System Data Acquisition User Guide Release 7 1 page 286 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Sample Plate 384 wells Wi23s456789 101112131415 161718192021 222324 SaS Pe POOOOOOO 08O OOOOOOO0O00O 222a aaan OQOQQQQQQQQQQ BOOOGOOOOOOO OOOOOOOOOOOO OOOOOOOO0OOOO OOOQOOOOOOO0O Sample Reference Control Negative Control Positive Control 222a Buffer 07010 ge Activation OGOE Quench MOODOQOOOGOSC toad OO OODOOOOOOO I960505660000 wash g Regeneration Set Well Data EFI IRL O O Q O 600 O000O0 0000 O0O0O0 O Q Q O Unassigned Reagent Plate 96 walls BOOOQOAL Concentration ug ml Sample only v By value
401. n the Group drop down box For more information please see Creating a New User Group on page 389 4 Assign Privileges Each user account can be assigned specific privileges The privileges displayed initially will be those defined in the user group selected in the previous step Privileges for the default user groups are shown in Table B 1 If needed change user account privileges by selecting or deselecting the check boxes next to each privileges e Administration Can administer the user database Review Can review changes and events Change Can change methods and configuration values Plate Can change sample plate properties e Run Can run experiments and analyses Table B 1 Default User Group Privileges Privilege Administrator Supervisor Developer Lab User Guest Administration Y Review V v Change vA V Plate v v Run vV v 5 Options Select the Password does not expire check box if desired This check box is deselected by default Deselecting this option will let user account passwords expire at the set PasswordTTL constant For more information on setting constants please see Administrator Constants on page 392 6 Click OK to save changes and exit Octet System Data Acquisition User Guide Release 7 1 page 386 Chapter B 21 CFR Part 11 Software Administrator Options Viewing and Changing User Account Settings To view and change user account settings 1 Right click on the user a
402. n the Sample Plate Map NOTE Shift clicking in the Sample Plate Map mimics the head of the instru ment during the selection Designating Standards To designate standards 1 In the Sample Plate Map select the wells to define as standards 2 Click the Standard button below the Sample Plate Map see Figure 5 3 or right click and select Standard The standards are marked in the plate map and the Sample Plate Table is updated 3 Select the concentration units for the standards using the Concentration Units drop down list above the Sample Plate Table Octet System Data Acquisition User Guide Release 7 1 page 74 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Concentration Units u Basic Quantitation Experiment Quantitation 96 1 fmf ston x Plate Definition Sensor Assignment Review Experiment Run Experiment oJ In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and right click to efter modify well data Assay Settings Sample Plate Table me Basic Quanttation Concentration units pami x Export impot Ern Well Sample ID Replicate Group Type Conc pg ml Dilution Factor Information Al Time s Shake speed OBI Standard ma Quantitation 120 200 loa Genel aa ion Standard nie 0E Se ion Standard nja
403. n tray after use check box see Figure 7 38 Sensor Tray Replace sensors in tray after use y 1 2 3 4 5 6 a 8 9 10 11 12 Legend Unassigned sensors R Missing sensors Remove Fill Fill Plate Figure 7 38 Replace Sensors in Tray After Use Check Box NOTE Biosensors can be regenerated up to a max of 11 times per experiment Octet System Data Acquisition User Guide Release 7 1 page 252 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Entering Biosensor Information To enter information about a biosensor 1 Optional Double click in any cell in the Lot Number column to enter the biosensor lot number All wells in the Lot Number column for that biosensor type will automatically populate with the lot number entered see Figure 7 39 Optional Double click a cell in the Information table column Enter or edit the biosen sor information as appropriate see Figure 7 39 NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu Well Sensor Type Lot Number Information Al SA Streptavidin 10102020 tj f B1 SA Streptavidin 10102020 Undo C1 SA Streptavidin 10102020 D1 SA Streptavidin 10102020 Cut E1 SA Streptavidin 1010
404. naging the Runtime Binding Chart 0 c cece cece cence eee nen e ence eneeas 331 Managing Experiment Method Files ccc ccc cece e eee e cence eee ee ene eeaeens 338 Octet System Data Acquisition User Guide Release 7 1 page 276 Chapter 8 Kinetics Experiments Octet RED384 and QK384 INTRODUCTION A basic kinetics experiment enables you to determine the association and dissociation rate of a molecular interaction After starting the Octet system hardware and the Octet System Data Acquisition software follow the steps in Table 8 1 to set up and analyze a quantita tion experiment Table 8 1 Setting Up and Analyzing a Kinetic Experiment Step Select a kinetics experiment in the Experiment Wizard or open a method file fmf See Starting a Basic Kinetics Experiment on page 277 Define a sample plate or import a sample plate definition Defining the Sample Plate on page 278 Define a or import a reagent plate optional Working with a Reagent Plate on page 299 Specify assay steps Defining a Kinetic Assay on page 302 Assign biosensors to samples Run the experiment Assigning Biosensors to Samples on page 313 Running a Kinetics Experi ment on page 324 Software Data 1 Acquisition 2 iale 2 3 4 5 6 Data Analysis 7 i 8 View and process the raw data Analyze the data Octet System Data
405. ncentration units pg ml Sample Plate 384 wells Reagent Plate Molerconcentraton units aM x W123 4 5 6 7 8 9 1011121314151617 18192021 222324 Well Sample ID Replicate Group Type Conc uig ml MW kD Molar AMOOQOODODO OO OOO9OO0C000O OM Proteina Load BIOQOQOOQOOQOOOOOOOCOOOOOOCO00O O07 Proteina Load COOOOODOOOOOOOOO OO000000 A 1XKinetics Butter Buffer DIOOOOOOOOOOOOOOOOOOOOOOO ce EOOOODOOOOOO OOO9O0O00000O0 FIOOOQOOO00O0 OQOOOCO0OO er cCOOOOCOOOAOAOOOOOOQOQOQOOQOOQQOQ Gh HOQOOQOQOOQOOOQOOOOOOOOOOOOOO er 1 OQCOOODODOODOOOOO O000000O g ffer JOOOOCOOOOOQOOQOQOOQOQOQOQOQOOQQOQOQQQQQ f ffer K OQOOOODOOOO OOOOO O0O0C00000 iti ffer ILOOQOQOQOQOOOOOOOOOOOOOOOOOO iter MOOC OQOOOOOCOOOOOO OO00000O ffer NOOOOOQOQOQOOQOQOQQOQOOQOOQOQOOQQQQOQOQQOQ r SS OO OOOOOOOOO 0 0O0000000 a P O Unassigned Import ji Export Remove Reagent Plate 96 wells a Set Well Data Clear Data Copy to Clipboard x SK liv Extended Sample Types 3 k m 013 1X Kinetics Buffer ASISTeNe O A15 Sample joc Sample Sites e gt OC Set Well Data H O O Or AO OO C Well Information Concentration ug ml Sample only Unassigned Import Export Sample ID By value human 19G Diution series Replicate Group Starting value E 7
406. nd methods Kinetics 96 data hlgG ProA Kinetics Kinetics Runtime Binding Chart eon x Current Binding Charts Sensors to Chet Plate Status So Plate Legend Kinetics Assay 1 SelectAll a Sinten d CS Ritalin Sane eee 72345678 910112 P Selected Kinetics Assay 3 A A Processing B B Processed sensor D2 3 O Reserved sensor E2 E E Date Eror FsensorF2 Fsensorc2 F F O Serextrall sensor H2 G G z H H Subtract reference sensors Assay Step Status Experiment Progress Step 17 of 17 Step details Assay 3 of 3 Elapsed time Total exp time Extend Current Step 10s 10s eee Eguiara 5270 8 5270 s 25713 25713 1200 rpm e gt Go to Next Step Flip Data Binding nm l l I l H I l I l l I I l I I I l l l L o 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 Time sec Sensor A2 Sensor B2 Sensor C2 Figure 7 53 Runtime Binding Chart Window Octet System Data Acquisition User Guide Release 7 1 page 268 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Opening the Runtime Binding Chart After an experiment is run you can open and review the Runtime Binding Chart at any time 1 Click File gt Open Experiment 2 Inthe dialog box that appears select an experiment folder and click Select Viewing Reference Subtracted Data If the experiment includes reference biosensors you can display reference subtracted data in the chart by
407. ndo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 159 Replicate Groups When samples are assigned to a Replicate Group the Octet System Data Analysis software will automatically calculate statistics for all samples in that group The average binding rate average concentration and corresponding standard deviation as well CV are presented in the Results table for each group see Figure 6 19 Protein Group 1 0 66 0 01 1 5 604 5 17 8 29 Protein Group 1 0 66 0 01 1 5 604 5 17 8 29 Protein Group 1 0 66 0 01 1 5 604 5 17 8 29 Protein Group 1 0 66 0 01 15 604 5 17 8 29 Anti Hu Group 2 0 6589 0 0052 0 8 602 5 915 15 Anti Hu Group 2 0 6589 0 0052 0 8 602 5 9 15 15 AntiHu Group 2 0 6589 0 0052 08 602 5 9 15 1 5 AntiHu Group 2 0 6589 0 0052 0 8 602 5 9 15 1 5 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 24 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 2 4 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 24 AntiMo Group 3 0 6773 0 0087 1 3 635 3 15 4 24 Protein Group 4 0 6544 0 0073 11 594 6 12 9 2
408. nerates more data points per second and monitors faster binding events better than a slower acquisition rate A lower acquisition rate allows the software enough time to per form more averages of the collected data Typically more averaging leads to reduced noise and thus better signal to noise ratios Therefore the frequency setting should be deter mined based on consideration of the binding rate the amount of signal generated in your assay and some experimentation with the settings Table 5 11 Advanced Settings for Octet QK Octet RED and Octet RED96 Item Description Acquisition rate e High sensitivity quantitation 0 3 Hz averaging by 40 Octet QK The average of 40 data frames is reported as one data point One data point is reported every 3 3 seconds Standard quantitation 0 6 Hz averaging by 5 The aver age of five data frames is reported as one data point One data point is reported every 1 6 seconds Acquisition rate e High sensitivity quantitation 2 Hz averaging by 50 The Octet RED and average of 50 data frames is reported as one data point Octet RED96 Two data points are reported per second Standard quantitation 5 Hz averaging by 20 The aver age of 20 data frames is reported as one data point Five data points are reported per second Sensor offset Recommended sensor offset for quantitation 3 mm mm Octet QK only Default Sets acquisition rate and sensor offset to the defaults
409. netics 384 295 kinetics 96 231 defined 144 removing quantitation 384 149 153 quantitation 96 74 78 reagent plates quantitation 384 167 removing controls or reference wells quantitation 384 157 quantitation 96 81 well information tooltip 241 well types Activation kinetics 384 281 kinetics 96 218 Buffer kinetics 384 280 kinetics 96 218 Control kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 designating kinetics 384 282 kinetics 96 219 designating kinetics experiments 282 for kinetics experiments 220 282 Load kinetics 384 281 kinetics 96 218 Negative Control kinetics 384 280 quantitation 384 145 quantitation 96 71 Positive Control kinetics 384 280 quantitation 384 145 quantitation 96 71 Quench kinetics 384 281 kinetics 96 218 Received quantitation 384 145 quantitation 96 71 Reference kinetics 384 280 kinetics 96 218 quantitation 384 145 quantitation 96 71 Regeneration kinetics 384 281 kinetics 96 218 removing designated type 220 Sample kinetics 384 280 Octet System Data Acquisition User Guide Release 7 1 page 39 kinetics 96 218 Standard quantitation 384 145 quantitation 96 71 Unknown quantitation 384 145 quantitation 96 71 Wash kinetics 384 281 kinetics 96 218 well volumes Octet QK384 20 27 Octet RED384 20 27 wells annotating 82 225 288 annotating individual kinetics 384 289 kinetics 96 226 quantitation 384 157 quantitation 96 8
410. netics 96 233 quantitation 384 163 quantitation 96 88 exporting binding data 127 204 plate definition kinetics 384 297 kinetics 96 233 quantitation 384 163 quantitation 96 88 Runtime Binding Chart to a data file 127 204 272 337 Runtime Binding Chart to a graphic 127 204 272 337 Runtime Binding Chart to a graphic file 273 337 Exporting dialog box figure 127 204 Extend Current Step button 270 Extend Current Step dialog box figure 271 335 extending duration of the active step 270 335 F factory loaded biosensor types deleting 49 FBServer7 folder installation location 381 FBServerConfig exe file 381 File Compliant figure 62 File History menu 34 File menu described 32 figure 33 list of menu commands 33 File menu commands listed table 33 File Not Compliant figure 62 File Type selection figure 61 Fill Plate menu 253 316 Filtering threshold parameter 239 305 Flip Data check box 125 269 334 Flip Data function viewing inverted data 269 ForteBio GxP Server 7 0 exe 372 ForteBio GxP Server desktop icon figure 397 ForteBio GxP Server module installing 371 Octet System Data Acquisition User Guide Release 7 1 page 17 ForteBio technical support contacting 13 ForteBio Web Site menu 38 fractional use of regeneration and neutralization wells figure 112 189 Fuse symbol 13 G general settings kinetics 384 330 GetMethodInfo automation interface command 349 GetRun
411. ng Chart To scale the Runtime Binding Chart 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box select Fullscale or Autoscale Octet System Data Acquisition User Guide Release 7 1 Managing Runtime Binding Charts page 203 Adding a Runtime Binding Chart Title To add a Runtime Binding Chart title 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box enter a graph title or subtitle Selecting a Runtime Binding Chart Legend To select a Runtime Binding Chart legend 1 Right click the chart and select Properties 2 Inthe Runtime Graph Properties dialog box see Figure 6 64 select one of the fol lowing legends Sensor Location Sample ID Sensor Information e Concentration Dilution F Runtime Graph Properties Es Title Subtitle Legend Sensor Location Sensor Information Sample ID Concentration Dilution Figure 6 64 Selecting a Runtime Binding Chart Legend NOTE Text for Sample ID Sensor Information or Concentration Dilution is taken from the Plate Definition and Sensor Assignment tabs and must be entered before the experiment is started 3 Click OK Octet System Data Acquisition User Guide Release 7 1 page 204 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Viewing Multiple Runtime Binding Charts To view multiple Runtime Binding Charts click Window g
412. ng Experiment Method Files Menu Bar Command Description Toolbar Button File gt Open Method Enables you to select and open a method file fmf File File gt Save Method Saves one method file or all method files Saves a method file File or amp before the experiment is run File gt Save Method Saves a method file to anew name so that the original file is not File As overwritten Octet System Data Acquisition User Guide Release 7 1 page 275 CHAPTER 8 Kinetics Experiments Octet RED384 and QK384 INTPOGUCHON is seccivecereceneene nay E E ceadewpinvamad seven Revenue eects 276 Starting a Basic Kinetics Experiment 0 cece cece eee e eee e eee e ene een eens 277 Defining the Sample Plate cece cece cence nen n eee e nen sirop iE Aies 278 Managing Sample Plate Definitions cc cece cece cece eee eee e eee eneaenenees 296 Working with a Reagent Plate ccc cece cece cence een ee nee ene e een en eee eneens 299 Defining a Kinetic Assay ccc cece cece cence ene n ence ence een e neste eeneenaes 302 Assigning Biosensors to Samples ccc cece cence eee ence eee eens ences eeeneens 313 Reviewing Experiments ccc ccc c eee ee eee n enn enn eeneeneeneeees 322 SAVING EXPeriMents lt i ici diaesasd dices ane anders and aides ewan E EEE EEE Te EEE IRE DE AEE alae 323 Running a Kinetics Experiment 0 cece ccc eee n ence eee eee eeeeennenee 324 Ma
413. ng Wells in the Sample Plate Map 219 Designating Well Types 219 Entering Sample Information 221 Replicate Groups aoaaa 226 Editing the Sample Table 231 Managing Sample Plate Definitions 232 Exporting a Plate Definition 233 Importing a Plate Definition 234 Defining a Kinetic Assay 5 236 Defining Step Types 006 236 Building an Assdy 00 eeeee 241 Assigning Biosensors to Samples 249 Reviewing Experiments 258 Saving Experiments eeeee 259 Saving an Experiment to the Template Folder an ree er ee iioa 260 Running a Kinetics Experiment 260 Loading the Biosensor Tray and Sample Plate caniae rand wiGAmowe nantes 260 Starting the Experiment 261 Run Experiment Window Settings 264 Stopping an Experiment 266 Managing the Runtime Binding Chart 267 Opening the Runtime Binding Chart268 Viewing Reference Subtracted Data 268 Viewing Inverted Data 269 Aligning Data by a Selected Step 270 Extending or Skipping an Assay Step270 Terminating a Step to Begin the Next Step 271 Magnifying the Runtime Binding Chart 271 Scaling a Runtime Binding Chart 271 Adding a Runtime Binding Chart Title271 Selecting a Runtime Binding Chart Legend 271 Viewing Multiple Runtime Binding Charts 272 Exporting or Printing the Runtime Binding Octet System Data Acquisition User
414. ng the Audit Trail The Audit Trail displays a historical log of user system and software events recorded during user sessions To view the Audit Trail click Security gt View Audit Trail n C Audit Trail Project Machine b E E Date Time 2011 02 14 13 00 53 2011 02 14 13 18 01 2011 02 14 13 42 07 2011 02 14 13 42 45 2011 02 14 13 43 30 2011 02 14 13 44 09 2011 02 14 13 49 09 2011 02 14 13 49 14 2011 02 14 13 49 30 2011 02 14 13 49 34 2011 02 14 13 50 59 2011 02 14 13 54 47 2011 02 14 14 18 46 Project Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Antigen Antibody screen Figure 4 18 Audit Trail Machine JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS JRICHARDS Action User login User login User logout User login User logout User login User login User logout User login User logout User login User login User login Description Octet System Data Acquisition User Guide Release 7 1 Compliance Features page 63 gt NOTE Events shown in the Audit Trail are those associated with the user account that is currently logged in and active
415. nm min for a user specified time min Filtering The amount of data seconds to average when computing the sig nal change or gradient threshold Octet System Data Acquisition User Guide Release 7 1 page 240 Chapter 7 Kinetics Experiments Octet RED96 QK and QK 4 Click OK to save the newly defined step The new step type appears in the Step Data List 5 Repeat the previous steps for each step type to create until all the desired steps are added see Figure 7 26 Step Data List Add Remove Threshold Params Name Time Shake speed Type Threshold Equilibration 10 1000 3 Custom r Pro Immobilization 120 1200 LZ Loading O Baseline 600 1200 b Baseline r Association 300 1000 Z Association m Dissociation 600 1000 Z Association m Regeneration g00 1000 3 Custom m Neutralization 10 1000 3 Custom m Equilibratian2 10 1000 3 Custom r Figure 7 26 Step Data List Displaying Step Types 6 To delete a step type from the list click the corresponding row in the Step Data List and click Remove or press the Delete key Copying and Editing Step Types To define a step type by copying an existing one click the step type row in the Step Data List and click Copy The copied step type appears at the end of the Step Data List To define a step type by editing an existing one 1 Double click the cell in the step s Name Time or Shake speed column and then enter a new value Or right click the cel
416. nor Oy Sample ID z By value Unknown O Reference IgG Standard Dilution series Replicate Group Starting value 1 Series operator w Well Information v Sample Diluent IES ORETAKI 2 Dilution orientation 883 Right 888g Left g Down g Up a ee L d Figure 5 14 Adding Sample Annotations from the Sample Plate Map Annotating Wells in the Sample Plate Table To annotate an individual well in the Sample Plate Table 1 Double click the table cell for Sample ID or Well Information 2 Enter the desired information in the respective field see Figure 5 15 Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 83 NOTE A series of Sample IDs may also be assembled in Excel and pasted into the Sample Plate Table Sample Plate Table Concentration units g ml v Export Import Well Sample ID Replicate Group Type Conc g ml Dilution Factor Information a G3 IgG Standard Standard 5 n a Sample Diluent H3 IgG Standard Standard 2 5 n a Sample Diluent A4 Abl Unknown n a 2 Sample Diluent B4 Ab2 Unknown n a 2 Sample Diluent C4 Ab3 Unknown n a 2 Sample Diluent D4 Ab4 Unknown n a 2 Sample Diluent E4 Ab5 Unknown n a 2 Sample Diluent F4 Abb Unknown n a 2 Sample Diluent G4 Ab Unknown n a 2 Sample Diluent H4 Abs Unknown n a 2 Sample Diluent A5 Abl Unknown nja 2 Sample Diluent E
417. not displayed when the software is launched click the Experiment Wizard toolbar button 4 or click Experiment gt New Experiment Wiz ard Ctrl N from the Main Menu m In the Experiment Wizard select New Quantitation Experiment see Figure 6 1 left w Select a type of quantitation experiment see Table 6 2 for options Table 6 2 Quantitation Experiment Selection Quantitation Experiment Description Basic Quantitation A standard quantitation assay Basic Quantitation with A standard quantitation assay that enables regeneration of Regeneration biosensors Octet System Data Acquisition User Guide Release 7 1 page 142 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Table 6 2 Quantitation Experiment Selection Quantitation Experiment Description Advanced Quantitation A standard two or three step quantitation assay that enables signal amplification for higher detection sensitiv ity a Basic Quantitation Experiment Am Pite Defintion Sensor Assignment Review Experiment Run Experiment O eee iia ol Read Head Setting 16 Channels a a ror Aaa Well Sample ID Replicate Group Type Conc ug ml Dilution Factor Information snge any Time 8 Shake speed Quantitation 120 400 Sample Plate PX Experiment Wizard e les Semja Plane 384 Wells 123 45 6 7 8 9 1011121314 15161718192021222924 AOO0 00000000000 O00OO0000d
418. ns may be less than the number of sample columns as the buffer columns are reused Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incubated in regeneration buffer to speed rpm remove bound analyte Neutralization The duration time and shaking speed of the neutralization step Time s and Shake where the biosensor is incubated in neutralization buffer after the speed rpm regeneration step Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For example an acidic pre conditioning buffer maximizes the binding competence of Protein A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 137 Table 5 17 Advanced Quantitation Assay Parameters Parameter Description Regeneration The number of regeneration neutralization cycles that a biosen cycles sor undergoes before reuse NOTE In an Advanced Quantitation experiment this option is only available if the first step biosen sor incubation in sample is performed online Selecting a Custom Assay You can select a
419. nsor Assignment window 254 318 biosensor types changing 246 311 biosensors assigning quantitation 384 173 quantitation 96 96 assigning to samples 249 313 automatically adding experiment tray maps 256 320 changing locations kinetics 96 252 changing type 320 designating reference 105 110 182 187 257 321 entering information 252 315 preparing 68 removing from sensor tray maps 253 317 replaying in the biosensor tray 251 315 viewing available 48 biosensors reference designating 258 browser window functions 47 Buffer well type kinetics 384 280 kinetics 96 218 Buffer Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Buffer Time and Shake speed parameter 135 212 building assays 241 By value option 76 151 222 285 C capabilities Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 22 Octet RED384 instrument 18 Octet RED96 instrument 17 Octet System Data Acquisition User Guide Release 7 1 page 9 cascade arrangement organizing windows 37 Cascade menu 37 Change Password dialog box figure 387 Change Projects menu 64 changing administrator password 387 assay step name figure 247 311 biosensor Location Method 1 253 316 biosensor location Method 2 254 317 biosensor type figure 247 311 biosensor type in the Assay Definition window 258 322 biosensor type in the Sensor Assignment window 254 31
