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Octet System Data Analysis User Guide

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1. Working with Experiments page 79 Ec ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics S File Help Data Selection Processing lt Analysis S Loaded Data Summary higG Pro Kinetics Sensor Tray 1 23 Sensors from 1 sa Dra EST LE CAUsers wms Documents User Guides 7 0 higG ProA Kinetics fa AE a i Unassigned E ExperimentType KINETICS StartDateTime 4 21 2011 5 14 11 PM MachineName RED ALPHA 5 UserName labuser PlateName 110420 PlateName2 Unassigned Instrument Type OctetRED96 110420_001 frd A1 Z Assay Fow StepType Step Assay Step Sensor N Data Name fee To ee None Step Data Name 1 Regeneration 10 1000 Custom 7 Equilibration 1 2 Equilbration 120 1200 Baseline 2 2 ProA Immobilization 1 3 ProA Immobilization 600 1200 Loading 3 3 Baseline 1 s gt 4 Ba Baseline 2 4 Association 1 Cs Association 5 Association n 0 5 Dissociation 1 N Dissociation S E Desktop 6 Dissociation S 1 6 Regeneration 1 Sy Libraries 7 Neutralization ie Custom 7 7 Neutralization 1 JR Wesley McGinn Straub 8 Regeneration 1 h i Computer lej Activation 3 Neutralization 1 cig Network He Quenching EF Control Panel Paes 10 Regeneration 1 Recycle Bin n Neutralization 1 J processed data export 12 Equilibration 1 di Workshop data 13 ProA Immobilization 1 14 Baseline 1 15 Association 1 1
2. Figure 3 3 Choose Server Address 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 Analsyis User Guide Release 7 1 page 32 Chapter 3 21 CFR Part 11 Compliance _ Connection to server Server address 192 168 1 78 Localhost 20002 Figure 3 4 Authentication Server Dialog Box 4 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 is listed as the Server in the Login dialog box Figure 3 5 coon O E Figure 3 5 Login Dialog Box GxP Server Information Octet System Data Analsyis User Guide Release 7 1 Starting a User Session page 33 STARTING A USER SESSION NOTE Before starting your first user session contact your administrator to determine the GxP Server module host location to use To start a user session 1 Launch the Data Acquisition or Data Analysis software by double clicking the respec tive desktop icon The Login dialog box displays Figure 3 1 on page 30 2 Confirm that the Server location is correct If not see Selecting a Server Location on page 30 e Ifthe local machine is to be used as the GxP serve
3. m r Figure 5 18 Quantitation Window Displaying Selected Step Data from a Kinetic Assay NOTE When step data from a kinetic assay is open additional quantitation experiments cannot be opened 3 Optional Change the sample type a Select wells in the sample plate map or sample rows in the table b Right click the selection in the plate map or table and select a sample type Octet System Data Analsyis User Guide Release 7 1 page 94 Chapter 5 Basic Kinetics Analysis 04 27 2011 384 higG Q ForteBio Data Analysis 7 0 Quantitation higG ProA Kinetics lelo jk File Help O Data Selection E Resuts E E Loaded Data higG ProA Kinetics 16 Sensors from 1 H Kretics ign X L Reference Subtraction Average of Group View Gy 04 27 11 384 K ProAhigG ed 2 Fip Data Show All Traces pe OctetREDIE Edt Bp hlgG ProA Kinetics 10 Sec OA Row Column F Ignore emors in files when loading Option G Ful Legends S Quantitation GB 04 27 11 384Q hig Binding Curve Graph m Desktop 0 30 6 9 120 150 180 210 240 270 300 330 360 390 420 450 480 510 540 570 600 Time sec Select samples from the table or Plate below to display the data Pia 2 3 4 6 6 7 8 8 18 Ht 2 Wc aculcod Gemoiah Senley A A 0000 Change to Standard O
4. Login name Full name Information Password Confirm password Password reminder 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 pasari cosa re Figure B 33 New User Dialog Box Octet System Data Analsyis User Guide Release 7 1 Accessing Administrator Options page 175 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 Administrator Add delete and change user accounts and groups Supervisor Review data and events e Developer Create run save and export data Lab User Only run experiments Guest No explicit privileges these must be assigned by the administrator If other user groups have been created by an administrator they will also be available for selection in the Group drop down box For more information please see Creating a New User Group on page 179 4 Assign Privileges Each user account can be assigned specific privileges The privileges displayed init
5. Selecting wells in the sample plate map Selecting a cell in the Well Type column of the results table Figure 5 5 Changing Sample Designations Excluding Including Samples from Analysis To toggle sample analysis in the Results window perform one of the following tasks Inthe sample plate map select the well s right click and select Exclude Wells to remove the samples from the analysis If the selection is already excluded from anal ysis select Include Wells to return the samples to the analysis Inthe results table to exclude wells de select the check box in the first column or right click selected rows and select Exclude Wells If the selection is already excluded from analysis click the check box for the desired rows or right click desired rows and select Include Wells Octet System Data Analsyis User Guide Release 7 1 page 82 Chapter 5 Basic Kinetics Analysis SSS Data Export MiG PA Krees ano ais i Table Column Known Conc Index Known C Sample Sensor Plate Sample Binding Wel C Fp X bog Y T bes gt i ott sets su V 0 NA E F 1 Associa Binding Rate v Calc Cone v k A iv 1 N A G4 G1 a Associa o naaa Wo2 oma e no n Ace Daa a 8 2 NA MAS 321 toes a D 4 NA B5 B2 1 Associa 3 Ee C2 1 Associa E o Da FOO Include Wells in Binding Rate Calcula
6. 5D Bl Desktop PULL EFFERRE Figure 5 20 Setting Concentration Values 5 Inthe Results window select a standard curve equation set the processing parameters and then click Calculate Binding Rate The binding rates will be calculated and displayed see Figure 5 21 For more details on analyzing quantitation data see Loading an Experiment for Analy sis on page 76 Octet System Data Analsyis User Guide Release 7 1 page 96 Chapter 5 Basic Kinetics Analysis ForteBio Data Analysis 7 0 Quantitation hlgG Pro Kinetics Se File Help Data Selection gt Results iy Loaded Data higG ProA Kinetics 16 Sensors from 1 S Kinetics py 04 27 11 384 K ProAhlgG aoe 5 Felene S jon Average of F Fip Data a e ve OctetRED9S Ede E hlgG ProA Kinetics 10 Ssec Al Ro Colu 7 Ignore errors in files when loading s Ato F Legends S Quantitation 04 27 11 384 Q higG Binding Curve Graph 04 27 2011 384 higG Q 0 30 60 90 120 150 180 210 240 270 300 330 360 390 420 450 480 510 540 570 600 Time sec m Desktop Select samples from the table or Plate below to display the data Pi 2 3 45 6 78s 9 1H 12 in rammooo gt Secret eee E ID sa Gre 5 F Fe 6 G1 z ref 741 BH H4 Associa Ref 8 A2 A5 Associa Unk 9 B2 EI B5 As
7. Figure 4 6 Data Selection Window Editing Sample Information Editing Processing Parameters To edit processing parameters 1 Modify the following parameters as appropriate Read time The amount of data that is analyzed e Zero concentration threshold Binding rates that are less than the zero con centration threshold are considered zero Low concentration threshold Clicking Calculate binding rate causes the initial rate to be calculated using both a linear and exponential equation The low concentration threshold determines which value is reported in the results table Changing this threshold can improve the precision of low concentration samples e Ifthe result from a linear fit is below the low concentration threshold then the value from the linear fit is reported in the analysis table e Ifthe result from a linear fit is greater than the low concentration threshold then the value from the exponential fit is reported in the analysis table Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 49 2 Inthe Results window select the cell to edit and enter a new value Or right click the cell to access a shortcut menu of edit commands The modified parameters are saved in the Settings_DataAnalysis ini file when you click Calculate Binding Data Data Selection 3 Results Standard Curve Equation Linear Point to Point x Standards Fitting Curve Unkn
8. Figure 5 1 Data Selection Window Loading an Experiment 3 Inthe Loaded Data directory click an experiment name to open it The experiment summary appears Figure 5 2 NOTE Multiple kinetics can be loaded but only one kinetic can be open at a time The 5 icon in the Loaded Data directory tree indicates the open experi ment Octet System Data Analsyis User Guide Release 7 1 page 78 Chapter 5 Basic Kinetics Analysis Experiment information and data files frd ForteBlio Data Analysis 7 0 Kinetics higG Pro Kinetics Wa File Help I Dms Seieren Procesan Arataa z ee emanon Simmmary higG ProA Krates Sansor Tay 1 16 Sensors from 1 z Kneis E 0427 11 IK PRANG BG Prod Kinetics I Qusttaten By 0477 11 O gG 06 27 2011 Bangs f avery Load Bare Aasocut Diesociat Outoa Oton Onton Canton Castor Outoa Barin Losan Basel asociat Ossos Castor Basen Lon n List of all available steps forthe assay Steps performed in the assay Figure 5 2 Data Selection Window Displaying Experiment Summary Information 4 Optional If any step types have been incorrectly assigned in the Octet System Data Acquisition software change them before beginning analysis To do so right click the step and select the correct step type from the shortcut menu Figure 5 3 Octet System Data Analsyis User Guide Release 7 1
9. Working with Experiments page 83 all Edit Sample Information Sample ID IgG Standard Sensor Tip Wel Type E Concentration 10 Replicate Group 10 1 Sensor Infomation Sample Diluent 0K Cancel Figure 5 8 Edit Sample Information Dialog Box 2 Enter the new information in the appropriate fields and click OK Editing Processing Parameters To edit processing parameters 1 Modify the following parameters as appropriate Read time The amount of data that is analyzed e Zero concentration threshold Binding rates that are less than the zero con centration threshold are considered zero e Low concentration threshold When you click Calculate Binding Rate the raw data are fit using both a linear and an exponential equation Both sets of fit ting data are not reported The user specified low concentration threshold deter mines which binding rates are taken from the linear fit and which binding rates are taken from the exponential fit Ifthe result of the linear fit is below the user specified low concentration threshold then this value is reported as the binding rate in the results table e Ifthe result of the linear fit is above the user specified low concentration threshold then the binding rate value obtained from the exponential fit is reported in the binding rate column of the results table 2 Inthe Results window select the cell that you want to edit and enter a new value Or righ
10. Loads an experiment Args d lt path gt Path to experiment data files Response OK r n Tf Error lt reason gt r n const char AUT_CMD_ANALYZE Analyze Runs an analysis Args LA p lt path gt Path to parameters INI file x lt path gt Path to XML information file tiple XML info files Response Error OK r n lt reason gt r n const char AUT_CMD_STATUS Status Returns status OK ready Busy running by an error optional can be mul Error Action was terminated Busy is followed by descriptive information on the progress of the o experiment complete Args none Response OK r n ZJ Busy r n Ey Running nn r n Error lt reason gt r n tendif INC_ANALYSIS_AUTOMATIONAPI_H Octet System Data Analsyis User Guide Release 7 1 page 154 Chapter A Using Octet384 Systems with an Automation Interface Octet System Data Analsyis User Guide Release 7 1 page 155 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 156 Installing the Data Analysis 7 0 21 CFR Part 11 Software cece cece eee e eee e es 159 Installing the ForteBio GxP Server Module 0 ce cece cece eee cnet ence ence ences 162 Administrator Account Setup cece cece cece nee e tence cence ene
11. Octet System Data Analysis 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 Welcome cce ccc ece cece eeeeee 5 About the Octet System a se 6 What s New in the Octet System Data Analysis Software Release 7 1 00eceeeeeeees 7 What s New in the Octet System Data Analysis Software Release 7 0 00eeeeeeee 18 Conventions and Symbols Used in This Guide 20 ForteBio Technical Support 20 Chapter 2 Getting Started 21 Launching the Octet System Data Analysis 7 1 SOMWONC riein ieii 22 Main Menu sessirrestsreistrrtearta 23 Chapter 3 21 CFR Part 11 Compliance 27 Octet System 7 021 CFR Part 11 Software OQVENMVICW wicencenitn tues peededs yeni ve 28 ForteBio GxP Server Module 29 Selecting a Server Location 30 Starting a User Session 0004 33 Compliance FeatureS 0 eeeeees 35 Experiment and Method File Compliance 36 Verifying Digital Signatures 36 Viewing the Audit Trail 38 Changing Projects During a User Session 40 Changing the User Password 41 Locking the Application 41 Ending a User Session 0 000 42 Chapter 4 Quantitative An
12. Apply al Export File txt Sensor Sample Sample Concentration Time 1 Binding 1 Time 2 Binding 2 a Location Location ID uM sec nm shift sec nm shift Al sample 1 0 13330 174 80 5 15571 474 60 5 21287 A2 sample 1 0 06667 174 80 4 69167 474 60 4 79429 A5 sample 1 0 00833 174 80 1 63218 474 60 1 76880 AB sample 1 0 00417 174 80 1 05697 474 60 1 16647 B1 sample 2 0 13330 174 80 2 99342 474 60 2 54185 a Figure 5 67 Report Data Types Processing Options Report Point Analysis Analysis Option S To use the available analysis options select the following from the Analysis window tab e Kinetics analysis Iso Affinity analysi S Steady State analysis Octet System Data Analsyis User Guide Release 7 1 Generating a Report page 147 di ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics File Help Data Selection C Processing Anais Curve Fit Vew _ Y Axis Scaling Repot Points Sepo Maize Sacked Grouped man Ato Sede Te bec 100 Associaton Oniy Individual Options Refesh Refesh FulScae Use 20 Pont Average Remove AL koad Dissociation Only Association and Dissociation Fitting View Model Fitting Local Ful Partial Gobal Ful Group By Rmax Linked Sensor 20 0 400 50 600 700 80 900 1
13. D IMPORTANT An important message for instances where the assay or proce dure will not work if not properly followed WARNING A warning informs the user that specific actions could cause irre versible consequences or damage Table 25 Octet Instrument Labels Symbol Definition A Electrical hazard A Heat hot ise FORTEBIO TECHNICAL SUPPORT You can contact ForteBio technical support at any of the locations listed in Table 26 Table 26 ForteBio Technical Support Main Office European Office Asia Office ForteBio Inc 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 Analsyis User Guide Release 7 1 page 21 CHAPTER 2 Getting Started Launching the Octet System Data Analysis 7 1 Software 0 cece eee ener e eee e ees 22 page 22 Chapter 2 Getting Started LAUNCHING THE OCTET SYSTEM DATA ANALYSIS 7 1 SOFTWARE 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
14. Subtraction Reference Wells Parallel Reference Sensors Double Reference Average Reference Sensors 0 1 000 2 000 1 000 2 000 f 600 1 200 1 800 Time sec Time sec Time sec Step 3 Align Y Axis A m H1 mm 41 H1 44 400M Step Baseline v Time Range sec From 1 0 To 299 0 hlgG A4 40 nM 2 70 Step 4 Inter step Correction a e ina A 240 i pe me J ign to Dissociation i Align to Baseline 210 T H a H Step 5 Process 1 80 H ze H Z Savitzky Golay Filtering 1 50 A N i too H a H i Step 6 View Results 0 30 i i Processed Results 0 60 if if H Sensor Summary 030 i i Report Points H i 0 00 ee eee i Step 7 Save Resuks o 200 400 600 800 1000 1200 1400 1600 1 800 2000 2 200 Save Processed Data Time sec Sensorgrams Sensorgrams q a T a Top View ave Raw Data Tra A A D D Row COS Ros S A RawData Z Fist Subtraction Second Subtraciion Z AignX Save Proc Parameters SensorAl B1 c1 01 E1 Fm c1 Figure 5 36 Processed Data in the Sensor Summary View NOTE In Figure 5 36 the data were processed using the Reference Well sub traction method Report Points The Report Points view displays the raw binding data in tabular format Figure 5 37 Report point analysis can also be performed in the An
15. a ERE I OMOFO OOOOH 2 E Subtraction D et ee ee ees ee A D SSS a mera EE OOO ROmEEOOCOnS Parallel Reference Sensors E l y Y E A e omarion FRO OO0OOO0OCOKL OBO GC aT Buiter Step 3 F Align Y Axis G a a H G oO Or E Edit Sample Properties Sample Step Association HE uH N NIMOY ONC y HO Copy To Clipboard Referend Time Range sec wT Exclude Wells for Analysis From 02 bea X Include Wells for Analysis Step 4 7 Inter step Comection Align to Dissociation Align to Baseline Step 5 Process T Savitzky Golay Fittering m 7 z kl Ligand Sensor Empty Buffer Load Sample O Empty Regeneration Process Data Step 6 View Results Processed Results Sensor Summary Wel Wel Sensor Sensor Wel Wel Well Sample Repor Points Number Location Senor Type fo _ Fe Name _ Number Location Tipe 10 Decay Scat eas 18 B3 _ Ligand Sensor SA Streptavidin 10420 18 i Empty See eae aE 19 C3 Ligand Sensor SA Streptavidin 110420_019frd 31 G4 Empty Association 1X Kinetics B eased 20 D3 _ Ligand Sensor SA Streptavidin 110420_020 rd 32 m Emy Associaton 1X Kinetics Ba anaa TAIE ae an gt Ee F3 Ligand Sensor SA Streptavidin 110420_022frd fae ces Same T yen Ere 23 G3 Ligand Sensor SA Streptavidin 110420_023 rd ZAKAR Sra 24 H3 Ligand Sensor SA Streptavi
16. if 4 10 H 12 1 E H 12 i SS o I A 060 fi i i 0 i 0 00 fom 02 To 04 Step 4 F rterstep Comection Ay lo Desoasten Aqn to Baseine Step 5 Process Smet sey Golay teng First Subtraction Second Subtraction sociation Dissociation Rest 0 00 0 10 tery Wray 0 05 0 10 015 E 0 20 0 25 0 30 0 35 300 Time sec B1 82 0 300 1 800 Time sec s00 1 800 Time sec 70 140 Time sec 210 m C1 C2 a o 30 180 270 Time sec 0 30 180 270 Time sec 30 180 270 30 180 270 Time sec Time sec lq 4 Dd Dl ar m e Fi a Ht Ske Figure 5 66 Types of Report Data Included by the Processing Options Sensor Summaries Octet System Data Analsyis User Guide Release 7 1 page 146 Chapter 5 Basic Kinetics Analysis 5 20 4 80 4 40 4 00 3 60 3 20 280 240 200 0 80 0 40 0 00 0 30 120 Association Dissociation Results 150 180 210 240 270 Time sec 300 330 360 390 420 450 480 Al 81 jar jor je r Time sec 174 7998 Time2 sec 474 5996 6 amp 1 Hi jaz ee c Report Point Analysis Input times are after beginning of Association Step 2 D2 E2 F2 c2 H2 lt gt Use 20 point average Apply
17. Average from tThe of amount of equilibrium state data to analyze from the time equilibrium was reached to the time at which the response should be calcu lated PROCESSING BATCH KINETICS ANALYSIS In batch mode multiple kinetic data sets may be processed without attended operation The Octet System Data Acquisition software analyzes experiment data using the data pro cessing parameters in the Settings_DataAnalysis ini file Batch mode processing may be performed using either a single or multiple ini files During batch processing sample well and sensor information may be substituted with new text a useful feature if the naming convention requires editing after data acquisition Sample Well information which includes Well Type Sample ID Description and Molar concentration can be replaced during batch processing by specifying a Settings_Welllnfo xml file during batch processing Sensor information as well as some sample information which includes Sensor Type Sensor Info Sample ID and Molar Concentration can be replaced by specifying a Settings_Tablelnfo xml file during batch processing If both Settings_Welllnfo xml and Settings_Tablelnfo xml are specified then the Sample ID and Molar Concentration values from Settings_Tablelnfo xml are used during batch processing while the corresponding information from Settings_Tablelnfo xml is ignored Creating a Kinetic Settings_DataAnalysis ini File To create a kinetic Settings_DataAn
18. BI zz Ligand Sensor SA Streptavidin B1 B Ligand Sensor SA Streptavidin C1 GEM Licand Sensor SA Streptavidin HI Ligand Sensor SA Streptavidin D1 B card Sensor SA Streptavidin D1 E Ligand Sensor SA Streptavidin El B igen Sensor SA Streptavidin Usend Sensor SA Streptavidin a FI PD Ligand Sensor SA Streptavidin F E Ligand Sensor SA Streptavidin BE ioo Sensor Gl Ea Ligand Sensor HI B Ligand Sensor H1 ez Ligand Sensor A2 Ligand Sensor A2 Ligand Sensor B2 HE Licand Sensor B2 E cand Sensor c2 E cand Sensor c2 B Ligand Sensor D2 Ligand Sensor D2 Ligand Sensor E2 HE oai Sensor Figure 5 16 Selecting contiguous left and discontiguous right biosensors in the Sensor location list 4 Align the data select an alignment option All Aligned to One Step Enables the following options rently selected step selected step Exporting Raw Data To export raw data 1 2 Click Export Aligned Step csv files Show All Steps Aligned Aligns all steps Aligns baseline steps and association steps to the start of the step Aligns all dissociation steps to the end of the step Align by Begin Point Aligns the displayed curves to the start of the cur Align by End Point Aligns the displayed curves to the end of the currently Align All Baselines Aligns all steps according to the baseline step data In the displayed dialog box navigate to a destination directory enter a filename and
19. D E M 83 25 E o D1 1 IgG Sta Sta E y o a w E E1 1 IgG Sta Sta Save Anahsis Settings 45 5 Gn F 1 IgG Sta Sta HE D V 46 25 E ci G1 1 IgG Sta Sta M471 HI H1 1 IgG Sta Sta a 48 200 A2 A2 1 IgG Sta Sta F B 49 10 E 2 B2 1 IgG Sta sta W 50 50 E c c2 1 IgG Sta Sta m 5 25 D2 D2 1 WG Sta Sta E 52 10 E2 E2 1 IgG Sta Sta R Pi m J a a sai ae Figure 4 19 Results Window 5 Select a standard curve equation from the drop down list e Linear Point to Point The Octet System Data Acquisition software connects the points of the standard curve with straight line segments e Dose Response 4PL Default Unweighted A symmetrical dose response curve No points are weighted during the curve fitting e Dose Response 4PL Weighted Y2 Anon symmetrical dose response curve with weighting applied as 1 Y2 Dose Response 4PL Weighted Y A non symmetrical dose response curve with weighting applied as 1 Y as Y increases weighting decreases e Dose Response 5PL Default Weighted Y2 A non symmetrical dose response curve with weighting applied as 1 Y2 e Dose Response 5PL Unweighted A symmetrical dose response curve No points are weighted during the curve fitting e Dose Response 5PL Weighted Y A non symmetrical dose response curve with weighting applied as 1 Y Octet System Data Analsyis User Guide Release 7 1 page 60 Chapter 4 Quantitat
20. Empty Reference Sensor Pome Md Select Ligand Sensor s for Data Analysis Step 5 Precess Y Savtzky Golay Fiteang We Wel Sensor Sensor We Wel Wet Me Procesa Data Number Location Serao ge ne i Samna Number Location Tye 10 Danpua u on Coy T 2e Shep G View Resuts ls en 4 E Processed Results a 5 G7 Ey zi Sorner Summary s m ay W Exety Repon Ports en Emoty T 4 Se 7 Save Rents m Ve os i JE Save Processed Data eee elec i i Sara Foor Dala m cI Tair Empty Save Proc Parameters s2 o2 my a B ety 9 E2 Ery 2 r ew oa m y F ee eee O ss n2 e l u Pate eT us Lom J a im n Figure 5 27 Parallel Reference Sensor Reference Subtraction Method Double Reference Corrects the binding data for signal due to system artifacts non specific binding and system drift This method requires one reference biosensor per ligand biosensor and one or more rows of reference buffer in the sample plate Octet System Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 103 UF Fortetio Data Analysis 7 0 Kinetics higG Pro Kinetics oa File Help UD Data Seinction 3 Processing Anas Seo 1 Data Selection Erara Sep 2 F Steacton Rederence Wels Sep 4 F kter aep Comection Ayn to Dissociation Nign to Baseine k Ligand Sensor Emp
21. Export File txt Opens a Save As dialog box so that you can save the Report Point Analysis table Results Information Sensor Location Ligand biosensor location Sample Location The well location of the sample in the sample plate Sample ID User specified ligand biosensor information Octet System Data Analsyis User Guide Release 7 1 page 112 Chapter 5 Basic Kinetics Analysis Concentration mM Sample concentration Time 1 sec Time at which the first binding measurement is acquired Binding 1 nm shift The binding signal at Time 1 Time 2 sec Time at which the second binding measurement is acquired Binding 2 nm shift The binding signal at Time 2 Step 7 Saving Results and or Processing Parameters In this step you can save the following parameters Raw data X Y data for the curves in the final Processed Results graph to a file format that can be imported to third party applications like Scrubber2 from BioLogic Software Processing parameter settings The processing parameters are set to the saved val ues the next time the experiment is loaded Binding chart To save the processed data 1 2 Click Save Processed Data Figure 5 38 In the displayed dialog box select a destination folder and click OK The Octet System Data Acquisition software generates a separate file xls for each bio sensor that includes the time nm shift and sample concentration for each processed curve
22. Remove All 125 Time sec 124 Use__ Point Average 125 Report Points view described 110 processed results figure 111 Report Selection form figure 142 reports generating 141 saving 24 Req Rmax kinetic analysis result 130 Residual view individual option figure 125 stacked option figure 124 Residual analyzed data 63 response calculated from the time window entered in the Steady State Analysis section 129 response maximum calculating 115 Response kinetic analysis result 129 Response steady state kinetics analysis option 118 Restart Server console figure 191 Restart Server desktop icon figure 190 restarting ForteBio GxP Server module 190 results color coding by category 135 grouping 126 table described 63 viewing options 107 Results table searching contents 133 Results window for a quantitation experiment figure 61 showing standards sample alerts figure 64 with calculated binding rates figure 96 returning to kinetics analysis mode 96 to the originally configured ForteBio GxP Server module settings 189 Rmax defined 115 kinetic analysis result 129 Rmax Error kinetic analysis result 129 Rmax unlinked 115 Octet System Data Analsyis User Guide Release 7 1 page 206 Rmax Unlinked option for Global Fitting curve fitting kinetics analysis option 115 running batch kinetics analysis 121 batch quantitative analysis 70 S Sample Alert described 65 threshold
23. 0 092 Calculated affinity constant Kp 0 001 and calculated RMax H KD 1 1E 06 o 5 7E 08M asuodsay gt p gt gt E3 8 S e z o B 8 30 10 20 Molecular Concentration uMi Figure 5 59 Steady State Analysis Graph DATA EXPORT OPTIONS The analysis results can be exported txt or csv or copied to the system clipboard Infor mation from the Data Selection Processing or Analysis windows can be selected to gener ate custom reports xls 433 ForteBio Data Analysis 7 0 Kinetics higG Pro Kenetics or x File Help E Duta Selection E Prmceseng Pree Carve Ferg y a to Araire Y Aas Scaling Fepot Ports o Socked Gapos Da Ato Sose Te bech 100 Addio Tatie Seve hiv Oona Refresh Retesh Rd Scale Use 20 Point Avernge Romom Ab Load 0 w w w wv w xo xO wO 1100 1x0 100 10 Window of interest From Stat of Rep Amonen 0 to 595 5 secs Osoite 0 to 8999 secs She Erin Sep Tans Response Cone nM Dase Lec Color Assoc Sampie Loc 7 XY Geach soiinty Steady State o R 2451 7 a m 1 ai x e oo y Ramona 1g um 7 a M 2 X 2 E 203 B3 e s 1 E Index Reapones 3 k 200 n3 B Bs 2 E a g 18s 67 a a 1 Cs 5 x 1621 167 Q J 2 c 6 12 an D o 1 t 7 x 10u55 an oo oe 2 t Pn 8 x LEL 47 i G 1 E f s x 1087 an G E 2 e H w oom o a ce 1 c te n oom 6 G3 Gi 2 2 oows o a EEN u 1 3B x o0 cd Baw 2 u 2606 e7 a 5 3 t