420. nsor 57 PSensor C6 sensor C Eni nso D7 sensor E6 sensorE7 sensor F6 Sensor F sensor G6 Isensor G7 sensor H6 sensor H Subtract reference sensors Plate Status Sensor Tray y 12 3456 7 8 9 101112 rommoOO gt D Figure 8 60 Subtract Reference Sensors check box in the Runtime Binding Chart NOTE Subtracting reference data in the Runtime Binding Chart only makes a visual change to the data on the screen The actual raw data is unaffected and the reference subtraction must be repeated during data analysis if needed Octet System Data Acquisition User Guide Release 7 1 page 334 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Viewing Inverted Data The data displayed in the Runtime Binding Chart can be inverted during real time data acquisition or data analysis after the experiment has completed To invert data select the Flip Data check box see Figure 8 61 Uncheck the box to return to the default data display Assay Step Status Experiment Progress Step 11 of 11 Step details Assay 2 of 2 Elapsedtime Total exp time Extend Current Step 20 5 20 s equilibration 1840 s 1 840 Ci 0 31 14 0 31 14 e A ooo oDe 1 5 Binding nm ety Sy es amp cs A pas 1 I CIOCCI 0 200 400 600 800 1000 1200 1400 1600 Time sec ees At ern DE sere DA See D n E H4 AS ern Bb Sees CE eat
421. nt amp F1 IgG Standard 5 Standard 5 Sample Diluent 9 G1 IgG Standard 2 5 Standard 25 Sample Diluent 10 H1 IgG Standard 1 Standard 1 Sample Diluent 11 A2 IgG Standard 200 Standard 200 Sample Diluent w u 4 96 standard plate 2 IKI m rf Figure 5 25 Example Sample Plate File csv Octet System Data Acquisition User Guide Release 7 1 Managing Assay Parameter Settings page 91 MANAGING ASSAY PARAMETER SETTINGS Modifying Assay Parameter Settings You can modify the assay parameter settings during sample plate definition However the changes are only applied to the current experiment To save modified parameter settings you must define a new assay For details on creating a new assay see Custom Quantitation Assays on page 129 Viewing User Modifiable Assay Parameter Settings To view the user modifiable settings for an assay click Modify in the Assay Settings box The Assay Parameters box will display Figure 5 26 The settings available are experiment dependent Plate Definition sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and rightclick to enter modify well data Assay Settings Sample Plate Table Assay Basic Quantitation Concentration units Lom X Export l Import RERA Wel
422. nt Click for a password reminder 3 Enter the New Password and Password reminder optional 4 Click OK to save changes and exit Changing the Administrator Password 1 Initiate a new administrator user session with the existing password 2 When the software launches select Change Password from the Security menu The Change Password dialog box will display NOTE The Change Password dialog box can also be accessed by right click ing on the administrator account in the Users Tab and selecting Set Pass word from the Tab menu Octet System Data Acquisition User Guide Release 7 1 page 388 Chapter B 21 CFR Part 11 Software Administrator Options lt lt mx Current password New password Confirm new password Password reminder Figure B 40 Administrator Change Password Dialog Box 3 Enter the Current password for your user account Click for a password reminder 4 Enter the New Password and Password reminder optional 5 Click OK to save changes and exit Group Administration The Groups Tab allows administrators to add and delete user groups as well as set and change group privileges For ForteBio GxP Server i Groups Projects Constants Events Name Privileges Info Administrator admin review change plate Administrators can add delete edit users and groups Supervisor review Supervisors can review data and events Developer change pl
423. nt and the run parameters An experiment method file provides a convenient initial template for subsequent experiments Open a method fmf and edit it if necessary NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Table 5 14 Managing Experiment Method Files Menu Bar Command Description Toolbar Button File gt Open Method Enables you to select and open a method file fmf File File gt Save Method Saves one method file or all method files Saves a method file File or before the experiment is run File gt Save Method Saves a method file to anew name so that the original file is not File As overwritten Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 129 CUSTOM QUANTITATION ASSAYS Defining a Custom Assay To define a custom assay 1 Click Experiment gt Edit Assay Parameters The Edit Assay Parameters dialog box appears see Figure 5 61 r 7 Edit Assay Parameters Available Assays Assay Parameters E Basic Quantitation Name Standard Assay Anti Penta HIS High sensitivity Anti Penta HIS Standard range Hig
424. nterface command 350 Present Stage menu 36 Print menu 33 Print Preview menu 33 print preview window 33 Print Setup dialog box 33 Print Setup menu 33 printing files 33 Runtime Binding Chart 128 205 273 338 prior to running an experiment 258 322 privileges assigning 385 project administration 390 Project drop down list 63 project selection figure 58 project settings changing 391 viewing 391 project based Audit Trail events figure 64 Octet System Data Acquisition User Guide Release 7 1 page 25 projects changing figure 64 deleting 392 editing 391 Projects tab 391 projects changing during a user session 64 properties for Octet System software displaying 38 Q QKe instrument replacing fuses 341 quantitation 384 144 Quantitation Data Repository setting Run Experiment window settings quantitation 384 196 quantitation 96 119 quantitation data repository user option 41 Quantitation Experiment Advanced Quantitation quantitation 384 142 Basic Quantitation 384 141 Basic Quantitation 96 69 Basic Quantitation with Regeneration 69 141 quantitation experiment defined 68 140 starting 69 141 Quantitation Shake Speed assay parameter quantitation 384 209 quantitation 96 132 Quantitation Shake Speed parameter quantitation 384 169 quantitation 96 92 Quantitation Time and Shake speed parameter 133 170 210 Basic Quantitation with Regeneration quantitation 96 93 Quantitation Time
425. ntitation Table 5 8 Advanced Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte For multi analyte experiments using multiple biosensor types per and Replicates per sample well and the number of replicate assays in each well per sensor type biosensor type Octet System Data Acquisition User Guide Release 7 1 Managing Assay Parameter Settings page 95 Table 5 8 Advanced Quantitation Assay Parameters Continued Parameter Description SampleTime s and The duration of data acquisition in seconds while the biosensor is Shake speed rpm incubated in sample and the sample platform orbital shaking speed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Buffer Time s and The duration of biosensor incubation in the first buffer in seconds Shake speed rpm and the sample platform orbital shaking speed rotations per minute Enzyme Time s The duration of biosensor incubation in seconds in the enzyme and Shake speed solution and the sample platform orbital shaking speed rotations rpm per minute 2nd Buffer Time s The duration of biosensor incubation in seconds in the second and Shake speed buffer solution and the sample platform orbital shaking speed rpm rotations per minute Detection Time s amp The duration of data acquis
426. ntitation 384 155 quantitation 96 80 parameter values quantitation 384 208 quantitation 96 131 projects 391 sample data in the Sample Plate Table kinetics 384 295 kinetics 96 231 standard concentration quantitation 384 151 quantitation 96 76 step type figure 241 306 editing step types 240 305 Electrical hazard symbol 13 electrical requirements Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 emptying waste container 340 ending a user session 66 enhanced legend options in the Runtime Binding Chart 12 entering annotations Octet System Data Acquisition User Guide Release 7 1 page 14 quantitation 384 157 quantitation 96 82 biosensor information displayed figure 252 316 procedure 252 315 entering an individual standard concentration quantitation 384 151 quantitation 96 76 environmental features Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 Enzyme Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Enzyme Time and Shake speed parameter 136 213 equipment classifications Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 events list options available 396 viewing 395 Events tab figure 395 example csv plate definiti
427. ntitation Experiments Octet RED384 and QK384 Selecting Wells in the Sample Plate Map There are several ways to select wells in the Sample Plate Map Click a column header or select adjacent column headers by click hold drag Figure 6 6 left To select non adjacent columns hold the Ctrl key and click the col umn header Click a row header or select adjacent row headers by click hold drag Figure 6 6 cen ter e Click a well or draw a box around a group of wells Figure 6 6 right Sample Plate Sample Plate Sample Plate Sample Plate 384 wells Sample Plate 384 wells Sample Plate 384 wells Modify rm 456 7 8 9 101112131415161718192021222324 YF 123 4 5 6 7 8 9 101112131415161718192021222324 Wei 23 45 6 7 8 9 1011121914 151617 18192021222924 OO OOO0O0OO000000 g ag B c c D DOOOOOOOOOOOOOOOOOQOOOOO ig E EROOOOOOOOOOOOOOOOO000000 E F FOOO0OOO0QOQO00000000000000000 F G cOOOOQOQOQOQOQQOQOQQOQQQQQQQ0Q00Q0Q a H HOOOQOQOQOQOQOQOQOOQOQQQOQQQQOQQQ00Q0QQ H t 1 O00000 0Q0000000000000000 J JJO OOQ u K O00000 KOO O K LOQOOQOQQQQQQQQQQ000000000 LOOOQOQQOQQQQQQQQ00Q00000000 IL IMOOOCOOOOOOCOOOO 000000000 MOO O M NOOQOOOQOQOQQQQ0Q0Q00000000000 NOQOQQOQ O000000 N OOQOOOQOOQOQOQQQQQQQQ0Q00000 hiistotetoleteteteteletelelelelelelolelolololole o OOOOQOQOQQ0Q0Q0Q0Q00000000000 PQ0000060660660660660660 POO0606660600600600600600d Standard Control O Unassigne
428. nts and analyses Figure B 42 New Group Dialog Box 2 Enter the Group name and Information optional 3 Privileges Each group can be assigned specific privileges Add group privileges by selecting or deselecting the check boxes next to each privilege Administration Can administer the user database e Review Can review changes and events e Change Can change methods and configuration values Plate Can change sample plate properties e Run Can run experiments and analyses 4 Click OK to save changes and exit Octet System Data Acquisition User Guide Release 7 1 page 390 Chapter B 21 CFR Part 11 Software Administrator Options Viewing and Changing Group Settings 1 Right click on the group and select Edit Group from the Tab menu or double click on the group The Edit Group dialog box will display bat Coup ii E Group name IDeveloper Information Developers can create run save and export data Privileges Administration administers the user database Review reviews changes and events Change can change methods and configuration values Plate can change sample plate properties Run can run experiments and analyses Figure B 43 Edit Group Dialog Box 2 If needed modify the group settings For more details on individual settings please refer to Creating a New User Group on page 389 3 Click OK to save
429. nts can be changed as needed see Figure 6 44 Octet System Data Acquisition User Guide Release 7 1 page 182 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Sensor Tray Sensor Tray 7 Replace sensors in tray after use of 3 Tray Format Heterogeneot VW i 2 3 4 5 6 9 10 11 12 TE Type Lot Number Information ALLIEN EEEE 7 BLOOD BBM c Prins C1 Protein A D1 Protein A i EAMAN ISECCESREEe z G1 Protein A Jmm mma y ree A2 Protein A FL ILIBSULERR RRR ven C2 Protein A GLILIBRBULBR BREE n HOSS 2 F2 Protein A G2 Protein A Legend Unassigned sensors R3 Missing sensors Hu Dratain A Figure 6 44 Tray Selection 7 To designate reference biosensors select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during acquisition 8 Optional Double click in any cell in the Lot Number column to enter a biosensor lot number All wells in the Lot Number column for that biosensor type will automatically populate with the lot number entered 9 Optional Double click in a cell in the Information column to enter biosensor informa tion for a particular cell NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z
430. o GMoreno George Moreno Guest run 00 11 23 External collaborator RBrown Richard Brown Supervisor review 00 12 32 JBlack John Black Developer change plate run 00 13 30 PSmith Paul Smith Lab User run 00 14 46 Administrator Administrator Administrator admin review change plate 1 day 22 17 19 Default administrator user Figure B 34 Tab Contents Sorted by Password Age Tab Menu Right clicking on an entry or on a blank area in the tab will display the Tab menu Tab menu options vary depending on the tab selected New User Edit User Set Password Delete User Figure B 35 Tab Menu Octet System Data Acquisition User Guide Release 7 1 page 384 Chapter B 21 CFR Part 11 Software Administrator Options User Account Administration The Users Tab allows administrators to add and delete user accounts as well as set and change individual user account privileges and passwords ForteBio GxP Server Admininstrz Users Groups Projects Constants Events Login Name Full Name Group Privileges Password Age Info Administrator Administrator Administrator admin review change plate 1 day 22 06 08 Default administrator user PSmith Paul Smith Lab User run 00 03 35 JBlack John Black Developer change plate run 00 02 19 RBrown Richard Brown Supervisor review 00 01 20 GMoreno George Moreno Guest run 00 00 12 External colaborator Figure B 36 Users Tab Creating a New User Acc
431. o ways to assign biosensors Select a column in the Sensor Tray Map right click and select a biosensor type from the drop down list see Figure 6 39 left Select a cell in the Sensor Type table column click the down arrow and select a bio sensor type from the drop down list see Figure 6 39 right Sensor Tray V Replace sensors in tray after use eee Eee eee ee d 7 ae 10_11_12 Bi A auto assign A auto assign i a A i Anti Human IgG Fc p aAnti Mouse IgG Fv B z H Protein A Anti MRES IgG Fv El Protein G c 0 Protein A ig F1 A protein L Protein G G1 ASA Streptavidin D D x W H1 AResidual Protein A Protein L A2 aAnti Penta HIS E SA Streptavidin E B2 acustom Residual Protein A A F l Anti Penta HIS m D2 A G Custom eal E2 if H Reference E Positive Control Legend Negative Control RR Missing sensors Ren Remove Fill Sample 1 Set Sensor Data 5 161718192021 222324 O Copy to Clipboard D Figure 6 39 Changing Biosensor Types in the Sensor Tray Map left and Sensor Type Column right Biosensor Assignment Using Heterogeneous Biosensor Trays The default Tray Format is Heterogeneous Heterogeneous biosensor trays contain a mix ture of biosensor types NOTE When using this Heterogeneous option the order of biosensor types in each tray must be identical 1 If Heterogeneous Trays is not displayed next to the Tray Format button click the but ton The
432. ode control character Standard 5 Open IME Standard 2 5 R er Standard 1 econversion Standard 200 nja Figure 5 8 Sample Plate Table Shortcut Menu of Edit Commands NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sam ple Plate Table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types Octet System Data Acquisition User Guide Release 7 1 page 78 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Designating Unknowns To designate unknowns in the Sample Plate Map select the wells to define as unknown right click and select Unknown The unknown wells are marked in the plate map and the sample plate table is updated see Figure 5 9 Plate Definition Sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and right click to enter modity well data Assay Se
433. oftware can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Table 8 12 Managing Experiment Method Files Menu Bar Command Description Toolbar Button File gt Open Method Enables you to select and open a method file fmf File File gt Save Method Saves one method file or all method files Saves a method file File or before the experiment is run File gt Save Method Saves a method file to anew name so that the original file is not File As overwritten Octet System Data Acquisition User Guide Release 7 1 page 339 CHAPTER 9 Maintenance Octet RED96 and Octet QK Systems eee eee eee eee e eee n tence nance 340 Octet RED384 and Octet QK384 Systems eee cece cece ee eee eee n eee enes 342 page 340 Chapter 9 maintenance OCTET RED96 AND OCTET QK SYSTEMS Cleaning the Octet Instrument NOTE If you use the Octet instrument regularly clean the interior horizontal surfaces daily with a Kimwipe tissue moistened with a 30 60 isopropyl alcohol solution Otherwise clean once a week or as needed To clean the Octet instrument 1 Turn off the power to the instrument 2 Open the system door 3 Wipe the biosensor and sample platform Figure 9 1 4 Carefully wipe the eight biosensor pickup tips 5 Allow the surfaces to dry for at least one
434. og box Runtime Binding Chart MANAGING EXPERIMENT METHOD FILES After you run an experiment the Octet System Data Acquisition software automatically saves the method file fmf which includes the sample plate definition biosensor assign ment and the run parameters An experiment method file provides a convenient initial template for subsequent experiments Open a method fmf and edit it if necessary NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Table 6 15 Managing Experiment Method Files Menu BarCommand Description Toolbar Button File gt Open Method Enables you to select and open a method file fmf File File gt Save Method Saves one method file or all method files Saves a method file File or before the experiment is run File gt Save Method Saves a method file to anew name so that the original file is not File As overwritten Octet System Data Acquisition User Guide Release 7 1 page 206 Chapter 6 Quantitation Experiments Octet RED384 and QK384 CUSTOM QUANTITATION ASSAYS Defining a Custom Assay To define a custom assay 1 Click Exp
435. omogeneous biosensor trays contain only one biosensor type NOTE Using the Homogeneous option will necessitate switching trays dur ing the experiment 1 Click Tray Format The Tray Format dialog box displays see Figure 5 41 and the Sensors box will be populated with the default biosensor type Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 107 r Tray Format Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical Homogeneous A different sensor tray is used for each sensor type Sensors Am Add Remove Change Move Up Move Down Figure 5 41 Tray Format Dialog Box 2 Select Homogeneous Click Add to select the first biosensor type see Figure 5 42 r Tray Format Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical Homogeneous A different sensor tray is used for each sensor type Sensors Anti Mouse IgG Fv Protein A Protein G Protein L SA Streptavidin Residual Protein A Anti Penta HIS Custom Figure 5 42 Selecting a Biosensor Type in the Tray Format Dialog Box 3 Repeat this step to add any additional biosensor types that will be used in the experi ment To remove a biosensor type select a biosensor type in the Sensor box and click Remove 4 Adjust the order of biosensor types
436. on 384 154 quantitation 96 79 assigning serial dilution quantitation 384 154 quantitation 96 79 selecting in the Sample Plate Map kinetics 96 219 quantitation 384 148 quantitation 96 73 window icons arranging 37 Window menu described 37 list of menu commands 37 windows organizing in a cascade arrangement 37 tiling vertically 37 Octet System Data Acquisition User Guide Release 7 1 page 40 Octet System Data Acquisition User Guide Release 7 1
437. on 384 173 quantitation 96 96 biosensors to samples 249 quantitation 384 173 quantitation 96 96 dilution factor to selected wells quantitation 384 154 quantitation 96 79 Octet System Data Acquisition User Guide Release 7 1 page 5 dilution factor to unknowns quantitation 384 153 quantitation 96 78 heterogeneous biosensor trays quantitation 96 101 heterogenous biosensor trays quantitation 384 178 homogenous biosensor trays quantitation 384 183 quantitation 96 106 molecular weight kinetics 96 221 molecular weight and molar concentration kinetics 283 privileges 385 Replicate Groups in the Sample Plate Map kinetics 384 290 kinetics 96 227 quantitation 384 159 quantitation 96 84 Replicate Groups in the Sample Plate Table kinetics 384 293 kinetics 96 229 quantitation 384 162 quantitation 96 87 sample concentrations by value kinetics 96 figure 223 sample concentrations using dilution series kinetics 384 286 kinetics 96 223 kinetics 96 figure 224 serial dilution to selected wells quantitation 384 154 quantitation 96 79 serial dilution to unknowns quantitation 384 153 quantitation 96 78 standard concentration quantitation 384 figure 151 quantitation 96 figure 76 standard concentrations using a dilution series quantitation 384 149 quantitation 96 74 step types in the sample plate figure 242 307 user group 385 user specified concentration to samples 222 285 user speci
438. on The duration time and shaking speed of the neutralization step Time s and Shake where the biosensor is incubated in neutralization buffer after the speed rpm regeneration step Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For example an acidic pre conditioning buffer maximizes the binding competence of Pro A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Regeneration The number of regeneration neutralization cycles that a biosen cycles sor undergoes before reuse Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 135 Advanced Quantitation Assay Parameters Edit Assay Parameters Available Assays Assay Parameters Basic Quantitation Name My Advanced Quant Assay IE Anti Penta HIS High sensitivity ae ore IE Anti Penta HIS Standard range Description Enter a short description of the assay here E High sensitivity Human IgG quantitation E Human IgG Quantitation 2 Immunogenicity Direct detection E Murine IgG Quantitation Time 8 Shake speed E Protein L Standard range Sample 120 al 1000 Offline E Standard Assay E My Basic Quant Assay
439. on file figure 235 299 example assay using one partial biosensor tray and biosensors from a second tray 113 190 example experiment using two biosensor trays figure 257 321 Exit menu 34 experiment prior to running 258 322 Experiment menu described 34 figure 35 list of menu commands 35 experiment method files managing 128 274 quantitation 384 205 quantitation 96 128 saving 33 saving to new name 33 experiment method files managing 274 338 experiment methods saving manually 114 191 Experiment Run Name setting Run Experiment window settings quantitation 384 196 quantitation 96 119 experiment settings advanced settings Octet QK384 198 330 data file location and names 2nd plate name barcode 264 328 Assay Type 328 assay type 264 Auto Increment File ID Start 264 Octet System Data Acquisition User Guide Release 7 1 page 15 328 kinetics data repository 264 328 plate name barcode file prefix 264 328 run name 264 328 general information Description 121 199 331 Machine name 121 199 330 User name 121 199 330 run settings Automatically save runtime charts 120 197 265 329 Delayed experiment start 265 329 Open runtime charts automatically 120 197 265 329 Set Plate Temperature 120 197 265 329 shake sample plate while waiting 120 197 265 329 Start After 265 329 experiment settings data file location and names quantitation 384 2nd Plate Name Ba
440. on for the file and click Save NOTE If you edit a saved experiment and want to save it without overwriting the original file click File gt Save Method File As and enter anew name for the experiment Octet System Data Acquisition User Guide Release 7 1 page 260 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Saving an Experiment to the Template Folder If you save an experiment to the factory installed Template folder the experiment will be available for selection To view templates select Experiment gt Templates gt Kinetics gt Experiment Name Figure 7 48 Follow the steps above to save an experiment to the Template folder located at C Program Files ForteBio DataAcquisition TemplateFiles D IMPORTANT Do not change the location of the Template folder If the Tem plate folder is moved from the factory set location the software may not func tion properly Experiment Instrument Window Help vV New Experiment Wizard Ctrl N Edit Assay Parameters Edit Sensor Types Set Plate Temperature Biomolecule kinetics AHC biosensor Kinetic Characterization_8CH_96W fmf Biomolecule kinetics AMC biosensor Screening_8CH_96W fmf Biomolecule kinetics AR biosensor Biomolecule kinetics SA biosensor Small Molecule and Fragment Kinetics SSA biosensor Kinetics Templates Quantitation Skip Step Stop Figure 7 48 Saved Experiments
441. on i i E Murine IgG Quantitation E Protein L Standard range E Standard Assay L E Time s Shake speed Basic Quantitation with Regeneration Quantitation 120 w 2 E High sensitivity assay with regeneration nan Protein L Standard range E Standard Assay My Basic Quant with Regen Assay Advanced Quantitation E Immunogenctty Enzyme Linked E Residual Protein A E Standard Assay Z Three Step Assay Description Enter a short description of the assay here sortype f Blue indicates a ForteBio built in assay and cannot be modified or deleted Duplicate Remove Cancel L 4 Figure 5 62 Defining a New Assay Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 131 Editing Assay Parameters To edit assay parameters 1 In the Edit Assay Parameters dialog box confirm that the new assay is selected in Available Assays see Figure 5 62 bottom 2 Modify the assay parameters as needed A complete list of parameters for each type of quantitation experiment follows this procedure 3 Click Save to accept the new parameter values The new assay is added to the system NOTE Not all parameters are available for all of the assays Basic Quantitation Assay Parameters E x Edit Assay Parameters Available Assays Assay Parameters E Basic Quantitation Name My Basic Quant
442. on rate Standard quantitation 5 0 Hz averaging by 20 Default Sensor offset mm distance to sensor tip from bottom of well Warming changing these settings could affect assay signal to noise Ifyou are unsure of how to use these settings please consult the Data Acquisition User Guide General Information Username Owner Machine name JRICHARDS Description Figure 6 57 Run Experiment Window Octet RED384 2 Confirm the defaults or enter new settings See Run Experiment Window Settings on page 196 for more information on experimental settings NOTE If you delay the experiment start you have the option to shake the plate until the experiment starts 3 To start the experiment click If you specified a delayed experiment start a message box displays the remaining time until the experiment starts Octet System Data Acquisition User Guide Release 7 1 Running a Quantitation Experiment page 195 If you selected the Open runtime charts automatically option the Runtime Binding Chart window displays the binding data in real time and the experiment progress see Figure 6 58 NOTE For more details about the Runtime Binding Chart see Managing Runtime Binding Charts on page 199 L g C Users Owner Documents Contracting Forte Bio User_Guides Data and methods 384 04 27 11 384 Q hig Quantitation Runtime Binding Chart Ee Curren
443. on software This example indicates that version 6 1 0 75 of the Data Acquisition software is controlling an Octet instrument using version 1 0 of the auto mation interface AUTOMATION COMMANDS Table A 1 summarizes the commands supported by the Octet System Data Acquisition soft ware automation interface NOTE The symbolic names are provided for C clients who connect using the interface as defined in the AutomationAPl h header file Table A 1 Commands Supported by the Automation Interface Command Symbolic Name Purpose Version AUT_CMD_VERSION Returns the version of the appli cation being automated the type of instrument it is control ling and the automation API ver sion Reset AUT_CMD_RESET Stops any running experiment and resets the instrument GetMethodinfo AUT_CMD_GETMETHODINFO Returns information about the resources required by given method file Run AUT_CMD_RUN Runs an experiment using a given method file GetRunInfo AUT_CMD_GETRUNINFO Returns information about the experiment currently running Octet System Data Acquisition User Guide Release 7 1 Chapter A Using Octet384 Systems with an Automation Interface page 350 Table A 1 Commands Supported by the Automation Interface Continued Command Stop Symbolic Name AUT_CMD_STOP Purpose Stops a running experiment ejecting the sensors if necessary Status Present AUT_CMD_STATUS AUT_CMD_PRESENT Returns
444. one click the step type row in the Step Data List and click Copy The copied step type appears at the end of the Step Data List To define a step type by editing an existing one 1 Double click the cell in the step s Name Time or Shake speed column and then enter a new value Or right click the cell to display a shortcut menu of editing commands see Figure 8 32 left NOTE Keyboard commands can also be used Ctrl x cut Ctrl c copy Ctrl v paste Ctrl z undo 2 Click the cell in the step s Type column then select another name from the drop down list see Figure 8 32 right Octet System Data Acquisition User Guide Release 7 1 page 306 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Step Data List Step Data List Add Copy Remove Threshold Params Add Copy Remove Threshold Params Name Time Shake speed Type Threshold Name Time Shake speed Type Threshold oar as aaa z custom z gt equilibration 120 1000 E Association m pooma poang i Dissociation gt Baseline a alia ears smn sop U Bassline z Association 300 Undo nesana Loading Dissociation 600 ae Association 300 1000 Activation r Regeneration 20 2 Dissociation 600 1000 H Quenching r Neutralization 20 Copy Regeneration 20 1000 aaa o Paste Neutralization 20 1000 zP r Assay Steps List Delete NewAssay Move Select All Assay Sample Plat Right to left Reading order Show Unicode
445. ontor O Unassignea O Standard Conto C Unassignea O Standard contol C Unassigned Unknown Reference O Reseved Unknown Reference O Reseved Figure 8 5 Selecting Wells in the Sample Plate Map Unknown Refrence Reserved NOTE Shift clicking in the Sample Plate Map mimics the head of the instru ment during the selection Octet System Data Acquisition User Guide Release 7 1 page 282 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Designating Well Types In the Sample Plate Map select the wells right click and select a sample type Figure 8 6 Plate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered Highlight one or more wells on the sample plate and right click to enter modify well data Read Head 8 Channels 16 Channels Sample Plate Concentration units ug ml Sample Plate 384 wells Reagent Plate Molar concentration units nM Wi2s456789 1011121314151617 18 192021 222324 Well Sample ID Replicate Group Type Conc j1g ml MW kD Molar Coi ASA aw WV WWW BDOOODOOOL Sample ar KE sBESOSS80 Se D EWOOOOOOO Control ov Load FIOOOOO000 6 O OOO HOOOOOO 1 OOOOOOO JIOOOOOOOO Buffer k O OOOOO LOQQQQQQQ M OOOOOOO
446. oo i Users Groups Projects Constants Events Login Name Full Name Group Privileges Password Age Info Administrator Administrator Administrator admin review change plate 1 day 22 06 08 Default administrator user Psmith Paul Smith Lab User run 00 03 35 JBlack John Black Developer change plate run 00 02 19 RBrown Richard Brown Supervisor review 00 01 20 GMoreno George Moreno Guest run 00 00 12 External collaborator Figure B 33 GxP Server Administration Window Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 383 Administrator Tabs Five tabs are available in the ForteBio GxP Server Administration window that contain the following options Users Tab Allows user and password management and individual privileges selec tion Groups Tab Allows user group management and group privileges selection e Projects Tab Allows project management and setup Constants Tab Allows setup of password requirements cached server credentials and screen lock due to inactivity e Events Tab Displays event logs for individual user accounts projects or machines To view the information contained on a tab just click on the tab Tab View Each tab displays a list of administrator entries and associated setting information that can be sorted by clicking on any of the column headers Login Name Full Name Group Privileges Password Age Inf
447. or D2 c sensor E1 sensor E2 D sensor Fl sensor F2 E sensor G1 sensor G2 F Sensor H1 sensor H2 G H Figure 6 62 Subtract Reference Sensors check box in the Runtime Binding Chart Octet System Data Acquisition User Guide Release 7 1 page 202 Chapter 6 Quantitation Experiments Octet RED384 and QK384 gt NOTE Subtracting reference data in the Runtime Binding Chart only makes a visual change to the data on the screen The actual raw data is unaffected and the reference subtraction must be re done in data analysis if needed Viewing Inverted Data The data displayed in the Runtime Binding Chart can be inverted during real time data acquisition or data analysis after the experiment has completed To invert data select the Flip Data check box see Figure 6 63 Uncheck the box to return to the default data display Experiment Progress Step 4 of 4 120s 120s Elapsed exp time 0 10 13 Total experimenttime 0 10 13 WFip Data 0 0 e N ye Binding nm 60 Time sec Bo C1 ee Et F2 G2 ews H2 H1 AZ 5 ocean 32S enaA aa Al masi E2 Figure 6 63 Data Inverted Using Flip Data Function Magnifying the Runtime Binding Chart To magnify the chart press and hold the mouse button while you draw a box around the chart area to magnify To undo the magnification right click the chart and select Undo Zoom Scaling a Runtime Bindi
448. ort contacting 13 Temperature field accessing 12 temperature range Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 Temperature Setting dialog box displayed figure 43 opening 35 temperature value default saving 44 temperature startup user option 42 Templates menu 35 templates viewing kinetics 384 324 kinetics 96 260 terminating a step in the assay 271 335 testing server 397 Threshold check box 238 threshold parameters Active Channels 239 304 Filtering 239 305 Gradient 239 305 listed table 239 304 Signal Change 239 304 Threshold Parameters dialog box 304 threshold applying to assay steps 238 304 throughput Octet QK instrument 24 Octet QKe instrument 22 Octet RED96 instrument 17 19 26 Tile menu 37 tiling windows vertically 37 Toolbar menu 34 toolbar Octet System Data Acquisition software 31 tooltip of well information 241 Tray Format button 106 types of wells control 71 145 reference 71 145 reserved 71 145 standard 71 145 unassigned 71 145 Unknown 71 unknown 145 U Unaligned menu 270 334 unassigned type of well 71 145 UNC folder names 347 undo magnification 125 202 271 335 Unknown well type quantitation 384 145 quantitation 96 71 unknowns assigning a dilution factor quantitation 384 153 Octet System Data Acquisition User Guide Release 7 1 page 36 quantitation 96 78 assigning serial dilution quantitation 384 153 q
449. ou do not want to use The software automatically selects the next available column s Method 2 Remove all columns from the Sensor Tray Map then select the col umns you want to use Method 1 In the Sensor Tray Map select the columns to not use and click Remove Or right click the selection and select Remove Figure 8 45 left The software automatically selects the next available biosensor columns in the tray Figure 8 45 right Click Fill Plate to return the Sensor Tray Map to the default layout Sensor Tray Replace sensors in tray after use MW 12 3 4 5 6 7 8 9 10 11 12 Legend O Unassigned sensors B Missing sensors Remove j Fill J Fill Plate Figure 8 45 Changing Biosensor Location Method 1 Sensor Tray V Replace sensors in tray after use F 1i 2 3 4 5 0 N 12 o w gt EE Ee ESS EES ULI O E z E E DES BARE FERBEAN m E ES Eg ES SGS0e0n DOoooog HOo0co0a Ea E E a Legend __ Unassigned sensors RRI Missing sensors Remove Fill Fill Plate Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 317 Method 2 1 Inthe Sensor Tray Map select all of the columns and click Remove Figure 8 46 top left Or right click the selection and select Remove All columns will be shown as Miss ing Figure 8 46 top right 2 Select the column s to use
450. ount To create a new user account 1 Right click anywhere in the Users Tab and select New User from the Tab menu or double click in a blank area The New User dialog box will display Login name Full name Information Password Confirm password Password reminder Group Supervisor Supervisors can review data and events Privileges _ Administration administers the user database v Review reviews changes and events Change can change methods and configuration values Plate can change sample plate properties Run can run experiments and analyses remo dosnt ore Figure B 37 New User Dialog Box Octet System Data Acquisition User Guide Release 7 1 Accessing Administrator Options page 385 2 Assign Account Details Enter the user s Login name Full name Information optional Password and Password reminder optional 3 Assign a User Group Select a user group from the Group drop down list The following default group selections are available e Administrators can add delete and change user accounts and groups Supervisors can review data and events e Developers can create run save and export data Lab Users can only run experiments e Guests have no explicit privileges these must be assigned by the administra tor If other user groups have been created by an administrator they will also be available for selection i
451. oup Type Conc jig ml Dilution Factor Informatio Assay Basic Quantitation OAT Standard nja Standard Assay le analyte a Standard nja Singi me PE Qe Standard nja ime s jake speed oa Standard nja uantitaton 120 400 s on Standard nja OK Standard nja Om Standard nja oa Standard nja OA Standard nja one Standard nja OB Standard nja eles Standard nja Sample Plate H s Sanus E tandar nja le Plate 384 well Sample Plate 384 wells Oma Standard nja P1234567 8 9 1011121314151617 18192021222324 03 Standard nja Standard andard N a Standard TO Control C Unassigned Unknown Reference Reseved lt u J Figure 6 7 Plate Definition Window Designating Standards To remove a well designation select the well s and click Unassigned Or right click the well s and select Clear Data Assigning Standard Concentrations Using a Dilution Series To assign standard concentrations using a dilution series 1 Inthe Sample Plate Map select the standard wells right click and select Set Well Data The Set Well Data dialog box displays see Figure 6 8 Octet System Data Acquisition User Guide Release 7 1 page 150 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Sample Plate Sample Plate 384 wells i 2 3 4 5 6 7 8 9 1011121314151617 18192021 222324 A Standard OO0O0000 Unknown Set Well Data E O Control O Refer
452. out overwriting the original file select File gt Save Method File As and enter a new name for the experiment Saving an Experiment to the Template Folder If you save an experiment to the factory installed Template folder the experiment will be available for selection To view templates click Experiment gt Templates gt Quantitation gt Experiment Name see Figure 6 55 Follow the steps above to save an experiment to the Template folder located at C Program Files ForteBio DataAcquisition TemplateFiles 1 IMPORTANT Do not change the location of the Template folder If the Tem plate folder is not at the factory set location the software may not function properly Instrument Window Help V New Experiment Wizard Ctrl N Edit Assay Parameters Edit Sensor Types Set Plate Temperature Kinetics Quantitation Advanced Quantitation Basic Quantitation Anti hIgG biosensor_16CH_96W fmf Basic Quantitation with Regeneration gt Anti hIgG biosensor_8CH_96W fmf Anti mIgG biosensor_16CH_96W fmf Anti mIgG biosensor_8CH_96W fmf Anti Penta HIS Dilution Factor Scouting_96W fmf Anti Penta HIS Spike Recovery Assay_96W fmf DirectDetectionImmunogenicity_16CH_384W fmf DirectDetectionImmunogenicity_16CH_96W fmf DirectDetectionImmunogenicity_8CH_96W fmf Protein A biosensor_16CH_96W fmf Protein A biosensor_8CH_96W fmf Protein A or G biosensor_16CH_96W fmf Protein A or G biosensor_8CH_96W
453. ove Fill Fill Plate Figure 7 43 Selecting a Sensor Tray Column 2 Right click in the Sensor Tray Map or click in a cell in the Sensor Type table column and select a biosensor type from the drop down list The biosensor type associated with the assay will shift location accordingly see Figure 7 44 In the example shown Streptavidin is the Sensor Type used for the current assay Column 1 was reassigned as AHC according to the heterogeneous tray being used Octet System Data Acquisition User Guide Release 7 1 page 256 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Sensor Tray V Replace sensors in tray after use ACEO OououL Lot Number Information A AN A BLIBO ae 4 C Anon ANC anhocre oo AHC Anti higG Fc Cd AHC Ant higG Fcc o E_IBOA anc antehigG Fe Cd SA Streptavidin F C C H SA Streptavidin s0000 aos HOO ae Legend __ Unassigned sensors RR Missing sensors a Remove Fill Fill Plate A3 SA Streptavidin B3 SA Streptavidin Sample Plat idi aat 5 3 4 e 6 7 8 9 10 11 12 a Sere a AOOOOOQOO 09 E SA sean G3 SA Streptavidi BOOCOO0O O sem COOOCO0O OO m srcsreptavain D A amp amp O B4 SA Streptavidin causes e9 pen E4 SA Streptavidin FOOOOQO OQ R eraran SA Streptavidi ILLL OO ia stisrerevey H OOOCO0O OO Legend Unassigned samples Figure 7 44 Assay Sensor Type Reassignment 3 Repeat the previous steps
454. pecific project Project list only ACCESSING THE GXP SERVER MODULE DIRECTLY The GxP Server module can be accessed by administrators directly without having to initi ate an administrator user session Direct access provides administrators with server testing options as well as access to all administrative functions discussed earlier in this section To access the GxP Server module directly Ifthe GxP Server module is installed on a network location Double click on the FBServerConfig exe file in the FBServer7 folder from the installed location File Edit View Tools Help Organize Include in library Share with Burn New folder _ see z 4 ForteBio Name Date modified Type Size gt DataAcquisition7 x 2 3 FBServer exe 12 3 2010 3 53 PM Application 2 966 KB gt DataAnalysis7 lt 3 FBServerConfig exe 12 3 2010 3 53 PM Application 7 821 KB FBServer7 3 FBServerMonitor exe 12 3 2010 3 54PM Application 6 909 KB amp ForteBio 2 10 2011 6 20PM __Internet Shortcut 1 KB e Globe ico 12 1 2010 4 21 PM Icon 25 KB E uninst exe 2 10 2011 6 20 PM Application 54 KB Figure B 53 Accessing the GxP Server on the Network Ifthe GxP Server module is installed on a local host computer Double click the ForteBio GxP Server desktop icon Octet System Data Acquisition User Guide Release 7 1 Accessing the GxP Server Module Directly page 397 ForteBio GxP Server
455. peed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Buffer Time s and The duration of biosensor incubation in the first buffer in seconds Shake speed rpm and the sample platform orbital shaking speed rotations per minute Octet System Data Acquisition User Guide Release 7 1 page 136 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 17 Advanced Quantitation Assay Parameters Enzyme Time s The duration of biosensor incubation in seconds in the enzyme and Shake speed solution and the sample platform orbital shaking speed rotations rpm per minute 2nd Buffer Time s The duration of biosensor incubation in seconds in the second and Shake speed buffer solution and the sample platform orbital shaking speed rpm rotations per minute Detection Time s amp The duration of data acquisition during the detection step in sec Shake speed rpm onds in an advanced quantitation assay NOTE A subset of data points may be selected for processing during data analysis Offline Choose this option to incubate sample with biosensors outside the Octet system Offline incubation is best performed on the ForteBio Sidekick biosensor immobilization station Reuse Buffer Allows buffer wells to be reused If unselected the number of buf fer columns must equal the number of sample columns If selected the number of buffer colum
456. pen Right Table 2 5 Octet QK System Specifications Item Description Equipment Classifications Product Classification Class 1 Detachable power cord Installation Overvoltage Category Category II Pollution Degree Degree 2 EMC Classification Group I Class A ISM Equipment EN55011 emissions EN61326 immunity Environmental Storage Temperature 20 to 70 C Optimum Operating Temperature 22 4 C Safe Operating Temperature 15 to 30 C Humidity Non condensing 10 to 80 Relative Humidity Indoor Use Only Operating Altitude 0 to 2 000 meters Compliance CE CSA Capabilities Protein quantitation Kinetic and affinity analyses kops Kar Kg Kp Binding specificity and cooperativity Kinetic screening of proteins peptides and other biomol ecules Recommended analyte molecular weight of 10 000 Da or higher Octet System Data Acquisition User Guide Release 7 1 page 24 Chapter 2 Octet System Specifications Table 2 5 Octet QK System Specifications Continued Item Description Sampling Format Required plate 96 well black flat bottom polypropylene microplate Greiner Bio One 655209 SBS standard microplate Single sample plate capacity Sample Volume 180 220 uL well 96 well plate Sample Types Purified samples common culture media crude lysates Biosensor Type Disposable single use fiber optic biosensors with optional reuse by regeneration Bios
457. perator Dilution orientation 3388 Right Down Left g up L Figure 8 11 Sample Plate Map Assigning Sample Concentrations Using Dilution Series 3 Select a series operator enter an operand and select the appropriate dilution orienta tion see Figure 8 12 Highest Concentration Lowest Concentration Figure 8 12 Concentration Representation in Dilution Series 4 Click OK The Sample Plate Table displays the standard concentrations Octet System Data Acquisition User Guide Release 7 1 page 288 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Annotating Samples You can enter annotations notes for multiple samples in the Sample Plate Map or enter information for an individual sample in the Sample Plate Table For greater clarity annota tion text may be displayed as the legend of the Runtime Binding Chart during data acqui sition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend Annotating Wells in the Sample Plate Map To annotate one or more wells 1 Inthe Sample Plate Map select the samples to annotate right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 8 13 enter the Sample ID and or Well Information and click OK Sample Plate 384 wells 123456789 1011121314151617 1819202122232
458. periment Run Experiment Assay 2 keg 0 02 30 of 0 09 20 fi In this step you can review the steps that make up the experiment moving the slider to change the active step peal Sensor Tray Sample Plate 384 wells 9 10 11 12 Wi2sa4 OO000 111213141516 171819202122 3334 Ow Danaa HOooooo HGGSG HG0eenn OOO0ooc oooeoco 3 L L E fal L E L Ionmoowb Ol Legend E Unassigned sensors ie Missing sensors Step Information Assay 2 Step 1 Type Sample Time 120s FlowRate 400 rpm Sensor Anti Human IgG Fe Figure 6 54 Review Experiment Window SAVING EXPERIMENTS After a run the software automatically saves the experiment information that you specified sample plate definition biosensor assignment assay settings to an experiment method file fmf If you set up an experiment but do not start the run you can manually save the experiment method To manually save an experiment method 1 Click the Save Method File button 5 or on the main menu click File gt Save Method File To save more than one open experiment click the Save All Methods Files button ga 2 In the Save dialog box enter a name and location for the file and click Save Octet System Data Acquisition User Guide Release 7 1 page 192 Chapter 6 Quantitation Experiments Octet RED384 and QK384 NOTE If you edit a saved experiment and want to save it with
459. periments Octet RED384 and QK384 Adding an Assay Through Replication A sample plate can include multiple assays that are the same replicates or different Each assay utilizes a new set of biosensors Replicates within a single assay will therefore use the same biosensor and replicates in different assays will use different biosensors To add a replicate assay to a plate 1 Inthe Assay Steps List select the steps to copy and click Replicate e To select adjacent steps press and hold the Shift key while you click the first and last step in the selection e To select non adjacent steps press and hold the Ctrl key while you click the steps 2 Inthe Replicate Steps dialog box click the Add as a new assay option Figure 8 40 CE Steps List NewAssay Move Up Mave Down I Damas Replicate Replicate P ime Assay paa psa Step Name Seg Type Sensor Type A oi equilibration _ equilibration p s AHC an WE Fe Capre ja E EE g sor on AHC an g BAe esn AnthlaG Fe Capture Neutralization 3 Custom Replicate Steps o pe fas te Replication Type Add as a new assay i Append to current assay Offset steps Sample steps only All Steps Sample steps will be adjusted Horizontally Vertically Figure 8 40 Adding a Replicate Assay to a Plate 3 Click the Offset steps check box and set the options as app