24. Analysis 2 Loaded Data Summary higG Pro Kinetics Sensor Tray 1 23 Sensors from 1 a parr 384 K ProAhigG CAUsers wms Documents User Guides 7 0 hIgG ProA Kinetics eg 195 Prod Kine oan Quantitation e por oec Unassigned m uzna DateTime 2172011 5 14 11 PM C 0272011 224 LE Remove Run ineName RED ALPHA 5 UserName labuser PlateName 110420 PlateName2 Unassigned Instrument Type OctetRED96 110420_001 frd A1 bd ProA Immobilization 600 a jati 600 i a70 04 27 11 384 K ProA higG Lj Data Reference io Jp Results U 04 27 11 384 Q hlgG b 04 27 2011 384 hlgG Q lj 96 J Acquisition J Analysis I higG ProA Kinetics J Screen Shots I Software v6 3 data files Figure 5 12 Closing a Kinetics Experiment Octet System Data Analsyis User Guide Release 7 1 page 88 Chapter 5 Basic Kinetics Analysis i ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics oo a File Help O Data Selection Processing Analysis Hy Loaded Data 23 Sensors from 1 ea C Users wms Documents User Guides 7 0 hlgG ProA Kinetics Gi higa Prem Kinetic i ii Unassigned 5 Quantitation pae 04 27 11 384QhlgG 04 27 2011 384 higG Q 4 21 2011 5 14 11 PM b 70 p S J 04 27 11 384 K ProA hig
25. Individual Options Refresh 6 Dna Sensor Location A1 Sensor Typ Association and Dissociation ws 1 80 Fitting Local E120 Full Partial 0 60 0 00 Global Ful S 200 400 600 Group By Rmax Linked Time sec Sensor Rmax Unlinked By Sensor Location B1 Sensor Typ Color Sensor 1 50 g 1 00 0 50 0 00 Results csv File sree as is Parameters Figure 5 61 Report Selection Form Association 0 to 300 secs Dissociation 0 to 900 secs o 200 400 600 Use Entire Step Times Time sec Sensor Location C1 Sensor Ty Ft Curves 1 50 Steady State Analysis Requiibium Ri Response a Average from 285 to 295 secs oo i ae ind _ 600 Calculate Response cl a Index include Color Sensor Location Experiment Summary Options a Report Selection Form Experiment Summary V Eqperiment Summary Processing V Raw and Aligned Data 7 Sensor Tray image 7 Sample Plate Image 7 Processed Results E Sensor Summary F Report Points Analysis Stack View V 7 Iso Affinty Sensor Tray Data Table Sample Plate Data Table Result Table V Steady State Analysis V Group Views Save To File C Users wms Documents Data Data Folder asia To use the available experiment summary options select the following from the Data Selec tion window tab Steps data table Assay steps data table Octet System Data A
26. Right click the project and select Delete Project 2 Click OK in the dialog box displayed Administrator Constants The Constants tab allows administrators to set GxP Server module constant settings These constants are applied to all user accounts and sessions C B ForteBio GxP Server Admininstration Users Groups Projects Constants Events Name Value CredentialsTTL 5 PasswordMinLength 0 PasswordSecure 0 PasswordTTL 180 UserIdleMin 15 Figure B 43 Constants Tab Octet System Data Analsyis User Guide Release 7 1 Accessing Administrator Options page 183 Available administrator constants and their associated value ranges are shown in Table B 3 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 maximum cache This allows the software to value operate in case the server is tem porarily down PasswordMin Minimum number of characters 0 Minimum 0 Length that a password must contain no maximum 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 and one punctuation character PasswordTTL Amount of time that a password 180 Minimum 0 is allowed to remain unchanged no maximum valu
27. Sensor Location Sensor Type Sensor Into Replicate Group Baseline Loc Sample ID SSGR 2 KO M kon l Ms kon Error k is 1 s kdes Error Remax Remax Error kobs 1 s Req Req Rmax Full X 2 Full RA2 SSG KD SSG Rmax Loading Well Location Losding Sample iD o amp File Help Data Selection CO Processing Anaise Curve Feng Step to Analyze P Associsbon Only D Dissociation Only View S Stacked D hdvis D Gaped Options Retresty Y Aes Scaling Repot Ports Ato Scale Tme bec 100 D Ra Scale Add to Tabie Use ZU Port Avenge Remove Al Lond Aswason and Dswaston Fitung View Model st x Fitina D Rai Pae H 0 w w w w rri XO 0 XO 100 W0 120 130 140 aa 7 j Group By Rmax Linked Tine sec Senser Remax Unlinked By Coker Senser Compound Window of interest From Start of Step Association 0 to 599 6 secs Dissociation O to 899 secs index haxe Remorse 9 Conc nM Dissoc Loc Cokr Assoc Sarge Loc ore 2 R a2 an E es 1 sn Eose Sep Dee u k ooa o rc E 1 2 ome o 4S 45 1 Fe Curves 4 E I4 GT a ca 1 6 k mi 83 03 oe 1 Sondy Sate Analysis E g 11655 417 E E4 T Requiem 1 E 2575 667 ry M 2 Okun n k o O amp ce 2 i 3 k ons o 43 H 2 nepika 85 te Ea E 27586 667 a 5 2 Tainaa Paparan 7 k 2367 B3 83 os 2 3 E 18797 167 c3 rey 2 Data Epot a E 11982 83
28. Step 3 Align YAXiS cc cece 104 Step 4 Interstep Correction 105 Step 5 Process 0 cece cece eens 106 Step 6 Viewing Results 107 Step 7 Saving Results and or Processing Parameters 6 c cece cee eee 112 Kinetics Andlysis 0 02 cceee eee ee 113 Curve Fitting Analysis 114 Steady State Analysis 118 Processing Batch Kinetics Analysis 119 Creating a Kinetic Settings_DataAnalysis ini File 119 Creating a Kinetic Settings_Wellinfo xml File Optional 0 ccccee nuns 120 Creating a Kinetic Settings_Tablelnfo xml File Optional ccccceeeeues 120 Selecting Experiments and Running the Batch Analysis 0ecceeeeeeuee 121 Kinetics Analysis Results 123 Fitting View and Residual View 123 Grouping Results for Viewing 126 Selecting Data for Viewing 127 Analysis Results Table 129 Working with the Analysis Results Table 131 Searching Analysis Results 132 Color Coding Data 06 05 134 Sorting Analysis Results 137 Working with Graphs 0006 138 1 AC 2 serrer telio tirn e 138 Iso Affinity Graphs a 0 000000 139 Steady State Analysis Graphs 140 Data Export Options 0664 140 Generating a Report 0 c0eee 141 Experiment Summary Options 142 Processing Options 0065 143 Analysis Options 00ee
29. This file is suitable for import into third party applications To save the raw data i 2 Click Save Raw Data Figure 5 38 In the displayed dialog box select a destination folder and click OK The Octet System Data Acquisition software generates one file xls that includes time and nm shift data for all of the biosensors To save the processing parameters 1 Click Save Proc Parameters Figure 5 38 The processing parameter values are saved as an ini file in the experiment folder Step 7 Save Results Save Proc Parameters Figure 5 38 Save Results Options Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis page 113 To print or copy a binding chart 1 Right click the chart and select Toolbar Figure 5 39 to access the printing and copy ing buttons the buttons will appear at the upper left of the binding chart ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics eee Fie Help QD Data Selecton Proceesrs EJ Anss Sep 1 Data Selection z Raw Data View R Sensor Sriection 260 eee Sensor to be Analyzed 240 ais A1 Fi o i 81 Fi 220 Ci Fn Ee a 2 00 1 1 GIF 1 Toolber Step 2 F Subtmetion 160 E Data Grid Relererce Wels 140 Parallel Reference Sensors i a dal Legend Box Dele Refernnor Color A 1 00 Average Relerence Sensors be E Step 3 F Aon Y foes Font su ow Step
30. not replicate groups The column is populated by opening Grouped view selecting up to three grouping parameter and activating Steady State under additional graphs The SSG Kp value is reported for the set of data within each pane of the Grouped view Repli cate grouping and global analysis are not used to determine this value SSG Rmax tThe steady state group Rmax value Use this feature to quickly view the Rmax value of steady state data for a group defined within Grouped view not repli cate groups The column is populated by opening Grouped view selecting up to three grouping parameter and activating Steady State under additional graphs The SSG Rmax value is reported for the set of data within each pane of the Grouped view Replicate grouping and global analysis are not used to determine this value e SSG RA2 The steady state group R 2 value Use this feature to quickly view the RA2 value of steady state data for a group defined within Grouped view not replicate groups The column is populated by opening Grouped view selecting up to three grouping parameter and activating Steady State under additional graphs The SSG R 2 value is reported for the set of data within each pane of the Grouped view Rep licate grouping and global analysis are not used to determine this value Loading Well Location Location of the sample well used during the load step of the experiment Cycle Number of biosensor regeneration cycles Octet
31. such as phage cells and lipoparticles on the biosensor surface Grouped View Displays graphs in custom groupings Choose this option to dis play graphs organized into groups according to sample attri bute or results category This is a highly useful feature when working with large data sets e Options Click to show the Grouped View Options dia log box e Refresh Updates the graph display Ignore errors in files when loading If this option is chosen the Octet System Data Acquisition soft ware ignores errors in data files All data files regardless of errors or runtime issues will be loaded for analysis Show All Traces Edit Legends Displays all binding curves Select the sample information displayed in the legend Options include Sensor Sample Sample ID Group and Concentra tion Octet System Data Analsyis User Guide Release 7 1 page 86 Chapter 5 Basic Kinetics Analysis Opening Binding Curve in Separate Window To open the binding curve chart in a separate window double click the graph Customizing Appearance of Graph or Binding Curve To customize the appearance of the graph or a binding curve see Figure 5 11 Right click the graph or a curve for a shortcut menu of display options Hover over a binding curve to display a tooltip of the XY coordinates e Right click the graph to view a shortcut menu of display options Right click a curve to view a shortcut menu of display opti
32. users groups projects and constants and view associated events These options can be accessed in the Octet System Data Acquisition and Data Analysis soft ware or by launching the ForteBio GxP Server module directly Data Acquisition and Data Analysis software Click Security gt Server Adminis tration Figure B 28 Security Help Verify Document Verify Document View Audit Trail View Audit Trail Change Project Change Password Change Password Change Project gt Server Administration Server Administration Lock Application Lock Application Logoff ng Data Acquisition Software Data Analysis Software Figure B 28 Security gt Server Administration Menu ForteBio GxP Server module on network location Double click the FBServerConfig exe file in the FBServer7 folder from the installed location Figure B 29 File Edit View Tools Help Organize Include in library 7 Share with 7 Burn New folder z i z 4 ForteBio p Name Date modified Type Size gt J DataAcquisition7 f A FBServer exe 12 3 2010 3 53 PM Application 2 966 KB gt J DataAnalysis7 A FBServerConfig exe 12 3 2010 3 53 PM Application 7 821 KB JL FBServer7 FBServerMonitor exe 12 3 2010 3 54PM Application 6 909 KB 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 5
33. 180 Edit Legends viewing options basic kinetics analysis 85 quantitative analysis 55 Edit Sample Information dialog box figure 50 editing a search 134 alert threshold value 64 experiments 81 processing parameters in the Results window figure 49 processing parameters kinetics 83 processing parameters quantitative 48 standard concentration information 48 82 well information 48 82 Electrical hazard symbol 20 electronic signature of method fmf and data frd files 36 ending a user session 42 equilibrium response 80 equilibrium state data analyzing 119 estimate of the goodness of the curve fit 130 Event Log figure 185 events listed in the Audit Trail 39 sorting in Audit Trail 39 tracking 185 viewing 39 186 Events tab 185 Exclude Wells display option 131 menu 47 Exclude Wells for Analysis menu 99 excluding data from analysis 116 sample from subsequent analyses 62 samples from analysis kinetics figure 82 samples from analysis quantitative 47 Octet System Data Analsyis User Guide Release 7 1 page 196 samples from analysis quantitative figure 47 wells from analysis described 99 wells from the biosensor table figure 116 Exit menu 24 experiment method file 76 experiment method file loading 24 experiment summary options 142 experiment quantitation described 44 experiments closing all kinetics 87 quantitative 57 closing one kinetics 87 quantitative 57 edi
34. 96 binding signal at Time 1 112 at Time 2 112 biosensor data viewing specific 127 biosensor number 62 biosensor types changing figure 98 biosensors selecting figure 97 selecting and confirming to analyze figure 106 selecting for analysis 79 biosensors selecting 97 BR AVG analyzed data 62 BR CV analyzed data 62 BR SD analyzed data 62 By Color analysis option 115 By Sensor analysis option 115 C Calc Conc analyzed data 63 calculated binding rates figure 96 calculated response at equilibrium 130 calibration curves 71 Case Sensitive Advanced Search option 133 Change Password dialog box figure 41 Change Password menu 25 Change Project menu 25 Change Well Type menu 98 changing administrator password 177 biosensor type figure 98 color of user selected results figure 135 constants 184 file type available for selection 37 group settings 180 project settings 182 projects during a user session 40 sample designations 81 quantitation analysis 46 sample designations figure 46 81 Octet System Data Analsyis User Guide Release 7 1 page 192 sample type 93 sample type in the sample plate map figure 94 sample type in the sample table figure 94 step type figure 79 user account password 177 user account settings 176 user password 41 Choose Install Location dialog box figure 157 159 Choose Start Menu Folder dialog box figure 157 160 163 closing all e
35. Analysis WORKING WITH GRAPHS The active analysis results are automatically presented in three graphical formats e XY Iso Affinity Steady State Analysis X Y Graphs The X Y graph is a scatter plot from user selected analysis results x and y variables Both axes may be presented on either a logarithmic or linear scale Logarithmic scale option XY Graph Iso Affinity Steady State X Response w C Log Y Cone uM x IY Log 30 ans Select the analysis result to plot from the drop down lists Qw 2 5 S 10 m 0 a m i o 0 02 0 04 0 06 0 08 ol Response Figure 5 56 X Y Graph An X Y plotting tool has been added to the Results tab of quantitation analysis Previously available only in kinetics analysis the X Y plotting tool graphs several important parame ters such as binding rate R2 calculated concentration and residual The axes may be inde pendently selected to by logarithmic In the example shown the calculated concentration is plotted versus the R2 Figure 5 57 Octet System Data Analsyis User Guide Release 7 1 Working with Graphs page 139 so Affinity Steady State x Re r ft Index kon 1 Ms D m n spyijucy be m n a Figure 5 57 X Y Plotting Tool Iso Affinity Graphs The Iso Affinity graph enables viewing of the continuum of kgis and Kon values that gener ate a single v
36. B 51 ForteBio GxP Server Configuration Window Use of the User Groups Projects Constants and Events tabs are described in Accessing Administrator Options on page 172 Octet System Data Analsyis User Guide Release 7 1 Accessing the ForteBio GxP Server Module Directly page 189 ForteBio GxP Server Module Testing The ForteBio GxP Server module can be tested to ensure it is accessible and functioning properly Wasn t sure about this functionality To test the ForteBio GxP Server module 1 Optional In the Connections to Clients box Figure B 52 make changes to the server settings if necessary Connection to clients Localhost Port 20002 Aep eest 7 Support UDP ping for discovery Figure B 52 Connection to Clients 2 Click Apply amp Test If the ForteBio GxP Server module is found and functioning properly the following message displays Figure B 53 Figure B 53 Message Confirmation of Found Server To return to the originally configured ForteBio GxP Server module settings click Default at any time Octet System Data Analsyis User Guide Release 7 1 page 190 Chapter B 21 CFR Part 11 Software Administrator Options RESTARTING THE FORTEBIO GXP SERVER MODULE If the host location of the GxP Server module cannot be found during user login or if you are unable to log in with valid credentials the ForteBio GxP Server module may be offline and must be re
37. 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 31 Tab View Example Tab Menu Right clicking an entry or a blank area in the tab displays the tab menu Tab menu options vary depending on the tab selected Octet System Data Analsyis User Guide Release 7 1 page 174 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 Creating a New User Account To create a new user account 1 Right click anywhere in the Users tab and select New User or double click in a blank area see Figure B 32 a ForteBio GxP Server Admininstration 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 32 New User Menu The New User dialog box displays Figure B 33
38. Confirm or edit the processing parameter settings for details see Editing Processing Parameters on page 48 Binding Rate Equation tThe curve fitting equation that models the binding data Initial Slope Calculates the initial slope of the acquired quantitation data nm second Choose this equation for a basic quantitation or basic quantita tion with regeneration experiment R equilibrium this equation is recommended for an advanced quantitation experiment that includes amplification This equation uses the calculated equilibrium not the initial slope to model the data Read Time The length of acquired data analyzed seconds Octet System Data Analsyis User Guide Release 7 1 Analyzing Data page 61 Zero Conc Threshold Calculated binding rates less than the zero concentra tion threshold are reported as zero in the results table e Low Conc Threshold Clicking Calculate Binding rate causes the initial rate to be calculated using both a linear and exponential equation The low concen tration threshold determines which value is reported in the results table If the result from a linear fit is below the low concentration threshold then the value from the linear fit is reported in the analysis table If the result from a linear fit is greater than the low concentration threshold then the value from the exponen tial fit is reported in the analysis table Changing this threshold can improve the precis
39. Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 109 Right click chart for chart display options Right click curve for curve display options aP CAUsers wms Documents UseF Guides 7 0 higG Pro Kinetics vee il on eee ee ee eee Po OA OO A R E 8 a 8 g 5 8 Time isee Figure 5 35 Binding Chart including Toolbar and Data Grid Sensor Summary The Sensor Summary view displays the binding charts generated during data processing Figure 5 36 The Sensor Summary view controls enable you to select the sensor data to display e Hover over a binding curve displays a tooltip with sample data e Clicka sensor tab or one of the arrow buttons I4 4 gt gt I in the Sensorgrams controls at the bottom of the window to view data for a specific biosensor Set the number of sensorgrams per row and the number of rows to display e Use the Top View check boxes to show or hide the raw data and subtraction graphs in the top row Octet System Data Analsyis User Guide Release 7 1 page 110 Chapter 5 Basic Kinetics Analysis G Data Selection 1 Processing E Analysis Step 1 Data Selection Raw Data By Sensor Subtraction By Sensor Align X By Sample ID Sample O Raw Data View Loc Conc nM Sensor Selection Sensors to be Analyzed Example Al B1 A2 B2 Reference Row m N w gt o os Step 2
40. J Data Ji Reference iJi Results D 04 27 11 384 Q hlgG B 04 27 2011 384 hlgG Q a ji 96 Ji 384 J Acquisition J Analysis I hlgG ProA Kinetics Ji Screen Shots _ Software v6 3 data files J Webinars J Webpage J Wikipedia a Music m Figure 5 13 Removing All Kinetics Experiments from Processing WORKING WITH RAW DATA Viewing Raw Data In the Processing window the Raw Data view enables you to conveniently examine the binding data To view raw data 1 Inthe Processing window the Processing tab and confirm that the Raw Data View option is selected Octet System Data Analsyis User Guide Release 7 1 Working with Raw Data page 89 Selected step 2 ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics File Help Y Scale Report Points Ato Ful TME 700 Use 29 Points Addto Tabie Click on a step below to align traces E Gec se 20 Average C Sensor Sensor Type Sensor info Raw Data Sensor Location HH Licend SA Strepta P y 3 00 HBB Lond SA Strepta i I Ligand SA Strepta 20044 i DD Ligand SA Strepta Sere i Ligand SA Strepta i i 7 Ligand SA Gtrepta 0 00 HE if 4 i _ _ i EE uoo H i AE a Ligand o 400 800 1 200 1600 2000 2400 2800 3200 3600 4 000 4400 4800
41. L PA 15 26318 7 a as 2 w 2773 B e 1 ts j 5 Figure 5 60 Data Export Options in the Analysis Window Octet System Data Analsyis User Guide Release 7 1 Generating a Report page 141 The data export options include Export Fitting Results Saves the binding data and analysis results for each biosen sor to a separate text file txt Export Table to csv File Saves the results table to a csv file that can be opened in a spreadsheet application Copy Table to Clipboard Saves the binding data and analysis results for the selected biosensors to the system clipboard GENERATING A REPORT NOTE Generating reports for large data sets may take a few minutes For faster report generation minimize the number of items selected for the report In particular the sensor summary for a large data set can be time consuming To generate a report 1 2 3 On the menu bar click File gt Save Report In the displayed dialog box select the information to include in the report Confirm the default location to which the file will be saved or specify a different loca tion Click Export Octet System Data Analsyis User Guide Release 7 1 page 142 Chapter 5 Basic Kinetics Analysis D Data Selection Processing Analysis Compound Window of Interest From Start of Step Curve Fitting View Step to Analyze Stacked Grouped Association Only
42. Point Average P Dissociation Only Association and Dissociation Fitting View Ws Fang Ful Partial Global Full Group By Rmax Linked Sensor Rmax Unlinked By 700 800 900 1 000 1 100 1200 1 300 1 400 Color Sensor Time sec Compound Window of Interest From Start of Step Association 0 to 599 6 secs Dissociation 0 to 900 secs d 3 g i Steady State Analysis R equilibrium Response Averagefrom 585 to 595 secs 0 1 2 3 4 5 6 7 8 9 10 n 12 13 14 15 16 eee ECE PEPE Figure 5 53 Changing the Color of User Selected Results 3 In the color palette that appears select a basic color or create a custom color To define a custom color click Define Custom Colors 4 Click OK in the color palette The selected color is applied to the binding curve and appears in the table Results can be color coded by category to group them for a global fit for example colored by compound then fit using global fit by color For the final display the wells can be re col ored without affecting the results Color Coding Analysis Results by Category To color code analysis results by category 1 Right click the analysis results table and select Set Color By 2 Make a selection from the shortcut menu Figure 5 54 In Figure 5 54 s example category sample concentration Octet System Data Analsyis User Guide Release 7 1 page
43. Ref o ea je Fis eh ee oe aa s c T a 100 E B1 1 IgG Sta Sta Sample Alet D 4 amp 2 50 Bic c1 1 IgG Sta Sta Daa E M43 25 Bo D 1 IgG Sta Sta r D T 44 10 E1 1 WG Sta Sta mer Ml 45 5 E F F 1 WG Sta Sia Save Analysis Settings ee HE i 4 amp 25 Bc G1 1 WG Sta Sta 7 F a7 1 HI H1 1 KG Sa sa i T 48 200 A2 A2 1 IgG Sta Sta i T 49 100 E 22 B2 1 IgG Sta Sta La 50 50 Hg c2 c2 1 IgG Sta Sta Mo 25 D2 D2 1 KG Sta Sta T 52 10 E2 E2 1 IgG Sta sta S i mmmn ra eae m r Figure 4 27 Results Window 3 Set the analysis options standard curve equation processing parameters standards sample alerts For more details see Analyzing Data on page 57 4 Click Save Analysis Settings The ini file is saved in the experiment folder 5 Optional Analyze each experiment using a different ini file repeat steps1 4 to create a ini file for each experiment in the batch Octet System Data Analsyis User Guide Release 7 1 page 70 Chapter 4 Quantitative Analysis Selecting Experiments and Running the Batch Analysis To select experiments and run the batch analysis 1 On the menu bar click File gt Quantitation Batch Mode The Quantitation Batch Model dialog box displays Figure 4 28 sel ai Quantitation Batch Mode Ini File Use the one in each folder Use one for all folders Output Folder U
44. Row 85 quantitative analysis All 54 Column 54 Row 54 reference subtraction applying during data processing 99 Reference Well menu 98 Reference Wells confirming subtraction figure 100 reference subtraction method 100 reference subtraction method figure 101 specifying figure 99 Refresh Fitting view option 124 Remove All Fitting view option 125 Remove Level Advanced Search option 133 removing all kinetics experiments from processing figure 88 Replicate Groups adding from the Sample Plate Table 52 analyzed data 62 assigning in the Sample Plate Map 50 assigning in the Sample Plate Table 52 defining 49 Replicate Groups displayed in Sample Plate Map figure 51 in Sample Plate Table figure 52 replicates 60 report data types analysis options kinetics analysis results figure 147 Experiment Summary options figure 143 Processing options processed data figure 145 raw data and aligned data figure 144 Report Point analysis figure 146 sensor tray and sample tray infor mation figure 144 Report point 1 10 kinetic analysis result 130 Report Point Analysis features Apply 111 Apply All 111 Export File 111 in the Analysis window 110 Input times after beginning of Association Step 111 Octet System Data Analsyis User Guide Release 7 1 page 205 listed 111 Use 20 point average 111 Report Point Analysis table 110 Report Points Add to Table 125 Fitting view option 124
45. Server module is hosted on a dif ferent subnet deselect the Localhost check box Enter the IP address of the computer hosting the GxP Server module Connection to server Server address 192 168 1 78 Localhost 20002 Figure B 19 Authentication Server 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 dialog box Octet System Data Analsyis User Guide Release 7 1 Administrator Account Setup page 167 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 reselected each time a new session is initiated Figure B 20 Login Dialog Box with Server Parameter Configured 4 Select Administrator from the User drop down list Figure B 20 5 Leave the Password blank set the Project to none and click OK Figure B 21 o na gt fort sio Server localhost 20002 User Administrator Password Project _ none Figure B 21 Login Dialog Box with Server User and Project Settings Configured The Change Password dialog box displays see Figure B 22 Octet System Data Analsyis User Guide Release 7 1 page 168 Chapter B 21 CFR Part 11 Software Administrat
46. System Data Analsyis User Guide Release 7 1 Kinetics Analysis Results page 131 Working with the Analysis Results Table To view a shortcut menu of display options Figure 5 51 right click the Analysis Results table 3 ForteBio Data Analysis 7 0 Kinetics higG Prod Kinetics eek File Help CD Osta Setecton Procesang Anses Y Aos Scaling Repot Ports B Stocked Groped Ato Scale Time ec 100 Adsto Table Swe Use 20 Port Average Remove A Lond 100 1100 1201300 1 400 Window of Interest From Stan of eo Asspoation 0 to 599 5 secs Dissociation D to 899 9 sees 500 600 100 1100 10 13001400 1 500 Advenced Search eaten Aep paon Feworee Conc hM Omeoc SetColor XY Gr ny Sad Sat 2693 7 a Set Calor By Grou f Reeporee Romi 2s 087 a ER j aes En 20196 23 B vi index Response Steady Siste Ansys 203 W 8 Lock Requabrum 16708 167 a Unlock Recporse Awerage trem 585 to S95 ses 1060383 03 Include Wells 10305 33 03 Exclude Wels Cakes Rasporse l 10346 47 E Sire Columns by Title 3 pm 2612 7 as Size Columns by Date i Export Fitting Espot Tabie to 2632 a AaB Rests esv Fle 2723 m 83 Cie f 233 n3 B Select All Rows swoon Betzee ve 7 e saecion 11041 ax D3 Group Selection Cte G a4 22 o 02 os Seve Osta Analyus Parameters hades Order Column Fip Date Back to Original Data Edit Sensor Sampl