460. plate at ambient 4 C IMPORTANT To save the new default temperature value you must restart the software Octet System Data Acquisition User Guide Release 7 1 Monitoring Experiments Remotely page 45 MONITORING EXPERIMENTS REMOTELY If the Octet system computer is connected to a local network experiment progress can be monitored remotely from any networked computer smartphone or mobile device using any web browser In addition instrument log files and previously run experiments can also be accessed remotely for review 1 From the Main Menu click File gt Options 2 Inthe Options dialog box Figure 3 18 select the Web Server check box Adjust the Port and Refresh settings and change the Connect as IP address if needed The default Refresh rate of 10 will refresh the experiment view in the web browser every 10 sec onds Click OK NOTE ForteBio recommends using the Port and Connect as IP address set tings shown as default in the Web Server box as they are unique to your par ticular Octet system r Options Data Files Port Refresh s Quantitation data repository C Temp cal Kinetics data repository C Temp Use old 5 0 file format for FRD files Use extended sample types Startup Simulation Temperature 30 al oc Tf no instrument is connected the x application is configured using the properties of the selected instrument pata opion
461. plate while plate until the experiment starts waiting Open runtime Displays the Runtime Binding Chart for the current biosensor dur charts auto ing data acquisition matically Automatically Saves an image jpg of the Runtime Binding Chart The binding save runtime data frd is saved as a text file regardless of whether a chart image is chart created Set plate tem Specifies a plate temperature and enters the temperature in the dia perature C log box If not selected the plate temperature is set to the default temperature specified in File gt Options The factory set default tem perature is 30 C NOTE If the actual plate temperature is not equal to the set plate temperature a warning displays and the Octet System Data Acquisition software provides the option to wait until the set temperature is reached before proceeding with the run continue without wait ing until the set temperature is reached or cancel the run Advanced settings are available for Octet RED384 and Octet QK384 systems The signal to noise ratio of the assay can be optimized by selecting different acquisition rates The acqui sition rate refers to the number of binding signal data points reported by the Octet system per second and is reported in Hertz per second A higher acquisition rate generates more Octet System Data Acquisition User Guide Release 7 1 page 198 Chapter 6 Quantitation Experiments Octet RED384 and QK384
462. plicate Group table column 2 Enter a group name see Figure 7 16 Octet System Data Acquisition User Guide Release 7 1 page 230 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Sample Plate Table Concentration units pg ml Z Molar concentration units nM kA Well Sample ID Replicate Group Type Conc ug ml MW kD Molar Conc nM Information a A4 Association Sample 10 150 66 67 1X Kinetics Buffer B84 Association 2 Sample 5 150 33 33 1X Kinetics Buffer c4 Association 3 Sample 25 150 16 67 1X Kinetics Buffer D4 Association 4 Sample 1 25 150 8 333 1X Kinetics Buffer QE4 Association 5 Sample 0 625 150 4 167 1X Kinetics Buffer F4 Association 6 Reference 1X Kinetics Buffer G4 Association 6 Reference 1X Kinetics Buffer H4 Association 6 Reference 1X Kinetics Buffer Figure 7 16 Add Replicate Group from the Sample Plate Table Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the Sample Plate Table To view edit com mands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE The right click menu is context dependant Right clicking on a cell where the value is not highlighted and in edit mode opens the Sample Plate Map menu used to designate sample types 3 Repeat the previous steps to assign new samples to the existing Replicate
463. quantitation 96 132 Quantitation Time parameter quantitation 384 169 quantitation 96 92 quantitative experiment analyzing 68 140 216 276 setting up 68 140 216 276 Quench well type kinetics 384 281 kinetics 96 218 quenching steps 237 303 R raw reference subtracted data viewing quantitation 384 201 quantitation 96 123 read head configuration kinetics 384 278 quantitation 384 143 reagent plate defining quantitation 384 166 modifying quantitation 384 299 Octet System Data Acquisition User Guide Release 7 1 page 26 reagent plate definitions saving 301 Reagent Plate Map 166 Reagent Plate Map figure 166 300 Reagent Plate radio button 166 reagent plates loading kinetics 384 324 Received well type quantitation 384 145 quantitation 96 71 recommended sensor offset 198 330 Reference well type 218 kinetics 384 280 quantitation 384 145 quantitation 96 71 reference biosensors designating 105 110 182 187 257 258 321 designating during acquisition 268 333 reference biosensors designating during acquisition quantitation 384 201 quantitation 96 124 Reference menu 124 201 268 333 reference wells defined 81 156 designating quantitation 384 156 quantitation 96 81 reference type of well 71 145 reference subtracted data viewing kinetics 384 332 kinetics 96 268 reference subtracted data viewing quantitation 384 201 quantitation 96 123 Refresh settings 45 Regeneration reserve
464. quantitation and kinetics experiments on the Octet instrument e Maintain the Octet instrument Use the optional Octet system 21 CFR Part 11 Compliance Validation module Octet System Data Acquisition User Guide Release 7 1 page 8 Chapter 1 welcome ABOUT THE OCTET SYSTEM The Octet system enables real time quantitation or kinetic characterization of biomolecular interactions A system includes the Octet instrument with the following components e Computer e Hardware Software Modules Data Acquisition and Data Analysis see Table 1 1 For more details on the Data Analysis software see the Data Analysis User Guide Table 1 1 Octet System Functions Octet Software Functions Data Acquisition Define a quantitation or kinetic experiment and save the s experiment for future use je Define custom assays e Run the experiment and acquire binding data View and save binding data to a user specified location Data Analysis Analyze binding data and view analysis results 2 ful Export or copy analysis results Generate a report of quantitation or kinetic results in table and graph formats For information on preparing samples for quantitation or kinetics experiments please see the appropriate ForteBio Octet Biosensor product instructions WHAT S NEW IN THE OCTET SYSTEM DATA ACQUISITION SOFTWARE RELEASE 7 1 The following features are new for the Octet Pro Data Acquisition software
465. r coded outlines as a visual indication of which wells are in the same group see Figure 5 18 Octet System Data Acquisition User Guide Release 7 1 page 86 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Sample Plate 96 wells V1 2 3 4 5 6 7 8 9 10 11 12 Figure 5 18 Replicate Groups Displayed in Sample Plate Map The Sample Plate Table will update with the Replicate Group names entered see Figure 5 19 Sample Plate Table Concentration units pg ml EA Export Import Well Sample ID Replicate Group Type Conc ig ml Dilution Facto OA IgGStandard 200 Standard 200 n a B1 IgGStandard 100 Standard 100 n a C1 IgGStandard 50 Standard 50 n a D1 IgG Standard 25 Standard 25 n a El IgGStandard 10 Standard 10 n a F1 IgGStandard 5 Standard 5 n a O G1 IgG Standard 2 5 Standard 2 5 n a H1 IgGStandard 1 Standard 1 n a OA2 IgGStandard 200 Standard 200 n a B2 IgG Standard 100 Standard 100 n a C2 IgG Standard 50 Standard 50 n a D2 IgG Standard 25 Standard 25 n a O E2 IgGStandard 10 Standard 10 n a O F2 IgGStandard 5 Standard 5 n a G2 IgGStandard 2 5 Standard 25 n a O H2 IgG Standard 1 Standard 1 n a O A3 IgG Standard 200 Standard 200 n a O B3 IgG Standard 100 Standard 100 nia O C3 IgGStandard 50 Standard 50 n a D3 IgG Standard 25 Standard 25 nia OE3 IgGStandard 10 Standard 10 n a O F3 IgGStandard 5 Standard 5 n a G3 IgG Standard 2 5 Standard 2
466. r of regeneration neutralization cycles that a biosen sor undergoes before reuse Regeneration cycles NOTE In an Advanced Quantitation experiment this option is only available if the first step biosen sor incubation in sample is performed online Selecting a Custom Assay You can select a custom assay when you define a sample plate To select a custom assay 1 In the Plate Definition tab click Modify in the Assay Settings box The Edit Assay Parameters dialog box displays see Figure 6 71 Plte Definition Sensor Assignment Review Experiment Q Run Experiment Read Head Quantitation 120 In this step all the information about the sample plate and its wells will be entered First check the assay settings Then highlight one or more wells on the sample plate and rightclick to enter modify well data Shake speed 400 8 Channels 16 Channels Sample Plate Table Concentration units gmt Zi Export l Import J Assay Settings i i j Well Sample ID Replicate Group Type Conc Dilution Factor Information Assay Basic Quantitation F P Eye ugim Standard Assay Single analyte Time s 9 Assay Parameter Available Assays Assay Parameters Basic Quantitation Single analyte Multiple analyte Anti Penta HIS High sensitivity Replicates per Anti Penta HIS Standar
467. r tray for each type of biosensor If the different types of biosensors are in the same tray change the biosensor type as appropriate The biosensor types shown in the Sensor Type table column are those designated during the kinetics assay definition In the example shown in Figure 7 36 the experiment includes three assays in the same wells The use of those wells by three different biosensors is indi cated by the pie chart colors NOTE The Sensor Type for the assay must be first be defined in the Assay Steps List on the Assay Definition Tab Changing the Sensor Type from the Sensor Assignment Tab will not update the assay Octet System Data Acquisition User Guide Release 7 1 page 250 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Plate Definition 2 Assay Definition Sensor Assignment Review Experiment Run Experiment In this step sensors are assigned to samples Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial tray Right click to assign a sensor type to selected sensors Sensor Tray Replace sensors in tray after use i 2 8 4 6 6 7 8 8 0 1 12 Well Sensor Type Lot Number Information L E A1__ sa Streptavidin Bi SA Streptavidin C C C1 __ SA Streptavidin 2 D1 _ SA Streptavidin E1 SA Streptavidin Fl SA Streptavidin
468. r user session 1 Launch the Data Acquisition or Data Analysis software by double clicking on the desk top icon Data Data Analysis Acquisition 7 0 CFR11 7 0 CFR11 Figure B 24 Data Acquisition and Data Analysis Desktop Icons The Login dialog box will display Octet System Data Acquisition User Guide Release 7 1 Starting an Administrator User Session page 379 Figure B 25 Login Dialog Box 2 Confirm that the Server location is correct If not please see Administrator Account Setup on page 374 3 Select Administrator from the User drop down list on E z fort sio Server localhost 20002 User Administrator Password Project none Figure B 26 Administrator User Name Selection 4 Enter your password in the Password text box Click for a password reminder if needed Octet System Data Acquisition User Guide Release 7 1 page 380 Chapter B 21 CFR Part 11 Software Administrator Options fort sio Server localhost 20002 User Administrator Password Project Reminder Employee number Figure B 27 Password Reminder 5 Select a project from the Project drop down list if required fort sio Server localhost 20002 User Administrator Password eeeecceece Project none Antigen Antibody screen Cell Culture screen Receptor Ligand screen Figure B 28 Project Selection 6 Click
469. racterization_8CH_96W fmf Kinetics gt Biomolecule kinetics AR biosensor Screening_16CH_384W fmf gt r Quantitation Templates Skip Step l Stol z Biomolecule kinetics SA biosensor Screening_8CH_96W fmf Small Molecule and Fragment Kinetics SSA biosensor Figure 8 53 Saved Experiments in the Template Folder RUNNING A KINETICS EXPERIMENT D IMPORTANT Before starting an experiment ensure that the biosensors are properly rehydrated For details on how to prepare biosensors see the appro priate biosensor product insert Loading the Biosensor Tray Sample and Reagent Plates To load the biosensor tray sample plate and reagent plate 1 Open the Octet instrument door lift the handle up and present the instrument stage click the Present Stage button 2 Place the biosensor tray sample plate and reagent plate on the appropriate stage so that well A1 is located at the upper right corner see Figure 8 54 a Place the rehydration plate and biosensor tray on the biosensor stage left plat Octet System Data Acquisition User Guide Release 7 1 Running a Kinetics Experiment page 325 form b Place the sample plate on the sample stage middle platform c Place the reagent plate on the reagent stage right platform Well A1 Position Figure 8 54 Octet Instrument Stage Platform IMPORTANT Ensure that the bottom of the sample plate reagent plate and biosensor
470. rature 22 4 C Safe Operating Temperature 15 to 30 C Humidity Non condensing 10 to 80 Relative Humidity Indoor Use Only Operating Altitude 0 to 2 000 meters Compliance CE CSA Capabilities e Protein quantitation Kinetic and affinity analyses kops Ka Kg Kp Binding specificity and cooperativity Kinetic screening Octet System Data Acquisition User Guide Release 7 1 page 26 Cc hapter 2 Octet System Specifications Table 2 6 Octet QK384 System Specifications Continued Item Description Sampling Format Required plates 96 well black flat bottom polypropylene microplate Greiner Bio One 655209 or similar SBS standard microplate 384 well black flat bottom polypropylene Greiner Bio One 781209 384 well black tilted bottom polypropylene micro plate ForteBio 18 5076 or 18 5080 SBS standard microplate e Two plate stations Test volume e 180 300 uL in a 96 well plate non destructive and recoverable e 80 130 uL in a 384 well plate non destructive and recoverable e 40 100 uL in a 384 well tilted bottom microplate 384TW non destructive and recoverable Sample Types Purified samples common culture media crude lysates Biosensor Type Disposable single use fiber optic biosensors with optional reuse by regeneration and or re racking Biosensor Tray Type 8 x 12 format 96 biosensor tip tray green color Automation Optics and Mechanic
471. ray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate Sensor Tra lie os Tray Format Homogeneous trays Em E E Dmm E Siam EOM EM roammoonr OOS9OCO OO99OOO0O0 Legend Unassigned samples Legend j RRA Missing sensors Remove Fill Fill Plate Sample Plate 7 1 9 10 11 12 BS cs DS Lot Number Information Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A a WW Figure 5 44 Biosensor Assignment using Homogeneous Trays and Two Biosensor Types 6 To view the biosensor assignments in another tray click the Sensor Tray button and select a tray number from the drop down list The Sensor Tray Map and table for the tray selected will be shown see Figure 5 39 Octet System Data Acquisition User Guide Release 7 1 page 110 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Sensor Tray 7 Replace sensors in tray after use of 4
472. rcode 196 Assay Type 196 Auto Increment File ID Start 197 Experiment Run Name 196 Plate Name Barcode 196 Quantitation Data Repository 196 quantitation 96 2nd Plate Name Barcode 119 Assay Type 119 Auto Increment File ID Start 120 Experiment Run Name 119 Plate Name Barcode 119 Quantitation Data Repository 119 Experiment type selecting for the Octet RED384 142 for the Octet RED96 70 Experiment Wizard 34 described 40 figure 40 opening 35 starting kinetics experiments 384 277 Experiment Wizard button 69 141 217 277 Experiment wizard starting experiment quantitation 384 141 experiments adding assays 248 313 kinetic starting 384 277 96 217 monitoring remotely 45 remote view via web browser figure 47 reviewing kinetics 96 258 saving manually 259 323 saving to the factory installed Template folder 260 324 starting 261 325 quantitation 384 194 quantitation 96 117 stopping 36 stopping in progress 266 331 Octet System Data Acquisition User Guide Release 7 1 page 16 quantitation 384 199 quantitation 96 122 Export button 88 Sample Plate Map kinetics 96 233 export options Copy the Runtime Binding Chart quantitation 384 205 quantitation 96 128 Export the Runtime Binding Chart to a graphic file quantitation 384 204 quantitation 96 127 Print the Runtime Binding Chart quantitation 384 205 quantitation 96 128 save the binding data quantitation 384 204 quantitation 96 127 Export Plate
473. rder of biosensor types listed in the Sensor box will be used as the default tray assignment see Figure 6 48 F Tray Format Heterogeneous Sensor trays may contain various sensor types but all sensor trays used are identical Homogeneous A different sensor tray is used for each sensor type Sensors Protein G Move Up L Figure 6 48 Biosensor Types List Order in Sensor Box 5 Click OK The software will automatically calculate the number of biosensor trays needed and assign biosensors types to each tray In the example shown in Figure 6 49 Protein A and Protein G biosensor types will be used for the multiple analyte experiment using two replicates Four homogeneous bio sensor trays two for each biosensor type will be needed for the experiment The Tray 1 Sensor Tray Map will be displayed by default Octet System Data Acquisition User Guide Release 7 1 page 186 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Piate Definition B Sensor Assignment Review Experiment Q Run Experiment In this step sensors are assigned to samples If you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate Sensor Tray Sensor Tray 7 Replace sensors in tray after use a Tayi xj of 4 Tray Format Homogeneous trays 4 Well Sensor T
474. re B 4 Installation Progress The installation wizard displays the Completing the Data Acquisition 7 0 Setup Wizard dialog box Figure B 5 i Data Acquisition 7 0 Setup ol Completing the Data Acquisition 7 0 Setup Wizard Data Acquisition 7 0 has been installed on your computer Click Finish to dose this wizard Figure B 5 Completing the Data Analysis 7 0 Setup 6 Click Finish to complete the installation Octet System Data Acquisition User Guide Release 7 1 Installing the Data Analysis 7 0 21 CFR Part 11 Software page 369 INSTALLING THE DATA ANALYSIS 7 0 21 CFR PART 11 SOFTWARE To install the Data Analysis 7 0 21 CFR Part 11 software 1 Insert the software CD into your CD drive 2 Navigate to the window listing the files located on the installation CD 3 Double click DataAnalysis CFR 7_0_0_x exe to launch the installation wizard see Figure B 6 i Data Analysis 7 0 Setup SIE Welcome to the Data Analysis 7 0 Setup Wizard for 21 CFR part 11 This wizard will guide you through the installation of Data Analysis 7 0 Itis recommended that you dose all other applications before starting Setup This will make it possible to update relevant system files without having to reboot your computer Click Next to continue Figure B 6 Data Analysis 7 0 for 21 CFR Part 11 Software Setup Wizard 4 Click Next to display the Choose Install Location dialog box Figure B 7 i3 Data Analysis
475. riment type for the Octet RED384 142 for the Octet RED96 70 in the Experiment Wizard 70 from a set of predefined ForteBio quantitation or kinetics method templates 35 molar concentration units 222 284 molar concentration units in the Plate Definition window figure 222 285 non adjacent steps to add and copy 243 308 project in the Audit Trail 63 Runtime Binding Chart legend kinetics 384 336 kinetics 96 271 quantitation 384 203 quantitation 96 126 server location 53 wells in the Sample Plate Map kinetics 384 282 Octet System Data Acquisition User Guide Release 7 1 page 32 kinetics 96 219 quantitation 384 148 quantitation 96 73 wells in the Sample Plate Map kinetics 384 281 selecting the Web Server in the Options dialog box figure 45 selectively display the acquisition for a data column 267 331 quantitation 384 199 quantitation 96 122 Send Commands Command Field figure 349 Sensor Assignment tab 48 96 100 173 177 303 Sensor Assignment window 96 100 173 177 303 displayed figure 250 314 Sensor Assignment Window for Basic Quantitation without Regeneration figure 97 100 174 177 sensor offset 198 330 Octet QK384 20 27 Octet RED384 20 27 Sensor offset Octet QKe advanced settings 121 Sensor Tray map color codes 122 199 267 331 sensor tray maps 256 automatically adding 256 320 changing biosensor locations 252 257 removing biosensors 253 317 re
476. riments Octet RED384 and QK384 L x CAUsers Owner Documents Contracting Forte Bio User_Guides Data and methods 384 04 27 11 384 K ProA higG Kinetics Runtime Binding Chart ston x Current Binding Charts Sensors to Chart Plate Status Plate Legend Kinetics Assay 1 SelectAll ss lt Rengon kin Selected Kinetics Assay 2 1234 EZ B 9 1011421914151617 10192021222524 SensorA7 A E 1 Processing 1 B E i Processed 1 sensor D6 a H O Reseved SensorE6 Sensor E7 E H od Data Eror HeensorFs Sensor F7 i Se Fail sensorGs Sensor G7 F a H Siar Bsensor He Sensor H7 G j H LT mim Subtract reference sensors Assay Step Status Experiment Progress Step 11 of 11 Step details Assay 2 of 2 Elepsedtime Total exp time Extend Current Step 20 s 20s 3 equilibration 1840 8 1840 s 0311 osia Jono e s l gt Go to Next Step Flip Data 40 35 l i I l l l 25 i l I l l 0 200 400 800 Time sec 600 1200 1400 Sensor AG Sensor B6 Sensor C6 Figure 8 58 Runtime Binding Chart Window Opening the Runtime Binding Chart After an experiment is run you can open and review the Runtime Binding Chart at any time 1 Click File gt Open Experiment 2 Inthe dialog box that appears select an experiment folder and click Select Viewing Reference Subtracted Data If the experiment
477. ropriate see Table 8 5 on page 309 for more information If the replicate assay uses the same sample columns as the original assay do not choose the Offset steps option If the replicate assay uses a different sample column select Offset steps and the appropriate options Sample steps only offsets the sample wells by the value specified under Sam ple steps will be adjusted The offset will not be applied to reagent wells such as buffer loading regeneration neutralization and detection Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 313 All Steps offsets all wells in the assay including sample and reagent wells by the value specified under Sample steps will be adjusted 4 Click OK The new assay appears in the Assay Steps List 5 Continue to add assay steps as needed ASSIGNING BIOSENSORS TO SAMPLES After you define the sample plate and assay s click the Sensor Assignment tab or click the arrow to access the Sensor Assignment window The color coded Sensor Tray and Sample Plate Map show the locations of the biosensors associated with the samples Figure 8 41 NOTE When using a 96 well plate with the 8 channel read head do not put biosensors in columns 2 4 6 8 10 and 12 if the biosensors will be returned to the biosensor tray and not discarded If the biosensors will be ejected biosen sors can be placed in all columns NOTE Ifan experiment includes more t
478. rs to samples 249 quantitation 384 173 quantitation 96 96 dilution factor to selected wells quantitation 384 154 quantitation 96 79 Octet System Data Acquisition User Guide Release 7 1 page 5 dilution factor to unknowns quantitation 384 153 quantitation 96 78 heterogeneous biosensor trays quantitation 96 101 heterogenous biosensor trays quantitation 384 178 homogenous biosensor trays quantitation 384 183 quantitation 96 106 molecular weight kinetics 96 221 molecular weight and molar concentration kinetics 283 privileges 385 Replicate Groups in the Sample Plate Map kinetics 384 290 kinetics 96 227 quantitation 384 159 quantitation 96 84 Replicate Groups in the Sample Plate Table kinetics 384 293 kinetics 96 229 quantitation 384 162 quantitation 96 87 sample concentrations by value kinetics 96 figure 223 sample concentrations using dilution series kinetics 384 286 kinetics 96 223 kinetics 96 figure 224 serial dilution to selected wells quantitation 384 154 quantitation 96 79 serial dilution to unknowns quantitation 384 153 quantitation 96 78 standard concentration quantitation 384 figure 151 quantitation 96 figure 76 standard concentrations using a dilution series quantitation 384 149 quantitation 96 74 step types in the sample plate figure 242 307 user group 385 user specified concentration to samples 222 285 user specified concentration to standards quan
479. rting quantitation 384 164 quantitation 96 89 Plate Definition window Designate Unknown Wells figure 78 153 Designating Standards figure 74 149 Export button figure 233 234 Import button figure 234 Octet System Data Acquisition User Guide Release 7 1 page 24 kinetics experiments 282 selecting concentration units figure 222 285 molar concentration units figure 222 285 plate definitions importing kinetics 384 298 kinetics 96 234 plate name barcode file prefix 264 328 Plate Name Barcode setting Run Experiment window settings quantitation 384 196 quantitation 96 119 plate temperature range 43 plate temperature setting 43 Port 2002 default server settings 54 Positive control 218 Positive Control well type kinetics 384 280 quantitation 384 145 quantitation 96 71 post condition biosensors 12 Post condition sensors parameter 134 211 Advanced Quantitation quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 Pre condition sensors parameter Advanced Quantitation 136 213 quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration 134 211 Precondition sensors parameter Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 preparing biosensors 68 preparing samples for quantitation or kinetics experiments 8 Present automation interface command 350 Present Stage
480. s e Up to 16 biosensors in parallel e Ability to integrate the Octet instrument with a laboratory automated robotic system for automated plate and bio sensor tray handling e 16 channel biosensor manifold e Optical interferometer Sample plate platform temperature range From 4 C above ambient to 40 C 2spectrometers one dedicated spectrometer per eight biosensors Throughput Up to 16 biosensors in parallel maximum of 384 tests unat tended e Two microplates either 96 or 384 well at once Only one plate can be used for samples The second plate is used for reagents Octet System Data Acquisition User Guide Release 7 1 Octet QK384 System Specifications page 27 Table 2 6 Octet QK384 System Specifications Continued Item Description Orbital Flow Static or 100 1 500 rpm Capacity Dimensions 30 1 H x 31 5 W x 31 4 D 76 5 cm H x 80 cm W x 79 8 cm D Weight 150 Ib 68 kg Electrical e Mains AC 100 240 V 5 0 2 0 A 50 60 Hz single phase Requirements e Power consumption 195 W 240 W peak Table 2 7 Sensor Offset and Well Volumes for Octet RED384 and Octet QK384 Recommended Minimum Fill Volume pL 96 well plate 384 well plate 384 well tilted bottom Greiner Bio One Greiner Bio One plate ForteBio 384TW 3 200 80 40 4 200 80 60 5 225 100 80 6 250 120 100 7 300 130 100 Octet System Data Acquisition User Guide Release 7 1 page 28 Chapter 2 Octet Sy
481. s quantitation 384 2nd Plate Name Barcode 196 Assay Type 196 Auto Increment File ID Start 197 Experiment Run Name 196 Plate Name Barcode 196 Quantitation Data Repository 196 quantitation 96 2nd Plate Name Barcode 119 Assay Type 119 Auto Increment File ID Start 120 Experiment Run Name 119 Plate Name Barcode 119 Quantitation Data Repository 119 Experiment type selecting for the Octet RED384 142 for the Octet RED96 70 Experiment Wizard 34 described 40 figure 40 opening 35 starting kinetics experiments 384 277 Experiment Wizard button 69 141 217 277 Experiment wizard starting experiment quantitation 384 141 experiments adding assays 248 313 kinetic starting 384 277 96 217 monitoring remotely 45 remote view via web browser figure 47 reviewing kinetics 96 258 saving manually 259 323 saving to the factory installed Template folder 260 324 starting 261 325 quantitation 384 194 quantitation 96 117 stopping 36 stopping in progress 266 331 Octet System Data Acquisition User Guide Release 7 1 page 16 quantitation 384 199 quantitation 96 122 Export button 88 Sample Plate Map kinetics 96 233 export options Copy the Runtime Binding Chart quantitation 384 205 quantitation 96 128 Export the Runtime Binding Chart to a graphic file quantitation 384 204 quantitation 96 127 Print the Runtime Binding Chart quantitation 384 205 quantitation 96 128 save the binding data quantitation 38
482. s Save Method File As Open Experiment Save Experiment As Print Ctrl P Print Preview Print Setup 1 Example Quantitation Method file fmf 2 BHO81908 4 ADAM titration_LABUSERO81908_ExpMethod fmf File History 3 LABUSERO90811_ExpMethod fmf Options Exit Figure 3 4 File Menu Table 3 1 File Menu Commands Menu Command Toolbar Function Button Open Method File 4 Opens an experiment method file fmf Close Method File N A Closes the active experiment method file but does not save changes Save Method File 5 Saves the active experiment method file fmf Save All Method Files re Saves all open method files fmf Save Method File As N A Allows the active experiment method file to be saved as a new file without overwriting the original method file Open Experiment N A Opens an experiment folder Save Experiment N A Saves the active experiment Print N A Opens the Print dialog box to print a file Print Preview N A Opens a print preview window of a method file Print Setup N A Opens the Print Setup dialog box to print a file Octet System Data Acquisition User Guide Release 7 1 page 34 Chapter 3 Getting Started Table 3 1 File Menu Commands Continued Menu Command Toolbar Function Button File History N A Displays a list of previously opened files Options N A Opens the Options dialog box Please refer to Octet System Data Acquisition Options on page 40 for more information on
483. s select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during acquisition 3 Optional Double click in any cell in the Lot Number column to enter the biosensor lot number All wells in the Lot Number column will automatically populate with the lot number entered 4 Optional Double click in a cell in the Information column to enter biosensor informa tion for a particular cell NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 99 NOTE For greater clarity annotation text may be displayed as the legend of the Runtime Binding Chart during data acquisition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend 5 Optional for the Octet RED96 instrument only After an assay is completed the biosen sors can be returned to the biosensor tray or ejected through the biosensor chute to an appropriate
484. s 222 284 sampling format Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 sampling volume Octet RED96 instrument 17 Save All Method Files menu 33 Save Experiment menu 33 Octet System Data Acquisition User Guide Release 7 1 page 31 Save Method File As menu 33 Save Method File menu 33 Save to File menu 39 saved experiments in the Template folder figure 260 324 saving all method files 33 binding data 127 204 273 337 default temperature value 44 experiment method files 33 experiment method files to a new name 33 experiment methods 114 191 experiments manually 259 323 experiments to the factory installed Template folder kinetics 384 324 kinetics 96 260 quantitation 384 192 quantitation 96 115 modified parameter settings 91 167 reagent plate definition kinetics 384 301 quantitation 384 167 scaling Runtime Binding Chart kinetics 384 335 kinetics 96 271 quantitation 384 202 quantitation 96 126 screen components Octet System Data Acquisition software 31 Security menu availability 32 compliance features figure 59 described 36 figure 37 selecting adjacent steps to copy and add 243 308 concentration units 222 284 concentration units in the Plate Definition window figure 222 285 custom assays quantitation 384 214 quantitation 96 137 experiment method file opening function 33 Expe
485. s all windows in a cascade arrangement Tile Tiles all windows vertically Arrange Icons Arranges the minimized window icons in a row at the bot tom of the main software screen Open Windows Lists of windows currently open in the Main Screen Octet System Data Acquisition User Guide Release 7 1 page 38 Chapter 3 Getting Started Help Menu The Help menu provides access to software and instrument support information Data Acquisition User Guide Fl ForteBio Web Site About ForteBio Data Acquisition Figure 3 10 Help Menu Table 3 6 Help Menu Commands Menu Command Toolbar Function Button Data Acquisition User N A Opens the online Data Acquisition Guide Software User Guide ForteBio Web Site N A Opens a web browser and displays the ForteBio web page www forte bio com About ForteBio Data Displays software user and instru Acquisition ment information NOTE Clicking on the ForteBio logo in the upper right corner of the Main Screen also displays the About ForteBio Data Acquisition window Status Bar The Status Bar is located at the bottom of the Main Screen and displays current instru ment and experiment status as well as the plate temperature instrument Ready Experiment Not Started Plate temp 30 C Figure 3 11 Status Bar In the 21 CFR Part 11 version of the Data Acquisition software the Status Bar will also dis play the User and Project name entered at
486. s experiments 8 Present automation interface command 350 Present Stage menu 36 Print menu 33 Print Preview menu 33 print preview window 33 Print Setup dialog box 33 Print Setup menu 33 printing files 33 Runtime Binding Chart 128 205 273 338 prior to running an experiment 258 322 privileges assigning 385 project administration 390 Project drop down list 63 project selection figure 58 project settings changing 391 viewing 391 project based Audit Trail events figure 64 Octet System Data Acquisition User Guide Release 7 1 page 25 projects changing figure 64 deleting 392 editing 391 Projects tab 391 projects changing during a user session 64 properties for Octet System software displaying 38 Q QKe instrument replacing fuses 341 quantitation 384 144 Quantitation Data Repository setting Run Experiment window settings quantitation 384 196 quantitation 96 119 quantitation data repository user option 41 Quantitation Experiment Advanced Quantitation quantitation 384 142 Basic Quantitation 384 141 Basic Quantitation 96 69 Basic Quantitation with Regeneration 69 141 quantitation experiment defined 68 140 starting 69 141 Quantitation Shake Speed assay parameter quantitation 384 209 quantitation 96 132 Quantitation Shake Speed parameter quantitation 384 169 quantitation 96 92 Quantitation Time and Shake speed parameter 133 170 210 Basic Quantitation with Regeneration
487. s for the LOAD command const char AUT SWITCH DATASET d Parameter switches for the ANALYZE command const char AUT SWITCH PARAMS p const char AUT_ SWITCH XMLINFO x COMMAND API const char AUT CMD VERSION Version Returns the version of the app being automated and the API version Args none Response App product version e g 6 3 1 12 1 0 r n const char AUT CMD LOAD Load Loads an experiment Args d lt path gt Path to experiment data files Response OK r n Error lt reason gt r n Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 363 const char AUT CMD ANALYZE Runs an analysis Args p lt path gt _ x lt path gt tiple XML info files Response const char AUT CMD STATUS oR r n Error lt reason gt r n Analyze Path to parameters INI file Path to XML information file optional can be mul Status Returns status OK ready Busy running Error Action was terminated by an error Busy is followed by descriptive information on the progress of the experiment complete Args none Response OK r n Busy r n Running nn r n Error lt reason gt r n endif INC_ANALYSIS AUTOMATIONAPI H Octet System Data Acquisition User Guide Release 7 1 page 364 Chapter A Using Octet384 Syst
488. s in tray after use a of 4 Tray Format Homoge Tray 1 T Lot Number Informa Tray 3 ann ey Tray 4 G C1 Protein G D1 Protein G E1 Protein G F1 Protein G G1 Protein G H1 Protein G A2 Protein G B2 Protein G HERR REREREEe e F2 Protein G 2 isi G2 Protein G L Unassigned sensors RRI Missing sensors eS Figure 6 50 Tray Selection 7 To designate reference biosensors select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during acquisition 8 Optional Double click in any cell in the Lot Number column to enter a biosensor lot number All wells in the Lot Number column for the biosensor type selected will auto matically populate with the lot number entered Optional Double click in a cell in the Information column to enter biosensor informa tion for particular cell NOTE Edit commands Cut Copy Paste Delete and shortcut keys Cut Ctrl x Copy Ctrl c Paste Ctrl v Undo Ctrl z are available in the table To view edit commands double click the cell This highlights the value and allows it to be edited Next right click to view the edit menu NOTE For greater clarity annotation text may be displayed as the legend of the Runtime Binding Chart during data acquisition but annotations must be entered be
489. s selected in the Run Experiment window Figure 7 53 the Runtime Binding Charts are automatically displayed when data acquisition starts The Runtime Binding Chart window displays the assay step status experiment progress and the elapsed experiment time The Runtime Binding Chart is updated at the start of each experimental step The active biosensor column is color coded A green B magenta C orange D purple E olive F black G red H blue within the Sensor Tray Map Used sensor columns that are inactive are colored black Active sample columns are colored green Each assay in the experiment is represented by Assay X in the Current Binding Charts box To selectively display data for particular assay 1 Click the corresponding Assay number 2 Select a subset of sensors for a displayed column under Sensors to Chart box see Figure 7 53 WARNING Do not close the Runtime Binding Chart window until the experi ment is complete and all data is acquired If the window is closed the charts are not saved To remove the chart from view minimize the window The Octet System Data Acquisition software saves the Runtime Binding Chart as dis played at the end of the experiment For example modifying a chart by hiding the data for a particular biosensor will cause this data not to be included in the bitmap image generated at the end of the run L x C Users Owner Documents Contracting Forte Bio User_Guides Data a
490. s the Sensor Types dialog box to view current biosensor types add new biosensor types and remove biosensor types See Managing Biosensor Types on page 48 for more information Set Plate Temperature N A Opens the Temperature Setting dialog box that displays the current sample plate tem perature and allows users to change the cur rent temperature setting of the instrument See Setting the Plate Temperature on page 43 for more information To set the default temperature see Defining a New Default Sample Plate Temperature on page 44 Templates N A Allows users to select from a set of pre defined ForteBio quantitation or kinetics method templates Skip Step N A Skips the step in the method that is currently executing kinetics experiments only Octet System Data Acquisition User Guide Release 7 1 page 36 Chapter 3 Getting Started Table 3 3 Experiment Menu Commands Continued Menu Command Toolbar Function Button Stop gt Stops the experiment Data from the active biosensor is not saved but all data prior to the active biosensor will be available Instrument Menu The Instrument menu provides direct control of Octet instrument functions Instrument Window Hel Reset Stop Shaker Present Stage Figure 3 7 Instrument Menu Table 3 4 Instrument Menu Commands Menu Command Toolbar Function Button Reset N A Resets the instrument and the log in th
491. s you to insert the appropriate tray in the Octet instrument Reference Biosensors To designate reference biosensors select the desired biosensors in the Sensor Tray Map right click and select Reference The reference biosensors are marked with an R NOTE Reference biosensors may also be designated in the Runtime Binding Chart during acquisition Octet System Data Acquisition User Guide Release 7 1 page 258 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Changing the Biosensor Type The biosensor type used in the assay must be selected in the Assay Definition window To change the biosensor type 1 Click the Assay Definition Tab 2 Inthe Assay Steps List click the cell in the Sensor Type column to change 3 Select from the drop down list see Figure 7 46 IMPORTANT Ensure that the same biosensor types are selected in both the Assay Definition and the Sensor Assignment windows or the experiment can not be run Assay Steps List New Assay Move Up Move Down Remove Replicate Eara Assay Sample Step Name Step Type Sensor Type Assay Time i Equlibration 3 Custom SA Streptavidin la 1 2 ProA Immobilization IZ Loading ESA Streptavidin il 3 Baseline k Baseline SAHC Anti higG Fc Ca 1 4 Association lal Association pep taal ate 1 3 Dissociation Association Sosa Super Streptavi 1 11 Regeneration Custom E Custom i 12 Neutralization 3 Custom sA
492. sample well and the number of replicate assays in each well sor type per biosensor type Quantitation Time s The duration of data acquisition seconds while the biosensor is incubated in sample NOTE A subset of data points may be selected for processing during data analysis Quantitation Shake The sample platform orbital shaking speed rotations per min speed rpm ute Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 133 Basic Quantitation with Regeneration Assay Parameters a Edit Assay Parameters Available Assays Assay Parameters Basic Quantitation Name My Basic Quant with Regen Assay IE Anti Penta HIS High sensitivity E Anti Penta HIS Standard range High sensitivity Human IgG quantitation Single analyte Multiple analyte Human IgG Quantitation E Replicates persensortype 1 2 Immunogenicity Direct detection Murine IgG Quantitation Time 8 Protein L Standard range La Standard Assay My Basic Quant Assay Regeneration 5 400 2 sic Quantitation with Regeneration aie High sensitivity assay with regeneration Siesia 5 4 ate Ea Protein L Standard range V Pre condition sensors Post condition sensors Standard Assay Regeneration cycles 3 Ea vanced Quantitation E Immunogencity Enzyme Linked Residual Protein A Standard Assay Three Step Assay Description Enter a short description of the assay here Shake spe
493. se step types are assigned to col umns in the Sample Plate or Reagent Plate maps To build an assay 1 Select a step type in the Step Data List 2 Inthe Sample Plate Map double click the column that is associated with the selected step type For information about sample plate wells mouse over a well to view a tool tip see Figure 7 28 Sample Plate 96 wells VW 12 3 4 5 6 7 8 9 10 11 Assayed samples O Unassigned samples Figure 7 28 Tool Tip of Well Information The selected wells are marked with hatching for example and the step appears in the Assay Steps List see Figure 7 29 with an associated Assay Time Octet System Data Acquisition User Guide Release 7 1 page 242 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Plate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment fi In this step the assay steps will be assembled from the Step Data List Select a group of sensors and append the currently selected step into the current assay with a double click or right click for more options Sample Plate 96 wells 2 Step Data List Tine Wah Seis secede ter VW i123 4 6 6 7 8 9 10 11 12 Add l Copy l Remove Threshold Params A O O O O O O O 1 Name Time Shake speed Type Threshold B O O O O Beeasec a a i toa Cc O0 O00000
494. se 7 1 Defining the Sample Plate page 281 Table 8 2 Types of Sample Wells Icon Description Activation Activation reagent Makes the biosensor competent for binding Quench Quenching reagent Blocks unreacted immobilization sites on the bio sensor surface Load Ligand to be immobilized loaded on the biosensor surface Wash Wash buffer Regeneration Regeneration reagents dissociate the analyte from the ligand Selecting Wells in the Sample Plate Map There are several ways to select wells in the Sample Plate Map e Click a column header or select adjacent column headers by click hold drag Figure 8 5 left To select non adjacent columns hold the Ctrl key and click the col umn header e Click a row header or select adjacent row headers by click hold drag Figure 8 5 cen ter e Click a well or draw a box around a group of wells Figure 8 5 right Sample Plate Sample Plate Sample Plate 384 wells Sample Plate 384 wells 3 456 7 8 9 1011121314 151617 18192021222324 OO OOO ODO OOOO OOO0O 000000 OO OOONOODOOCOOOO 000000 OOOOOCOOOOOCO0000000 OO0OO0O0000000000 W123 45 6 7 8 9 1011121314 151617 18192021222324 EN 229990299999999 39892999 vozrszc Ir0nmoo0 oOOOO0O0OQOQOQOQOQOQQQQ0Q0Q0000000 POOOOQQQQ0Q000000000000000 Sample Plate Sample Plate 384 wells Modify Fi E 3456 7 8 91011121314151617 18192021222324 vozarzc zonmgonr OQ Standard C
495. sensor Trays If you are using a partial tray of biosensors some biosensors are missing specify the miss ing columns in the Sensor Tray Map 1 Select the column s without biosensors and click Remove or right click the selection and select Remove If the number of specified biosensors in the Sensor Assignment tab is less than the number required to perform the assay the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay 2 To view the additional biosensor tray that is required for the assay select Tray 2 from the Sensor Tray drop down list Figure 5 48 In the example shown Tray 1 is a partial tray that does not contain enough biosensors for the assay To designate a second tray select Tray 2 from the Sensor Tray drop down list Figure 5 48 top The Sensor Tray Map will then display the additional biosensors required for the assay Figure 5 48 bot tom Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 113 Sensor Tray Sensor Tray Sensor Replace sensors in tray after use of 2 Tray Drop ot Type Lot Number Information Down A List B1 Protein A C1 Protein A D1 Protein A E1 Protein A F1 ProteinA G1 Protein A H1 Protein A A2 Protein A B2 Protein A BOBO MME EEE o rona DIDI ee ES runa D aS
496. sensor pickup tips Figure 9 5 Octet Instrument Side Panel Removed 4 Gently clean the biosensor pickup tips with a Kimwipe moistened with a 30 60 iso propyl alcohol solution Remove any debris left from the biosensor hub 5 Allow the biosensor pickup tips to dry for at least one minute 6 Replace the side cover and then turn on the instrument Replacing Fuses Two replaceable fuses are located on the left back panel of the Octet instrument power supply Figure 9 6 D WARNING Turn off and unplug the instrument before replacing the fuses Octet System Data Acquisition User Guide Release 7 1 page 344 Chapter 9 Maintenance Fuses Figure 9 6 Octet Instrument Power Supply Back Panel To replace the fuses 1 Using a small screwdriver gently pop the fuse drawer out 2 Remove the expired fuse and place a new one in the holder WARNING Only use 5 amp slow blow fuses 3 Reinstall the fuse drawer Octet System Data Acquisition User Guide Release 7 1 page 345 APPENDIX A Using Octet384 Systems with an Automation Interface OVEIVIEW sir sariscerieieg eriti in s paw E wredenvareede E EEE E EE OE E 346 Design of the Automation Interface 1 0 0 0 ccc cece cece cece cee e teen en tetneeee 346 Automation Commands ssssiessisrred si eb eens sta dccanibe eo eden aed ween eae Seema oe 349 Octet System Data Acquisition User Guide Release 7 1 page 346 Chapter A Using O
497. sensor type biosensor type Quantitation The duration of data acquisition in seconds while the biosensor is Time s and Shake incubated in sample and the sample platform orbital shaking speed rpm speed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incubated in regeneration buffer to speed rpm remove bound analyte Neutralization The duration time and shaking speed of the neutralization step Time s and Shake where the biosensor is incubated in neutralization buffer after the speed rpm regeneration step Octet System Data Acquisition User Guide Release 7 1 Managing Assay Parameter Settings page 171 Table 6 7 Assay Parameters Basic Quantitation with Regeneration Parameter Description Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For example an acidic pre conditioning buffer maximizes the binding competence of Pro A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Regeneration The number of regeneration neutralization cycles that a