47. a Data Export n amp oon o G3 G4 2 a F 2 g omz 0 H3 A 1 HI 3 Export Export Table to n E ooe o H y 2 HI 3 n ene u k 26206 667 AB Has i A2 en Copy Table to 15 x 26318 667 B 2 A2 ti Clipboard 6 x 275 83 B3 E cs 1 B2 7 k 22918 33 B3 Hs 2 B2 0 one ar Save Data Analysis Parameters 8B x 17742 167 a3 cs 1 c2 a A A an a anan ana an a a an i m F Index Figure 5 43 Save Data Analysis Parameters Button Analysis Window Steady State Analysis To analyze the processed kinetic data 1 Set the analysis options for more details see Table 5 1 on page 85 2 Click Calculate Response to display the analysis results For more information on viewing results see Kinetics Analysis Results on page 123 Excluding Data from the Analysis To exclude specific data from the analysis remove the check mark next to the row in the analysis results table Or right click the selected row s and select Exclude Wells Steady State Kinetics Analysis Options e R equilibrium Fits the binding curve to a 1 1 model and uses the calculated Req to determine the steady state affinity If this option is selected you first must perform a curve fitting kinetic analysis e Response Takes the average response from the user specified time window and uses it to calculated the steady state affinity Octet System Data Analsyis User Guide Release 7 1 Processing Batch Kinetics Analysis page 119
48. a group name see Figure 4 12 Sample Plate Table Concentration units Molar concentration units mM Well Sample ID Replicate Group Type Conc jig ml MW kD Molar Conc nM Information a Ad Association Sample 10 150 66 67 1X Kinetics Buffer B4 Association 2 Sample 5 150 33 33 1 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 1 Kinetics Buffer G4 Association 6 Reference 1X Kinetics Buffer H4 Association 6 Reference 1X Kinetics Buffer Figure 4 12 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 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 Analsyis User Guide Release 7 1 Working with Experiments page 53 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 Mul
49. accommo date all of the data Report Points e Time sec A user specified time point in the experiment The Octet System Data Acquisition software computes the response at that time point Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis Results page 125 Use ___ Point Average Each data point represents an average of the number of data points specified centered around the time point chosen Add to Table Adds the response computed for the user specified time point to the analysis results table Up to 10 response points can be added to the table Remove All Removes all of the response data for user specified time points from the analysis results table ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics Sie a File _Help OD Data Selection C Prockssing Anaivsis Curve View _ Y Axis Scaling Report Points Step to Analyze Stacked Grouped ta Auto Scale Time sec 100 Association Only Individual Options Refresh Refresh Full Scale Use 20 Point Average Dissociation Only Sensor Location A1 Sensor Type SA Streptavidin Sensor Info Replicate Group 1 KD M 4 811E 10 kon 1 Ms 1 36505 kdis 1 s 6 566E 05 kobs 1 s 9 168E 03 z 7E i o 8 i o 8 Full Partial o 300 600 900 1 200 o 300 600 300 1 200 Time sec Time sec Global Full Group By Rmax Linked Sensor Rmax UnLinked By C
50. 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 ora set period of inactivity is reached A new user session is initiated each time a user accesses the software S NOTE For details on how to install the ForteBio GxP Server module see Appendix B 21 CFR Part 11 Software Administrator Options on page 155 NOTE The ForteBio GxP Server is required for 21 CFR Part 11 NOTE The GxP Server can be installed in multiple locations with user selection of the employed copy at the launch of the Acquisition or Analysis software although a single copy per network is recommended by ForteBio to ensure that all records are saved to one location Octet System Data Analsyis User Guide Release 7 1 page 30 Chapter 3 21 CFR Part 11 Compliance SELECTING A SERVER LOCATION NOTES Please contact your administrator to determine best location to use for the GxP Server module Once the GxP Server module host location is selected this location should be used as the default selection for the user account It does not need to be rese lected 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
51. click Save Quantitating Raw Data To quantitate raw data from a selected step 1 In the Raw Data view select the step to quantitate and click Quantitate Selected Step Figure 5 17 Octet System Data Analsyis User Guide Release 7 1 page 92 Chapter 5 Basic Kinetics Analysis Step 2 Subtraction Reference Wells Parallel Reference Sensors Double Reference Average Reference Sensors Step 3 F Align Y Axis Step Association Time Range sec From 0 2 To 04 4 Ome ra oy 109 ea Sensor location C Sensor Step 4 F Inter step Comection Ak dl ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics o B amp File Help T Data Selection 3 Processing Analysis Y Scale Report Points Points cen Click on a step below to align traces Ext Legends Average 3 00 2 00 100 0 00 j 400 800 4800 5 200 1 200 1600 2000 2400 2800 3200 3600 4 000 4 400 Time sec This will quantitate the currently selected step Equilibration and close this file Do you want to proceed itep selected Equilibration Sensor Location Well Location 2 500 3 000 3 500 Time sec 2 000 Al C1 60 50 0 40 30 20 f i i i i i i i i i i i i i i i i i i ow i 0 00 4 000 4 50
52. data Results table NOTE If multiple experiments are open the report will include a separate worksheet for each experiment Octet System Data Analsyis User Guide Release 7 1 Exporting Data page 73 To save a quantitation results report 1 Onthe menu bar click File gt Save Report or click the Save Report button The Report Selection dialog box displays see Figure 4 30 ES Report Selection Ini File Experiment Summary Plate Map Standard Curve M Result Table XY Graph Group View File Name ExcelReport Figure 4 30 Report Selection Dialog Box 2 Select the components from the analysis to be exported enter a file name and click Save The report is saved to the data folder Octet System Data Analsyis User Guide Release 7 1 page 74 Chapter 4 Quantitative Analysis Octet System Data Analsyis User Guide Release 7 1 page 75 CHAPTER 5 Basic Kinetics Analysis Working with Experiments 0 cc cece cece cence ada ttti ene eee KEERAS TEAR 76 Working with Raw Data ccc cece cence ence ence nen enn nen en eee enee nea enes 88 Processing Kinetic Data cece ccc ccc cee cece nee e eee kt eate E iini 96 Kinetics Analysis lt 2sc00s 00sancietscvhee padeeseies eradedaubader borne abddeawevune wre 113 Processing Batch Kinetics Analysis 0 cece cece eee cee n cnet ence ence teen ees 119 Kinetics Analysis Results 00 0 0 cece c
53. down list and select an entry Figure 3 16 2 Audit Trail ec E Machine JRICHARDS Date Time role Antibody screen Machine Action Description 2011 02 Cell Culture screen JRICHARDS User login 2011 02 RESTS RICHARDS User login 2011 02 14 13 42 07 Antigen Antibody screen JRICHARDS User logout 2011 02 14 13 42 45 Antigen Antibody screen JRICHARDS User login Figure 3 16 Viewing a Specific Project in the Audit Trail NOTE Selections can be made in either one or both of the Project or Machine drop down lists The list only displays events for the selected entries Figure 3 17 Octet System Data Analsyis User Guide Release 7 1 page 40 Chapter 3 21 CFR Part 11 Compliance C Audit Trail f eae Project Receptor Ligand screen M Machine Date Time Project Machine Action 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 3 17 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 you can switch to another project in the Data
54. location To select a server location NOTE You must select the host location of the GxP Server module during the login process You can use the GxP Server on the local host computer where the Data Acquisition or Data Analysis software is installed or from a network location 1 Launch the Data Analysis software by double clicking the Data Analysis desktop icon The Login dialog box displays Figure 3 1 Figure 3 1 Login Dialog Box Octet System Data Analsyis User Guide Release 7 1 Selecting a Server Location page 31 2 Click browse to select a Server location The Authentication Server dialog box displays Figure 3 2 F Connection to server Server address localhost v Localhost 20002 Figure 3 2 Authentication Server Dialog Box 3 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 click the Localhost check box Change the Port number if necessary 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 x More than one server was found Please choose one 192 168 1 78 JRICHARDS 192 168 1 78 JRICHARDS
55. 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 Analsyis User Guide Release 7 1 Launching the Octet System Data Analysis 7 1 Software page 25 Security Menu The Security menu is only available in the 21 CFR Part 11 version of the Octet System Data Analysis software NOTE The Security menu is only available in the CFR 11 version of the Octet System Data Analysis software For complete details on menu options refer to Compliance Features on page 35 Security Help Verify Document View Audit Trail Change Password Change Project Server Administration Lock Application Log Off Figure 2 4 Security Menu Table 2 2 Security Menu Commands Menu Command Function Verify Document Utility that tests if a method fmf or data frd file was created using a CFR version of the ForteBio software View Audit Trail Displays the recorded events for CFR docu mentation Events may be viewed by project or machine Change Project Change Password Switches active projects or run experiment without a project title none Edits password for active user Server Administration Modifies settings for users groups projects and constants Lock Application Disabled the Octet System Data Analysis software with a screen lock A password is requi
56. reference subtraction Subtracted Data Binding curves after the user specified reference subtraction method is applied Align Y Binding curves after user specified Y alignment Align X Binding curve association steps aligned at the same time point Octet System Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 107 gt ForteBio Data Analysis 7 0 Kinetics higG Prod Kinetics reer File Help D Data Selection O Processing Analysis 3205 270 280 240 240 44 210 20 4 1 80 160 i Step 2 T Subtraction E 120 E Reference Wells 1 20 Parallel Reference Sensors 080 ai Double Reference re Average Reference Sensors i 060 Step 3 7 Align Y Axis on 030 Step Association X 0 40 Time Range sec i i i i i i i Fom 02 To 04 0 1 000 2 000 3 000 4 000 5 000 0 1 000 2 000 i Time sec Time sec Step 4 T Inter step Correction Align to Dissociation Align Y Aignto Baseline 270 i Step 5 Process Z Savitzky Golay Fitering 240 Process Data 210 Step 6 View Results 1 80 Processed Results 5 Sensor Summary i Report Points 10 Step 7 Save Results ise oso oa 0 00 i i i i H H 0 1 000 i 3 000 i 1 0 200 400 600 800 1 000 1 200 1 400 Time sec Time sec Figure 5 32 Processed Results View 3 Click Save Proc Parameters to save the proces
57. tab The Settings_Tablelnfo xml file is saved to the experiment folder NOTE If there is an existing Settings_TableInfo xml file in the experiment folder it will be overwritten The original Settings_Tablelnfo xml file that contained information entered during data acquisition is deleted Right click the analysis table and select Edit Sample Sensor Information Enter the new information for Sensor Type Sensor Info Sample Info and Molar Con centration and then close the dialog box The Settings_Tablelnfo xml file is saved to the experiment folder Octet System Data Analsyis User Guide Release 7 1 Processing Batch Kinetics Analysis page 121 Selecting Experiments and Running the Batch Analysis To select experiments and run the batch analysis 1 Select File gt Kinetic Batch Mode The Quantitation Batch Mode dialog box displays Figure 5 44 223 ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics Load a Folder Quantitation Batch Mode Kinetics Batch Mode Save Report Options Exit a Kinetics Batch Mode z bife Use the one in each folder Use one for al folders Outpt Folder Use the oignal data folder Use this folder Selected Folders Add Folders Remove Selected Satin Folder Qus Analyze Data Figure 5 44 Kinetics Batch Mode Quantitation Batch Mode Dialog Box 2 Set the batch mode options Use the one in each fol
58. the corresponding table at the bottom of the window 3 Optional Copy the sensor tray map or sample plate map to the system clipboard right click the map and select Copy to Clipboard The clipboard contents can be saved as a graphic file for drawing applications Selecting Biosensors To select biosensors 1 Inthe Step 1 Data Selection pane select the Sensor Selection option Figure 5 22 Data Selection Raw Data View or Sensor Selection E Data Selection C2 Processing Analysis Step 1 Data Selection Sensor Tray Map Sample Plate Map LABUSER090813 O Raw Data View F 1 2 3 4 5 6 7 8 9 wna Wt 23 45 G7 8 9101112131415 16 17 18 19 20 21 22 23 24 Sensor Selection AIOE mc CyYC YC C C C C Vala ihe LoL O Sensors to be Analyzed gt HY N N N N de B ry a Example B e Bc AS Ligand Sensor gt gt IO n SRA A1BT Streptavidin SA S D molar cone 4 167 eal laara N c Bc rT VVC IOC IDC Wat majam em am AARTEEN 2Y YY Y UF AEE DO BMOBOOO0COCO Basse 5 a NEA Nal NA E Not Na 4 ICICI Step 2 V Subtraction EO AN 1 VO IC IO IO IO IODC Reference Wells x E Nesi J GIGI Parallel Reference Sensors FV NC K Double Reference iii S I S a L Average Reference Sensors Gi
59. will be available in the Processing window Octet System Data Analsyis User Guide Release 7 1 page 80 Chapter 5 Basic Kinetics Analysis Number of biosensors selected for analysis i ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics oo File Help GD Data Selection Processing O Anatysis Loaded Data S Kinetics Gp 04 27 11 384 K ProAhigG 16 Sensors from 1 04 27 11 384 Q hlgG G 04 27 2011 384 higG Q Number Location m i B2 Ligand Sensor C Users wms Documents User Guides 7 0hlgG ProA Kinetics 110420_002frd G g z oe fg 1 C2 _ Ligand Sensor CAUsersnms Documents User Guides 7 O higG ProA Kinetics 110420_003 rd ie on 1 D2 Ligand Sensor C Users wms Documents User Guides 7 0 higG ProA Kinetics 110420_004 fre ny Reference 1 E2 Ligand Sensor CAUsers wms Documents User Guides 7 0 higG ProA Kinetics 110420_005 frd L Results 1 F2 Ugerd Sensor CAUsers wms Documerts User Guides 7 O hloG ProA Kinetics 110420_006 frd U 04 27 11 384 Q higG 1 G2 Ligand Sensor Ci Users wms Documents User Guides 7 0 hlgG ProA Kinetics 110420_007frd D 04 27 2011 384 hlgG Q 1 H2 Ligand Sensor CAUsers wms Documents User Guides 7 0 hlgG ProA Kinetics 110420_008frd J 1 A3 Ligand Sensor CAUsers wms Documents User Guides 7 0 hlgG ProA Kinetics 110420_009rd
60. you Click Fit Curves Octet System Data Analsyis User Guide Release 7 1 page 118 Chapter 5 Basic Kinetics Analysis ii ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics ieee File Help 0 Data Selection 3 Processing Analysis Curve Fitting View Y Ais Scaing Repot Points Step to Analyze Stacked Grouped Aways Ato Scale Time Gec 100 B Association Oniy Individual Options Refresh Refresh Ful Scale Use 20 Point Average Dissociation Only Association and Dissociation Fitting View Model 1 1 a 250 e Fitina 20 EE a Lo zs i Ful Partial 1 50 f j E E f Global Ful 1 00 F tS Group By Rmax Linked on A ga i Sensor Rmax UnLinked By eae Color Sensor 0 00 S H Compound 0 100 20 30 40 50 6 amp 0 70 80 0 1000 1100 1200 130 1 400 Window of Interest From Statt of Step Association 0 to 599 6 secs Dissociation 0 to 900 secs as Time sec Ft Curves Index Include Response Conc nM Dissoc Loc Color Assoc Sample Loc Cycle Sensor Locatic XY Graph Iso Affnity Steady State Steady State Analysis 4 E 16625 167 3 1 a x Index E log Y Response 7 R equilibrium 5 x 16621 167 3 E 2 ci a Response 6 k 1052 83 D3 E 1 D1 Index Response hvengetom SEE lto BS es 7 e s es o Mo 2 m s E 1119 417 E3 B 1 E1 s 9o w oa B Be o par mo k ono 0 G3 G4 1 a
61. 0 5 000 400 600 Time sec A1 A1 51 81 C1 C1 Figure 5 17 Processing Window Raw Data View Quantitating a Selected Step 2 In the system prompt that displays click Yes to proceed with the quantitation The selected step data is displayed in a quantitation window Figure 5 18 By default samples are designated as unknowns For more details on viewing the quantitation data see Viewing Binding Curves on page 84 Octet System Data Analsyis User Guide Release 7 1 Working with Raw Data page 93 gt ForteBio Data Analysis 7 0 Quantitation hlgG ProA Kinetics ajaa File Help Data Selection DO Resuts By Loaded Data higG ProA Kinetics 16 Sensors from 1 B E Knetics ign XL Reference Subtraction Average of Group View Gy 04 27 11 384 K ProAhlgG anx O z i E Rip Data Show al Traces 1 ve OctetRED9S Eq BD hidG ProA Kinetics 10 Sec A c Column F Ignore errors in les when loading Ortons Ato Ful Legends S Quantitation 04 27 11 384 QhlgG Binding Curve Graph E 04 27 2011 384higG Q 0 30 60 90 120 150 180 210 240 270 300 330 360 390 420 450 480 510 540 570 600 Time sec m Desktop Select samples from the table or Plate below to display the data a d UUE roammooory IORQRBELTTELER Y pococceeeoooce Deere eeaae EE EE iseebageeanaws z
62. 0 90 100 110 120 130 140 150 160 170 180 190 200 210 22 Concentration ug ml 907029 Mock T50 Testing Beta2 DR4PL Table Column Known Cone wl Index Plate F C Sample Dilutio Bindin Known Type Sai Pas So tne a ae Be O E 47 1 0 00286 N A Our Nie 000000000009 oe a B M31 1 0 00282 N A Unk Ne 44 E7 1 0 01791 N A Unk N 0000 0000 3 5 1 m 1 0 01927 N A oi NA 1 D MWO M6 1 G7 1 0 01977 N A Unk N2 7 l H7 1 0 01976 N A Unk N E Q O OOOOOS E m n 1 tts kG tm o y 3 1 B8 1 0 03365 N A Unk N F O Q QOOOOO0000 10 1 E ce 1 0 03528 N A Unk N Swe we Cos Cos Ge Co DOOOO ioe m 1 0 03249 N A Ne Wo 121 E8 1 0 05550 N A Unk N2 16 HACAAOAAOCOAOAOAOAA ei heene oe a B 141 E G9 1 0 05185 N A Unk NH W 15 1 e 1 0 04240 N A Unk Nz lM 16 1 Mes 1 0 07058 N A Unk N 1 ira a7 4 4 annnm aiia DD ie wee Figure 1 2 Quantitation Analysis Updated Interactive Binding Graph and Group View Octet System Data Analsyis User Guide Release 7 1 page 8 Chapter 1 welcome Separate binding graphs are displayed based on the sensor type Figure 1 3 0 180 0 160 0 140 0 120 gt Binding Rate 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 t Concentration pg ml Figure 1 3 Separate Bi
63. 00 c 301 SA Gre D4 Associa Sta 4 00 4E SA Sre E4 Associa Sa 5 00 2 D 5 Fl SAGtre F4 Associa Re 6 N A F eca EE G4 Associa Re 6 N A E 7m 6 Oo H4 Associa Ref 6 N A 8 A2 A5 Asocia Unk 1 NA F B5 Associa Unk 2 N A G 12 E C5 Associa Unk 3 N A a if D5 Associa Unk 4 N A 12 E5 Associa Unk 5 N A HIIIIIIIIIITI e eee 4 m Figure 4 16 Viewing Binding Curves Octet System Data Analsyis User Guide Release 7 1 Analyzing Data page 57 Closing Experiments To close an experiment in the Loaded Data directory tree right click the experiment name and select Remove Run see left side of Figure 4 17 To close all experiments in the Kinetics or Quantitation folder right click the folder and select Remove All see right side of Figure 4 17 File Help C Data Selection Results fa Data Selection J Results 2 Loaded Data a P Looded Dat I H Kinetics E oaded Data 7 oe aa E Kinetics Se Remove All Quantitation 201 Basic quantitation data Prot sensor amp 2011 03 01_ multi analyte 3 LS Open Explorer gt proAproGproL muttianalyte 2 amp X1021 2490 002 002 L Remove Run a EX8130 2409 037 0427 11 384 Q hlgG 04 27 2011 384hlgG Q E hloG ProG Q Figure 4 17 Closing a Selected Experiment left or All Exper
64. 00 t E10 E10 Ucros 1 23545 Standards Sample Alerts ype Threshold Do not use alerts Save Analysis Settings Kap APCS APPS SPSS SKIS Figure 5 9 Editing processing parameters in the Results window Viewing Binding Curves To view binding curves in the sample plate select a well s or in the sample plate table select a row s To select non adjacent rows or wells press and hold the Ctrl key while clicking the wells or rows X ForteBio Data Analysis 7 0 Quantitation higG ProG Q Lo S te fie Help OD Osta Seiection E Bemas 5 Losded Data higG ProG E 04 27 11 384 K ProAhigS E higG ProA Kinetics Quareaneon By 04 27 11 384 2 higG GB 04 27 2011 384 MG Q E higG PGG E Desktop Gh Gy Libraries UR Wesley McGinn Straub i Computer ho Sewo Co Sensor Sampie Sampie Twe Reckcat Krenn Cone by fly Windown7 05 Ci om PrtenG AY Oa 2 w F Hai OVO RW Orive ki 10 Prina 01 2 0 100 H Sak xeroxscans migration O 2c PotenG CI Ou 9 s BD Lenovo Recovery Q 30 PrnG DI On s 235 W shared fbserverd 5 ae PotenG Et Osa 10 10 ge SOC sr O nG FT a 5 5 H Wesley Meginnstraub s Phone ea ProtenG GT Oa 25 25 Gig Network 7w ProtanG HI m 1 1 B Control Panel 8 a2 T PrtenG Az a 200 20 W Recycle Bin 9 92 PrtenG 82 x 100 100 ub junk 1c2 PrvenG C2 Om so 102
65. 000 1100 1200 1300 1400 Color Time sec Residual View Window of Interest From Start of Step Association O to 599 5 secs 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1 500 Time sec Index Include Response Conc nM Dissoc Loc Color Assoc Sample Loc g a XY Graph Iso Afinity Steady State Sees TEE xe roe x 24685 667 B 2 1 Elos eine x 20496 33 B3 1 E Index Response x 20563 33 B 2 E iR x 1678 167 fe 1 Ce x 1658 167 2 c 25 g k 10603 83 D3 1 fi a a k 1005 83 3 2 C x 123 4v7 E 1 BaF 2 x 10946 417 E 2 E 3 7 x 26172 667 A 1 a 3 b x 2632 667 a3 2 r 15 x 2m3 B3 B3 1 E x 232 33 B 2 E o 1 1708 167 3 1 i i e x 17881 167 e 2 t G amp 1104 83 D 1 i is p7 Save Data Analysis Parameters a Index Figure 5 68 Report Data Types Analysis Options Kinetics Analysis Results XY Graph so Affinity Steady State XY Graph Iso Affinity Steady State i Fitting Result Iso Affinity Graph Steady State Analysis iting Results 01 Model Equation 5 H Response E 7 0 08 Rmax Conc JKD Conc Es 2s Y Weighting None E Results SES F Chi 2 DoF 0 0000 R 2 0 990202 H RMax 0 092 0 001 KD 1 1E 06 5 7E 08M 10 20 Molecular Concentration ul Figure 5 69 R
66. 1 u umo an 0 oO 1 Aa Ready Sane inays 15 417 B5 u 1 Recuitrass 257 5 687 N M 2 7 bs oor o G3 Gi 2 he Te ee omn o H Hi 2 2m 7 A faa 2 Caled Fespers 230 3 od m z F 1 67 a cs 2 H las Owe boon 12 en 03 05 28 d eee 1208 an 8 Es 2 ytaka ona o a Gs 2 oom o n 45 2 f 2155 333 B e 2 See moot w2 6 oa a 2 A AA EN 1 an 03 o 2 Cis una 417 o u a ndes ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics 8 File Help lt Data Selection C Procesang Anaives Conve Fang Step to Anahyze Aasociation Oniy Dasocation Oriy Assocation and Ossccuton Modei 1 4 Fans Local era Pats O Geos AN Group By Prax Lre G Serer Rma Lhiked ey Color O Sanar Campan Window of Interest From Stat of Step Aemcaton to 5956 scs Ossocistion 0 to 8999 scs XY Gah ino Mfinnty teady Sate x Index I Los Y Response M tos S os Use Entre Smp Times oe 05 Index Response Fe Orvosi 05 m Steady State Arayan et Requitrs bad wr amp 15 Aragoien S85 lo 595 secs k Caadate Response bed as Ones Export w 4 Ha Epotfang Epot Table to a Ge es save pet Bien a E os Ss Save Data Ansys Parameters A o 2 Figure 5 55 Color Coded Analysis Results Sorted by Color 2 Click the column header again to sort the results in ascending order Octet System Data Analsyis User Guide Release 7 1 page 138 Chapter 5 Basic Kinetics
67. 1 000 1100 1200 1300 1400 1 500 Time sec R equilibrium Conc nM Dissoc Loc Color Assoc Sample Loc XY Graph iso Affinty Steady State 26318 667 A3 x index Os vf 22757 3833 B3 E cs 22918 33 3 B3 B5 Index Response 17742 167 3 Hi cs TE 17879 167 c3 3 gt 18 318 14 12 16 17 18 19 2 21 Index Figure 5 50 Selecting Analysis Results for Viewing in the Fitting View and Residual View Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis Results page 129 Analysis Results Table Each row in the Analysis Results table displays the results for one set of association dissoci ation data By default the Fitting and Residual views include all of the results in the table Kinetic analysis results Index Numbered order of the curves processed The index is useful to sort back to the original order It is also useful in the graphing applications in the lower right win dow pane Include X indicates data included in the analysis If this field is blank the data is not included in the analysis Color tThe color of the biosensor binding curve in the Fitting and Residual view Sensor Location Location of the biosensor in the sensor tray map Sensor Type The type of biosensor chemistry Sensor Info Information about the biosensor that was entered in the Octet System Da
68. 119 kinetic Settings_Tablelnfo xml file creating 120 kinetic Settings_Welllnfo xml file creating 120 kinetics analysis mode returning to 96 kinetics analysis results 123 Kinetics Batch Mode menu 24 Kinetics Batch Mode Quantitation Batch Mode dialog box figure 121 kinetics experiment closing 87 Octet System Data Analsyis User Guide Release 7 1 page 200 starting 76 km error kinetic analysis result 130 km kinetic analysis result 130 Known Conc 63 kobs 1 s kinetic analysis result 130 kon 1 Ms kinetic analysis result 129 kon Error kinetic analysis result 129 L launching Octet System Data Acquisition software 22 Legend by view option 126 license information displaying 26 ligand biosensor location 111 ligand biosensors defined 96 Linear Point to Point 59 list options 186 Load Standards menu 60 Loaded Data Directory Tree 45 Loaded Data directory tree 76 loading experiment for analysis 76 experiment method file 24 Loading Well Location kinetic analysis result 130 location of the biosensor in the sensor tray map 129 of the sample well used during the load step of the experiment 130 Lock Application menu 25 locking a user session 41 Logoff menu 25 Lot Number analyzed data 62 Low concentration threshold processing parameters basic kinetics 83 Quantitative Analysis 48 M Mass Transport 114 mass transport rate constant 130 matching search term with searchable t
69. 136 Chapter 5 Basic Kinetics Analysis ForteBio Data Analysis 7 0 Kinetics higG Pro Kinetics lolo be File ae Curve Fitting Sep to Analyze D Association Only lt Data Selection C Processing lt Ansiyes Stacked Auma Retesh Faas Scaling Repot Ports Ato Scale Tene Goch 100 D Ful Scale Addto Table Use 20 Port Average Remove Al D Dissociation Only Associaton and Dissocistion Modei 1 1 gt Fane D Local ha Gobel Ful Group By D Remax Linked Sener Raa Unlinked By P Color Sensor P Compound Patail Window of interest Frem Start of Step Fasociation 0 to 5996 secs Dissociation 0 to 899 9 secs Use Gime Sep Times R Orres Steady State Anaha Requiteum Data Epor Epor Feng Epot Table to a Fie Sare Repat Coge Teele Save Data Analynis Paameters E a FRBRERETLLTAAREGRTE CR Fitting View Advanced Search Set Color Set Color By Group Set Color By Lock Unlock Include Wells Exclude Wells Sze Columns by Title Sue Columns by Date Size Columns by Both Select All Rows invert Selection Group Selection Cte Order Column Fip Data Back to Original Data ForeBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics Edit Sensor Semple information Dissoc Loe Assoc Sample Loc Cycle
70. 22 01 Administrator JRICHARDS Project added Receptor Ligand screen 2011 02 13 18 23 05 Administrator JRICHARDS Project added Antigen Antibody screen 2011 02 13 18 24 59 Administrator JRICHARDS Project added Cell Culture screen 2011 02 13 19 15 19 Administrator JRICHARDS User login 2011 02 13 19 33 26 Administrator JRICHARDS User login 2011 02 13 20 27 13 Administrator JRICHARDS User login Figure B 46 Event Log Events are tracked for individual user accounts projects and machines By default a histori cal log of all events recorded on the active ForteBio GxP Server module displays Octet System Data Analsyis User Guide Release 7 1 page 186 Chapter B 21 CFR Part 11 Software Administrator Options Viewing Events To view events for a specific user account project or computer click the User Figure B 47 Project or Machine drop down list and select an entry User Project Machine any nA me Project Machine Type Info rator JRICHARDS User login 2011 PSmith rator JRICHARDS User logout 2011 RBrown rator JRICHARDS User login 2011 02 07 16 20 31 Administrator JRICHARDS User login 2011 02 07 16 47 42 Administrator JRICHARDS User logout any Date Administrator 201 Figure B 47 Viewing Events from the User Drop Down List NOTE Selections can be made in either one or all of the User Project or Machine drop down lists The list then only displays ev
71. 3 03 os 2E a k 1208 4n 6 es 2 G EEA 5 k oom o 3 65 2 7 a ooa o 3 HS 2 Takk 3 k 21535 33 83 ou 2 Save Repor S Aem 5 E 17432 167 a ce 2 7 E 106 833 03 pe 2 ar aca 3 k 11573417 6 Es E z x 0 Figure 5 54 Setting Data Color by Category Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis Results page 137 Sorting Analysis Results To sort results by any category column header 1 Click a column header The results are displayed in descending order In Figure 5 55 the results were color coded by sample concentration and then sorted ForteBio Data Analysis 7 0 Kinetics higG Prod Kinetics o g fle Help D Date Setectin Procesing Araves y i pe Curve Fang View YAn Seaing Ragot Ports Sep to Arwiyoe Sacked Grapes Ba Atosi Time ech 100 Addto Isti Save esocastion Ory navos Opora Raden Fetes Full Sos Use 20 Port Average Remove Al Load Desonston Only Association and Dissociation Modei iat Faing ha Pot G s Fa Gop by Rena Uric G Senor Rma Unlrkes By Cole Sense Compound Window of interest From Start of Step Aemosten O to 5996 secs Dissociation 0 Remorse Cone iM Dsscloe Cor Mosoc Sermale Loc Op XY Geach Liso anty Stendy State f w2 an 5 e5 1 x inde M loo Y Response z P bog eae a es 1 x ten C ome o H3 HS 1 i index Response 1767 a a
72. 39E 05 kdis Error 3 016E 07 Rmax 1 1633 om 1E3 23 33 43 om 1E3 253 3B 43 Vie 02 02 0 04 Sensor Location F2 Sensor Type AMC Anti migG Baseline Loc F8 Assoc Sample Loc F10 05 Sample ID Fab Dissoc Loc F12 Conc nM 200 Response 1 1601 o KD M 3 950E 09 kon 1 Ms 2 295E04 kon Error 8 385E01 kdis 1s 9 065E 05 kdis Error 3 274E 07 Rmax 1 1761 v om Traces 3 4 of 4 I4 4 P Pl NumberRows 2 NumberColumns A Z Show Resuts Z Show Residual Select Fields Figure 1 6 Editable Individual View b The user can select the fields to display in the individual view by clicking Select Fields Figure 1 7 Traces 3 4 of 4 l4 4 gt gt i Number Rows 2 amp Number Columns 4 V Show Results V Show Residual Figure 1 7 Select Fields Menu Option The Choose Fields from Result Table dialog box displays Figure 1 8 c Inthe Available Fields column select desired fields click gt to move the fields to the Chosen column and then click OK EE Choose Fields from Result Table Chosen Sensor Location Sensor Type Sensor Info Replicate Group Baseline Loc Assoc Sample Loc Sample ID Dissoc Loc Cone nM kdis 1 s kdis Error OK Cancel Figure 1 8 Choose Fields from Result Table Octet System Data Analsyis User Guide Release 7 1 page 10 Chapter 1 welcome The information on the individua
73. 4 Chapter 5 Basic Kinetics Analysis ForteBio Data Analysis 7 0 Kinetics higG Prot Kmetics file Help ols Be GEA Step 2 M Sutwecton Relemce Weis Frenkel Releeerce Sarao Sep Ul Ain Yas Sep Association gt Tene Range pec From 02 To 04 Step amp F Interaten Comection Aio Desccuton App to Baseine Figure 5 63 Report Data Types Processing Options Raw Data and Aligned Data Sensor tray images UF Fortetio Data Analysis 7 0 Kinetics higG ProA Kinetics Sample plate data images From 01 To 258 Step 4 IY inter tep Comecton Apn Deman At Baseine Step 5 Process Satz Goley Fitemng Process Data Bi Ligand Sensor Empty bd Select Ligand Sensor s for Data Analysis 110029_c01 ke Step View Renate Processed Resuts Sensor Summary Regot Ports Step 7 Save Rosats Save Processes Data Save Raw Data Save Prec Parameters Sensor tray data table E 11040 002i 110420 003d ifs eles Eusi fz Barer ese iz alli Sample plate data table Figure 5 64 Report Data Types Processing Options Sensor Tray and Sample Tray Information Octet System Data Analsyis User Guide Release 7 1 Generating a Report page 145 EF ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics sion x Subtractes Data 27 1 i 240 i 210
74. 4 KB Figure B 29 Installation Location ForteBio GxP Server module on a local host computer Double click the ForteBio GxP Server desktop icon Figure B 30 Octet System Data Analsyis User Guide Release 7 1 Accessing Administrator Options page 173 ForteBio GxP Server Figure B 30 ForteBio GxP Server Desktop Icon NOTE When accessing the ForteBio GxP Server module directly additional tools are also provided to test server functionality Please see Accessing the ForteBio GxP Server Module Directly on page 187 for more information The ForteBio GxP Server Configuration window displays Administrator Tabs Five tabs are available in the ForteBio GxP Server Configuration window Users Allows user and password management and individual privileges selection Groups Allows user group management and group privileges selection Projects Allows project management and setup Constants Allows setup of GxP server parameters e Events Displays event logs for individual user accounts projects or machines Click any of the tabs to view the respective information contained within the tab Tab View Each tab displays a list of administrator entries and associated setting information that can be sorted by clicking any of the column headers Figure B 31 Login Name Full Name Group Privileges Password Age Info GMoreno George Moreno Guest run 00 11 23 External collaborator RBrown Richard
75. 5 200 igand Time sec HB oi lt Step 3 F Align Y Axis a pe A Bt Ct D Et F mm G H1 so f a ae i n e eo oa me en ea m Time Range sec al HME J From 0 2 To 0 4 Align by Begin Point All Steps Aligned Align All Baselines Align by End Point Al Aligned to One Step All Steps Aligned by step Equilibration Sensor Location 7 Show Step Dividers Export Aligned Step csv files J Quantitate Selected Step Step 4 Inter step Correction itep selected Equilibration Sensor Location Well Location 0804 0 60 H Eos 0 20 i 300 f E Time sec A1 A1 51 581 C1 C1 D1 D1 E1 E1 F1 F1 1 000 1500 2000 2500 3 000 Time sec 3 500 4000 4500 5 000 m G1 G1 H1 H1 A2 A1 62 81 C2 C1 D2 D1 A mmg C p g F mm G H1 2 E1 F2 F1 G2 G1 A2 mm 62 C2 D2 m 2 F2 G2 H2 H2 H1 Raw data from all steps displays all biosensors Raw data from selected step displays all bio by default sensor data for the selected step by default Figure 5 14 Processing Window Raw Data View Selected 2 View the step data and align the binding curves click a step bounded by lines in the Raw Data chart NOTE The lines represent individual assay steps Populate the step charts below wit
76. 6 View Results Processed Results Sensor Summary Report Points Step 7 Save Results nm Save Processed Data ne igs 0 500 1 000 1 500 2 000 2 500 3 000 3 500 4 000 4 500 5 000 0 200 400 600 800 1 000 Time sec Time sec Al 8 C1 A1 A1 81 51 C1 C1 All step data for biosensor C1 Selected step data for biosensor C1 Figure 5 15 Processing Window Raw Data View Displaying Data from a Single Selected Biosensor C1 3 Select which biosensor data to display To view the data from a selected biosensor click the biosensor in the table The step charts will display all of the binding data for the selected biosensor and the data from the selected step aligned starting at y 0 e To display data from multiple biosensors in the step charts select the biosensors in the Sensor location list To select a contiguous block of biosensors from the list hold down the Shift key and click the first and last biosensors in the group e To select non contiguous biosensors hold down the Ctrl key and click the desired biosensors e To include all biosensor data in the step charts click Show All Sensors Octet System Data Analsyis User Guide Release 7 1 Working with Raw Data page 91 Sensor location Color Sensor Sensor Type Sensor Info Sensor location Color Sensor Sensor Type Sensor Info Al GEM Licend Sensor SA Streptavidin HEMI Ligand Sensor SA Streptavidin
77. 6 Dissociation 1 17 Regeneration 1 18 Equilibration 2 19 ProA Immobilization 2 3 1 Figure 5 3 Changing a Step Type 5 Inthe Sensor Tray tab confirm the biosensors to be analyzed The first group of biosensors is automatically selected for analysis Biosensors that are assigned to the same type of assay step and have the same assay step times are displayed in the same color providing convenient identification of mul tiple types of assays executed in one experiment and using one biosensor tray red fj in Figure 5 4 Only biosensors of the same color processed simultaneously This pro vides a convenient way to identify multiple experiments on a biosensor tray 6 Select particular biosensors for the analysis a Click a biosensor To select non adjacent biosensors press and hold the Ctrl key while you click the biosensors b Select a column s or row s To select non adjacent columns or rows press and hold the Ctrl key while you click the columns or rows c Draw a box around the biosensors using the mouse The number of biosensors selected for analysis in the current tray will be displayed in the upper right corner of the Sensor Tray tab 7 Choose the Ignore error in files option when loading to load data files regardless of whether a runtime error was identified This enables data visualization even if a sensor error occurred during runtime NOTE Only the selected biosensors
78. 7 0 Kinetics hiqG Pro Kinetics 2 a File Help WD Date Selection CJ Processing Anais Curve Fring Sep to Analyte Y Aes Scaling Report Ports __ Stacked Grouped r Ato Scale Time sec 100 Addto Table Save naval Options Retreat Feres Fill Scale Use 20 Part Average Remove AL Load Fitting View D Ra Panal Gobal Ful Group By D Rmax Linked Sensce Fmax Unlinked By Coke Senser Compound 2x0 3o 400 xO 600 mo 20 so Tene sec 1400 1100 120 Window of interest From Stat of Step Associaton 0 to 5996 secs Dissociation 0 to 00 secs No Data n sistie Advanced Search ce Fat ep eee hcd Set Color a x 2461 6867 a Set Color By Group x index zji Y omea Bose x 247 667 a Set Color By x 20413 n3 63 Index Response Steady State Anahyus B T l Requittus x a 24 B Response x Av agebom 585 lo 595 secs x Tach Wels x Exclude Wells 22 Calouate Response x F 4 x Size Columns by Title Nie 2 Data Boot w ax ooo o G3 Size Columns by Data Epot Filing Spat Table to Nook oom 63 Size Columns by Both Rests ow Fle 12 x 002 0 43 18 i amp oos o K3 Select All Rows A rae Copy Tabie to u x 2e 667 a katia Opboae 5 2608 687 a ee or 6 x 2357 a3 83 aaa iaaa o 1 2 3 4 Save Data Analysis Pammeters ito pac Order Column nex Flip Data Back t
79. A unique number assigned to each data point during data analysis Dilution factor tThe dilution factor used to prepare the assay sample The dilution factor is multiplied by the well concentration to determine the calculated concentra tion Well concentration The concentration of the analyte determined from the stan dard curve The well concentration is multiplied by the dilution factor to determine the calculated concentration Flip tInverts the magnitude of all data Used during analysis of large particles where negative signals can be observed Information Annotations about the sample e Replicate Group A set of replicate values organized as a set to facilitate calculation of statistics BRAVG The average binding rate of the replicate group e BRSD The standard deviation of the binding rate of the replicate group BRCV The coefficient of variance of the binding rate of the replicate group e Concentration avyg The average concentration of the replicate group e Concentration SD The standard deviation of the concentration of the replicate group e Concentration CV The coefficient of variance of the concentration of the repli cate group Sensor Type tThe biosensor chemistry utilized in the assay Lot Number The lot number of the biosensor tray used in the assaySample The well location in the sample plate Sample ID The name of the sample entered in the Octet System Data Acquisition softwar
80. Acquisition or Data Analysis software without having to log out To change projects during a user session 1 Click Security gt Change Projects A list of projects assigned to your user account displays with the active project high lighted Figure 3 18 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 3 18 Changing Projects 2 Select the desired project from the list The selected project becomes the active project for the user session Octet System Data Analsyis User Guide Release 7 1 Compliance Features page 41 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 displays Figure 3 19 Current password New password Confirm new password Password reminder Figure 3 19 Change Password 3 Enter the Current password for your user account Click for a password reminder 4 Enter the New Password confirm the new password and optionally enter a Password reminder 5 Click OK to save the changes and exit Locking the Application The Data Acquisition or Data Analysis software can be locked during a user session to pre vent another us
81. Baseine z Ph 5 Time Range ees 0 40 f roperties_ From O1 To 2998 o Step 4 F Interstep Comection 0 00 f Ngnto Dessocsation 0 100 200 xo 400 500 e0 700 200 xo 100 10 1X0 1X0 140 150 A to Baseline T me sec Step 5 Procesa VY Sevtsicy Goley Fitenng al ae 5 es Se a yr Sm Sa gt gt ce 2 Process Data Report Point Analysis Step 6 View Resuts Foul ines ae die beyrning ol Assouaten Step Pucesed inate Teel eck SS4 791 Tene2 eck 149454 Use 20 pont average footy foo A Expon Fie va Sensor Summary Recon Ports Sensor Samle Samoe Conceriralon Tael Gn nol Time 2 Gndro2 prikan Erm AT M Resoctation 7 E m Save i MO maon E7 53479 za uasal zanas 1 a 7 z 8 Ba Association B3 sa 22 nas 197658 Save Proc Pammeters Bt Pa Amannan n rE JIRI IUR 3 man Sa Figure 5 39 Binding Chart Shortcut Menu 2 Select the desired command bel Opens a dialog box that enables you to save the chart in several different for mats cfx txt data only xml properties only bitmap or metafile E Opens a dialog box that enables you to copy the chart in several different for mats data only bitmap or metafile to the system clipboard ie Opens a dialog box that enables you to print the chart KINETICS ANALYSIS In the Analysis window two types of kinetics analysis are available Curve fitting Determines the kinetic constants k kg and the affinity constant Kp by fitting the data to a speci
82. Click the Standard Curve Within Plate check box Figure 1 19 when multiple data sets are loaded Binding rates and concentrations are calculated according to the standards in the individual plate Standard Curve Equation Linear Point to Point X Load ES 4 Standard Curve Within Plate gt a Curve by Sensor Type Processing Parameters Binding Rate Equation R equilibrium x Read Time 120 00 secs Zero Conc Threshold 0 0001 BR Low Conc Threshold 0 003 BR Calculate Binding Rate Data Export Figure 1 19 Standard Curve Within Plate Check Box b When you click the Standard Curve by Sensor Type check box Figure 1 20 stan dard curves are generated based on sensor types and sample binding rates and concentrations are calculated according to the standards with the same sensor type Standard Curve Equation Linear Point to Point x Load Select Standard Curve Within Plate M Standard Curve by Sensor Type Pr tessing Parameters Binding Rate Equation R equilibrium x Read Time 120 00 secs Zero Conc Threshold 0 0001 BR Low Conc Threshold 0 003 BR Figure 1 20 Standard Curve by Sensor Type Check Box Octet System Data Analsyis User Guide Release 7 1 page 16 Chapter 1 welcome c Click Load Standards to load three saved standard curves Standard 1 Standard 2 and Standard 3 see Figure 1 21 and click Select Standards 254 ee L me o
83. G B2 WG Se 100 100 12 PretenG C2 Ge Me 50 s 102 Prete G D2 Was a 25 25 12 TB anc WG Ow m w ard Prete F2 GS we 5 5 1G2 ss PretenG G2 KGa Se 25 25 1 H2 PrtenG H2 Ge 3 1 1 1A ProtenG A3 Ge 3 200 200 183 PrtenG B3 WGs Se 10 00 103 Gu a 50 s Figure 4 26 Data Selection Window 2 Set the data viewing options refer to Table 4 1 on page 54 The Results window displays Figure 4 27 Octet System Data Analsyis User Guide Release 7 1 Processing Batch Quantitation Analysis page 69 7 ForteBio Data Analysis 7 0 Quantitation higG ProG Q ee 2 File Help O Data Selection Resuits Standard Curve Equation Group View Linear Point to Point a Daens Ato pu Refresh Use standards from loaded file T Calibrate within plate Processing Parameters Binding Rate Equation Read Time 120 00 secs Zero Conc Threshold 0 0001 BR Low Conc Threshold 0 003 BR No Data Available Calculate Binding Rate Data Export hlgG PoGaQ Standard Sample Alerts Type Threshold Table Column Known Conc Index Known Dilution C Sample Sensor Plate Sample Type Bin X B bog Y E Log mee P aias e7 8 9 wn 38 N A Mc ce 1 Sampe Re Binding Rate v Caic Cone Max Residual a 10 ADD JV 39 NA Hi te He 1 Sample
84. IP socket NOTE The Localhost option can be useful in developing the automation cli enton 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 Analysis 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 Analysis Automation API KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KK KKK KK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK Copyright c 2011 ForteBio All rights reserved KKK KK KKK KKK KK KKK KK KKK KKK KKK KK KKK KKK KK KKK KKK KKK KKK KK KKK KKK KKK KKK KK KK KKK KKK HE ADER 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 Octet System Data Analsyis User Guide Release 7 1 page 152 Chapter A Using Octet384 Systems with an Automation Interface 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 the
85. J 384 IE B3 Ligand Sensor CAUsers wms Documents User Guides 7 0 hlgG ProA Kinetics 110420_0104rd B Acquisition 1 C3 Ligand Sensor C Users wms Documents User Guides 7 0 higG ProA Kinetics 110420_011 frd B To PR 1 D3 Ligand Sensor C A Users wms Documents User Guides 7 0 higG ProA Kinetics 110420_012rd H vo aa 1 E3 Ligand Sensor CAUsers wms Documents User Guides 7 0 hlgG ProA Kinetics 110420_013 frd dh Software v6 3 data files p 1 F3 Ligand Sensor CAUsers wms Documents User Guides 7 0 hlaG ProA Kinetics 110420_014frd D Webinars 5 1 G3 Ligand Sensor C Users wms Documents User Guides 7 O hlgG Pro Kinetics 110420_015 frd J Webpage 1 H3 Ligand Sensor C Users wms Documents User Guides 7 0 higG ProA Kinetics 110420_0164rd Ji Wikipedia 1 A4 Ligand Sensor CAUsers wms Documents User Guides 7 0 hlaG ProA Kinetics 110420_017frd r H a Music Figure 5 4 Selecting Biosensors for Analysis Analyzing Binding Data To analyze the binding data 1 Start an analysis session and select the experiment s to use a Confirm or change the biosensor and sample type selected for the analysis b Process the data compile binding curves with or without reference subtraction 2 Analyze the binding data Curve fitting analysis Determines the kinetic constants k kg and the affinity constant Kp from fusing a specified binding model Steady state analysis Determines the affinity constant Kp from the ca
86. Options S Group Graphs By Graph Size in Pixels Fametamow B Auto Size Width 1 5 x Height Fred Size Width 300 4 7 Height 200 Legend by Graph Options Assoc Sample Loc v v ues V Individual Column Names B Legend by Column Name Additional Graphs X Axis V Labels V Titles Y Axis V Labels V Titles Residuals Steady State XY so Affinity J Grid Lines V Step Dividers Data Options Show as of Rmax V Show Curve Fits Use Included Traces Only Display Traces in Table Color Figure 5 48 Grouped View Options Dialog Box 2 From the drop down lists select up to three categories for grouping The following Grouped view options are available Group Graphs By Select up to three categories for grouping the data across three independent parameters Legend by Select up to two categories to include in the graph legends Figure 5 49 Additional Graphs Select other graphs to display with the analyzed fitted data Data Options Click the Use Included Traces Only check box to graph only the biosensors that are included in the analysis marked with an X in the analy sis results table Graph Size in Pixels Options for graph size and the number of graphs to dis play per row Graph Options Options for graph labels and other graph dis
87. PraenG 02 Om s as 182 TM ons s 10 10 12 FL ten c E eo Figure 5 10 Selecting Sample wells or Rows to Display in the Binding Curve Graph Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 85 Viewing Options Table 5 1 Viewing Options in the Data Selection Window Option Description Align X Choose this option if there is an artifact at the beginning of the binding step that you want to remove Enter a time seconds at which to start the alignment Reference Subtrac tion Average of If the experiment includes reference biosensors choose the Reference Subtraction option and select one of the following All Computes the average binding curve from the ref erence wells and subtracts this average from each sam ple curve Row lfarowincludes both samples and references the Octet System Data Acquisition software computes the average reference curve for the row and subtracts this curve from the samples in the same row Column lIf a column includes both samples and refer ences the Octet System Data Acquisition software com putes the average reference curve for the column and subtracts this curve from the samples in the same col umn Flip Data The Flip Data function inverts signals from positive to negative or from negative to positive This is used most often when the observed nm shift is negative due to the presence of large ana lytes
88. R FBServer7 Space required 17 3MB Space available 177 2GB ForteBio Inc www fortebio com Figure B 11 Choose Install Location 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 12 533 ForteBio GxP Server 7 0 Setup p Choose Start Menu Folder Choose a Start Menu folder for the ForteBio GxP Server 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 FForteBio 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 12 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 13 Octet System Data Analsyis User Guide Release 7 1 page 164 Chapter B 21 CFR Part 11 Software Administrator Options 33 ForteBio GxP Server 7 0 Setup cys Installing Please wait while ForteBio GxP Server 7 0 is being installed Create shortcut C Users wms AppData Roaming Microsoft Windows Start Menu Pr 4 Create short
89. Reference well H1 will j At pt E be subtracted from 7 ODOR g sample wells E FOROn E Dotie Reference 7 N Selected subtraction _ sse F Sno a method ee anvas wi a e a iH HOR Gal From 02 To 04 Rep 4 I7 eer sep Corector Myr to Dssscsten Agr to Baeeine B Ligand Sensor Empty Buller P Load P Sample Reference Wer Empty ff Select Ligand Sensor s for Data Analysis Reference well H1 190420_001 fed 11042000214 110420_003 ed 110620_004 fed Figure 5 25 Confirming the Reference Well is Subtracted from the Sample Wells If an experiment includes reference biosensors and reference wells the Octet System Data Acquisition software offers multiple reference subtraction methods for data processing Reference Wells cCorrects binding data for system drift For example drift is mea sured by the interaction of the immobilized biosensors with the assay buffer This method requires at least one row of reference wells in the sample plate If more than one row of reference wells is selected checked the signals are averaged and the average signal is subtracted from the samples Octet System Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 101 ForteBio Data Analysis 7 0 Kinetics higG Pro Kinetics le Step 3 F Ap Y Ace Sep Baseine X Time Range sec from 01 To 2998 roa 7mooD DI Step 4 F breeratep Comect
90. Release 7 1 page 189 Lot Number 62 plate 62 quantitative analysis Index parameter 62 r2 COD 63 Replicate Groups 62 Residual 63 Sample ID 62 sensor 62 Sensor Type 62 well concentration 62 Well Information 63 analyzing binding data 80 binding data kinetics 80 binding data quantitative 57 entire time duration of selected step 115 equilibrium state data 119 experiments 44 processed kinetic data curve fittng analysis 114 steady state analysis 118 applications closing 24 Apply All Report Point Analysis feature 111 Apply Report Point Analysis feature 111 applying reference subtraction during data processing 99 sample alerts 65 standards alert 64 assigning different colors to binding curves 134 Replicate Groups in the Sample Plate Map 50 Replicate Groups in the Sample Plate Table 52 Assoc Sample Loc kinetic analysis result 129 Association amp dissociation analysis option 114 Association only analysis option 114 Association analysis option 115 Audit Trail described 38 listing events 39 sorting events 39 viewing 38 Auto Scale Fitting view option 124 Autoplay dialog box 156 Average from steady state kinetics analysis option 119 Average Reference Sensors reference subtraction method figure 104 Octet System Data Analsyis User Guide Release 7 1 page 190 reference subtraction method described 103 Baseline Loc kinetic analysis result 129 bas
91. Sa File Help O Data Selection C Processing 9 Ansivss Vias Sealing Repot Ports Sacked Goed Maaja Ato Scale Time bec 100 Addio laie Seve Individual Opbons Retest Refresh Full Scale Use 20 Pont Average RemoveAl Load Time nec Window of Interest From Stat of Step Asocion 0 to 5886 secs Oweociaton 0 to 0 secs Use Entre Step Temes Fi Curves nn Index include Reserse Conc pM Disscc Lec Coker Asoc Sampie inc Cyee Sensor Locate XY Getoh lso Hingy Reedy Sate Steady State Arahyais 4 16625 167 a c Steady State Analysis manek R equibaum 5 162 167 a a a ee Response 6 1062833 03 D4 DI La Response Average from 505 to 595 secs f7 105 an D3 E o D gju Paart 8 119 47 a i ee G 2 AKD Cone s 5 z a Y wega nee 10 a Ge 61 gt Data Epot m G3 G sas 00373 Boot Boot 3 a i fe Table to pot eae 43 awe R 2 0 0972 J n RMax 2 8476 fable to 20 128 Gpboad B Bs KD 1 0608 p es os 214E0M Save Data Anaien Parameters 9 f o 2 a p Molecuitar Cancantration AM L Figure 5 45 Analysis Window with Sample Curve Fitting Results Fitting View and Residual View When the analysis is completed the fitting view displays the processed binding data and the fitted binding curve red for all analyzed biosensors Figure 5 46 The residual view dis plays the difference between the raw binding data and the fitted curve for all ana
92. Sa 00 Do not use alerts ip a 0 0 F T 44 10 E1 1 IgG Sta sa 00 cae k M 4 5 i Fl 1 WGI s oa TP 4 S V 46 25 E ci G1 1 WG Sta sa 00 5 Ml a 1 ch H1 1 WG Sta sa 0 0 _ 3 V 48 200 He A2 1 WG Sta sa 03 7 15 W 49 100 E 52 B2 1 bGSta sa 01 M50 50 fe c2 1 WG Sta sa 0 1 MoH 2 E o D2 1G Sta sa 0 0 10 T 52 10 He E2 1 IgG Sta sa 0 0 _ ee ma a ran 7 002 003 09 aI m Binding Figure 4 20 Results Window for a Quantitation Experiment Octet System Data Analsyis User Guide Release 7 1 page 62 Chapter 4 Quantitative Analysis Working with Analyzed Data On the Results window the following parameters see columns define the analyzed data Check boxes toggle the corresponding well s data between inclusion and exclusion from the data analysis To exclude a sample from subsequent analyses de select the corresponding bio sensor number in the results table and click Calculate Binding Rate to re ana lyze Or select one or more wells in the results table right click and select Exclude Wells To include a sample in subsequent analyses checkmark the corresponding bio sensor number in the results table and click Calculate Binding Rate to re ana lyze Or select one or more wells in the results table right click and select Include Wells e Plate A unique number assigned to individual sample plates Sensor The biosensor number Index
93. Selection ax Format xs csv V Ini File V Experiment Summary v Plate Map V Standard Curve V Result Table X Y Graph Select and Order Columns W File Name ExcelReport __o __ cancel Figure 1 23 Report Selection Dialog Box The Select And Order Columns dialog box displays Figure 1 24 all Select And Order Columns C Figure 1 24 Select and Order Columns Dialog Box b Select and order the columns and click OK c On the Report Selection dialog box Figure 1 23 click OK On the generated report Results tab the selected columns and the desired column order are displayed accordingly 14 For the Octet Pro Software Data Analysis CFR version all Edit options were disabled Octet System Data Analsyis User Guide Release 7 1 page 18 Chapter 1 welcome WHAT S NEW IN THE OCTET SYSTEM DATA ANALYSIS SOFTWARE RELEASE 7 0 Table 1 2 lists and describes the new features in the Octet System Data Acquisition soft ware Release 7 0 Table 1 2 Octet System Data Analysis Software New Features for Release 7 0 New Software for 21 CFR Part 11 New Software for the ForteBio GxP Server Module Updated Procedure for Launching the Data Analysis 7 0 Software Updated Security Menu The Data Acquisition and Data Analysis software for 28 Octet systems is available in an optional 21 CFR Part 11 version t