498. ser Guide Release 7 1 Defining the Sample Plate page 221 Entering Sample Information NOTE You must specify sample analyte concentration and molecular weight otherwise the Octet System Data Acquisition software cannot com pute a Kp value If the sample concentration is not specified only kyand kops are calculated You can also annotate any well with Sample ID or Well Infor mation and assign Replicate Groups Assigning Molecular Weight and Molar Concentration 1 Inthe Sample Plate Map select the sample wells right click and select Set Well Data 2 Inthe Set Well Data dialog box enter the analyte molecular and molar concentration Figure 7 5 Sample Plate 96 wells Fai z 3s 4 5 6 7 8 9 10 1 12 A O Sample z B Reference D Cc oO Control fe Negative Control p Positive Control EOOod D uffer F Activation D GOO Quench 9 H z Load E Wash Oe T Regeneration Set Well Data Clear Data gt s Copy to Clij Set Well Data v Extended S 2 3 L gt Well information Concentration ug ml Sample only v Sample ID By value 1 Dilution series Replicate Group Starting value Fee Well Information k 2 Dilution orientation 8838 O Right 8883 Olet Well Data Sample only Don g Molecular Weight and Molecular Weight kD 150 oO aa ii Molar Concentration Molar Concentration nM 66
499. sic Quantitation with Regeneration Parameter Description Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For example an acidic pre conditioning buffer maximizes the binding competence of Pro A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Regeneration The number of regeneration neutralization cycles that a biosen cycles sor undergoes before reuse Advanced Quantitation Assay Parameters r j 7 Assay Parameters Available Assays Assay Parameters E Advanced Quantitation Single analyte Multiple analyte E Immunogencity Enzyme Linked Replicates per sensortype 1 Residual Protein A er j E BAECS imaisi a PISROR E Three Step Assay Sample 20 S 1000 F Offline Buffer 120 1000 V Reuse Buffer Enzyme 120 1000 F 2nd Buffer 120 1000 Detection 120 E 1000 _ Regeneration Time s Shake speed Regeneration 5 1000 Neutralization R 1000 Pre condition sensors _ Post condition sensors Regeneration cycles 3 Blue indicates a built in assay OK Cancel i Figure 5 29 Assay Parameters Advanced Qua
500. sition User Guide Release 7 1 page 30 Sample Plate and Reagent Plate Layouts for an Advanced Quantitation Experiment 16 Channel Read Head figure 167 Sample Plate File csv example figure 90 165 sample plate format changing kinetics 384 280 quantitation 384 144 Sample Plate Map Setting a Dilution Series figure 75 150 223 286 sample plate shaker stopper 36 Sample Plate Table Shortcut Menu of Edit Commands figure 77 80 152 155 231 232 295 296 sample plate temperature recorded in log file 12 sample plates adding assays 248 313 assigning biosensors to samples 249 313 assigning step types to 242 307 defining kinetics 96 218 quantitation 384 142 quantitation 96 70 defining kinetics 384 278 importing definitions kinetics 384 298 kinetics 96 234 sample step types for kinetic assays listed table 236 Sample steps only option 244 309 Sample steps will be adjusted by vertically by one row option 244 309 Sample steps will be adjusted by X columns option kinetics 384 309 kinetics 96 244 Sample Time and Shake Speed parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 sample types Octet QK instrument 24 Octet QK384 instrument 26 Octet QKe instrument 22 Octet RED384 instrument 19 Octet RED96 instrument 17 sample volume Octet QK instrument 24 Octet QKe instrument 22 samples changing biosensor type 320 designating kinetics experiments 21
501. sors Assay Sample Step Name Step Type Sensor Type a i 11 Regeneration J Custom SA Streptavidin 1 12 Neutralization J Custom SA Streptavidin 1 11 Regeneration J2 Custom SA Streptavidin 4 12 Neutralization Custom SA Streptavidin 1 11 Regeneration 3 Custom SA Streptavidin 1 12 Neutralization 3 Custom SA Streptavidin 1 i Equlibration 3 Custom SA Streptavidin 1 rA ProA Immobilization IZ Loading SA Streptavidin i 3 Baseline ke Baseline SA Streptavidin 1 5 Association IC Association SA Streptavidin 1 3 Dissociation I Association SA Streptavidin 1 11 Regeneration Custom SA Streptavidin C Equlibration Custom SA Streptavidin ProA Immobilization IZ Loading SA Streptavidin SA Streptavidin SA Strantavictiny Legend O Unassigned Samples Pie charts Figure 7 47 Review Experiment Window SAVING EXPERIMENTS After an experiment is run the software automatically saves the experiment information that you specified sample plate definition biosensor assignment assay settings to an experiment method file fmf If you set up an experiment but do not start the run you can manually save the experiment method To manually save an experiment 1 Click Save Method File 2 or on the main menu click File gt Save Method File If there is more than one open experiment and you want to save all of them click Save All Methods Files 2 Inthe Save dialog box enter a name and locati
502. starting the GxP Server module 398 Resume automation interface command 350 resuming user session 66 Reuse Buffer parameter Advanced Quantitation quantitation 384 172 quantitation 96 95 Review Experiment window 114 191 258 322 Review Experiment window figure 114 191 259 323 reviewing experiments kinetics 96 258 Run automation interface command 349 Run Experiment tab 117 Run Experiment window Octet RED RED96 and QKe figure 117 194 Run Experiment window settings 2nd Plate Name Barcode 119 196 Assay Type 119 196 Auto Increment File ID Start 120 197 Experiment Run Name 119 196 Plate Name Barcode 119 196 Quantitation Data Repository 119 196 Run Experiment window Octet RED and Octet RED96 figure 262 326 run name 264 328 run settings quantitation 384 Delayed Experiment Start 197 Start After setting 197 quantitation 96 Delayed Experiment Start 120 Start After setting 120 run settings listed quantitation 384 197 quantitation 96 120 running experiment settings 119 196 Runtime Binding Chart adding title 271 336 quantitation 384 203 quantitation 96 126 copying kinetics 384 338 kinetics 96 273 exporting to a graphic file 273 337 exporting to a graphic or data file 127 204 272 337 magnifying 271 335 quantitation 384 202 quantitation 96 125 managing Octet System Data Acquisition User Guide Release 7 1 page 29 kinetics 96 267 opening 268 332 quantitation
503. status during a running experiment OK ready Busy running Waiting waiting for a condi tion to be resolved Error experiment was termi nated by an error Busy is followed by descriptive information on the progress of the experiment complete Octet 384 only Open the door and move the stage to the presentation posi tion Resume AUT_CMD_RESUME Indicates that the Waiting con dition has been resolved new sensor tray installed Continues the experiment Close AUT_CMD_CLOSE Closes the door if it is open Homes the read head on an Octet 384 instrument Cleanup AUT_CMD_CLEANUP Closes open MDI windows Only valid when not busy Useful when using the Run command without the s option Octet System Data Acquisition User Guide Release 7 1 Automation Commands page 351 Typical Automation Session The following example is a typical automation session that illustrates the use of the auto mation commands to run an experiment NOTE Commands sent from the client application are designated as SEND Responses received from the Octet System Data Acquisition software are des ignated as RECV Connecting to the Data Acquisition Software SEND Version r n RECV 6 1 0 30 Pegasys 1 0 SEND Status r n RECV OK Preparing for an Experiment SEND Cleanup RECV OK SEND GetMethodInfo mC MethodFiles Q001 fmf r n RECV OK p96 0 t1 s Anti Human IgG Fc Startin
504. stem Specifications Octet System Data Acquisition User Guide Release 7 1 page 29 CHAPTER 3 Getting Started Starting the Octet System and Data Acquisition Software 00 cece eee eee ee 30 Software Overview cece eee cee een e ene n ene cent cee e een een eeee eee ean eens 31 Octet System Data Acquisition Options 0 cece cece eee een ene e een en ees 40 Setting the Plate Temperature 6 0 ccc ce cece cece eee nee e een e een e nee eneneenes 43 Monitoring Experiments Remotely 00 cece cece cence eee e ence ene e eee eeeeaeeee 45 Managing Biosensor Types 0 cece cece eee ener nee ksss S ESNS KRANIN EEKANNA 48 page 30 Chapter 3 Getting Started STARTING THE OCTET SYSTEM AND DATA ACQUISITION SOFTWARE gt NOTE The installation shall be performed by ForteBio Inc personnel only WARNING If the Octet system is not used as specified injury to the user and or damage to the instrument may result NOTE Do not position the Octet instrument such that it is difficult to discon nect the power For information about how to connect the Octet instrument to the computer please refer to the insert sheet that is provided with the Octet instrument To start the system and software 1 Turn on the computer 2 Turn the Octet instrument on using the power switch located on the external electrical box NOTE The instrument requires a minimum of one
505. stru ment during the selection To remove a well designation select the well s and click Unassigned Or right click the well s and select Clear Data Octet System Data Acquisition User Guide Release 7 1 page 82 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Annotating Samples You can enter annotations notes for multiple samples in the Sample Plate Map or enter information for an individual sample in the Sample Plate Table For greater clarity annota tion text may be displayed as the legend of the Runtime Binding Chart during data acqui sition but annotations must be entered before the experiment is started If the annotation is entered after the experiment is started it will not be available for display as a legend Annotating Wells in the Sample Plate Map To annotate one or more wells 1 Inthe Sample Plate Map select the samples to annotate right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 5 14 enter the Sample ID and or Well Information and click OK Sample Plate Sample Plate 96 wells P_i es a A A LI H Q Unknown B OO contro Q Cc O Negative Control O Positive Control DIOOC ference E wales Q F He Set Well Data C Clear Data F G O O Set Well Data Copy to Clipboard H vV Extended Sample Typ Well Information Concentration ig ml Standard only O Standard co
506. sword Project _ none Figure 4 8 Login Dialog Box 2 Confirm that the Server location is correct If not please see Selecting a Server Loca tion on page 52 3 From the User drop down list select your login name Octet System Data Acquisition User Guide Release 7 1 Starting a User Session page 57 NOTE To start an down list administrator session select Administrator in the User drop Login fort sio localhost 20002 5 Figure 4 9 Username Selection Enter your password in needed Administrator PSmith RBrown the Password text box Click for a password reminder if E E Remin Employee number der Figure 4 10 Password Reminder 5 Select a project from the Project drop down list if required Octet System Data Acquisition User Guide Release 7 1 page 58 Chapter 4 21 CFR Part 11 Compliance fort sio Server localhost 20002 User JBlack Password eeececceece Cell Culture screen Receptor Ligand screen Figure 4 11 Project Selection 6 Click OK The Data Acquisition or Data Analysis software will now launch and start the user ses sion During the session the user account and project selected at login display in the software status bar Experiment Not Started Plate temp 35 C Project Antigen Antibody screen amp User JBlack John Black F
507. t New Window Exporting or Printing the Runtime Binding Chart To export the Runtime Binding Chart as a graphic or data file 1 Right click the chart and select Export Data 2 Inthe Exporting dialog box see Figure 6 65 select the export options and click Export r Exporting Export EMF WMF BMP JPG PNG Export Destination ClipBoard OFile Browse Printer Export Size Millimeters Inches Points Width 152 400 101 600 Millimeters Large Font Figure 6 65 Exporting Dialog Box Table 6 14 Runtime Binding Chart Export Options Text Data Export Task Export Option Export Result Destination Text EMF WMF Data BMP JPG or PNG Save the v Click File gt Creates a tab delimited text binding Browse to file of the numerical raw data data select a folder from each biosensor Open and enter a file the file with a text editor name such as Notepad Export the v Click File gt Creates a graphic image Runtime Browse to Binding select a folder Chart toa and enter a file graphic file name Octet System Data Acquisition User Guide Release 7 1 Managing Experiment Method Files page 205 Table 6 14 Runtime Binding Chart Export Options Continued Task Export Option Export Result Destination Copy the vV Clipboard Copies the chart to the sys Runtime tem clipboard Binding Chart Print the v Printer Opens the Print dial
508. t Binding Charts Sensors to Chart Plate Status lt a a Plate Legend Sern SelectAll jensor Tray jample Plate een DN OP 412 345 67 8 9104112 P7123 4567 es 10nt211415161718192021222324 Selected Semple Column 3 All E i RoSoscscscececs Processing Sample Column 13 B E Patthar ttt Processed Efe 0 0 0 20 0 0 0 DE Sle oo oo ooo Di Em fee 000000 Data Error Fil H ko o o o o ooo Sensor Feil CHR EEE rd itatetatetstetetetstotstotstt H 0 00 Subtract reference sens i Experiment Progress Step 4 of 4 120s 120s Elapsed exp time 0 10 13 Total experimenttime 0 10 13 E Flip Data Binding nm N N 0 10 20 30 40 50 60 70 80 90 100 110 120 Time sec c a Ba 1 D E Ff 1 H a2 B2 c2 m ee a Geis Figure 6 58 Runtime Binding Chart 4 Optional Click View gt Instrument Status to view the log file see Figure 6 59 The experiment temperature is recorded at the beginning of every experiment as well as each time the manifold picks up a new set of biosensors Instrument events such bio sensor pick up manifold movement integration time biosensor ejection and sample plate temperature are recorded in the log file WARNING Do not open the Octet instrument door when an experiment is in progress If the door is opened the data from the active acquisition step is lost The data acquired in previous steps is s
509. t File ID Start 197 Experiment Run Name 196 Plate Name Barcode 196 Quantitation Data Repository 196 quantitation 96 2nd Plate Name Barcode 119 Assay Type 119 Auto Increment File ID Start 120 Experiment Run Name 119 Plate Name Barcode 119 Quantitation Data Repository 119 Experiment type selecting for the Octet RED384 142 for the Octet RED96 70 Experiment Wizard 34 described 40 figure 40 opening 35 starting kinetics experiments 384 277 Experiment Wizard button 69 141 217 277 Experiment wizard starting experiment quantitation 384 141 experiments adding assays 248 313 kinetic starting 384 277 96 217 monitoring remotely 45 remote view via web browser figure 47 reviewing kinetics 96 258 saving manually 259 323 saving to the factory installed Template folder 260 324 starting 261 325 quantitation 384 194 quantitation 96 117 stopping 36 stopping in progress 266 331 Octet System Data Acquisition User Guide Release 7 1 page 16 quantitation 384 199 quantitation 96 122 Export button 88 Sample Plate Map kinetics 96 233 export options Copy the Runtime Binding Chart quantitation 384 205 quantitation 96 128 Export the Runtime Binding Chart to a graphic file quantitation 384 204 quantitation 96 127 Print the Runtime Binding Chart quantitation 384 205 quantitation 96 128 save the binding data quantitation 384 204 quantitation 96 127 Export Plate Definition window kinetics 384 297 ki
510. t description of the assay here E High sensitivity Human IgG quantitation E Human IgG Quantitation 2 Immunogenicity Direct detection E Murine IgG Quantitation Time 8 Shake speed E Protein L Standard range Sample 120 1000 Offline E Standard Assay E My Basic Quant Assay Basic Quantitation with Regeneration Enzyme 120 1000 I High Snoey assay with regeneration 2nd Butter 120 z 1000 E Protein L Standard range IE Standard Assay Detection 120 a 1000 E My Basic Quant with Regen Assay amp Advanced Quantitation Time 3 Shake speec E Immunogencity Enzyme Linked Regeneration 5 ge 1000 E Residual Protein A j l E Standard Assay Neutralization 5 t 1000 E Three Step Assay Pre condition sensors Post condition sensors Bf My Advanced Quant Assay m g Regeneration cycles Single analyte Multiple analyte Replicates per sensor type 1 Buffer 120 t 1000 t V Reuse Buffer Pi EHLE Regeneration Blue indicates a ForteBio built in assay and cannot be modified or deleted pipe anew Figure 6 70 Assay Parameters Advanced Quantitation L Table 6 18 Advanced Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte For multi analyte experiments using mu
511. ta Acquisition User Guide Release 7 1 Defining a Kinetic Assay page 303 Table 8 3 Sample Step Types for Kinetic Assays Continued Step Type Step Description Custom Can be used for an activity not included in any of the above step types Activation Used when employing a reagent to chemically prepare the biosensor for loading Quenching Used to render unreacted immobilization sites on the biosensor inactive Creating Step Types Click the Assay Definition tab or click the 5 arrow to access the Assay Definition window see Figure 8 29 The Step Data List shows the types of assay steps that are available to build an assay By default the list includes a baseline step To create different types of assay steps 1 Click Add 2 In Assay Step Definition dialog box Figure 8 29 specify the step information a Choose a step type b Optional Edit the step name c Set the step time and shake speed Time range 2 to 48 000 seconds Shake speed range 100 to 1 500 rpm or 0 Piate Definition Assay Definition Sensor Assignment Review Experiment Run Experiment In this step the assay steps will be assembled from the Step Data List Select a group of sensors and append the currently selected step into the current assay with a double click or right click for more options Time in s Shake speed in rpm Sample Plate 384 wells Step Data List ra 2 EEI 7 J FEER Ada
512. tation 384 163 quantitation 96 88 importing quantitation 384 164 quantitation 96 89 Plate Definition window Designate Unknown Wells figure 78 153 Designating Standards figure 74 149 Export button figure 233 234 Import button figure 234 Octet System Data Acquisition User Guide Release 7 1 page 24 kinetics experiments 282 selecting concentration units figure 222 285 molar concentration units figure 222 285 plate definitions importing kinetics 384 298 kinetics 96 234 plate name barcode file prefix 264 328 Plate Name Barcode setting Run Experiment window settings quantitation 384 196 quantitation 96 119 plate temperature range 43 plate temperature setting 43 Port 2002 default server settings 54 Positive control 218 Positive Control well type kinetics 384 280 quantitation 384 145 quantitation 96 71 post condition biosensors 12 Post condition sensors parameter 134 211 Advanced Quantitation quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 Pre condition sensors parameter Advanced Quantitation 136 213 quantitation 384 173 quantitation 96 96 Basic Quantitation with Regeneration 134 211 Precondition sensors parameter Basic Quantitation with Regeneration quantitation 384 171 quantitation 96 94 preparing biosensors 68 preparing samples for quantitation or kinetics experiments 8 Present automation i
513. te to equilibrate Octet System Data Acquisition User Guide Release 7 1 page 194 Chapter 6 Quantitation Experiments Octet RED384 and QK384 The time required for temperature equilibration depends on the temperature that your application requires and the initial temperature of the sample plate For specific biosen sor rehydration times see the appropriate biosensor product insert Starting an Experiment To start the experiment 1 Click the Run Experiment tab or click the arrow to access the Run Experiment win dow see Figure 6 57 Plate Definition Sensor Assignment Review Experiment Run Experiment Data File Location and Names Prior to pressing Go confirm the Assay Assay type Basic Quantitation Standard Assay Quantitation data repository CAUsers Owner Documents ForteBio Experiment run name sub directory Experiment_1 EA Total experimenttime Plate name barcode file prefix 110408 0 09 20 2nd Plate name barcode Auto incrementfile ID start 1 a Data files will be stored as follows CATemp Experiment_1 110408_001 frd C Temp Experiment_1 110408_002 frd CATemp Experiment_1 110408_003 frd Run Settings J Delayed experiment start Z Open runtime charts automatically Start after s 600 F Automatically save runtime chart v Shake sample plate while waiting V Set plate temperature C 37 Advanced Settings Acquisiti
514. ted in regeneration buffer to speed rpm remove bound analyte Octet System Data Acquisition User Guide Release 7 1 Custom Quantitation Assays page 211 Table 6 17 Assay Parameters Basic Quantitation with Regeneration Parameter Description Neutralization The duration time and shaking speed of the neutralization step Time s and Shake where the biosensor is incubated in neutralization buffer after the speed rpm regeneration step Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For example an acidic pre conditioning buffer maximizes the binding competence of Pro A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Regeneration The number of regeneration neutralization cycles that a biosen cycles sor undergoes before reuse Octet System Data Acquisition User Guide Release 7 1 page 212 Chapter 6 Quantitation Experiments Octet RED384 and QK384 Advanced Quantitation Assay Parameters Edit Assay Parameters Available Assays Assay Parameters Basic Quantitation Name My Advanced Quant Assay IE Anti Penta HIS High sensitivity a p IE Anti Penta HIS Standard range Description Enter a shor
515. tem Data Acquisition User Guide Release 7 1 page 224 Chapter 7 Kinetics Experiments Octet RED96 QK and QK Sample Plate 3 S z Z 9 10 11 IonmooWwb 00000 2 6080808 006006000 0 Wash O Unassigned Wl Regeneration Set Well Data Clear Data r ES x Copy to Clij vV Extended S Concentration ug ml Sample only v By value Dilution series Starting value 10 Series operator x Well Information Series operand 2 Dilution orientation 3888 Right 38883 O Left Well Data Sample only g Down g up Molecular Weight kD 150 Molar Concentration nM L d Figure 7 8 Sample Plate Map Assigning Sample Concentrations Using Dilution Series 3 Select a series operator enter an operand and select the appropriate dilution orienta tion see Figure 7 9 Highest Concentration Lowest Concentration Figure 7 9 Concentration Representation in Dilution Series 4 Click OK The Sample Plate Table displays the standard concentrations Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 225 Annotating Samples You can enter annotations notes for multiple samples in the Sample Plate Map or enter information for an individual sample in the Sample Plate Table For greater clarity annota tion text may be displayed as the leg
516. ter 8 Kinetics Experiments Octet RED384 and QK384 IMPORTANT If you intend to analyze the data from a sample using the Inter step correction feature in the Octet System Data Acquisition software the assay must use the same well to perform baseline and dissociation for the sample Replicating Steps Within an Assay To copy steps and add them to an assay 1 In the Assay Steps List select the step s to copy and click Replicate for example in Figure 8 36 step rows 1 4 are selected To select adjacent steps press and hold the Shift key while you click the first and last step in the selection To select non adjacent steps press and hold the Ctrl key while you click the desired steps 2 Inthe Replicate Steps dialog box see Figure 8 36 click the Append to current assay option 3 Click the Offset steps check box and set the options as appropriate For more details on offset options see Table 8 5 Assay Steps List New Assay Move Up Move Down Remove rire Asse Sone Plate Step Name Step Type Sensor Type 1 equilibration m a Custom AHC Anti hlgG Fe Capture eee yt feccang Id Bioeaeg_ avcoengerecepum 1s seins I seine nig r capt pa 1 assosaon fd Associer AAC igo Fe Capt L EET Assay Time Replicate Steps Replication Type Add as a new assay Append to current assay al Sample steps only Offset steps All Steps Sample