94. The following default user groups are available and the privileges assigned to each are shown Table B 2 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 Guests Have no explicit privileges these must be assigned by the administra tor Octet System Data Analsyis User Guide Release 7 1 Accessing Administrator Options page 179 Table B 2 Default User Group Privileges Privilege Administrator Supervisor Developer Lab User Guest Administration Review v v Change s v Plate x v Run v4 v Creating a New User Group To create a new user group 1 Right click anywhere in the Groups tab and select New Group or double click in a blank area The New Group window displays Figure B 38 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 experiments and analyses Figure B 38 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 de selecting the check boxes next to each privilege Administration Can ad
95. Tmel Binding 1 Tme2 Bindng2 z Sep 7 Save Resuts Location Location 10 nM ec rmshit ec amshift a am a AA Association 667 594 79 2552173 149458 2354297 E Al A4 Association 66 7 594 79 2580133 149458 2401262 81 B4 Association 333 59479 2122761 149458 1 971658 Save Proc Parameters B1 B4 Association 333 59479 2158242 149458 2 018022 c1 C4 Association 167 594 79 1 737875 149458 1 64411 cl C4 Association 167 594 79 1 748121 1494 58 1 660586 D1 D4 Association 833 594 79 1 115573 1494 58 1 087051 5 Figure 5 37 Report Points View of Processed Results Report Point Analysis Features Input times after beginning of Association Step The Octet System Data Acquisi tion software measures the sample binding nm shift at Time 1 within the associa tion step and Time 2 within the dissociation step Both time points refer to time in seconds after the beginning of the association step You can edit Time 1 or Time 2 Use 20 point average Each reported nm shift in the table represents an average of 20 data points centered around the time point specified Apply lf you modify Time 1 or Time 2 click Apply to re analyze the sample binding of the active ligand biosensor at the new time points Report points can also be determined in the Analysis window Apply All If you modify Time 1 or Time 2 click Apply All to re analyze the sample binding of all ligand biosensors at the new time points
96. a Acquisition and Data Analysis software Octet System Data Analsyis User Guide Release 7 1 Compliance Features page 37 t amp Vey Forte Bio gt example files gt Quantitation non CFR Z Search Quantitation Organize New folder Favorites m Documents library En Arrange by E Desktop Quantitation W Downloads Name Date modified Type Recent Places LABUSER090811_072 frd 2 14 2011 12 08 PM_ FRD File GE Libraries LABUSER090811_071 frd 2 14 2011 12 08 PM__FRD File Cs LABUSERO90811_070 frd 2 14 2011 12 08 PM FRD File Music LABUSERO90811_069 frd 2 14 2011 12 08 PM_ FRD File S Pictures LABUSER090811_068 frd 2 14 2011 12 08 PM__FRD File B Videos LABUSERO90811_067 frd 2 14 2011 12 08 PM FRD File LABUSERO090811_066 frd 2 14 2011 12 08 PM__ FRD File Homegroup LABUSERO90811_065 frd 2 14 2011 12 08 PM FRD File LABUSERO90811_064 frd 2 14 2011 12 08 PM_ FRD File 1 Computer Ell i File name X Data Files frd File Type Figure 3 11 Selecting Method or Data Files To change the file type available for selection click the file type box and select a differ ent format Figure 3 12 File name v DataFiles d Method File fmf Data Files frd XML Files xml ee All Files Figure 3 12 Changing File Type 3 Select the desired file and click OK A message displays in the Verify Digital Signature dialog box indicating file compl
97. a Analsyis User Guide Release 7 1 page 14 Chapter 1 welcome o Ba A3 2 N A o E A3 3 N A o B1 B3 1 N A o B3 B3 2 N A or es B3 3 N A o Mia c3 1 N A o E c c3 2 N A 01 c5 c3 3 N A o fo D3 1 N A o E o D3 2 N A o E os D3 3 N A o Qe E3 1 N A o E3 E3 2 N A o 65 E3 3 N A o Grn F3 1 N A o E F3 2 N A o E s F3 3 N A o Ba G1 N A Figure 1 17 Cycle Column for Multiple Analyte Data Sets 10 The binding rates of an imported standard curve are displayed in the result table Figure 1 18 The name of the standard curve is displayed in the Plate column C Plate Sensor Sample Sample Type Binding Ho A3 A3 N A Sta 1 60895 E B3 B3 N A Sta 1 03574 BE o loaded c3 c3 N A Sta 0 52679 B o standard D3 D3 N A Sta 0 31084 E cuve B3 E3 N A Sta 0 16615 B F3 F3 N A sa 0 10902 E o l G3 G3 N A Sa 0 08135 Sta StandardCurve fsc Sta StandardCurve fsc sa Ea StandardCurve fsc sa StandardCurve fsc sa Fy StandardCurve fsc Sta StandardCurve fsc Sta StandardCurve fsc oO Sta StandardCurve fsc Oo Sta Ea StandardCurve fsc sa B Standardcurve fsc sa StandardCurve fsc Sta Figure 1 18 Loaded Standard Curve Example Octet System Data Analsyis User Guide Release 7 1 What s New in the Octet System Data Analysis Software Release 7 1 page 15 11 On the Quantitation Analysis tab 2 there is a new standard curve GUI feature a
98. ad and analyze an experiment e Re analyze an experiment To load an experiment for analysis 1 Onthe desktop click the 5 icon Or click the Windows Start button and select All Pro grams gt ForteBio gt ForteBio Data Analysis 7 0 The Data Selection window displays 2 Load an experiment a Right click the experiment folder in the workstation directory tree and select Load Folder or on the menu bar click File gt Load a Folder b In the Load Folder dialog box enter the folder name or click the Browse button and select the desired folder and then click Load The experiment is added to the Loaded Data directory tree Figure 5 1 Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 77 273 ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics 6 gia Data File Help H Quantitation O Data Selection Processing Analysis iy Loaded Data Quantitation Ji Acquisition fe Analysis a B i Ji Data Load Folder f Acquisition fee jG ProG Analysis sei Dpape 3 B higG ProA Kinetics 1 J Results New Folder J Data J Screen Shots Rename Folder hlgG ProG Q Software v6 3 data files Delete Folder Reference Webinars Bis Results d Webpage Collapse E Wikipedia Refresh yb My Music My Pictures E My Videos B Saved Games a Searches 4 9 Computer
99. al Remove experiments from the batch select the corresponding folders and click Remove Selected Forte Oota Anaiysts 2 2 Quamttation g Pro Q ae Fa Hele D oas semen ate Mark Ti Retewree Ranmen Aownged F a na dhe A meme Sen ee Ea Laari Select Foisor as Feito Remove Saecos Fatu et Procemed C inan ums Documares Data Data Fokder 04 200 080410 High Seratovty Premed Cronan Doomen Data Data Folder 04 2090 Standart Q assay 0 1 ay hrsheeyy u sus gy SRS SESee r Figure 4 29 Selecting Experiments for Batch Analysis 6 Click Analyze Data EXPORTING DATA Raw data or quantitation result reports can be exported Saving Raw Data To save raw data 1 In the Results window Figure 4 21 click Save Raw Data 2 Inthe displayed dialog box select a destination directory 3 Enter a filename and click Save The raw data are saved as a csv file that can be opened in a spreadsheet application such as Microsoft Excel software Saving a Quantitation Results Report All information in the results window can be saved to a report The Octet System Data Acquisition software generates an Excel spreadsheet xls file that includes the current con tents of the results window Calibration curve s Octet System Data Analsyis User Guide Release 7 1 page 72 Chapter 4 Quantitative Analysis Sample plate map that shows the user selected type of
100. alue of Kp providing a convenient way to view both kinetic and affinity data The value of the affinity constant Kp is the ratio of the association rate kon and dissociation rate ky A single value of Kp can therefore be obtained from varying values of kon and kgj lt for example a Kp value of 1 uM can be the result of kg 1x10 3 1 S and kj 1x10 3 1 Ms or kgj 1X10 2 1 S and k 1x10 4 1 Ms Each Iso Affinity plot has two red lines that correspond to a single Kp value The position of the Kp lines is determined by taking the average of all Kp values and plotting one redline 10 fold lower than the average and one red line 10 fold higher than the average Steady State lso Affinity Graph SL 51py m in E2 E3 E4 E5 E6 E7 E8 kon 1 Ms Figure 5 58 Iso Affinity graph X axis k Y axis kg Octet System Data Analsyis User Guide Release 7 1 page 140 Chapter 5 Basic Kinetics Analysis Steady State Analysis Graphs The Steady State Analysis graph Figure 5 59 displays the results from the steady state analysis see Steady State Analysis Graphs on page 140 The graph plots the response or Req vs concentration and the curve fit XY Graph Iso Affinity Steady State Steady State Analysis Fitting Results 0 1 Model Equation Response Rmag Conc KD Conc Y Weighting None Results Chi 2 DoF 0 0000 R 2 0 990202 FiMax
101. alysis 43 Working with Experiments 44 Loading an Experiment for Analysis 44 Editing Experiments 4 46 Viewing Binding Curves 53 Closing Experiments 04 57 Analyzing Data 6 cece eee e eens 57 Analyzing Binding Data 57 Specifying Analysis Settings 58 Working with Analyzed Data 62 Saving Standards Datd 00 00e 66 Saving Analysis SettingS 0 66 Processing Batch Quantitation Analysis 67 Creating a Settings_DataAnalysis ini File 68 Selecting Experiments and Running the Batch Analysis a an 70 Exporting Ddtd sses 71 Saving Raw Data 0 eeeeeee 71 Saving a Quantitation Results Report 71 Chapter 5 Basic Kinetics Analysis 75 Working with Experiments 76 Octet System Data Analsyis User Guide Release 7 1 page 2 Starting a Basic Kinetics Experiment 76 Loading an Experiment for Analysis 76 Analyzing Binding Data 80 Editing Experiments 81 Viewing Binding Curves 84 Closing Experiments 00 0005 87 Working with Raw Datd 04 88 Viewing Raw Data 88 Exporting Raw Data 91 Quantitating Raw Data 91 Processing Kinetic Datd 96 Step 1 Sensor Selection 96 Step 2 Reference Subtraction 99
102. alysis 7 0 Quantitation higG ProG Q File Help Data Selection OQ Results 5 Loaded Data higG ProG Q e ae a Align X Reference Subtraction Average of Flip Data Show All Traces Group View 2011_03_01 _ mutti analyte 1 10 Sec A Row Column F Ignore erorsinfies when loading Options d 2011_03_01 _ muti analyte GQ 2011_03_01 _ muti analyte E proAproGproL multianalyte 2 EX1021 2490 002 002 lt EX8130 2409 037 Pro A Quant from QC QQ Bperiment_36 Bperiment_37 I Bperiment_40 I Experiment_44 jj testReferenceSubtraction 04 27 11 384Q higG Gj 04 27 2011 384 higG Q BP riG Poco wn Binding Curve Graph nm 0 10 20 30 40 50 60 70 80 ol 70 TA Time sec ff 04 27 11 384 K ProA hlgG JD 04 27 11 384 Q hlgG Select samples from the table or Plate below to display the data Figure 4 3 Data Selection Window Opening an Experiment 5 Repeat steps 2 3 to load and open another experiment Octet System Data Analsyis User Guide Release 7 1 page 46 Chapter 4 Quantitative Analysis NOTE When multiple experiments are loaded select an experiment by click ing its tab above the binding chart in the Data Selection window or click the experiment name in the Loaded Data directory tree Editing Experiments The Octet System Data Acquisition software
103. alysis ini file 1 2 3 Load and open a kinetic experiment that will be included in the batch process Click the Processing tab Enter processing parameters For more details see Processing Kinetic Data on page 96 Click Process Data Click the Analysis tab This creates a Settings_DataAnalysis xml file in the experiment folder NOTE To batch process data sets with individual ini files create an ini file for each experiment in the batch Octet System Data Analsyis User Guide Release 7 1 page 120 Chapter 5 Basic Kinetics Analysis Creating a Kinetic Settings_Welllnfo xml File Optional To create a kinetic Settings _Welllnfo xml file 1 2 3 4 Load and open a kinetic experiment that will be included in the batch process Click the Processing tab and select Sensor Selection In the sample plate map right click a welland select Edit Sample Properties Enter the new information for Well Type Sample ID Description and Molar Concen tration and then close the dialog box Click Process Data or Save Proc Parameters The Settings_Welllnfo xml file is saved to the experiment folder Creating a Kinetic Settings_Tablelnfo xml File Optional To create a kinetic Settings_Tablelnfo xml file 1 2 3 4 5 Load and open a kinetic experiment that will be included in the batch process Click the Processing tab Enter processing parameters Click Process Data Click the Analysis
104. alysis window the data will be added to the Report Point Analysis table NOTE Click a sensor tab at the bottom of the binding chart to view data for a particular biosensor Octet System Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 111 ki ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics S File Help O Data Selection Processing Analysis Step 1 Data Selection Raw Data View Association Dissociation Results Sensor Selection Sensors to be Analyzed A1 F1 B1 F1 z C1 F1 1 F1 E1 F1 G1 F1 x Step 2 V Subtraction Reference Wells gt Parallel Reference Sensors Double Reference Average Reference Sensors Step 3 F Align Y Axis Step Baseline 7 Time Range sec From 01 To 299 79 Step 4 T Inter step Correction Aign to Dissociation 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 130 1400 150 Align to Baseline Time sec Step 5 Process ee _ T Savitzky Golay Fitering Al SR eT FS RE NF Ye TT ee fD2 af E2 fT Process Data Report Point Analysis Step 6 View Results Input times are after beginning of Association Step Processed Results 7 ere Time sec 594 7919 Time2 sec 1494 584 Use 20 pointaverage Apply Apply Al Export Fie ta O heath Sensor Sample Sampe Concentration
105. at TM sA tre A4 Associa Unk 1 N A B O diang io Unknown 181 EBB saoe Ba Associa Unk 2 N A 2c1 SA Stre C4 Associa Unk 3 N A ic 1 X 10 Changeto Control 3 D1 SA Stre D4 Associa Unk 4 N A Change to Reference 4 E1 SA Ste E4 Associa Unk 5 N A D O O sia Sarin boomed 5 Fl I SA Stre F4 Associa Ref 6 N A E O ca B G4 Associa Ref 6 N A 7H E H4 Associa Ref 6 N A Feo 8 a2 A5 Asocia Unk 1 N A liceo 982 E B5 Associa Unk 2 N A 1 c2 C5 Associa Q Unk 3 N A 1 D2 D5 Associa Unk 4 N A H 162 E5 Associa Unk 5 N A 169 ER beencio M Rf 6 N a Figure 5 19 Changing the Sample Type in the Sample Plate Map or Sample Table 4 Seta standard concentration value in the sample table double click the Conc cell and enter a value Figure 5 20 To access a shortcut menu of editing commands right click the cell Octet System Data Analsyis User Guide Release 7 1 Working with Raw Data page 95 iF ForteBio Data Analysis 7 0 Quantitation higG ProA Kinetics o S Z File Help O Data Selector LO Reats Hay Loaded Data higG ProA Kinetics 16 Sensors from 1 oak By 0427 11 384 K PAKS E hig ProA Kinetics 10 Se SA EF igram oms n fies when loading A Guanttation By 04 27 11 I4 AhkG Gy 04 27 2011 384 hG Q 210 450 48 510 54 570 600
106. ata Analysis 7 0 Setup Wizard dia log box Figure B 9 i Data Analysis 7 0 Setup S Completing the Data Analysis 7 0 Setup Wizard Data Analysis 7 0 has been installed on your computer Click Finish to dose this wizard lt Back Finish Cancel H Figure B 9 Completing the Data Analysis 7 0 Setup 7 Click Finish to complete the installation Octet System Data Analsyis User Guide Release 7 1 page 162 Chapter B 21 CFR Part 11 Software Administrator Options INSTALLING THE FORTEBIO GXP SERVER MODULE The ForteBio GxP Server module can be installed and run from the following locations e Alocal host computer where the 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
107. ata Selection Results 5 Loaded Data H Kinetics H Quantitation Figure 4 1 Data Selection Tab 2 Load an experiment right click the experiment folder in the workstation directory tree and select Load Folder or on the menu bar click File gt Load a Folder 3 In the Loading Files dialog box enter the folder name or click the Browse button _ select the desired folder and click Load The experiment is added to the Loaded Data directory tree see Figure 4 2 example Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 45 i Data Selection E Loaded Data E Kinetics E Quantitation GD Data Selection Results S Loaded Data Kinetics E Documents and 5 A ae BG ForteBio 2011_03_01 _ multi analyte 1 aao ee a E 20110301 _ muti analyte 2 amp BH081908 44 E aesa Sn pro analyte EX1021 2490 002 002 Load Folder EX8130 2409 037 Open Explorer Pro A Quant from QC New Folder gt Emperiment_36 Rename Folder f Delete Folder Loaded Data Directory Tree E Experiment _44 Expand Qj testReference Subtraction Refresh a 04 27 11 384 Q higG 04 27 2011 384 higG Q hlgG ProG Figure 4 2 Data Selection Window Loading an Experiment 4 Inthe Loaded Data directory click the experiment name to open The binding curves sample plate and sample plate table appear Figure 4 3 il ForteBio Data An
108. ate Window To open the binding curve chart in a separate window double click the graph Customizing Appearance of Graph or Binding Curve To customize the appearance of the graph or a binding curve see Figure 4 16 Right click the graph or a curve for a shortcut menu of display options Hover over a binding curve to display a tooltip of the X Y coordinates e Right click the graph to view a shortcut menu of display options Right click a curve to view a shortcut menu of display options e Right click the graph and select Toolbar Toolbar buttons enable you to save copy or print the graph ForteBio Data Analysis 7 0 Quantitation higG Prod Kinetics gt 5 a File Help O Data Selection E Results 5 Loaded Data higG ProA Kinetics 16 Sensors from 1 6 Kinetics z E 0427 11 384 K ProAhigG ee ee E T el anye E Instrument Type OctetRED95 Edt eis 10 See AI Row Column Ignore errors in files when loading tions Auto Ful Legends 6 Quantitation Binding Curve Graph 300 0 6 9 120 150 180 210 240 270 30 330 360 30 420 450 480 510 540 570 600 a M Desttop Time sec Select samples from the table or Plate below to display the data Via 2 3 4 ss S10 ti i in Sensor C Sensor Sample Sample Type Repicat Known Conc VY Y yore oa MM saGr M4 Associa Sa 1 o B 18 SA Stre B4 Associa Sta 2 0 0 2c1 SA Sre C4 Associa Sa 3
109. ays Figure B 36 Current password New password Confirm new password Password reminder Figure B 36 Change Password Dialog Box Administrator Octet System Data Analsyis User Guide Release 7 1 page 178 Chapter B 21 CFR Part 11 Software Administrator Options NOTE You can also access the Change Password dialog box by right clicking on the administrator account in the Users tab and selecting Set Password from the tab menu 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 Figure B 37 allows administrators to add and delete user groups as well as set and change group privileges ForteBio GxP Server Admininstra 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 plate 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 37 ForteBio GxP Server Administration When a user account is assigned to a user group the privileges defined in the group are also applied to the individual user account
110. cut C Users wms AppData Roaming Microsoft Windows Start MenulPr Create shortcut C Users wms Desktop ForteBio GxP Server ink Create shortcut C Users wms AppData Roaming Microsoft Windows Start MenulPr Create shortcut C Users wms Desktop Restart Server ink 3 Output folder C Program Files ForteBio 7 CFR FBServer7 Create shortcut C Users wms AppData Roaming Microsoft Windows Start Menu Pr Created uninstaller C Program Files ForteBio 7 CFR FBServer 7 uninst exe Execute C Program Files ForteBio 7 CFR FBServer7 FBServer exe S Execute C Program Files ForteBio 7 CFR FBServer7 FBServer exe 2 s 4 ForteBio Inc www fortebio com lt Back Next gt Cancel Figure B 13 Installation Progress The installation wizard displays the Completing the ForteBio GxP Server 7 0 Setup Wiz ard dialog box Figure B 14 33 ForteBio GxP Server 7 0 Setup iss 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 14 Completing the ForteBio GxP Server Software 7 0 Setup 7 Click Finish to complete the installation Octet System Data Analsyis User Guide Release 7 1 Administrator Account Setup page 165 ADMINISTRATOR ACCOUNT SETUP To set up the administrator account 1 Launch the Octet System Data Acquisition or Data Analysis software by double clicking the respecti
111. cut menu of editing commands File Help TJ Data Selection I Resuits Standard Curve Equation E Group View Linear Point to Point z E Options Ato Full Refresh Load Standards Save Standards Standard Fitting Curve Unknown amp Control E Use standards from loaded file 0400 Calibrate within plate 0 360 Processing Parameters Binding Rate Equation 0 320 0 280 Read Time 120 00 secs 0 240 Zero Conc Threshold 0 0001 BR Z aa Low Conc Threshold 0 003 BR 3 0160 0 120 Calculate Binding Rate 0 080 Data Export noe m oo 10 2 3 40 50 60 70 80 90 100 110 120 120 140 150 160 170 18 190 200 210 220 230 240 Standard Sample Alerts Concentration ug ml Type Threshold Max Residual 10 Sample Sensor Plate Sample ID Binding Rate Well Conc fip Cale Conc Beth Min and Max Residual I Sample Aet F Do not use alerts 7 009 E IgG Stan 00181877 9 96 Save Analysis Settings e K amn on O0000000 wi S 0000OG80 7 e v S aH o 4 v J 7 978 7 KG Stan 00090943 498 v 4 a em SES 8 1 aoma me Oo cj m Figure 4 21 Results Window Displaying Standards Sample Alerts Octet System Data Analsyis User Guide Release 7 1 Analyzing Data page 65 Applying Sample Alerts The Sample Aler
112. d wells and excluded wells become included wells You must re run the analysis to apply the inverted settings Order Columns Opens a dialog box that enables you to change the order of the table columns Searching Analysis Results The complete contents of the Analysis tab results table is searchable using the Advanced Search tool The search result is a highlighted set of table rows that meet the specified search criteria The set of rows selected before activation of the Advanced Search dialog box may be combined with the results of the search using ALL AND and OR opera tors specified within the Advanced Search dialog box Advanced Search Dialog enove Level_ Seach Optone Column Name Operator Value A x n eep current Sensor Location gt Starts with x selection implies OR i Search only current selection implied AND Saved Searchs Selected Search Search Details Case Sensitive Include Excluded Traces Treat Empty Cells as a Match Search Name NewSearch Save Figure 5 52 Advanced Search Dialog Box Advanced Search options Column tThe column of the results table searched Operator The method of matching the search term with the searchable text Options include Starts with Ends with Contains Does not contain and Is empty Value The search term for a single level Add Level Adds one additional search level to the search T
113. damage to the instrument may result nect the power NOTE For information about how to connect the Octet instrument to the NOTE Do not position the Octet instrument such that it is difficult to discon computer refer to the insert sheet that is provided with the Octet instrument To launch the system and the Octet Data Analysis software 1 Turn the Octet instrument on using the power switch located on the external electrical box NOTE The instrument requires a minimum of one hour warm up time It is recommended that you leave the instrument on for a minimum of eight hours prior to use 2 Launch the Data Analysis software by double clicking the Data Analysis desktop icon NOTE When using the CFR 11 version of the Octet System Data Analysis soft ware you are required to log in and start a user session before the software launches For more information refer to Starting a User Session on page 33 Launching the Octet System Data Analysis software application displays the main screen Figure 2 1 Octet System Data Analsyis User Guide Release 7 1 Launching the Octet System Data Analysis 7 1 Software page 23 Main Menu n ForteBio Data Analysiq 7 0 gt 5 x File Securi Data Selection iy Loaded Data Kinetics amp Quantitation W Desktop Figure 2 1 Main Screen for Data Analysis Main Menu The main menu is located in the uppe
114. der Analyzes each experiment using the ini file found in the same experiment folder e Use one for all folders Analyzes all experiments using a single ini file that is selected by the user Well Information Specifies a Settings_Welllnfo xml file in the experiment folder that contains four types of sample information e Well Type e Sample ID e Description e Molar Concentration This feature can be used to edit sample information after data acquisition It is use ful for example if naming conventions within a project change over time and the sample information used during data acquisition requires updating Octet System Data Analsyis User Guide Release 7 1 page 122 Chapter 5 Basic Kinetics Analysis Select a Well Information file only if you edited an experiment in data analysis For more information about editing an experiment see Editing Experiments on page 46 A Settings_Welllnfo xml file will be put in the experiment folder of any experiment that has been edited in the Octet System Data Acquisition software Select a well information file if the Use one for all folders option is selected If no xml file is specified the well information from the original data acquisition file will be utilized Table Information Specifies a Settings_Tablelnfo xml file in the experiment folder that contains four types of sensor sample information e Sensor Type Sensor Info Sample ID e Molar Concentration Thi
115. din 110420_024 frd q j 3 I Ae E 4 F P pam Figure 5 24 Specifying Reference Wells 4 Exclude wells from analysis a In the sample plate map select the wells b Right click and select Exclude Wells for Analysis Figure 5 24 Step 2 Reference Subtraction Reference subtraction is optional and is not required for all applications There are two types of references used in Octet experiments reference biosensors and reference wells Reference biosensors Used as a references throughout the entire assay for exam ple biosensors without active capture molecules Reference wells Contain only assay buffer and are used to measure system drift To apply reference subtraction during data processing 1 In the Step 2 Subtraction pane select the Subtraction method The subtractions that will be executed based on the subtraction method biosensor designation and sample plate well designation are listed in the Sensors to be Analyzed box If the subtraction method is not compatible with the sensor tray map and the sample plate map a question mark is displayed in the Sensors to be Analyzed box 2 Confirm the biosensor subtraction in the Sensors to be Analyzed box Octet System Data Analsyis User Guide Release 7 1 page 100 Chapter 5 Basic Kinetics Analysis 0 Fortelio Dets Analysis 7 0 Kinetics higG Prod Kinetics op g a m Damm Doai ee ge ee E BE E E S A AOLIO N
116. dit Legends 85 Ignore errors in files when loading 85 in the Data Selection window ta ble 85 Reference Subtraction Average of 85 Show All Traces 85 in the Data Selection window table 54 quantitative analysis Align X 54 Edit Legends 55 Flip Data 54 85 Grouped View 54 Ignore errors in files when loading 54 in the Data Selection window ta ble 54 Reference Subtraction Average of 54 Show All Traces 54 selecting data 127 W web browser opening 26 Weighted Y2 59 well concentration 62 well designation 62 Well Information analyzed data 63 batch mode option kinetics 121 quantitation 70 editing 48 well location Octet System Data Analsyis User Guide Release 7 1 page 212 in the sample plate 62 in the sample plate or reagent plate 129 wells excluding from analysis 99 Window of Interest From Start of Step analysis option 115 X X Y graph described 138 displayed figure 138 Y Y Axis Scaling Auto Scale 124 Fitting view option 124 Full Scale 124 Y axis aligning figure 105 Z Zero concentration threshold processing parameters basic kinetics 83 Quantitative Analysis 48 Octet System Data Analsyis User Guide Release 7 1 page 213 Octet System Data Analsyis User Guide Release 7 1 page 214 Octet System Data Analsyis User Guide Release 7 1 page 215 Octet System Data Analsyis User Guide Release 7 1 page 216 Octet System Data A
117. dministrator Password Project none Figure B 25 Login Dialog Box with Server User and Project Settings Configured 4 Enter your Password Click for a password reminder Figure B 26 if necessary fort sio localhost 20002 Administrator Reminder Employee number Figure B 26 Password Reminder 5 If required select a project from the Project drop down list Figure B 27 Octet System Data Analsyis User Guide Release 7 1 Starting an Administrator User Session page 171 fort sio Server localhost 20002 User Administrator Password eeececceece Cell Culture screen Receptor Ligand screen Figure B 27 Login Dialog Box with Project Selections 6 Click OK The Octet System Data Acquisition or Data Analysis software launches and initiates the administrator session During the session the administrator account and project selected at login are displayed in the Data Acquisition software status bar NOTE Administrator and user sessions are automatically closed after a period of inactivity set using the UserldleMin constant Please see Administrator Constants on page 182 for more information Octet System Data Analsyis User Guide Release 7 1 page 172 Chapter B 21 CFR Part 11 Software Administrator Options ACCESSING ADMINISTRATOR OPTIONS The 21 CFR Part 11 software Server Administration options allow administrators to mange
118. dministrators to add and delete user projects Proj ects are selected when a new user session is initiated in the Octet System Data Acquisition or Data Analysis software allowing all user system and software events for a particular proj ect to be monitored 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 40 Projects Creating a New Project To create a new project 1 Right click anywhere in the Projects tab and select New Project or double click ina blank area The New Project window displays Figure B 41 Project name Information Figure B 41 New Project 2 Enter the Project name and Information optional 3 Click OK to save changes and exit Octet System Data Analsyis User Guide Release 7 1 page 182 Chapter B 21 CFR Part 11 Software Administrator Options Viewing and Changing Project Settings To view and change project settings 1 Right click on the project and select Edit Project or double click on the project The Edit Project window displays Figure B 42 Project name Receptor Ligand screen Information Affinity Screen Figure B 42 Edit Project 2 If needed modify the project settings 3 Click OK to save changes and exit Deleting a Project To delete a project 1
119. e Group Type The well designation Standard Unknown Reference or Control Octet System Data Analsyis User Guide Release 7 1 Analyzing Data page 63 Binding Rate The rate of sample binding to the biosensor computed by the Octet System Data Acquisition software using the binding rate equation specified Known Conc The user specified standard concentration that was entered during sample plate definition Calc Conc The sample concentration computed from the standard curve e Residual Residual Expected standard concentration Calculated standard concentration Expected standard concentration r2 COD The r of the curve fit used to determine the binding rate Well Information User specified notes about the wells Sample Plate Map The sample plate map displays well data and can be used to select which type of results to display Select the type of results to display in the sample plate map Show Table Column drop down list For example select Calc Conc to display the computed sample concen trations on the map Results Table The results table displays detailed results for each well in the plate map Sorting Results Table Entries The information in the results table can be sorted in ascending or descending order based on the values in any of the columns To sort the entries in ascending alphanumeric order click a column header To sort the entries in descending order click
120. e 2 ee ae F pa nw g a a 15 7 a 2 l F A 3 j A 5 2 a F x Tr an s S le 05 lt gt j f w on oea 0 TE TN ae a rire rr rrr rrr Tt ret rr a aE i TET i E a i ETT rrr 0 200 400 600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 Concentration ug ml Figure 1 21 Three Standard Curves Generated by Sensor Type The Select Standards dialog box Figure 1 22 displays with all of the standard curves including the one in the plate Bel sclect Standards File Name vs St Standard 2fsc V Standard 3fsc Figure 1 22 Select Standards Dialog Box d Click to select the standards you want to use and click OK e On the Standard Curve Equation dialog box Figure 1 19 on page 15 click Calcu late Binding Rate Binding rates concentrations are calculated based on the selected standard curves 12 An exported standard curve path is displayed on the saved report on the Standard Curve tab Octet System Data Analsyis User Guide Release 7 1 What s New in the Octet System Data Analysis Software Release 7 1 page 17 13 A customized report feature allows users the flexibility to select and order columns on the saved report and the report setting is saved as the default for future reports To use this feature a On the Report Selection dialog box Figure 1 23 click Save Report gt Select and Order Columns gt OK al Report
121. e Release 7 1 page 130 Chapter 5 Basic Kinetics Analysis e kobs 1 s Observed binding rate For the 2 1 and 1 2 models the Octet System Data Acquisition software computes two kops values km tThe mass transport rate constant km error The standard error of the mass transport rate constant Req The calculated response at equilibrium that is determined from a fit of the binding data Req Rmax Ratio of Req to Rmax Full X2 A measure of the goodness of curve fitting not directly related to a param eter estimate It is the sum of squared deviations where deviation is the difference between the actual data point and the fitted curve There is one value for each curve fit Values close to zero indicate a good curve fit Full R2 R2 is the coefficient of determination COD It is an estimate of the good ness of the curve fit and is not directly related to the estimate of a specific parameter Values close to 1 0 indicate a good curve fit e Report point 1 10 Up to 10 report points can be added to the analysis results table using the Report Points feature in the Analysis window The column heading of each report point is time value used to generate that report point For example if a report point is generated at 100 seconds the column heading is X 100 e SSGKp The steady state group Kp value Use this feature to quickly view the steady state derived Kp values of groups defined within grouped view
122. e UserldleMin Idle time allowed during a user 15 Minimum 0 session after which the session is no maximum automatically closed value Octet System Data Analsyis User Guide Release 7 1 page 184 Chapter B 21 CFR Part 11 Software Administrator Options Creating a New Constant To create a new constant 1 Right click anywhere in the Constants tab and select New Constant or double click in a blank area The New Constant window displays Figure B 44 Constant name Value Figure B 44 New Constant 2 Enter the Constant name and Value Refer to Table B 3 for a list of available constants and value ranges 3 Click OK to save changes and exit Viewing and Changing Constants To view and change constants 1 Right click the constant and select Edit Constant or double click the constant The Edit Constant dialog box displays Figure B 45 Constant name UserIdleMin Value 15 Figure B 45 Edit Constant Dialog Box 2 If needed modify the constant settings For more information on available constants and their values see Table B 3 on page 183 3 Click OK to save changes and exit Octet System Data Analsyis User Guide Release 7 1 Accessing Administrator Options page 185 Deleting a Constant To delete a constant 1 Right click the constant and select Delete Constant 2 Click OK in the dialog box displayed Event Log The Events tab allows administrators to view all th
123. e Information Figure 5 51 Analysis Results Table Shortcut Menu Analysis results table display options Advanced Search Searches the contents of the results table of the Analysis tab Multiple levels and operators are available Searches may be combined using AND OR operator and saved see Figure 5 52 Set Color Opens the color palette that enables you to choose a color for the selected results see Figure 5 53 Set Color By Group Color codes the results according to the groups set in the Grouped View Options dialog box see Figure 5 48 Set Color By Enables you to color code results according to a user selected cate gory from the analysis results table see Figure 5 54 Include Wells Removes the X in the Include column for the selected biosensors Re run the analysis to include these biosensors in the analysis Exclude Wells Adds an X in the Include column for the selected biosensors Re run the analysis to exclude these biosensors from the analysis Size Columns by Title Automatically sets the column width to fit the column title Octet System Data Analsyis User Guide Release 7 1 page 132 Chapter 5 Basic Kinetics Analysis Size Columns by Data Automatically sets the column width to fit the data Select All Rows Selects all biosensors in the table and displays the data in the Fit ting view and graphs Invert Selection Changes the wells status so that included wells become exclude
124. e Selected Step menu 91 quantitating raw data for a selected step figure 92 from a selected step described 91 Quantitation Batch Mode dialog box figure 70 Quantitation Batch Mode menu 70 quantitation experiment described 44 quantitation results report saving 73 quantitation results reports exporting data 71 Quantitation window displaying selected step data from a kinetic assay figure 93 R R equilibrium binding rate equation 60 steady state kinetics analysis option 118 r2 COD analyzed data 63 r2 of the curve fit 63 rate of association 129 rate of dissociation 129 ratio of Req to Rmax 130 raw data exporting 71 91 saving 71 viewing 88 Raw Data view 88 Read time processing parameters basic kinetics 83 Quantitative Analysis 48 reference biosensors defined 96 specifying 97 reference buffer wells defined 96 Reference subtraction average of methods figure 58 Reference Subtraction Average of viewing option basic kinetics analysis 85 quantitative analysis 54 reference subtraction methods Average Reference Sensors 103 Double Reference 102 Double Reference figure 103 for data processing 100 Parallel Reference Sensor figure 102 Parallel Reference Sensors 101 Reference Wells 100 Reference Wells figure 101 Octet System Data Analsyis User Guide Release 7 1 page 204 Reference Subtraction option 54 Reference Subtraction options basic kinetics analysis All 85 Column 85
125. e nee enaeneneeas 165 Starting an Administrator User Session ccc cece eee eee eee eee ence eee eneens 169 Accessing Administrator Options 0 cece cece cece cece e tence ence cnet ences 172 Accessing the ForteBio GxP Server Module Directly cece cece eee eee e eee 187 Restarting the ForteBio GxP Server Module ccc cece cece eee e ence eee eeeeenee 190 Octet System Data Analsyis User Guide Release 7 1 page 156 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 or E drive 2 Double click DataAcquisition CFR 7_0 0_x exe to launch the installation wizard see Figure B 1 lt 3 Data Acquisition 7 0 Setup a Welcome to the Data Acquisition 7 0 Setup Wizard for 21 CFR part 11 This wizard will guide 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 Fig
126. e of Methods 2 Confirm the sample designations for details see Changing Sample Designations on page 46 Octet System Data Analsyis User Guide Release 7 1 Analyzing Data page 59 3 Confirm the standard concentrations for details on changing standard concentration see Editing Standard Concentration or Well Information on page 48 4 Click the Results tab and select samples to include in the analysis for details see Excluding Including Samples from Analysis on page 47 i ForteBio Data Analysis 7 0 Quantitation higG ProG Q leoleo File Help Data Selection B Resuts Standard Curve Equation Group View Linear Point to Point Options Ato Full Refresh E Use standards from loaded file Calibrate within plate Processing Parameters Binding Rate Equation Read Time 120 00 secs Zero Conc Threshold 0 0001 BR Low Conc Threshold 0 003 BR No Data Available Calculate Binding Rate Data Export hlgG ProGQ Standard Sample Aerts Type Threshold Table Column Known Conc v Index Known Sample Type Bin X E bog Y E Log m y isas e7 e 910m1 38 NA EE c ce 1 Sampe Ref Binding Rate Cale Cone Ma A POCO 7 39 Na Mrs He 1 Same Fat gt enne Lae Sa ee oe ao No Data ce B a 100 E B1 1 IgG Sta Sta Sample Alet D B 42 50 ca c1 1 IgG Sta Sta
127. e user system and software event infor mation recorded by the ForteBio GxP Server module 2 ForteBio GxP Server Admininstration ES Users Groups Projects Constants User Project Machine Date Time Login Name Project Machine Type Info 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 2011 02 13 15 42 32 Administrator JRICHARDS User login 2011 02 13 16 35 41 Administrator JRICHARDS User login 2011 02 13 16 57 39 Administrator JRICHARDS User login 2011 02 13 16 59 25 Administrator JRICHARDS User login 2011 02 13 17 45 50 Administrator JRICHARDS User login 2011 02 13 18
128. eV YO YO VC a NYY NY NHI SHI MHI WY OWI EY n Step 3 X Align Y Axis HIC OCO Cy ye M Y o Step Baseine AATA TETTA PL Time Range sec From 1 0 To 1190 Reference Sensor Empty k Ligand Sensor Sample unset Reference Well tep 4 Inter step Correction k Select Ligand Sensor s for Data Analysis Align to Dissociation Align to Baseline Well Wel Sensor Sensor All Well Well Well Sample tion Molar Step 5 Process Number Location Sensor Type Info File N Number Location Type ip Description nh Saviteky Golay Filtering 26 B4 ir 5 Process Datal 27 c4 Empty 2 B1 unset 28 D4 Empty 3 a Sampe Analytel 41 Step 6 View Results 29 E4 Empty aaa Eso at eee eth b Processed Results 30 F4 Empty R i f ai pena eee e E 5 E1 Sample Analyte 41 Report Points 6 AL unset ji Step 7 Save Results iga SA Streptavidin Z B Sarok JAn Save Processed Data 34 B5 LigandSensor SA Streptavidin LABUSEROI 8 HM unset 35 c5 Ligand Sensor SA Streptavidin LABUSEROS 3 n unset ave Raw Data 1 t i 36 D5 LigandSensor _ SA Streptavidin LABUSEROS y 10 a unset a Figure 5 22 Selecting Biosensors in the Processing Window 2 Specify reference biosensors a In the sensor trap map select the appropriate biosensors b Right click and select Change Sensor Type gt Reference Sensor Figure 5 23 Octet System Data Analsyis User Guide Release 7 1
129. ece cece cen e nen n nent ke En ene ee een enenes 123 Working with Graphs 0 cece ccc cece cnn cence ence ene nee en een eeenneneneens 138 Data Export Options op scenie ee aa E EE a E a a TEE ele esdasas 140 Generating a Report ssssssssrsssesssesessessessscesseressosscrosesesressere 141 Octet System Data Analsyis User Guide Release 7 1 page 76 Chapter 5 Basic Kinetics Analysis WORKING WITH EXPERIMENTS Starting a Basic Kinetics Experiment A basic kinetics experiment enables you to determine the association and dissociation rate of a molecular interaction After an experiment is run start a data analysis session double oe click the icon on the desktop There are several ways to start a basic kinetics experiment Use the Experiment wizard e Open a method file fmf An experiment method file fmf is automatically saved after you define and run an experiment 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 re analyze 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 Loading an Experiment for Analysis A data analysis session can be used to e Lo
130. ed rows are marked in the Alert column in the analysis table Figure 4 25 Index TFlip Alert Plate Sensor Sample Sample ID Type 0 x 1 A4 A4 Ab1 Unknown 1 x 1 B4 B4 Ab2 Unknown 2 x 1C4 c4 Ab3 Unknown 3 1 D4 D4 Ab4 Unknown 4 1 E4 E4 Ab5 Unknown 5 1 F4 F4 Ab6 Unknown 6 1G4 G4 Ab7 Unknown 7 x 1 H4 H4 Abs Unknown 8 x 1A5 A5 Ab1 Unknown 9 x 1 B5 B5 Ab2 Unknown 10 x 1 c5 c5 Ab3 Unknown 1 1 D5 D5 Ab4 Unknown 12 1E5 E5 Ab5 Unknown 13 1 F5 F5 Ab6 Unknown 14 1G5 G5 Ab7 Unknown Figure 4 25 Alert Column SAVING STANDARDS DATA After analysis the standards data can be saved for use with other quantitation experiments to do so 1 Inthe Results tab see Figure 4 20 on page 61 click Save Standards 2 Inthe displayed dialog box select the file folder and enter a filename fsc 3 Click Save SAVING ANALYSIS SETTINGS To save the analysis settings in the Results and Data Selection windows click Save Analysis Settings A Settings_DataAnalysis file ini is saved in the experiment folder These settings are dis played the next time the experiment is loaded NOTE The Settings_DataAnalysis ini file is also automatically saved when you click Calculate Binding Rate The Settings_DataAnalysis ini file may also be used during batch processing Octet System Data Analsyis User Guide Release 7 1 Processing Batch Quantitation Analysis page 67 PROCESSING BATCH QUANTITATION ANALYSIS In batch mode multiple quantitation da
131. eeaee 146 Appendix A Using Octet384 Systems with an Automation Interface 149 Automation Interface Overview 150 Design of the Automation Interface 150 Automation Interface Control Setup 151 Analysis Automation API 151 Appendix B 21 CFR Part 11 Software Administrator OPtlONS seid ese sieiesieie sce Pate ters anes 155 Installing the Data Acquisition 7 0 21 CFR Part 11 Software assonans 156 Installing the Data Analysis 7 021 CFR Part 11 SOW ONC s etsisi aiiin iiE e ate 159 Installing the ForteBio GxP Server Module162 Administrator Account Setup 165 Starting an Administrator User Session 169 Octet System Data Analsyis User Guide Release 7 1 page 3 Accessing Administrator Options 172 Administrator Tabs 65 173 User Account Administration 174 Group Administration 178 Project Administration 181 Administrator Constants 182 Event LOG 0 cece ccc e eee n eee e nes 185 Accessing the ForteBio GxP Server Module Directly 187 Restarting the ForteBio GxP Server Module190 Octet System Data Analsyis User Guide Release 7 1 page 4 Chapter 1 Octet System Data Analsyis User Guide Release 7 1 page 5 CHAPTER 1 Welcome Aboutthe Octet Systemi ccicssscaadoveccutadeleasads E EE E E EEE E 6 What s New in the Octet System Data Analysis Software Release 7 1 000 00 7 What s New in the Oc
132. elease 7 1 Restarting the ForteBio GxP Server Module page 191 2 3 Restart Server oe CMDLINE Starting service x a Figure B 56 Restart Server Console Octet System Data Analsyis User Guide Release 7 1 page 192 Chapter B 21 CFR Part 11 Software Administrator Options Octet System Data Analsyis User Guide Release 7 1 page 187 Index Symbols fmf files method files 76 Numerics 1 to 2 Bivalent Analyte Model 114 2 to 1 HL Model 114 A About ForteBio Data Analysis menu 26 accessing GxP Server module 187 Add Folders menu 70 122 Add Level Advanced Search option 132 Add to Table Fitting view option 125 adding Replicate Group from the Sample Plate Table figure 52 Additional Graphs view option 126 administrator constants 183 administrator password changing 177 Advanced Search dialog box figure 132 Advanced Search options Add Level 132 Case Sensitive 133 Column 132 Include Excluded Traces 133 listed 132 Operator 132 Remove Level 133 Search All 133 Search all but keep current selection implies OR 133 Search only current selection implies AND 133 Treat Empty Cells as Match 133 Value 132 Advanced Search tool 132 Advanced Search display option 131 Affinity constant 129 affinity constant KD 80 alert threshold value editing 64 Align All Baselines alignment option 91 Align by Begin Point alignment option 91 Align by End Point align
133. elease 7 1 page 54 Chapter 4 Quantitative Analysis Viewing Options Table 4 1 Viewing Options in the Data Selection Window Option Description Align X Select this option if there is an artifact at the beginning of the binding step to remove Enter a time seconds at which to start the alignment Reference Subtrac tion Average of If the experiment includes reference biosensors select the Ref erence Subtraction option and select one of the following All Computes the average binding curve from the ref erence wells and subtracts this average from each sam ple curve Row lfarowincludes both samples and references the Octet System Data Acquisition software computes the average reference curve for the row and subtracts this curve from the samples in the same row Column lIf a column includes both samples and refer ences the Octet System Data Acquisition software com putes the average reference curve for the column and subtracts this curve from the samples in the same col umn Ignore errors in files when loading Show All Traces If this option is selected the Octet System Data Acquisition software ignores errors in data files All data files regardless of errors or runtime issues will be loaded for analysis Displays all binding curves Flip Data The Flip Data function inverts signals from positive to negative or from negative to positive This is used most often when the obser
134. enables you to change sample designations standard concentrations or exclude samples from analysis For example you can exclude a standard that does not meet the sample r or residual threshold then re analyze the data You can also modify some processing parameters Changing Sample Designations To change sample designations 1 Click the Data Selection tab then perform one of the following tasks Inthe sample plate map select the well s right click and select one of the fol lowing options see left image in Figure 4 4 e Change to Standard e Change to Unknown Change to Control e Change to Reference e Edit Sample Information Inthe results table right click a table cell and make a selection from the drop down menu see right image in Figure 4 4 Table Column Known Cone Change to Standard Change to Unknown Change to Control Change to Reference Edit Sample Information Selecting wells in the sample plate map F 1234567 8 9101112 roanmooo r Include Selected Rows Exclude Selected Rows Set Color Set Color By Group Set Color By b Size Columns by Title Size Columns by Data Size Columns by Both Select All Rows Invert Selection Order Columns Edit Sample Information Selecting a cell in the Well Type column of the results table Figure 4 4 Changing Sample Designations Octet System Data Analsyis User Guide Release 7 1 Wo
135. ents for the entries selected Figure B 48 User Black Mi Project Receptor Ligand scr z Machine ny x 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 48 Selected Entries In addition to the specific user project and machine selections the following list options are also available any Displays all user project or machine events none Displays all user and machine events not associated with a specific project Project list only Octet System Data Analsyis User Guide Release 7 1 Accessing the ForteBio GxP Server Module Directly page 187 ACCESSING THE FORTEBIO GXP SERVER MODULE DIRECTLY Administrators can directly access the ForteBio GxP Server module without initiating an administrator user session Direct access provides server testing options as well as access to all administrative functions discussed earlier in this section To access the ForteBio GxP Server module directly e Ifthe ForteBio GxP Server module is installed on a network location Double click the FBServerConfig exe file in the FBServer7 folder from the installed location Figure B 49 File Edit View Tools Help Organize Include in library Share with Burn New folder Ey fi O p 4 JL ForteBio Name Date modified Ty
136. eport Data Types Processing Options Iso Affinity and Steady State Analysis Graphs Octet System Data Analsyis User Guide Release 7 1 page 148 Chapter 5 Basic Kinetics Analysis Octet System Data Analsyis User Guide Release 7 1 page 149 APPENDIX A Using Octet384 Systems with an Automation Interface Automation Interface Overview 0 cece cece cece cence eee e eee eeseesensensens 150 Design of the Automation Interface 1 0 0 0 cece cece nec c eee nent eee ee te entnenes 150 Octet System Data Analsyis User Guide Release 7 1 page 150 Chapter A Using Octet384 Systems with an Automation Interface AUTOMATION INTERFACE OVERVIEW The Octet System 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 Figure A 1 ag Options Automation 7 TCP IP Pot 20001 s E Localhost Serial RS232 Pot 1 Figure A 1 Options for Automation An example application for testing the automation interface AutomationClient exe is included in the applications and Dynamic Link Libraries DLLs installed with the Octet Sys tem Data Acquisition software The file is located in the C Program Files ForteBio Data Analysis directory NOTES The automation interface can be used with Octet384 systems only The examples that follow are illustrated using a TCP IP connectio
137. er from interrupting a session or experiment When the application is locked any experiments started will continue to run To lock the Octet System Data Acquisition software application click Security gt Lock Application The Octet System Data Acquisition software is placed in locked mode immediately and the Application Locked window displays Figure 3 20 Octet System Data Analsyis User Guide Release 7 1 page 42 Chapter 3 21 CFR Part 11 Compliance fort sio ee cee JBlack John Black Figure 3 20 Application Locked Mode 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 Log Off 2 Click OK in the dialog box displayed Octet System Data Analsyis User Guide Release 7 1 page 43 CHAPTER 4 Quantitative Analysis Working with Experiments 0 ccc cece cece cence ence nee een e ene n een eeenaenenes 44 Analyzing Dat sscc0 ctcica coaeiad hace tne vegs chads Ee o a EA REE ee aeagdua EKES 57 Saving Standards Data cece ccc eee eee een en EEEN ene REENEN RERNE WER 66 Saving Analysis SettingS cece cece cece ce een iritat kortia ken E i 66 Processing Batch Quantitation Analysis ccc eee c cece teen eee e enn enone 67 Ex
138. er logout 2011 02 14 13 49 30 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 49 34 Antigen Antibody screen JRICHARDS User logout 2011 02 14 13 50 59 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 54 47 Antigen Antibody screen JRICHARDS User login 2011 02 14 14 18 46 Antigen Antibody screen JRICHARDS User login Figure 3 14 Audit Trail Octet System Data Analsyis User Guide Release 7 1 Compliance Features page 39 NOTE Events displayed in the Audit Trail are those associated with the user account that is currently logged in and active only Sorting Events in the Audit Trail Events in the Audit Trail can be sorted by clicking any of the column headers Figure 3 15 Date Time Project Machine Action Description 2011 02 14 13 00 53 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 18 01 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 42 07 Antigen Antibody screen JRICHARDS User logout 2011 02 14 13 42 45 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 43 30 Antigen Antibody screen JRICHARDS User logout Figure 3 15 Events Listed in the Audit Trail Viewing Events for a Specific Project or Computer By default the events initially displayed in the Audit Trail are those associated with the proj ect selected at login and the machine computer currently being used To view events for a specific project or computer click the Project or Machine drop
139. erage of all reference biosensors Step 3 Align Y Axis In order to fit curves correctly they must be aligned to a common reference point upon both the X and Y axes Alignment along the X axis is achieved during assay due to the parallel movement of all biosensors Alignment along the Y axis is achieved using Align Y Axis by specifying both a step and time with which to execute the alignment The time range from the specified step will be used to calculated an average and that aver age will then be set to y 0 For example for alignment to the baseline select baseline and specify the time within the baseine step to set to an average y 0 To align to association 1 Select the Align Y Axis option and make a selection from the Step drop down list 2 Confirm the time range defaults or enter new start and finish times If you choose to align to the association step set the shortest time range possible at the beginning of the association step to align Y 0 Octet System Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 105 Parallel Reference Sensors Double Reference Average Reference Sensors Align Y Axis The time range over which the data are averaged to align Y 0 4 E Inter step Correction Align to Dissociation Align to Baseline Step 5 Process V Savitzky Golay Filtering Process Data Step 6 View Results Processed Results Sensor Summary Report P