517. tet RED384 listed table 330 Octet RED96 listed table 266 Sensor offset Octet QKe 121 Align to Step menu 270 aligning binding data to the beginning of a user selected step 270 334 All steps option 244 309 analysis options viewing 40 analyzing quantitative experiment 68 140 216 276 annotating individual wells in the sample plate table kinetics 384 289 kinetics 96 226 quantitation 384 157 quantitation 96 82 one or more wells 82 225 288 annotations entering 225 288 quantitation 384 157 quantitation 96 82 Append as new assay option 244 309 Append to current assay option 244 309 Append to current assay option 243 Application Locked dialog box figure 66 applications closing 34 Arrange Icons menu 37 arranging window icons 37 Assay Definition tab 237 Assay Definition window 237 Assay number 267 assay parameter settings modifying quantitation 384 167 quantitation 96 91 assay parameter values editing quantitation 384 208 quantitation 96 131 assay parameters Advanced Quantitation quantitation 96 94 Basic Quantitation for 384 model 169 for 96 model 92 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 Assay Parameters box 91 assay parameters Basic Quantitation Multiple Analyte quantitation 384 209 quantitation 96 132 Quantitation Shake Speed Octet System Data Acquisition User Guide Release 7 1 page 4 quantitation 384 209 quantitation 96 132 Quantitat
518. the buffer columns are reused Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incubated in regeneration buffer to speed rpm remove bound analyte Neutralization The duration time and shaking speed of the neutralization step Time s and Shake where the biosensor is incubated in neutralization buffer after the speed rpm regeneration step Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 173 Table 6 8 Advanced Quantitation Assay Parameters Parameter Description Pre condition Performs a set of regeneration neutralization steps prior to the sensors start of the experiment The pre conditioning settings are equiva lent to the time and rpm settings for the regeneration in the assay For example an acidic pre conditioning buffer maximizes the binding competence of Protein A biosensors Post condition Post conditions biosensors after Basic Quantitation with Regener sensors ation allowing re racked biosensors to be stored in a regenerated state Regeneration The number of regeneration neutralization cycles that a biosen cycles sor undergoes before reuse NOTE In an Advanced Quantitation experiment this option is only available if the first step biosen sor incubation in sample is performed online ASSIGNING BIOSENSORS TO SAMPLES After the sample plate is defined biosensors must be assigned to
519. the samples NOTE When using a 96 well plate with the 8 channel read head do not put biosensors in columns 2 4 6 8 10 and 12 if the biosensors will be returned to the biosensor tray and not discarded If the biosensors will be ejected biosen sors can be placed in all columns Biosensor Assignment in Single Analyte Experiments In a single analyte experiment only one biosensor type is assigned to each sample and only one analyte is analyzed per experiment NOTE For single analyte experiments the Single Analyte option must be selected in the Assay Parameters dialog box For more information please see Managing Assay Parameter Settings on page 167 Click the Sensor Assignment tab or click the 5 arrow to access the Sensor Assignment window see Figure 6 35 Octet System Data Acquisition User Guide Release 7 1 page 174 Chapter 6 Quantitation Experiments Octet RED384 and QK384 The software generates a color coded Sensor Tray Map and Sample Plate Map that shows how the biosensors are assigned to the samples by default Piate Definition B Sensor Assignment Review Experiment Run Experiment In this step sensors are assigned to samples Tf you have a partial sensor tray it can be accomodated by selecting the missing sensors and clicking Remove Only the first sensor tray can be a partial plate Sensor Tray Replace sensors in tray after use VW 1i 2 3 4 5 1
520. tic analysis The available biosensor types display in the Sensor Assignment tab Users can add custom biosensors as needed Viewing Available Biosensor Types To view the available types of biosensors from the Main Menu click Experiment gt Edit Sensor Types The Sensor Types dialog box will display Figure 3 20 r Sensor Types Quantitation Sensors Kinetics Sensors Add Anti Mouse IgG Fv AHC Anti hIgG Fc Capture Protein A Delete APS Aminopropylsilane Protein G AR Amine Reactive Protein L SSA Super Streptavidin SA Streptavidin Custom Residual Protein A AHC Beta 1 Anti Penta HIS Custom k Figure 3 20 Sensor Types Dialog Box Octet System Data Acquisition User Guide Release 7 1 Managing Biosensor Types page 49 Adding a Biosensor Type To add a biosensor type 1 From the Main Menu click Experiment gt Edit Sensor Types 2 Inthe Sensor Types dialog box Figure 3 21 click Add next to the Quantitation Sen sors or Kinetic Sensors box depending on the type of biosensor that will be added 3 Inthe Add Sensor dialog box enter a name for the biosensor type and click OK r Sensor Types x Quantitation Sensors Kinetics Sensors Add Anti Mouse IgG Fv AHC Anti hIgG Fc Capture Protein A Delete APS Aminopropylsilane Protein G AR Amine Reactive Protein L SSA Super Streptavidin SA Streptavidin Residual Protein A Add Sensor Anti P
521. ting Automation Client example application 348 Octet instrument to computer 30 to a TCP IP socket connection locally using localhost 348 Connections to Clients box figure 397 constants changing 394 creating new 393 deleting 394 viewing 394 Constants tab figure 392 constants administrator listed table 393 contacting ForteBio technical support 13 Control well type 218 kinetics 384 280 quantitation 384 145 quantitation 96 71 control type of well 71 145 controls 156 defined 81 156 designating 156 quantitation 384 156 quantitation 96 81 conventions used in this guide 13 copying assay steps 243 308 Runtime Binding Chart kinetics 384 338 kinetics 96 273 quantitation 384 205 quantitation 96 128 step type kinetics 384 305 kinetics 96 240 creating csv file for import 90 assay step type figure kinetics 384 303 kinetics 96 238 different types of assay steps 237 303 new constants 393 new user account 384 new user group 389 step types 237 303 Current Binding Charts box 331 custom assays defining quantitation 384 206 quantitation 96 129 selecting quantitation 384 214 quantitation 96 137 custom biosensors 48 custom steps 237 303 D Data Acquisition 21 CFR Part 11 software overview 52 Data Acquisition desktop icon 30 Data Acquisition Software New Features 12 Data Acquisition User Guide menu 38 Octet System Data Acquisition User Guide Release 7 1 page 11 Data Acquisition
522. ting this will be presented Starting an Experiment Using the Experiment Wizard 1 If the Experiment Wizard is not displayed when the software is launched click the Experiment Wizard toolbar button 4 or click Experiment gt New Experiment Wiz ard Ctrl N from the Main Menu 2 Inthe Experiment Wizard click New Kinetics Experiment see Figure 7 1 left 3 Click the arrow button The Basic Kinetics Experiment window displays Figure 7 1 right ix Basic Kinetics Experiment cael fol 9 Phte Defintion Assay Defintion Sensor Assignment Review Experiment Run Experiment In this step all the information about the sample plate and its wells will be entered Highlight one or more wells on the samole plete end rightclick entevnodify well deta Sample Plate 96 wells Sample Plate Table 9 10 11 12 Concent OCCO Mo ri A OOOO Well Sample ID Replicate Group Type Conc ug ml MW KD Molar Conc nM Information MIND Q JO Or OOOC ae rommooOOrY IX Experiment Wizard ee Choose an option to start E New Quantitation Experiment Q Unassigned na Gee Basic Quantitation Basic Quanttation wth Regeneration Advanced Quantitation E New Kinetics Experiment Basic Kinetics 6 Figure 7 1 Starting a Kinetics Experiment with the Experiment Wizard Octet System Data Acquisition User Guide R
523. tion window 258 322 biosensor type in the Sensor Assignment window 254 318 constants 394 group settings 390 project settings 391 projects during a user session 64 sample plate format kinetics 384 280 quantitation 384 144 sample plate format figure 144 280 user account passwords 387 user account settings 386 user password 65 well designations kinetics 384 295 kinetics 96 231 changing location of a reserved column quantitation 384 146 quantitation 96 72 changing projects figure 64 Choose Install Location dialog box figure 367 369 Choose Start Menu Folder dialog box figure 367 370 373 cleaning biosensor pickup tips 343 cleaning Octet instrument 340 342 Cleanup automation interface command 350 Close automation interface command 350 Close Method File menu 33 closing active method file 33 application 34 color codes 122 199 267 331 color coded wells displaying how biosensors interrogate a 384 well plate 8 channel or 16 channel read head 143 279 a 96 well plate 8 channel or 16 channel read head 143 279 compliance Octet QK instrument 23 Octet QK384 instrument 25 Octet QKe instrument 21 Octet RED384 instrument 18 Octet RED96 instrument 16 compliant features 21 CFR Part 11 59 Conc column 76 151 concentration representation in dilution series figure 224 Concentration Units drop down list 73 Connect as IP address changing 45 Octet System Data Acquisition User Guide
524. tion and or re racking Biosensor Tray Type 8 x 12 format 96 biosensor tip tray green color Automation e Up to 16 biosensors in parallel e Ability to integrate the Octet instrument with a laboratory automated robotic system for automated plate and bio sensor tray handling Optics and Mechanics 16 channel biosensor manifold e Optical interferometer Sample plate platform temperature range from 4 C above ambient to 40 C e 16 spectrometers one dedicated spectrometer per biosen sor Throughput Up to 16 biosensors in parallel maximum of 384 tests unat tended e Two microplates either 96 or 384 well at once Only one plate can be used for samples The second plate is used for reagents Octet System Data Acquisition User Guide Release 7 1 page 20 Chapter 2 Octet System Specifications Table 2 2 Octet RED384 System Specifications Continued Item Description Orbital Flow Static or 100 1 500 rpm Capacity Dimensions 30 1 H x 31 5 W x 31 4 D 76 5 cm H x 80 cm W x 79 8 cm D Weight 150 Ib 68 kg Electrical e Mains AC 100 240 V 5 0 2 0 A 50 60 Hz single phase Requirements e Power consumption 195 W 240 W peak Table 2 3 Sensor Offset and Well Volumes for Octet RED384 and Octet QK384 Recommended Minimum Fill Volume pL 96 well plate 384 well plate 384 well tilted bottom Greiner Bio One Greiner Bio One plate ForteBio 384TW 3 200 80 40
525. tion sensors Postcondition sensors Regeneration cycles 3 Blue indicates a built in assay L x ane L Figure 5 28 Assay Parameters Basic Quantitation with Regeneration Table 5 7 Assay Parameters Basic Quantitation with Regeneration Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte and Replicates per sensor type For multi analyte experiments using multiple biosensor types per sample well and the number of replicate assays in each well per biosensor type Quantitation The duration of data acquisition in seconds while the biosensor is Time s and Shake incubated in sample and the sample platform orbital shaking speed rpm speed rotations per minute NOTE A subset of data points may be selected for processing during data analysis Regeneration The duration time and shaking speed of the regeneration step Time s and Shake where the biosensor is incubated in regeneration buffer to speed rpm Neutralization Time s and Shake speed rpm remove bound analyte The duration time and shaking speed of the neutralization step where the biosensor is incubated in neutralization buffer after the regeneration step Octet System Data Acquisition User Guide Release 7 1 page 94 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Table 5 7 Assay Parameters Ba
526. titation 384 151 quantitation 96 76 assigning molar concentration kinetics 96 221 association steps 236 302 Audit Trail described 62 illustrated figure 62 list options 64 selecting a project 63 sorting 63 viewing 62 Authentication Server dialog box 53 Auto Increment File ID 264 328 Octet System Data Acquisition User Guide Release 7 1 page 6 Auto Increment File ID Start Run Experiment window settings quantitation 384 197 quantitation 96 120 Auto Scroll to bottom check box 39 Automatically save runtime chart setting 120 197 265 329 automation for Octet QK384 26 for Octet RED384 19 Automation box 346 Automation Client example application connecting 348 automation interface commands Cleanup 350 Close 350 GetMethodInfo 349 GetRunInfo 349 Present 350 Reset 349 Resume 350 Run 349 Status 350 Stop 350 Version 349 automation interface control setup 346 automation interface design 346 automation session typical 351 Automation user option 43 AutomationAPI h header file 349 AutomationClient exe 346 baseline step 237 303 basic kinetics experiment 216 276 Basic Kinetics Experiment window figure 277 Basic Quantitation Assay Parameters listed table 92 131 169 208 Multiple Analyte quantitation 384 209 quantitation 96 132 quantitation 384 Multiple Analyte and Replicates per Sensor Type parameter 169 Quantitation Shake Speed param eter 169 Quantitation Time param
527. titation data files frd are saved Click Browse to select another data location NOTE It is recommended that you save the data to the local machine first then transfer to a network drive Experiment Run Name sub directory Specifies a subdirectory name for the data files frd that are created The software generates one data file for each biosensor Plate name barcode file reader required prefix 2nd Plate name barcode A user defined field where you can enter text or a barcode barcode A user defined field where you can enter text or a barcode barcode reader required for a second plate Octet System Data Acquisition User Guide Release 7 1 Running a Quantitation Experiment page 197 Table 6 9 Data File Location and Name Continued Item Description Auto Incre Each file is saved with a number after the plate name For example if ment File ID the Auto Increment File ID Start number is 1 the first file name is Start xxx_001 frd The following Run Settings are available on the Run Experiment Tab Table 6 10 Run Settings Item Description Delayed experi Specifies a time delay for the start of the experiment Enter the num ment start ber of seconds to wait before the experiment starts after you click Q Start after Enter the number of seconds to delay the start of the experiment Shake sample If the experiment has a delayed start time this setting shakes the
528. to assign locations for the remaining biosensor types in the tray IMPORTANT Ensure that the biosensor types selected in the Assay Definition window have assigned column s in the Sensor Assignment window or the experiment cannot be run Using Partial Biosensor Trays If you remove biosensors from the Sensor Tray Map and there are not enough remaining biosensors for the experiment the software automatically adds a second tray of biosensors and assigns the biosensors that are required for the assay s The experiment in the example shown in Figure 7 45 includes three assays and Tray 1 does not include enough biosensors for the experiment To view the additional biosensor tray that is required for the assay select Tray 2 from the Sensor Tray drop down list Figure 7 45 top The Sensor Tray Map will then display the additional biosensors required for the assay Figure 7 45 bottom If necessary change the location of these biosensors Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 257 Sensor Tray v Replace sensors in tray after use Sensor Tray of 2 10_11 BS SA Streptavidin 10102020 C5 SA Streptavidin 10102020 DS SA Streptavidin 10102020 E5 SA Streptavidin 10102020 F5 SA Streptavidin 10102020 G5 SA Streptavidin 10102020 H5 SA Streptavidin 10102020 SA Streptavidin 10102020 SA Streptavidin 10102020 SA Streptavidin 10102020 SA Strepta
529. to the assay as described earlier Sample Plate 384 wells ABO ZO A Add Assay Step Insert Assay Step Assayed samples Figure 8 37 Start New Assay Copy to Clipboard OUOU Start New Assay Show Sample Types Show Pie Charts O Unassigned samples Octet System Data Acquisition User Guide Release 7 1 page 310 Chapter 8 Kinetics Experiments Octet RED384 and QK384 Inserting or Adding an Assay Step To insert an assay step 1 Select a step in the Step Data List 2 Inthe Assay Steps List select the row above where you want to insert the step 3 Inthe Sample Plate Map right click the column to which the step will be applied and select Insert Assay Step The step is inserted into the Assay Steps List To add an assay step 1 Select a step type in the Step Data List 2 Inthe Sample Plate Map right click the column to which the step will be applied and select Add Assay Step The step is added to the end of the Assay Steps List Selecting a Biosensor for the Assay To select the biosensor type associated with the assay click the Sensor Type arrow for any step in the assay and select a sensor type from the drop down list Figure 8 38 The biosensor type will automatically update for every assay step Assay Steps List New Assay Move Up Move Down Remove Replicate Pop ime Assay Sample Plate Step Name Step Type Sensor Type Assay Time 1 Al 1 equilibration 3
530. tration Lock Application Logoff Figure B 30 Security Menu ForteBio GxP Server module on network location Double click on the FBServerConfig exe file in the FBServer7 folder from the installed location File Edit View Tools Help Organize 7 Include in library Share with 7 Burn New folder BES v i z 4 ForteBio Name Date modified Type Size gt DataAcquisition7 E A FBServer exe 12 3 2010 3 53PM Application 2 966 KB gt DataAnalysis7 z A FBServerConfig exe 12 3 2010 3 53PM Application 7 821 KB JL FBServer7 FBServerMonitor exe 12 3 2010 3 54PM Application 6 909 KB we ForteBio 2 10 2011 6 20PM __Internet Shortcut 1KB Globe ico 12 1 2010 4 21 PM Icon 25 KB E uninst exe 2 10 2011 6 20 PM Application 54 KB Figure B 31 Accessing the GxP Server on the Network Octet System Data Acquisition User Guide Release 7 1 page 382 Chapter B 21 CFR Part 11 Software Administrator Options ForteBio GxP Server module on a local host computer Double click the ForteBio GxP Server desktop icon ForteBio GxP Server Figure B 32 Security Menu NOTE When accessing the ForteBio GxP Server module directly additional tools are also provided to test server functionality Please see Accessing the GxP Server Module Directly on page 396 for more information The ForteBio GxP Server Administration window will display L
531. trument 23 biosensor tray type 24 biosensor type 24 capabilities 23 compliance 23 dimensions 24 electrical requirements 24 environment 23 equipment classifications 23 mechanics 24 optics 24 orbital flow capacity 24 sample types 24 sample volume 24 sampling format 24 temperature range 24 throughput 24 Octet QK system specifications 23 Octet QK384 sensor offset 20 27 well volumes 20 27 Octet QK384 instrument automation 26 capabilities 25 compliance 25 dimensions 27 electrical requirements 27 environment 25 equipment classifications 25 mechanics 26 optics 26 sample types 26 sampling format 26 weight 27 Octet QK384 instrument figure 25 Octet QK384 system specifications listed table 25 Octet QKe and Octet RED Run Experiment window advanced settings listed table 266 Octet QKe instrument biosensor tray type 22 biosensor type 22 capabilities 22 compliance 21 dimensions 22 displayed figure 21 electrical requirements 22 environment 21 equipment classifications 21 mechanics 22 optics 22 orbital flow capacity 22 sample types 22 sample volume 22 sampling format 22 temperature range 22 throughput 22 weight 22 Octet QKe system specifications listed table 21 Octet RED instrument replacing fuses 341 Octet RED system warm up 30 Octet RED384 sensor offset 20 27 starting Octet System Data Acquisition User Guide Release 7 1 page 22 kinetics experiment with the Exper iment wizar
532. ttings Sample Plate Table Assay Basic Quantitation Concentration units hovel x Export Import Sarel Well Sample ID Replicate Group Type _ Conc pg ml Dilution Factor Information DA Standard 1 nja Time s Shake speed OB Standard 200 n a Quantitation 120 200 oa Standard 100 n a on Standard 50 nja OEI Standard 25 nja OFf Standard 10 nja oa Standard 5 nja OH Standard 2 5 nja Oaz Standard 1 nja Os Standard 200 nja oc Standard 100 nja a Sample Piate Ope Standard 50 n a F Sample Plate 36 wells Or Stondard 25 ai F i 2 a Ore Standerd 10 n a A O G2 Standard 5 n a Standard 2 5 n a B Standard 1 n a Control Standard 200 n a c Negative Control andem 100 wes S Standard 50 n a D Positive Control Standard 25 n a E Reference Standard 10 n a B Standard 5 nja F Set Well Data 25 Clear Data ja G Copy to Clipboard H v Extended Sample Types O standard Control Unassigned O Unknown _ Reference O Reserved Figure 5 9 Plate Definition Window Designate Unknown Wells S To remove a well designation select the well s and click Unassigned Or right click the well s and select Clear Data Assigning a Dilution Factor or Serial Dilution to Unknowns To assign a dilution factor or serial dilution to unknowns 1 Inthe Sample Plate Map select the unknown wells see Figure 5 9 2 Right click and select Set Well Data The Set Well Data dialog box displays see Figure
533. ture 1 A5 1 Loading L Loading ASA Streptavidin 1 Ag 1 Baseline ke Baseline 9 AAHC Anti hlgG Fc Capture 1 Al3 1 Association a cenaam Aart je ad el 1 Ag 1 Dissociation kK Dissociation SSA Super Streptavidin 1 Al 2 Regeneration 3 Custom Custom 1 A5 2 Neutralization 3 Custom AHC Beta 1 0 29 00 Figure 8 51 Assay Definition Window Changing the Biosensor Type REVIEWING EXPERIMENTS Before running an experiment you can review the sample plate layout assays and assay steps as well as the biosensors assigned to each assay in the experiment In the Review Experiment window Figure 8 52 move the slider left or right to highlight the biosensors and samples associated with an assay step or click the gt arrows Alter natively select an assay step to view the biosensors and samples associated with it Octet System Data Acquisition User Guide Release 7 1 Saving Experiments page 323 Slider D Plate Defnit Assay Definition Sensor Assign Review Experiment Run Experiment In this step you can review the steps that make up thd experiment moving the slider to change the active step Assay 1 20s Step 10 1000 rpm y lella ainz Sensor Tray Sample Plate 384 wells 4 6 7 8 9 10 11 12 W123 4 5 67 8 9 1011121314 15161718192021 222324 MODO DOO OOOO OOO 9000000007 OQO O000 vOZErxc TOmMIOODY OO00000000 roaTmmoowr
534. turning to default layout 253 316 Sensor Type arrow 246 Sensor Type table column 249 Sensor Types dialog box opening 35 Sensor Types dialog box figure 48 Sensors to Chart box figure 267 serial dilution assigning to selected wells quantitation 384 154 quantitation 96 79 serial dilution assigning to unknowns quantitation 384 153 quantitation 96 78 serial port RS 232 346 server location selecting 53 server testing 397 Set Plate Temperature setting kinetics 384 329 kinetics 96 265 quantitation 384 197 quantitation 96 120 Set Plate Temperature menu 35 Set Well Data dialog box 76 151 221 Set Well Data dialog box figure 290 setting assay step threshold parameters figure 239 304 plate temperature 43 system and data preferences 40 setting assay step threshold parameters figure 239 Setting Default Temperature dialog box 44 setting temperature figure 43 setting up administrator account 374 setting up quantitative experiment 68 140 216 276 Octet System Data Acquisition User Guide Release 7 1 page 33 settings advanced run experiment 120 197 329 shake sample plate while waiting setting 120 197 265 329 Shake Speed parameter quantitation 384 169 quantitation 96 92 shortcut keys 226 showing main toolbar 34 status bar 34 Signal Change threshold parameter 239 304 significant digits data display 42 user option 42 simulation user option 43 Single Analyte assa
535. u options and toolbar buttons are described in this section Octet System Data Acquisition User Guide Release 7 1 page 32 Chapter 3 Getting Started File View Experiment Instrument Security Window Help qaaa Figure 3 3 Main Menu and Toolbar NOTE The Security menu is only available in the 21 CFR Part 11 version of the Octet System Data Acquisition software File Menu The File menu Figure 3 4 allows users to open and save method files view experiments print files and set system and software options A method file fmf contains sample plate configuration sample plate table information sensor assignments and assay step information that allow the Octet instrument and soft ware to run an experiment When the run is complete the data in the experiment folder can then be reviewed NOTE When using the 21 CFR Part 11 version of the Octet System Data Acqui sition software only 21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11 version of the software can be opened Files generated using the non compliant version of the software or with a non compliant system cannot be opened and a message indicating this will be presented Octet System Data Acquisition User Guide Release 7 1 Software Overview page 33 View Experiment Instrument Security Window Help Open Method File Ctrl O0 Close Method File Save Method File Ctrl S Save All Method File