140. ering k Ligand Sensor Empty Buffer Load Sample Reference Well O Empty Re Seen teas k Select Ligand Sensor s for Data Analysis Processed Results Sensor Summary Wel Wal Sensor Sensor Well Well Well Sample Mc Repott Points Number Location Sensor Type Info eae 0 Number Location Type 1D Duayen Step 7 Save Results cma 2 AZ _ Ugand Sensor 110420_009 4rd 1 DEE Al Buffer Kinetics Buffer 1X Kinetics Buffer eT m B2 tigani Sen 110420_010frd E Buffer Kinetics Buffer 1X Kinetics Buffer j C2 _ Ligand Sensor 110420_011 frd 2 c Buffer Kinetics Buffer 1X Kinetics Buffer 12 D2 Ligand Sensor 110420_012frd 4 ot eter Renetca titer 1XKretice Baer 1a E2 imna sensor en ora Sa ses Rese ee 14 F2__ Ugand Sensor 110420_014frd fs om mw 7 i 15 G2 __ Ligand Sensor 110420_015frd hl ne 12 Ligand Senor 710420 efa Alu 7 a Buffer habeas Figure 5 31 Selecting and Confirming the Biosensors to Analyze 2 Click Process Data The processed binding curves are displayed with Raw Align Y and Align windows e The processing parameters are automatically saved to the Settings_DataAnalysis ini file in the data folder The processing parameters may also be saved by clicking Save Proc Parameters These processing settings are displayed the next time the experiment is loaded The processed results Figure 5 32 include e Raw Data Binding curves with no
141. erver Administration menu 25 server location selecting 30 Set Color By Group display option 131 Set Color By display option 131 Set Color menu 134 Set Color display option 131 Set Well Data dialog box figure 50 setting concentration values figure 95 data color by category 136 setting up administrator account administrator account setting up 165 Settings_DataAnalysis ini file creating 68 Settings_DataAnalysis xml file 119 Settings_Welllnfo xml 119 Settings_Welllnfo xml file 70 shortcut menu of display options viewing 131 Show All Steps Aligned alignment option 91 Show All Traces viewing options basic kinetics analsys 85 quantitative analsys 54 Size Columns by Data display option 132 Size Columns by Title display option 131 sorting analysis results by any category 137 Audit Trail events 39 results table entries in ascending order 63 results table entries in descending order 63 specifying analysis settings 58 reference biosensors 97 Reference Wells figure 99 SSG KD kinetic analysis result 130 Stacked Fitting view option 124 standard concentration information editing 48 standard curve equation selecting 59 standard error of Rmax 129 standard error of the mass transport rate constant 130 Octet System Data Analsyis User Guide Release 7 1 page 209 standard error of the rate of association 129 standard error of the rate of dissociation 129 standards alert applying 64 standard
142. ext 132 mathematical model generates fitted view 114 Max Residual threshold value 63 measure of the goodness of curve fitting 130 menu bar Octet System Data Acquisition software 23 menu commands listed 24 method files generated 36 Octet System Data Analsyis User Guide Release 7 1 page 201 opening 76 Min Sample r2 threshold value 63 Model options 1to1114 1 to 2 Bivalent Analyte Model 114 2 to 1 HL Model 114 Mass Transport 114 Model curve fitting kinetics analysis option 114 modified parameters saving basic kinetic analysis 83 quantitative analysis 49 molar concentration of the sample used in the association step 129 multiple kinetic data sets processing 119 multiple quantitation data sets processing 67 N New Group window 179 New Project window 181 new software for 21 CFR Part 11 new feature 18 new software for ForteBio GxP Server module new feature 18 non equivalent surface capacity 115 non specific binding of sample 101 number of biosensor regeneration cycles 130 numbered order of the curves processed 129 O observed binding rate 130 Octet instrument labels 20 Octet instrument to computer connecting 22 Octet System Data Acquisition software launching 22 main toolbar 23 Octet system described 6 opening binding curve chart in a separate window kinetics 86 quantitative 56 Kinetics Batch Mode 24 online Data Acquisition User Guide 26 Quantitatio
143. fied binding model Steady state analysis Determines the affinity constant Kp from the calculated or measured equilibrium response Octet System Data Analsyis User Guide Release 7 1 page 114 Chapter 5 Basic Kinetics Analysis Curve Fitting Analysis To analyze the processed kinetic data specify the curve fitting options Steps to analyze e Curve fitting model e Type of fitting local or global to apply to the data Step time to analyze Curve Fitting Kinetics Analysis Options e Steps to Analyze Select the step s to include in the analysis association dissocia tion or both Association only Generates kops Dissociation only Generates kgis Association amp dissociation Generates kobs Kon Kadis aNd Kp Model The mathematical model that is used to generated the fitted view e 1 1 Model Fits one analyte in solution binding to one binding site on the sur face 2 1 HL Model Fits the binding of one analyte in solution to two different binding sites on the surface Kinetic parameters are calculated for two interac tions koni konz k is1 k isz Kpr Kp2 e 1 2 Bivalent Analyte Model Fits the binding of one bivalent analyte to a monomeric immobilized ligand Kinetic parameters are calculated for two inter actions kony Konv Kgist Kdis2 Kp1 Kp2 The model is available in the Analysis tab Model menu in Kinetics mode Mass Transport A Heterogeneous Ligand model that fits the bind
144. fined during acquisition or analysis as a group For each group the average binding rate average concentration and corresponding stan dard deviation CV are calculated To define replicate groups 1 Enter replicate grouping information in the Results table right click and select Edit Sample Information Figure 4 8 Octet System Data Analsyis User Guide Release 7 1 page 50 Chapter 4 Quantitative Analysis Index Include Color SensorLocation Sensor Type Sensor nfo Replicate Group BaselineLoc 2 x E SA Streptavidin 3 c3 29 x E 2 SA Streptavidin 3 c3 22 x D2 SA Streptavidin 4 D3 23 x D2 SA Streptavidin 4 D3 24 x E2 SA Streptavidin 5 E3 235 x a SA Streptavidin 5 E3 2 x E o SA Streptavidin 6 F3 2 x ae Fo SA Streptavidin 6 F3 2 x ee co SA Streptavidin 6 G3 29 x ae c2 SA Streptavidin 6 G3 3 x E SA Streptavidin 6 H3 no x He SA Streptavidin 6 H3 320 x a 3 SA Streptavidin 1 A3 Figure 4 8 Edit Sample Information NOTE Replicate Group information can also be entered in the Octet System Data Acquisition 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 In the Set Well Data dialog box see Figure 4 9 enter a name in the Replicate Group box and click OK Set Well Data Well Information Dilution Fact
145. h detailed views of an individual step by clicking inside the step boundaries The All Steps Aligned by step xx chart displays all of the assay data aligned by the step selected in the Raw Data chart Figure 5 15 Octet System Data Analsyis User Guide Release 7 1 page 90 Chapter 5 Basic Kinetics Analysis Selected biosensor Selected step 23 ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kirfetics File Help Data Selection Processing G Analysis Step 1 Data Selection Step 2 Subtraction Reference Wells Parallel Reference Sensors Double Reference Average Reference Sensors 800 1 200 1 600 2 000 2400 2 800 3 200 3600 4000 4400 4800 5 200 Time sec Step 3 1 Align Y Axis E iooni D2 Ligand s secon e uy SO 3 E Time Range sec From 02 To 04 lt m D Align by Begin Poit All Steps Aligned Align All Baselines Align by End Point All Aligned to One Step All Steps Aligned by step Equilibration Sensor Location Show Stop Dividers Export Aligned Step esv files J l Quantitate Selected Step Step 4 F Inter step Correction Align to Dissociation Align to Baseline Step 5 Process Savitzky Golay Filtering Process Data itep selected Equilibration Sensor Location Well Location 3 20 280 240 2 00 1 60 1 20 0 80 Step
146. hat 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 During user sessions the GxP Server module manages 29 and stores this recorded information Includes new screen captures of latest system desktop 22 icons and procedural text This menu now provides the following functions 25 e Verify document utility that tests if a method fmf or data frd file was created using a CFR version of the ForteBio software View Audit Trail Displays the recorded events for CFR documentation Events may be viewed by project or machine Change Project Switches active projects or run experiment without a project title none Change Password Edits password for an active user Server Administration Modifies settings for users groups projects and constants Lock Application Disables acquisition soft ware with screen lock Logoff Exits program as user Octet System Data Analsyis User Guide Release 7 1 What s New in the Octet System Data Analysis Software Release 7 0 page 19 Table 1 2 Octet System Data Analysis Software New Features for Release 7 0 Replicate Groups Replicate groups can be assigned as the sample plate is defined during experiment setup For quantitation experiments average binding rate average concentra tion and co
147. he AND operator applies to all levels Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis Results page 133 Remove Level Removes the selected search level Case Sensitive Requires that the case of all characters uppercase and lowercase of the search results match the search term Include Excluded Traces Includes all data acquisition traces within the search regardless of exclusion during analysis Treat Empty Cells as Match Returns empty cells of the column as positive matches useful for searches in which cells were inadvertently left empty during plate assignment or sample annotation Search Options Search All Specifies all text within the Analysis table as searchable regardless of the set of rows selected before activation of the Advanced Search dialog The search return is a highlighted set of rows in the table that match the search the search criteria Search all but keep current selection implies OR Specifies all text in the Analysis table as searchable regardless of the set of rows selected before open ing the Advanced Search dialog box Search only current selection implies AND Specifies the text as the set of rows selected beforeopening the Advanced Search dialog box Searching Contents of Results Table To search the contents of the Results table 1 nu FWD On the Analysis tab right click a cell in the Results table and select Advanced Search gt Edit Search U
148. i ance status Compliant or Non Compliant Figure 3 13 Octet System Data Analsyis User Guide Release 7 1 page 38 Chapter 3 21 CFR Part 11 Compliance r Verify Digital Signature Fle 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 Fie Documents ForteBio Quantitation non CFR LABUSERO90811_072 frd This file is not 21 CFR Part 11 compliant or was generated on a non 21 CFR Part 11 compliant system Figure 3 13 File Compliant top File Not Compliant bottom Viewing the Audit Trail The Audit Trail displays a historical log of user system and software events recorded during user sessions To view and display the Audit Trail click Security gt View Audit Trail Figure 3 14 i C Audit Trail eal Project Machine Date Time Project Machine Action Description 2011 02 14 13 00 53 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 18 01 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 42 07 Antigen Antibody screen JRICHARDS User logout 2011 02 14 13 42 45 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 43 30 Antigen Antibody screen JRICHARDS User logout 2011 02 14 13 44 09 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 49 09 Antigen Antibody screen JRICHARDS User login 2011 02 14 13 49 14 Antigen Antibody screen JRICHARDS Us
149. ially will be those defined in the user group selected in the previous step Table B 1 outlines the privileges for the default user groups If needed change user account privileges by selecting or deselecting the check boxes next to each privileges Administration Can administer the user database e 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 g Review Td Y Change S v Plate s v Run v x 5 Options Click the Password does not expire check box if desired By default this check box is not selected Clicking this option will let user account passwords expire at the set PasswordTTL constant For more information on setting constants see Admin istrator Constants on page 182 6 Click OK to save changes and exit Octet System Data Analsyis User Guide Release 7 1 page 176 Chapter B 21 CFR Part 11 Software Administrator Options Viewing and Changing User Account Settings To view and change user account settings 1 On the Users tab right click the user account and select Edit User or double click the user account The Edit User window displays Figure B 34 Login name 1 Full name Richard Brown Information Group Superv
150. ic kinetics experiment 76 batch analysis running 121 batch mode kinetics analysis 119 quantitation analysis 67 batch mode options kinetics 121 quantitative 70 Table Information kinetics 122 Use one for all folders kinetics 121 quantitation 70 Use the one in each folder kinetics 121 quantitative 70 Use the original data folder 70 Use this folder 70 Well Information kinetics 121 quantitation 70 batch process data sets with individual ini files 119 Binding 1 nm shift 112 Binding 2 nm shift 112 binding chart copying 113 including toolbar and data grid 109 printing 113 shortcut menu figure 113 viewing in separate window figure 108 binding curve chart opening in a separate window 56 86 binding curves after user specified reference subtraction method is used 106 after user specified Y alignment 106 assigning different colors 134 association steps aligned at the same time point 106 customizing appearance 56 86 displaying all ligand biosensors 124 from each biosensor 124 viewing basic kinetic analysis 84 quantitative analysis 53 with no reference subtraction 106 Octet System Data Analsyis User Guide Release 7 1 page 191 binding data analyzing kinetics 80 analyzing quantitative 57 binding data analyzing 80 Binding Rate Equation processing parameter 60 binding rate equations initial slope 60 R equilibrium 60 Binding Rate analyzed data 63 binding rates calculated figure
151. iments right in the Quantitation or Kinetics Folder ANALYZING DATA More than one experiment can be opened during a session If multiple quantitation experi ments are open the analysis includes the data from all of the biosensors that are selected in the Results tab NOTE When analyzing a large number of experiments batch mode may be more convenient For more details on batch analysis see Processing Batch Quantitation Analysis on page 67 Analyzing Binding Data To analyze the binding data 1 Start an analysis session and select the experiment s to use Select a standard curve equation If the sample plate does not include standards load a standards file fsc Confirm or set new values for the processing parameters wk WN Calculate the binding rate Octet System Data Analsyis User Guide Release 7 1 page 58 Chapter 4 Quantitative Analysis NOTE For information on preparing biosensors see the product insert packed with the biosensors For information on data acquisition see the Data Acquisi tion User Guide Specifying Analysis Settings To specify analysis settings 1 If the experiment includes reference biosensors click the Reference Subtraction Aver age of check box Figure 4 18 and select to average the data by one of the following All Computes the average binding curve from the reference wells and sub tracts this average from each sample curve e Row lfar
152. ing of the analyte taking into account two steps 1 transport of the analyte from the bulk solution to the surface and 2 molecular interaction of the analyte with the ligand Fitting Local If this option is selected the Octet System Data Acquisition software computes kinetic constants for each curve The constants that are calculated depend on the steps that are analyzed association only dissociation only or association and dissociation Full lf this option is selected the Octet System Data Acquisition software assumes that the off rate eventually reaches the pre association baseline and forces the curve fit to that point e Partial lf this option is selected the Octet System Data Acquisition software does not assume the dissociation will reach the pre association baseline Fitting Global Full If this option is chosen an analysis includes all of the binding curve data in the group and the Octet System Data Acquisition software generates kinetic constants for the entire group The kinetic constants that are calculated depend on the model selected Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis page 115 By Sensor Groups all data from one biosensor for example Biosensor A1 together and applies a global fit to the group By Color Groups all data that is the same color and applies a global fit to that group For more details on defining colors by sample attributes see Working
153. ion Aign to Dissociation Align to Baseline Ligand Sensor Empty Buffer IP Load We Sample Reference Well O Emply 4P kd Select Ligand Sensor s for Data Analysis Step 5 Process E Saveri Goiny Rtenng Process Data F Naber Locaton Twe ci i Ocna E 87 GII Regenerston Regeneron Bufer Ghrone pH 1 5 Step amp View Rosts Sap pee Ee faced Roane S8 O HI Regeneration Regeneration Buiter Giycine pH 1 5 Serwor Summary 9O OA O Be netics Bffer Knetics fer Roped Fotis 9 B2 Be Knees Ber Kneis Ber Step 7 Save Rests sO C2 Bie Koea ater Kirton Bie aol s oz lor ics Bier Baek Save Raw Det Ee netics Ber Kreis Der a s O F2 Biller Koela Biler Kirti Bute 35 Baffler Kinetics Buffer Kinetics Buffer 6 Kinetics Buffer Figure 5 26 Reference Wells Subtraction Method where Biosensor H1 is the Reference e Parallel Reference Sensors Corrects data for system artifacts or non specific bind ing of the sample to the biosensor surface This method requires one reference bio sensor for each ligand biosensor Octet System Data Analsyis User Guide Release 7 1 page 102 Chapter 5 Basic Kinetics Analysis ForteBio Data Analysis 7 0 Kinetics higG Prof Kinetics le 8 Seo X I7 Agn Y Ais Sep Baseine al Time Range sec From 01 To 2888 Step 4 7 htersteo Comection l Ligand Sensor
154. ion of low concentration samples 9 Click Calculate Binding Rate The standard curve and results table display Figure 4 20 Standard Curve 03 ForteBio Data Analysis 7 0 Quantitation higG ProG Q File Help Data Selection Resuts Standard Curve Equation P Group View Saale Linear Point to Point z Sie Ato Full _Refresh y lt ne Standard Fitting Curve Unknown amp Control E Use standards from loaded file an Calibrate within plate 0 360 Processing Parameters 0 220 Binding Rate Equation ae 0 240 Read Time 120 00 secs 2 0 200 Zero Conc Threshold 0 0001 BR 3 Low Conc Threshold 0 003 BR ae 0 120 0 080 Calculate Binding Rate 600 0 000 Data Epot 1 2 30 50 60 70 8 90 100 110 120 130 140 150 160 170 180 190 200 210 220 Concentration ug ml higG ProG Q Standard Sample Alerts Type Threshold Table Column Known Conc Index Known Dilution C Sample Sensor Plate Sample Type Bin X Log SSeS P 123456 7sownn 38 NA Mc ce 1 Sample Re 00 Binding Rate MaRe 10 A 000A V 3 wa Mts H 1 o Sampe Re 0 0 D G Z a w MA oO T Sa 0x Binding Rate c F 4 10 E B1 1 IgG Sta sa 0 1 Sample Alert D V 42 50 E c1 1 WG Sta sta 0 1 E T 483 25 B o D1 1 gGSta
155. isor 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 a Figure B 34 Edit User Dialog Box 2 If needed modify the user account settings For more details on individual settings see Creating a New User Account on page 174 3 Click OK to save changes and exit Deleting User Accounts To delete a user account 1 On the Users tab right click the user account and select Delete User 2 Click OK in the dialog box displayed Octet System Data Analsyis User Guide Release 7 1 Accessing Administrator Options page 177 Changing User Account Passwords To change a user account password 1 On the Users tab right click the user account and select Set Password The Change Password dialog box displays Figure B 35 Figure B 35 Change Password Dialog Box 2 Enter the New Password confirm the new password and provide a Password reminder optional 3 Click OK to save changes and exit Changing the Administrator Password To change the administrator password 1 Initiate a new administrator user session 2 When the software launches on the main menu click Security gt Change Password The Change Password window displ
156. itting view option 124 Full X2 kinetic analysis result 130 Full analysis option 114 Fuse symbol 20 G generating a report 141 graph display customizing 108 Graph Options view option 126 Graph Size in Pixels view option 126 graph customizing appearance 56 86 graphical formats 138 Group Graphs By view option 126 group settings viewing 180 Group Type analyzed data 62 Grouped View options Additional Graphs 126 Data Options 126 Graph Options 126 Graph Size in Pixels 126 Groups Graphs By 126 Legend by 126 Grouped View Options dialog box figure 126 Grouped View viewing options quantitative analysis 54 Grouped Fitting view option 124 grouping data by color 115 by sensor 115 grouping results for viewing 126 GxP Server module Octet System Data Analsyis User Guide Release 7 1 page 198 accessing 187 restarting 190 testing 189 H Heat hot symbol 20 Heterogeneous Ligand model 114 icons Data Acquisition 6 Data Analysis 6 Ignore error in files option 79 Ignore errors in files when loading viewing option basic kinetics analysis 85 quantitative analysis 54 Include Excluded Traces Advanced Search option 133 Include Wells display option 131 menu 47 Include kinetic analysis result 129 including sample in subsequent analyses 62 samples from analysis 47 Index parameter working with analyzed data quantitative analysis 62 Individual Fitting view option 124 information ana
157. ive Analysis NOTE The Octet System Data Acquisition software uses the data from the standards in all of the open experiment s to generate one standard curve Standards with the same concentration are treated as replicates Remove any standards or samples that you do not want to include in the analysis For more details on excluding samples see Excluding Including Samples from Analysis on page 47 Alternatively an experiment can be analyzed using only the standards from the same experiment plate or from a user selected experi ment 6 Optional If multiple experiments are open and you want to analyze an experiment using the standards from the same experiment plate click the Calibrate within plate check box NOTE When two quantitation datasets are opened you have the option to gt merge data across plates This happens by default if the Calibrate within plate check box is not checked Further to this replicate groups of standards will be merged and the statistics will be calculated across the entire new repli cate group BUT replicate groups of unknowns will not be merged S NOTE You can navigate between multiple experiments using the tabs above the sample plate map 7 Optional Analyze the data using standards from another experiment a Click Load Standards b In the displayed dialog box select a standard curve fsc and click Open c Click the Use standards from loaded file check box 8
158. jacent rows hold down the Shift key while you click the first and last row in the selection To select non adjacent rows hold down the Ctrl key while you click the rows of inter est The Fitting view Residual view and graphs X Y iso affinity and steady state are updated after each data selection After a kinetics analysis is completed the default Fitting and Residual views display the data for all biosensors and samples Octet System Data Analsyis User Guide Release 7 1 page 128 Chapter 5 Basic Kinetics Analysis ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics gt a File Help Curve Fitting View _ Y Axis Scaling Report Points Step to Analyze Stacked Grouped home Auto Scale Time sec 100 Add to Table Save Association Only Individual Options Refresh C Refresh Full Scale Use 20 Point Average Remove Al Load Dissociation Only Association and Dissociation ful Partial Global Full Group By Sensor Color Rmax Linked Rmax Unlinked By Sensor Compound Window of Interest From Start of Step Association O to 599 5 secs Dissociation 0 to 899 9 secs Use Entire Step Times Steady State Analysis 100 0 11 E 0 00 0 100 200 30 400 50 60 700 800 900 20 30 40 50 6 700 W 1 000 1 100 1 200 1300 1 400 Time sec Residual View
159. l view is changed based on the user selection Figure 1 9 Sensor Location B1 Sensor Type AMC Anti mlgG Fc Capture Sensor Location B1 Sensor Type AMC Anti mlgG Fe Sensor Location F1 Sensor Type AMC Anti migG Fe OED 1 E3 Traces 1 2 of 4 I4 4 P Pl Number Rows 2 E Number Columns n M Show Results V Show Residual Figure 1 9 Individual View Modified 2E3 3E3 453 6 An Apply All option has been added for the Group View graph To access this option on the Group View right click a graph and select Graph Options Figure 1 10 gt Apply All check box Copy To Clipboard gt at Graphic Options a Save to File Zoom In Title Show Font Sie 14 i Graph Options ca X Axis V Labels V Titles From 0 To 119 8 Y Axis V Labels V Titles 7 Auto Scale From 0 To 6 477 Axis Font Size Title 32 Label 32 Legends V Show Font Size 12 S V Grid Lines V Step Dividers apes Figure 1 10 Graph Options Octet System Data Analsyis User Guide Release 7 1 What s New in the Octet System Data Analysis Software Release 7 1 page 11 7 New sensor types have been added to the existing sensor type pull down list To access the new sensor types a Right click the sensor or sample information or result table and select Edit Sample Informati
160. lculated or measured equilibrium response View the results in graphical and tabular formats 4 Export the results and generate a report Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 81 Editing Experiments The Octet System Data Acquisition software enables you to change sample designations standard concentrations or exclude samples from analysis For example you can exclude a standard that does not meet the sample r or residual threshold then re analyze the data You can also modify some processing parameters Changing Sample Designations To change sample designations 1 Click the Data Selection tab then do either of the following Inthe sample plate map select the well s right click and select an option from the shortcut menu Inthe results table right click a table cell in the Well Type column then make a selection from the drop down menu Ean C Romence Suttnacton avenga C hyre anons in as when ling 10 See fi Shom A Taer E an C Relmerce Suthacton Average oi C gnane emors in fies whan loading 1 0 See Show Al Tasos i Brcieg Curve Gigh 10 600 so 40 E 200 200 100 aw Tma sec Select samples trom the tabbo os Plate below to display the date 2 3 4 6 I 8 3 WWW ma Sope Some ap Core wat fiwe A 00000900000 a uauseRaik 0000000000 sent 0000000000 0000000000 0000000000 0000000000 0000000000 m UUBUSERIZ LABUSERIZ
161. lt defined 132 search term for a single level 132 search editing a 134 searching contents of the Results table 133 Security menu 25 Security menu commands listed 25 Select All Rows display option 132 selecting adjacent rows for viewing data 127 analysis results for viewing in the Fitting view and Residual view figure 128 biosensors 97 biosensors for analysis figure 80 biosensors for the analysis 79 biosensors in the Processing window figure 97 biosensors to be analyzed figure 106 contiguous and discontiguous biosensors in the Sensor location list figure 91 experiments and run the batch analysis 121 experiments and running the batch analysis 70 experiments for batch analysis figure 71 non adjacent rows or wells kinetics analysis 84 quantitative analysis 53 non adjacent rows for viewing data 127 sample wells or rows to display in the binding curve graph basic kinetic analysis figure 84 quantitative analysis figure 53 server location 30 standard curve equation 59 Sensor Info kinetic analysis result 129 Sensor Location kinetic analysis result 129 sensor summaries figure 145 Sensor Summary view defined 109 displayed figure 110 Octet System Data Analsyis User Guide Release 7 1 page 208 features 109 sensor tray map copying 97 using 97 Sensor Tray tab 79 Sensor Type analyzed data 62 kinetic analysis result 129 sensor analyzed data 62 Sensors to be Analyzed box 99 S