536. uantitation 96 78 designating quantitation 384 153 quantitation 96 78 updating assay times as steps are added to the assay figure 242 307 Runtime Binding Chart kinetics 384 331 kinetics 96 267 quantitation 384 199 quantitation 96 122 Use extended sample types user option 42 Use old 5 0 file format for FRD files user option 42 user account creating new 384 deleting 386 user account passwords changing 387 user account settings changing 386 viewing 386 user data files options 41 user data options 42 user group assigning 385 creating new 389 deleting 390 privileges 385 user groups default 388 User name setting 121 199 330 user options Automation 43 kinetics data repository 41 listed table 41 quantitation data repository 41 significant digits 42 Simulation 43 temperature 42 Use extended sample types 42 Use old 5 0 file format for FRD files 42 viewing 40 Web Server 43 user password changing 65 user session changing projects during 64 starting 56 starting an administrator 378 user sessions discontinuing 66 ending 66 Login dialog box 56 resuming 66 user startup options 42 user defined default start up temperature 12 UserldleMin constant 381 user modifiable settings for an assay quantitation 384 167 quantitation 96 91 username selection figure 57 Users tab 384 using Octet System Data Acquisition User Guide Release 7 1 page 37 heterogeneous biosensor trays kinetics
537. uantitation with Regeneration experiments and Advanced Quantitation multi step experiments for Regeneration R Neutralization N or Detection D Reserved wells are not available for use as Standards Unknowns Controls or References Octet System Data Acquisition User Guide Release 7 1 page 72 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Reserved Wells In a Basic Quantitation with Regeneration or an Advanced Quantitation experiment the Sample Plate Map includes gray wells These wells are reserved by the system and specify the location of particular sample types Reserved samples cannot be removed from the sample plate but you can change their col umn location To change the location of a reserved column or right click a col umn header in the Sample Plate Map and select Regeneration Neutralization or Detection Table 5 5 Reserved Well Requirements Reserved Well Must Contain Regeneration Regeneration buffer that is used to remove analyte from the bio sensor typically low pH high pH or high ionic strength Neutralization Neutralization buffer that is used to neutralize the biosensor after the regeneration step Detection Secondary antibody or precipitating substrate that is used with an enzyme antibody conjugate to amplify the analyte signal Sample concentrations are computed using the binding data from the detection wells Basic Quantitation with Regener
538. uilibration Loading AHC Anti hlgG Fe Capture 1 Ag 1 ELoading gt Baseline AHC Anti hlgG Fc Capture 1 Als ardor Z Association AHC Ant higG Fe Capture ssociation 1 Ag 1 C Dissociation Dissociation AHC Anti hlgG Fc Capture 1 Al 2 F Regeneration 2 Custom AHC Anti hlgG Fe Capture i AS 2 n Neutralization Custom AHC Anti hlgG Fe Capture 0 29 00 Assay Steps List New Assay Move Up Move Down Remove Replicate Dae Assay Sample Plate Step Name Step Type Sensor Type Assay Time 1 Al 1 equilibration 3 Custom AHC Anti hlgG Fe Capture 1 AS 1 Loading LZ Loading ASA Streptavidin 1 Ag 1 Baseline kk Baseline 9 AAHC Anti higG Fc Capture 1 A13 1 Association a Association PAR Aes abc os 1 Ag 1 Dissociation N Dissociation 455 Super Streptavidin 1 Al 2 Regeneration 2 Custom Custom 1 A5 2 Neutralization 3 Custom AHC Beta 1 0 29 00 Figure 8 39 Editing an Assay Step Name top or Sensor Type bottom in the Assay Steps List To reorder or remove an assay step 1 Select a step row in the Assay Steps List 2 Click the Move Up Move Down or Remove button located above the list T IMPORTANT An assay must have a baseline step followed by a set of associa tion dissociation steps to be analyzed The Octet System Data Acquisition software recognizes the baseline association dissociation set of steps Octet System Data Acquisition User Guide Release 7 1 page 312 Chapter 8 Kinetics Ex
539. umber Information A 29a e ae 49 41 42 Al_ AHC Anti hIgG Fc Capture auto assign B1 A uto assign _ A sae Ci ASA Streptavidin SA Streptavidin o AHC Anti higG Fc Capture B AHC Anti hIgG Fc Capture E1 ap a A mine Reactive E APS Aminopropylsilane F1 ASSA Super Streptavidin AR Amine Reactive G1 ACustom D SSA Super Streptavidin i awe Beta 1 E Custom aA F AHC Beta 1 al J Reference G Positive Control H Negative Control i Remove egenc Fill ig sensors Re Set Sensor Data Sample Copy to Clipboard Figure 7 42 Sensor Assignment Window Changing the Biosensor Type The biosensor types shown in the Sensor Assignment window were specified previously in the Assay Definition window and default locations are assigned automatically To assign biosensor types for heterogenous trays 1 Select the column location of the biosensor type see Figure 7 43 Sensor Tray V Replace sensors in tray after use VW 1 2 3 4 5 6 7 8 9 A00 10 _ 11 12 SA Streptavidin BOO co D coo HOOD nm LILO a SS OnE eS sA Streptavidn SA Streptavidin sa Streptavidn sA Streptavidn SA Streptavidin SA Streptavidin e SA Streptavidin SA Streptavidin SA Streptavidin SA Streptavidin SA Streptavidin SA Streptavidin SA Streptavidin SA Streptavidin SA Streptavidin SA Streptavidin Legend Unassigned sensors R3 Missing sensors Rem
540. ument status log figure 119 196 263 327 Instrument Status window 36 described 39 figure 39 logging 36 inverted data viewing in the Runtime Binding Chart 269 334 K kinetic data analysis 40 kinetics assays building 248 defining 236 step type requirements 236 302 kinetics data repository 264 328 kinetics data repository user option 41 kinetics experiments designating samples 218 designating well types 282 Plate Definition window 282 starting 384 277 96 217 L launching the Octet System Data Acquisition software 30 legend for Runtime Binding Chart selecting 271 336 quantitation 384 203 quantitation 96 126 license information displaying 38 list options available for events 396 listing windows currently open in the Main Screen 37 Load well type kinetics 384 281 kinetics 96 218 loading biosensor tray kinetics 384 324 kinetics 96 260 quantitation 384 193 quantitation 96 116 reagent plates kinetics 384 324 sample plate kinetics 384 324 Octet System Data Acquisition User Guide Release 7 1 page 19 kinetics 96 260 quantitation 384 193 quantitation 96 116 steps 236 302 LoadSensors 353 Localhost option 347 localhost default server settings 54 locking Data Acquisition software 65 Data Analysis software 65 logging in the Instrument Status window 36 Login dialog box administrator session figure 378 user session figure 56 Lot Number column 252 lower acquisition rate
541. used with OctetRED384 and OctetQK384 systems only For more information please refer to Appen dix A Using Octet384 Systems with an Automation Inter face on page 345 SETTING THE PLATE TEMPERATURE The settable plate temperature can range from ambient plus 4 C to a high of 40 C A fac tory set default plate temperature of 30 C is used as a system startup plate temperature and the experiment default temperature This default value can be customized by the user In addition the plate temperature setting can be changed for individual experiments when needed The current plate temperature displays in the Status bar at the bottom of the Main Screen Changing the Plate Temperature for Individual Experiments To set the plate temperature to a value other than the default setting for a specific experi ment 1 From the Main Menu click Experiment gt Set Plate Temperature 2 Click the Set temperature to field Figure 3 15 to the desired value or enter the pre ferred temperature and click OK r x Temperature Setting 2 Sample Plate Temperature Current temperature 30 e Set temperature to 35 C Figure 3 15 Temperature Setting Octet System Data Acquisition User Guide Release 7 1 page 44 Chapter 3 Getting Started 3 Allow sufficient time for the sample plate to equilibrate to the new temperature before beginning an experiment approximately 5 minutes for a plate at room temperature or 15
542. ustom Assay 2 Select the custom assay from the directory tree and click OK Octet System Data Acquisition User Guide Release 7 1 page 138 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Octet System Data Acquisition User Guide Release 7 1 page 139 CHAPTER 6 Quantitation Experiments Octet RED384 and QK384 INTPOGUCHON ins se cusvcdenererdins ner She nbadoobe rund E Reve de dpa 140 Starting a Quantitation Experiment 0 ccc cece eee e een ee nen eee n eens 141 Defining the Sample Plate cece cece een ence nent een E tenn ES 142 Managing Sample Plate Definitions ccc cece e cece cee cee eee e eee neaeneaens 163 Working with a Reagent Plate cece ccc cece cence ene nee ee eee e nen nee eens 165 Managing Assay Parameter Settings ec eee eee eee eee cent teen ene eneeas 167 Assigning Biosensors to Samples ccc cece cece een ence tence eee ence eeeeeeeeees 173 Reviewing Experiments 0 cece cece cence ene nnn ene een eeneeneenes 191 SAVING EXPeLriIMENts sier sssimerecas nitar id alee a ween ed EREE blade E EENE RE aid einew ala 191 Running a Quantitation Experiment cece cece eee eee een ene eee een eens 193 Managing Runtime Binding Charts 0 cece cence cece nee en ence nen ee nen eneeans 199 Managing Experiment Method Files cc cece ccc cece ence ence een ee ee eneens 205 Custom Quantitation Assays 1 0 cece
543. utomatically update for every assay step Assay Steps List NewAssay Move Up Move Down Remove Replicate erie Assay Sample Step Name Step Type Sensor Type Assay Time 1 Equlibration 4 Custom SA Streptavidin p 1 2 ProA Immobilization Loading ESA Streptavidin 1 3 Baseline k Baseline SAHC Anti higG Fc Ca 1 4 Association a aaaea EEan i ol 1 3 Dissociation Association ESSA Super Streptavi 1 1 Regeneration F Custom E Custom 1 12 Neutralization 3 Custom sAHC Beta 1 1 11 Regeneration F Custom 1 12 Neutralization J Custom 1 11 Regeneration J Custom SA Streptavidin Figure 7 33 Selecting an Assay Sensor Type NOTE The Sensor Type for the assay must be selected or changed from the Assay Steps List Changing the Sensor Type from the Sensor Assignment Tab will not update the assay Editing an Assay To edit the step type or the biosensor type 1 In the Assay Steps List To change the step type click the Step Name arrow and select a step name from the drop down list Figure 7 34 top To change the biosensor type click the Sensor Type arrow for any step in the assay and select a sensor type from the drop down list Figure 7 34 bottom The biosensor type will automatically update for every assay step NOTE The Step Name drop down list includes only the step types defined in the Step Data List Octet System Data Acquisition User Guide Release 7 1
544. verifying 60 dilution factor assigning to selected wells quantitation 384 154 quantitation 96 79 dilution factor assigning to unknowns quantitation 384 153 quantitation 96 78 dilution factor editing in sample table quantitation 384 155 quantitation 96 80 dilution series assigning sample concentrations kinetics 384 286 kinetics 96 223 assigning standard concentrations quantitation 384 149 quantitation 96 74 Octet System Data Acquisition User Guide Release 7 1 page 13 Dilution Series option 75 223 dimensions Octet QK instrument 24 Octet QK384 instrument 27 Octet QKe instrument 22 Octet RED384 instrument 20 Octet RED96 instrument 17 discontinuing user session 66 displaying acquisition for a data column 267 331 quantitation 384 199 quantitation 96 122 GxP Server location figure 377 Instrument Status window 34 license information 38 Octet System Data Acquisition software properties 38 step types figure 305 dissociation steps 236 302 E Edit Assay Parameters dialog box figure 129 206 Edit Assay Parameters dialog box opening 35 Edit Assay Parameters menu 35 edit commands 226 Edit Constant dialog box figure 394 Edit Project dialog box figure 392 Edit Sensor Types menu 35 editing assay parameter values quantitation 384 208 quantitation 96 131 assays 35 246 311 biosensor information figure 252 316 dilution factor in the sample table quantitation 384 155 quantitation 96 80 p
545. vidin 10102020 SA Streptavidin 10102020 SA Streptavidin 10102020 SA Streptavidin 10102020 SA Streptavidin 10102020 ERARRRRS Legend _ Unassigned sensors R3 Missing sensors Remove Fill Fill Plate Sensor Tray 7 Replace sensors in tray after use Sensor Tray of 2 2 3 4 5 12 Well Sensor Type Lot Number Information d A E E UL JL BE A1 SA streptavidin 10102020 B1 SA Streptavidin 10102020 BPI IL C1 SA Streptavidin 10102020 cm D1 SA Streptavidin 10102020 DOLL E1 SA Streptavidin 10102020 OOG Fl SA Streptavidin 10102020 G1 SA Streptavidin 10102020 H1 SA Streptavidin 10102020 A2 SA Streptavidin 10102020 cc a B2 SA Streptavidin 10102020 Legend __ Unassigned sensors RRA Missing sensors ao o Eje L SH HH LI Ir C2 SA Streptavidin 10102020 L_JL_ D2 SA Streptavidin 10102020 I E C C E2 SA Streptavidin 10102020 p a F2 SA Streptavidin 10102020 G2 SA Streptavidin 10102020 H2 SA Streptavidin 10102020 Remove Fil Fil Plate A3 SA Streptavidin 10102020 B3 SA Streptavidin 10102020 Figure 7 45 Example Experiment Using Two Biosensor Trays NOTE Up to two trays may be used per assay but only the first biosensor tray can be a partial tray During the experiment run the software prompt
546. visual change to the data on the screen The actual raw data is unaffected and the reference subtraction must be re done in data analysis if needed Octet System Data Acquisition User Guide Release 7 1 Managing Runtime Binding Charts page 125 Viewing Inverted Data The data displayed in the Runtime Binding Chart can be inverted during real time data acquisition or data analysis after the experiment has completed To invert data select the Flip Data check box see Figure 5 58 Uncheck the box to return to the default data display Experiment Progress Step 8 of 8 120s 120s Elapsed exp time 0 21 55 Total experimenttime 0 21 55 V Flip Data 0 0 0 5 1 0 1 5 E 20 D H a25 3 0 3 5 40 0 10 20 30 40 50 60 70 80 90 100 110 120 Time sec Sensor A1 Sensor B1 Sensor C1 Sensor D1 Sensor E1 Sensor F1 Sensor G1 Sensor H1 Figure 5 58 Data Inverted Using Flip Data Function Magnifying the Runtime Binding Chart To magnify the chart press and hold the mouse button while you draw a box around the chart area to magnify To undo the magnification right click the chart and select Undo Zoom Octet System Data Acquisition User Guide Release 7 1 page 126 Chapter 5 Quantitation Experiments Octet RED96 QK and QK Scaling a Runtime Binding Chart To scale the Runtime Binding Chart 1 Right click the chart and select Properties 2 Inthe Runtime Graph Prop
547. with regeneration Re fi E Protein L Standard range B Time s Quantitation 120 H 400 S Regeneration 5 H 400 Neutralization 5 H wo V Pre condition sensors _ Post condition sensors Regeneration cycles 3 B Blueindicates a built in assay L Figure 6 31 Modifying Assay Parameters Octet System Data Acquisition User Guide Release 7 1 M anaging Assay Parameter Settings page 169 Basic Quantitation Assay Parameters r y Assay Parameters Available Assays Assay Parameters amp Basic Quantitation Single analyte Multiple analyte I Anti Penta HIS High sensitivity Replicates per sensor type 1 E Anti Penta HIS Standard range E High sensitivity Human IgG quantitation 2 Human IgG Quantitation IE Immunogenicity Direct detection 2 Murine IgG Quantitation E Protein L Standard range Bj Standard Assay Time 6 Shake speed Quantitation 120 S 400 L Figure 6 32 Assay Parameters Basic Quantitation Assay Table 6 6 Basic Quantitation Assay Parameters Parameter Description Single analyte For single analyte experiments using only one biosensor type per sample well Multiple analyte and For multi analyte experiments using multiple biosensor types Replicates per sen per sample well and the number of replicate assays in each well sor type per biosensor type Quantitation Time s
548. x E c2 SA Streptavidin 6 G3 30 x Dy 2 SA Streptavidin 6 H3 31 x 2 SA Streptavidin 6 H3 322 x E 1 SA Streptavidin 1 A3 3 x E 1 3 SA Streptavidin 1 A3 4 x He 3 SA Streptavidin 2 B3 3 x E 3 SA Streptavidin 2 B3 3 x He c SA Streptavidin 3 c3 337 x He c SA Streptavidin 3 C3 38x HE bs SA Streptavidin 4 D3 2a x EE 2 QA Gtrantavidin 4 na z Figure 8 15 Replicate Group Color Coding NOTE Replicate Group information can also be entered in the Octet System Data Analysis software Assigning Replicate Groups in the Sample Plate Map To assign Replicate Groups in the Sample Plate Map 1 Select the samples you wish to group right click and select Set Well Data 2 Inthe Set Well Data dialog box see Figure 8 16 enter a name in the Replicate Group box and click OK Octet System Data Acquisition User Guide Release 7 1 Defining the Sample Plate page 291 Set Well Data m Well Information Concentration g ml Sample only Sample ID By value 40 human IgG E 3 Dilution series Replicate Group aN e E Series operator Y Series operand 2 Dilution orientation 3838 Right 8833 Left well Data Sample only 8 Down 3 _ Up Molecular Weight kD Molar Concentration nM k 4 Figure 8 16 Add Replicate Group from the Sample Plate Map 3 Repeat the previous steps to assign new samples to the existing
549. xperiment with the Exper iment wizard figure 278 well volumes 20 27 Octet RED384 instrument automation 19 capabilities 18 compliance 18 dimensions 20 electrical requirements 20 environment 18 equipment classifications 18 mechanics 19 optics 19 sample types 19 sampling format 19 weight 20 Octet RED384 instrument figure 18 Octet RED384 stage platform figure 193 Octet RED96 instrument biosensor tray type 17 19 26 biosensor type 17 19 26 capabilities 17 compliance 16 dimensions 17 electrical requirements 17 environment 16 equipment classifications 16 mechanics 17 optics 17 orbital flow capacity 17 20 27 sample types 17 sampling format 17 sampling volume 17 temperature range 17 throughput 17 19 26 weight 17 Octet RED96 instrument figure 16 Octet RED96 system specifications displayed figure 18 listed table 16 18 25 Octet system biosensor stage left and sample stage right figure 325 Octet System Data Acquisition software Main Menu 31 main toolbar 32 new features 12 starting 30 toolbar 31 Octet System Data Acquisition software Main Screen 31 Octet System Data Acquisition analysis options viewing 40 Octet system described 8 Offline parameter 136 213 Advanced Quantitation quantitation 384 172 quantitation 96 95 Offset steps option 244 309 Offset steps check box 243 Open Experiment menu 268 332 Open Experiment menu 33 Open Method File menu 33
550. y All Steps Sample steps will be Horizontally Vertically Figure 7 35 Adding a Replicate Assay to a Plate 3 Click the Offset steps check box and set the options as appropriate see Table 7 5 on page 244 for more information If the replicate assay uses the same sample columns as the original assay do not choose the Offset steps option If the replicate assay uses a different sample column select Offset steps and the appropriate options Sample steps only offsets the sample wells by the value specified under Sam ple steps will be adjusted The offset will not be applied to reagent wells such as buffer loading regeneration neutralization and detection All Steps offsets all wells in the assay including sample and reagent wells by the value specified under Sample steps will be adjusted 4 Click OK The new assay appears in the Assay Steps List 5 Continue to add assay steps as needed Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 249 ASSIGNING BIOSENSORS TO SAMPLES After you define the sample plate and assay s click the Sensor Assignment tab or click the arrow to access the Sensor Assignment window The color coded Sensor Tray and Sample Plate Map show the locations of the biosensors associated with the samples Figure 7 36 NOTE Ifan experiment includes more than one type of biosensor the software automatically creates a separate senso
551. y parameter quantitation 384 208 quantitation 96 131 single analyte experiment assigning biosensors quantitation 384 173 quantitation 96 96 Single Analyte parameter Advanced Quantitation quantitation 384 171 quantitation 96 94 Basic Quantitation with Regeneration quantitation 384 170 quantitation 96 93 133 quantitation 384 169 quantitation 96 92 Skip Step menu 35 specifying number of significant digits for the values of Molecular Weight Concentration and Dilution used during data analysis 42 Standard well type quantitation 384 145 quantitation 96 71 Standard button 73 148 standard concentration entering quantitation 384 151 quantitation 96 76 standard type of well 71 145 standards designating quantitation 384 148 quantitation 96 73 Start After setting kinetics 384 329 kinetics 96 265 quantitation 384 197 quantitation 96 120 starting administrator user session 378 an experiment 261 325 quantitation 384 194 quantitation 96 117 basic kinetics experiment 384 277 96 217 experiment from the Experiment wizard 141 kinetics experiment with the Experiment wizard figure Octet RED384 278 Octet System Data Acquisition User Guide Release 7 1 page 34 new assay 244 309 Octet System Data Acquisition software 30 quantitation experiment 69 141 user session 56 starting concentration value 76 151 222 285 startup temperature user option 42 Status automation interface command
552. y steps designated as Threshold will terminate when either the step time elapses or the threshold termination COOCOO F sgnal change H E Threshold nm 1 00 A Assayed samples The threshold is achieved when Channel 3 Binding ascends by threshold from step start Channel 4 Waa 7 Channel 5 Binding descends by threshold from step start Channel 6 Channel 7 Gradient Channel 8 hreshold nm min 0 10 SSSSS8S888 Duration min 5 00 The step is terminated when the threshold is achieved on ALL channels the meen Mi Bao ed when below threshold for the given dura the threshold is achieved on ANY ONE channel v Filtering Filtering is applied before the threshold is assessed Lx Fterwidth 100 Figure 7 25 Setting Assay Step Threshold Parameters NOTE If thresholds are applied the step is terminated when either the step time elapses or the threshold termination criteria is reached Table 7 4 Threshold Parameters Item Description Active Channels Specifies the instrument channels that monitor the threshold criteria for the assay step Select an option for terminating the step e The threshold is achieved on ALL channels e The threshold is achieved on ANY ONE channel Signal Change The threshold is a user specified amount of ascending or descend ing signal change nm Gradient The threshold is a binding gradient
553. ype Lot Number Information ES Ai_ Protein A Protein A a Protein A D1 Protein A E1 Protein A F1 Protein A G1 Protein A H1 Protein A A2 Protein A B2 Protein A C2 Protein A D2 Protein A E2 Protein A L F2 ProteinA G2 Protein A H2 Protein A Remove mm FiPete A3 Protein A B3 Protein A Sample Plate c3 Protein A 8 9 1011121314151617 18192021222324 D3 Protein A E3 Protein A F3 Protein A G3 Protein A H3 Protein A A4 Protein A B4 Protein A C4 Protein A Protein A Protein A Protein A Protein A Protein A Protein A Protein A C5 Protein A D5 Protein A k mW rTaTmMmmMovAaDwayYS Legend _ Unassigned sensors RRA Missing sensors 9 0O0O00000000000 O00000000000000 VOZErxAc TOMmMIIODyY RRERZR rc a m a Unassigned samples Figure 6 49 Biosensor Assignment using Homogeneous Trays and Two Biosensor Types 6 To view the biosensor assignments in another tray click the Sensor Tray button and select a tray number from the drop down list The Sensor Tray Map and table for the tray selected will be shown see Figure 6 44 Octet System Data Acquisition User Guide Release 7 1 Assigning Biosensors to Samples page 187 Sensor Tray Legend FOOCUSSOCGEED amp rx cHEOCOSECOSEED amp Sensor Tray v Replace sensor

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