162. lysis tab right click any cell in the Results table and select Advanced Search gt Edit Search 2 Select a saved search from the Saved Searches list 3 Click Load Search The parameters for the specified search are restored 4 Edit the search see steps 2 9 in Searching Contents of Results Table on page 133 The search can be saved by specifying a new name under Search Name and clicking Save The name of the saved search will appear in the Saved Searches list 5 Click OK to execute the search Rows that contain cells meeting the search criteria will be highlighted Color Coding Data You can assign different colors to the binding curves as a follows A particular color to user selected results This is useful when grouping for a global fit e Color according to a results category Color Coding User Selected Results To color code user selected results 1 Select one or more rows in the analysis table click the row header 2 Right click and select Set Color Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis Results page 135 4 3 ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics lola X File Help O Data Selection B Processing Analysis Curve Fitting View Y Axis Scaling Report Points Step to Anaize Sacked Grouped amon Ato Seale Tre ec 100 Association Only Individual Optons Refresh Refresh FulScae Use 20
163. lyzed bio sensors For more details on graph options see Working with Graphs on page 138 Octet System Data Analsyis User Guide Release 7 1 page 124 Chapter 5 Basic Kinetics Analysis Y Axis Scaling Report Points Stacked Grouped iia Auto Scale Time sec 100 _Addto Table _ Save individua Options Refresh Refresh Full Scale Use 20 Point Average Remove Al Load Fitting View i 100 200 300 400 500 600 700 800 900 1 000 1 100 1 200 1 300 1 400 Time sec Time sec Figure 5 46 Fitting View and Residual View Stacked Option NOTE In Figure 5 46 a local full fitting analysis was applied to the data For detailed information on graph display options see Step 6 Viewing Results on page 107 Fitting view options Stacked Displays the binding curves of all ligand biosensors in one graph Figure 5 46 Individual Displays the binding curve from each biosensor in a separate graph Figure 5 47 Grouped Displays graphs organized into groups according to sample attribute or results category This is a highly useful feature when working with large data sets e Options Click to display the Grouped View Options dialog box e Refresh Updates the graph display Y Axis Scaling e Auto Scale Scales the y axis to the data in each graph Full Scale Scales the y axis to in all graphs to the range needed to
164. lyzed data 62 Initial Slope equation 60 Input times after beginning of Association Step 111 installing Data Acquisition 7 0 21 CFR Part 11 software 156 Data Analysis 21 7 0 CFR Part 11 software 159 ForteBio GxP Server 162 ForteBio GxP Server module 162 interstep correction features Align to Baseline 105 Align to Dissociation 105 Invert Selection display option 132 Iso Affinity graph described 139 X and Y axis figure 139 K KD M kinetic analysis result 129 kdis 1 s kinetic analysis result 129 kdis Error kinetic analysis result 129 130 Octet System Data Analsyis User Guide Release 7 1 page 199 kinetic analysis results Assoc Sample Loc 129 Baseline Loc 129 Color 129 Conc nM 129 Cycle 130 Dissoc Loc 129 Full R2 130 Full X2 130 Include 129 Index parameter working with analyzed data kinetics analysis 129 KD M 129 kdis 1 s 129 kdis Error 129 130 km 130 km error 130 kobs 1 s 130 kon 1 Ms 129 kon Error 129 Loading Well Location 130 Report point 1 10 130 Req Rmax 130 Response 129 Rmax 129 Rmax Error 129 Sample ID 129 Sensor Info 129 Sensor Location 129 Sensor Type 129 SSG KD 130 table listed 129 kinetic analysis types Curve fitting 113 Steady state analysis 113 kinetic assay displaying selected step figure 93 kinetic constants 80 kinetic data analyzing 114 processing 96 kinetic Settings_DataAnalysis ini file creating
165. ment option 91 Align to Baseline interstep correction feature 105 Align to Dissociation interstep correction feature 105 Align X viewing option basic kinetics analysis 85 quantitative analysis 54 aligning Octet System Data Analsyis User Guide Release 7 1 page 188 the Y axis figure 105 to association 104 alignment options Align All Baselines 91 Align by Begin Point 91 Align by End Point 91 All Aligned to One Step 91 Show All Steps Aligned 91 All Aligned to One Step alignment option 91 analysis excluding samples 47 including samples 47 options listed 146 Analysis results table figure 117 Analysis results table display options Advanced Search 131 Exclude Wells 131 Include Wells 131 Invert Selection 132 listed 131 Order Columns 132 Select All Rows 132 Set Color 131 Set Color By 131 Set Color By Group 131 Size Columns by Data 132 Size Columns by Title 131 Analysis Results table shortcut menu figure 131 analysis results sorting by any category 137 analysis settings saving 66 specifying 58 Analysis window figure 115 Analysis window with sample curve fitting results figure 123 Analyze Data button 71 analyzed data Binding Rate 63 BR AVG 62 BRCV 62 BR SD 62 Calc Conc 63 Concentration avg 62 Concentration CV 62 Concentration SD 62 dilution factor 62 flip 62 Group Type 62 information 62 kinetics analysis Index parameter 129 Octet System Data Analsyis User Guide
166. minister the user database e 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 4 Click OK to save changes and exit Octet System Data Analsyis User Guide Release 7 1 page 180 Chapter B 21 CFR Part 11 Software Administrator Options Viewing and Changing Group Settings To view and change group settings 1 Right click on the group and select Edit Group or double click the group The Edit Group window displays Figure B 39 Group name Developer Information Developers can create run save and export data Privileges Administration administers the user database _ Review reviews changes and events W Change can change methods and configuration values Plate can change sample plate properties Run can run experiments and analyses Figure B 39 Edit Group Dialog Box 2 If needed modify the group settings For more details on individual settings see Cre ating a New User Group on page 179 3 Click OK to save changes and exit Deleting a User Group To delete a user group 1 Right click the group and select Delete Group 2 Click OK in the dialog box displayed Octet System Data Analsyis User Guide Release 7 1 Accessing Administrator Options page 181 Project Administration The Projects tab Figure B 40 allows a
167. module on the network that can then be accessed by all users 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 10 i33 ForteBio GxP Server 7 0 Setup CSS es Welcome to the ForteBio GxP Server 7 0 Setup Wizard This wizard will quide you through the installation of ForteBio GxP Server 7 0 It is 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 10 ForteBio GxP Server 7 0 Software Setup Wizard Octet System Data Analsyis User Guide Release 7 1 Installing the ForteBio GxP Server Module page 163 4 Click Next to display the Choose Install Location dialog box Figure B 11 5 3 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 CF
168. mpliance OCTET SYSTEM 7 0 21 CFR PART 11 SOFTWARE OVERVIEW 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 11 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 compli ance features and administrative functions specific to the 21 CFR Part 11 versions of the Data Acquisition and Data Analysis software NOTE The 7 0 21 CFR Part 11 Data Analysis software only opens data files generated in CFR data acquisition 7 0 21 CFR Part 11 files from software ver sion 6 X are fully compatible with the 7 X 21 CFR Part 11 software NOTE For details on how to install the Octet System Data Acquisition or Data Analysis software see Appendix B 21 CFR Part 11 Software Administrator Options on page 155 Octet System Data Analsyis User Guide Release 7 1 ForteBio GxP Server Module page 29 FORTEBIO GXP SERVER MODULE When the Data Acquisition or Data Analysis 7 0 21 CFR Part 11 software is launched users are prompted to logon to the ForteBio GxP Server module This initiates a user session where all system software
169. n 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 e 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 command or response is terminated with a new line CR LF sequence Parameters containing embedded spaces need to be enclosed in double quotes Octet System Data Analsyis User Guide Release 7 1 Design of the Automation Interface page 151 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 and select the appropriate port in the Automation box Figure A 1 NOTE The Octet System Data Acquisition software can be controlled via the Automation interface through a serial port RS 232 or a TCP
170. n Batch Mode 24 web browser 26 Operator Advanced Search option 132 Options menu 24 options for viewing results 107 Options Fitting view option 124 Octet System Data Analsyis User Guide Release 7 1 page 202 Order Columns display option 132 editing 48 83 editing in the Results window figure 49 P Parallel Reference Sensors reference subtraction method figure 102 described 101 Partial analysis option 114 plate number 62 preparing samples for quantitation or kinetics experiments 6 printing binding chart 113 Process Data button 106 processed data in the sensor summary view figure 110 saving 112 processing data 106 kinetic data 96 options listed 143 processing parameters basic kinetics Low concentration threshold 83 Read time 83 Zero concentration threshold 83 Quantitative Analysis Low concentration threshold 48 Read time 48 Zero concentration threshold 48 Processing window described 96 Raw Data view selected figure 89 Raw Data view displaying data from a single selected biosensor figure 90 Raw Data view quantitating a selected step figure 92 project administration 181 project settings changing 182 viewing 182 projects changing during a user session 40 creating new 181 deleting 182 Projects tab 181 properties for Octet System software displaying 26 Octet System Data Analsyis User Guide Release 7 1 page 203 Q Quantatition Batch Mode opening 24 Quantitat
171. n be followed by required and optional parameters Bach parameter starts with a switch definition a la dos unix com mand line followed by the ii parameter itself This allows parameters to 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 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 WAED Parameter switches for the LOAD command const char AUT_SWITCH_DATASET d Parameter switches for the ANALYZE command const char AUT_SWITCH_PARAMS pty 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 Octet System Data Analsyis User Guide Release 7 1 Design of the Automation Interface page 153 Response App product version e g const char AUT_CMD_LOAD Load 6 3elis12 LONEN
172. nalsyis User Guide Release 7 1 Generating a Report page 143 K ForteBic Data Analysis 7 0 Kinetics higG Pro amp Kinetics so z File Help O Dets Selection LE Processing Anshaa J Al Losses Data Summary higG ProA Kinetics Sensor Tray i 1 16 Sensors trom Mt E nui IK ProAhigS C Users wms Documents User Guides 7 nigG ProA Kinetics fa I biG Prod Knetcs ExpDescripton Unassigned GW Quertexen E T ONENESS E a71 aga Time 4211 2011 5 14 11 PM E 2201 38s O IMachineName RED ALPHA S L UserName labuser PisteName 110420 PimieName2 Unassigned Type OctetREDS6 190420_001 frg At 190420_002 fre B1 190420_003 re C1 190420_004 fra 01 190420_005 Md Et e 190420_008 tre F1 oo i f g F i f SUITOR ESET S BE Desktop piii Nimernkzabon HH Steps data table Assay steps data table Figure 5 62 Report Data Types Experiment Summary Options Processing Options To use the available processing options select the following from the Processing window tab e Raw and aligned data e Sensor tray image e Sample plate image e Processed results Sensor summary Sensor tray data table e Sample plate data table Report points NOTE When working with large data sets including the sensor summary in a report significantly increases the time required to generate the report Octet System Data Analsyis User Guide Release 7 1 page 14
173. nalsyis User Guide Release 7 1 page 217 Octet System Data Analsyis User Guide Release 7 1 page 218 Octet System Data Analsyis User Guide Release 7 1 page 219 Octet System Data Analsyis User Guide Release 7 1 page 220 Octet System Data Analsyis User Guide Release 7 1 page 221 Octet System Data Analsyis User Guide Release 7 1 page 222 Chapter 1 Octet System Data Analsyis User Guide Release 7 1
174. nding Graphs Displayed Based on Sensor Type 3 For Quantitation analysis user enterable time for the Beginning Time for Linear Fit ting displays in seconds Figure 1 4 Beginning Time er for Linear Fitting SE Calculate Binding Rate Figure 1 4 Beginning Time for Linear Fitting 4 For Kinetics analysis the Align Y Axis to Association time range is available from 0 0 to 0 0 Figure 1 5 an Step Association v Time Range sec From 0 0 To o o Figure 1 5 Beginning Time for Linear Fitting 5 On the Kinetics Analysis tab 3 there is a new GUI for the individual view Figure 1 6 a The user can edit the display of individual view at the bottom of individual view graph Octet System Data Analsyis User Guide Release 7 1 What s New in the Octet System Data Analysis Software Release 7 1 page 9 Y Axis Scaling Report Points w Stacked O Group Auto Scale Time sec 100 Add to Table Always Individual Options Refresh Refresh Full Scale Use 20 Point Average Sensor Location B2 Sensor Type AMC Anti mlgG Fc Capture Baseline Loc B8 Assoc Sample Loc B10 Sample ID Fab Dissoc Loc B12 Conc nM 200 Respe Sensor Location B2 a Sensor Type AMC Anti migG 06 Baseline Loc B8 1 Assoc Sample Loc B10 oF Sample ID Fab 08 Dissoc Loc B12 02 Conc nM 200 06 Response 1 158 o KD M 3 961E 09 pi kon 1 Ms 2 333E04 kon Error 7 831 E01 kdis 1 s 9 2
175. nge Password Change Project Server Administration Lock Application Log Off Figure 3 9 Security Menu Octet System Data Analysis Software NOTES The Server Administration 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 Octet System Data Analsyis User Guide Release 7 1 page 36 Chapter 3 21 CFR Part 11 Compliance 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 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 cannot be opened and a message indicating this will be presented 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 displays Figure 3 10 Verify Digital Signature i Figure 3 10 Verify Digital Signature 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 Dat
176. nsor SA Streptavidin 110420_020 rd Ligand Sensor 110420_021 frd F3 Ligand Sensor SA Streptavidin 110420_022 rd G3_ Ligand Sensor SA Streptavidin 110420_023frd H3 Ligand Sensor SA Streptavidin 110420_024frd ae ee T T Buffer Buffer Kinetics Buffer 1X Kinetics D1 Buffer Kinetics Buffer 1X Kinetics Buffer Buffer Kinetics Buffer 1X Kinetics Kinetics Buffer 1X Kinetics wl lt m r E I S Sisla p Figure 5 23 Changing the Biosensor Type NOTE The biosensor designations can also be edited in the sensor tray table Figure 5 22 on page 97 3 Specify reference wells a In the sample plate map select the appropriate wells b Right click and select Change Well Type gt Reference Well Figure 5 24 Octet System Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 99 3 ForteBio Data Analysis 7 0 Kinetics hIgG ProA Kinetics qa File Help Data Selection Processing Analysis E E jj Step 1 Data Selection Sensor Tray 1 Sample Plate Map 110420 Raw Data View a TT E E E E a N E S E E Sensor Selection oy g ie ABBR 0000000 ACHOEEROO0CEO Al 3 HBE OOO s Omm mOOCOnS ci i a _ BEE OOO co MMM OOOnd E1
177. o Original Data Edit Sensor Sample Information Figure 5 41 Excluding Wells from the Biosensor Table 2 Click Fit Curves The analysis results are displayed data from wells marked for exclusion will not be included Figure 5 42 Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis page 117 Index Include Response Conc nM Dissoc Loc Color Assoc Sample Loc Cycle Sensor Location Sensor Type 0 x 24616 6 amp 7 A E 1 Al SA Streptavidi 1 x 24659 6 amp 7 AB B 2 Al SA Streptavidi 2 x 2019 33 B3 E 1 B1 SA Streptavidi 3 x 20537 33 B3 E 2 B1 SA Streptavidi 4 x 16631 167 c3 E 1 ci SA Streptavidi 5 x 16554 167 03 ec 2 cI SA Streptavidi 6 x 1052 83 D3 E o 1 D1 SA Streptavidi 7 x 10278 83 D3 E p 2 D1 SA Streptavidi 8 x 11019 417 E E 1 El SA Streptavidi 9 x 1092 417 E3 E 2 El SA Streptavidi 1 x 26095 6 amp 7 Ag 1 A SA Streptavidi 1 x 26293667 AB es 2 A2 SA Streptavid 2 x 22646 B3 B3 E 1 B2 SA Streptavidi B x 22893 B3 B3 ys 2 B2 SA Streptavidi x 17631 167 03 c5 1 C2 SA Streptavidi v j i Figure 5 42 Analysis Results Table 3 Save the settings in the Analysis window click Save Data Analysis Parameters Figure 5 43 A Settings_DataAnalysis ini file is saved in the experiment folder These settings are displayed the next time the experiment is loaded NOTE The Settings_DataAnalysis ini file is also automatically saved when
178. oints Step 7 Save Results Save Processed Data Save Raw Data Save Proc Parameters Figure 5 30 Aligning the Y Axis NOTE The time window should be minimized to the beginning of the associa tion The data within this window is set to an average of zero and cannot be included in the final curve fit Step 4 Interstep Correction The interstep correction feature corrects misalignment between two steps due to system artifacts The association step can be aligned to the dissociation step or to the baseline IMPORTANT For the most effective interstep correction the baseline and dis sociation steps of an assay cycle must be performed in the same microplate well e Align to Dissociation Moves the association step on the Y axis to align the end of the association step with the beginning of the adjacent dissociation step e Align to Baseline Moves the association step on the Y axis to align the beginning of the association step with the end of the adjacent baseline step NOTE Interstep correction is not recommended for very fast kinetics because some kinetic information may be lost Octet System Data Analsyis User Guide Release 7 1 page 106 Chapter 5 Basic Kinetics Analysis Step 5 Process Savitzky Golay filtering removes high frequency noise from the data Its use is optional but is recommended unless the data being analyzed has less than 20 data points in a step To process the data
179. on Precessna EJ Anata Step 1 Osta Selection Raw Data View 7 7 Senor Section Senacen to be Analyzed A A AMF lef 2v2 z BIFIF22 3 B B CLF IFN al Oi iF2v2 ElFloFay2 c c AQF LEI z Step 2 7 Subtraction D D Reference Wels Paralel Reference Sensors E E Double Reterenice Average Reference Sensors F F Step 3 Z Apn Y Ais G G Sop Baseine z Tne Range ec H H Fom 01 To 2998 Stop amp 7 kterstep Corecton Monte i bi Ligand Sensor Reference Sensor Empty Buffer IP Load Sample Empty P Regeneration POF Saine k Select Ligand Sensor s for Data Analysis Step 5 Process F Seve Golsy Fema Process Data o 8 FS 7 1X Kinetics Buller Shap 6 Vow Ronite 3 G Bfer Aescciaton 1X Kinetics Buffer Processed Resuts Sensor S mmay 4 HS Bier Associeton 1X Kinetics Buffer Report Ports 4 AS Sample Association Kinetics Butler b Step 7 Save Reeuts 2 BS Sample Asocion Kinetics Buffer 3 Save Processed Data 4 ce Semple Associetion Kinencs Buffer 1 Save Raw Data D6 Sample Aascuation Kinetics Buller 8 Gene Bec Famnsten a 45 EE Sample Association Kinetics Buffer 4 4 fe Buffer Associston Kinetics Buffer 47 G Buller Aesodston Kretos Buller AR HB Piser Assertion Kineties P finr be m Figure 5 29 Average Reference Sensors Subtraction Method NOTE In Figure 5 29 AB1 A1 A2 A3 A4 4 Target biosensor B1 corrected for sample medium interference by the av
180. on Figure 1 11 Sample C Sample Type Binding 1 A3 N A Unk A3 Include Selected Rows B3 Exclude Selected Rows B3 B3 Set Color c3 Set Color By Group c3 Set Color By gt D3 Size Columns by Title D3 Size Columns by Data E3 Size Columns by Both E3 Select All Rows E3 F3 Invert Selection F3 Order Columns Edit Sample Information p ea Parallel Sorting Figure 1 11 Edit Sample Information Menu b On the Edit Sample Information dialog box click the Sensor Type drop down menu and select Add a Sensor Type Figure 1 12 a Edit Sample Information Figure 1 12 Edit Sample Information Dialog Box Octet System Data Analsyis User Guide Release 7 1 page 12 Chapter 1 welcome c On the Add a Sensor Type dialog box that displays in the Sensor Type field enter a sensor type and click OK Figure 1 13 all Add a Sensor Type Sensor Type NTA hokan Genoa Figure 1 13 Add a Sensor Type Dialog Box d On the Edit Sample Information dialog box Figure 1 12 click the Sensor Type drop down menu again to display the newly added sensor type NTA Figure 1 14 r a Edit Sampie Information T Sample ID N A Sensor Type Anti Human IgG Fe Well Type Anti Mouse IgG Fv Anti Penta HIS Concentration Protein A Protein G Replicate Group Protein L Residual Protein A Diluti
181. on Factor SA Streptavidin Custom Sensor Information Add a Sensor Type Figure 1 14 Displaying the Newly Added Sensor Type NTA Octet System Data Analsyis User Guide Release 7 1 What s New in the Octet System Data Analysis Software Release 7 1 page 13 8 Parallel sorting on the result table is now supported To perform this function a Right click the result table and select Parallel Sorting Figure 1 15 Plate C Sensor Sample Sample Type Da 01 i B4 Include Selected Rows u B ci Exclude Selected Rows 01 D4 o E4 Set Color u Ear Set Color By Group u E c Set Color By u E 01 A5 Size Columns by Title 01 B5 Size Columns by Data o B ci l 1 E Size Columns by Both u E s Select All Rows si fa Invert Selection 01 Eg H5 Order Columns 0 AB Edit Sample Information u ee u B c Parallel Sorting S a m Figure 1 15 Parallel Sorting Menu b On the Parallel Sorting dialog box that displays configure the sorting parameters for the desired results and click OK Figure 1 16 a Parallel Sorting Column Name Order by Sensor Type M Then by Index X Figure 1 16 Parallel Sorting Dialog Box The result table is re sorted based on the configured sorting parameters 9 A Cycle column has been added on the result table for Multiple Analyte data sets Figure 1 17 Octet System Dat
182. ons e Right click the graph and select Toolbar Toolbar buttons enable you to save copy or print the graph 3 ForteBiio Data Analysis 7 0 Quantitation higG Prost Kinetics lo ow Fie Help A Oses Saiecton gt Renel S osd na NIG ProA Krane 16 Sensors from 1 Kinetics nme E 04 27 11 384 K PreANGG ARX Reference Samaan enn F Ap Daa Show AbTaces C Omp Vew Iratrumert Type OctetREDS pat 7 aa 3 d J iyon ero r ties when loosing Legends Bendang Curve Graph 300 2 2a 210 1 80 Eis a 120 omw 06 on ow 0 y HH 5w w 20 w 27 W W MW W 4H so w T w Tome sec P Select samples trom the table or Plate below to display the data W Binding Curve Graph oe aa Was Be BUa Banding Curve Grech 300 2 GJ 3w ww w n wW m w w v v v s w M w Time sec Figure 5 11 Viewing Binding Curves Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 87 Closing Experiments To close an experiment in the Loaded Data directory tree right click the experiment name and select Remove Run see left side of Figure 5 12 To close all experiments in the Kinetics or Quantitation folder right click the folder and select Remove All see right side of Figure 5 12 i ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics f hoe File Help O Data Selection Processing
183. or nd g Ta a a a 000 ae Ato E 0 00 Window of Interest From Start of Step o 300 0 aT 1 200 o 300 a eae 1 200 Sensor Location Al Sensor Type SA Streptavidin Sensor Info Replicate Group 1 KD M 4 811E 10 kon 1 Ms 1 365E05 kdis 1 s 6 566E 05 kobs 1 s 9 168E 02 a 5 a a a Sensor Location B1 Sensor Type SA Streptavidin Sensor Info Replicate Group 2 KD M 4811E 10 kon 1 Ms 1 365E05 kdis 1 s 6 566E 05 kobs 1 5 4 610 02 Dissociation 0 to 899 9 secs Fit Curves o 300 600 300 1 200 o 300 600 300 1 200 Time sec Time sec A Conc nM Dissoc Loc Color Assoc Sample Loc Cycle XY Graph Iso Affinity Steady State 1 x dete EI too Y Repone B3 1 Index Response B3 2 d c3 1 c3 2 r gm D3 1 D3 2 a sa E3 1 E3 2 1 o e sees 2 o 20 Index Processed binding data and fitted curves Residual curves Figure 5 47 Fitting View and Residual View Individual Option NOTE The data for all biosensors and samples is displayed Octet System Data Analsyis User Guide Release 7 1 page 126 Chapter 5 Basic Kinetics Analysis Grouping Results for Viewing To group results for viewing 1 Select the Grouped option and click Options to display the Grouped View Options dia log box Figure 5 48 all Grouped View
184. or Unknown only Sample ID By value 2 Dilution series Replicate Group Starting value 1 1 Series operator v Well Information 1X Kinetics Buffer Series operand 2 Dilution orientation 888 C Right 883 Left 8 Down 8 Up k Figure 4 9 Set Well Data Dialog Box Add Replicate Group from the Sample Plate Map Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 51 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 NOTE When performing a Multiple Analyte experiment in Data Acquisition if the same Replicate Group name is used with different biosensor types they will be treated as separate 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 4 10 Sample Plate 96 wells OOSOOOOOOOOS Figure 4 10 Replicate Groups Displayed in Sample Plate Map The Sample Plate Table update
185. or Options i Change Passwor i The password has not been set for this user New password eeccccccce Confirm new password eeccccccce Password reminder Default Figure B 22 Change Password Dialog Box 6 Enter a New password and Password reminder optional and click OK The Octet System Data Acquisition or Data Analysis software launches and initiates an administrator user session that will allow access to administration options Octet System Data Analsyis User Guide Release 7 1 Starting an Administrator User Session page 169 STARTING AN ADMINISTRATOR USER SESSION Administrators initiate new user sessions the same way non administrative users do 1 Launch the Octet System Data Acquisition or Data Analysis software by double clicking the respective desktop icon see Figure B 23 Data Data Analysis Acquisition 7 0 CFR11 7 0 CFR11 Figure B 23 Data Acquisition or Data Analysis Software Desktop Icons The Login dialog box displays see Figure B 24 Losin fort sio Server localhost 20002 User Password Project Figure B 24 Login Dialog Box 2 Confirm that the Server location is correct If not see Administrator Account Setup on page 165 3 Select Administrator from the User drop down list Figure B 25 Octet System Data Analsyis User Guide Release 7 1 page 170 Chapter B 21 CFR Part 11 Software Administrator Options A
186. owincludes both samples and references the Octet System Data Acquisition software computes the average reference curve for the row and sub tracts this curve from the samples in the same row e Column lf a column includes both samples and references the Octet System Data Acquisition software computes the average reference curve for the column and subtracts this curve from the samples in the same column File Help By On off rate _HIGH teing wth Oke beta D Querttstin E 080410 High SernstrvtyG ProA HigG 250 100 50 25 10 5 By Randri Q assay 0 10 E ProtA_HighSens_OpSH_5A_091803 yevaed E a e IIIT I I BOGOCCOCOOCOOO ROSEI H0000 Binding Curve Graph D Osta Selecton TEY Rests Loaded Data Pret _HighSens_OpGH_SA_031803 revised O Kreas MET Ralerence Subtrcton Average d pT SI a Gy 0805101 SA Joad aredig bind Pret 7 iyon enor in les when loading hatnmert Type Octet RED Ea 19 s Sow M Traces _ Legends 10 1 i ooo 0 2 0 100 120 wo 160 Time sec 180 x0 c1 or g Select samples from the table or Plate below to display the data ft Sensor Sample Sarge ID 0 1019 0 03256 0 0108 0 003323 0 003323 0 0108 Gop P0001006 rd PO0O1_0O7 Ind O01 008 ind POO 008 rd P0001010 P0001 011 Ars P0001012 P0001 0131r P0001 O14 tnd P0001 0151r P0001 O16 rd Fie Name Figure 4 18 Reference Subtraction Averag
187. owns amp Controls Load Standards Save Standards 5 Use standards from loaded file v Calibrate within plate Processing Parameters Binding Rate Equation L Initial Slope v Read Time L sers Zero Conc Threshold 0 001 Low Conc Threshold ood Cet Copy Paste p Delete 1 000 1 200 Calculate Binding Ratel Concentration pg ml an Data Export LE isic quantitation data Prot sensor AdvQ_online1 st_regen l SDA Save Report Show Table Column Known Conce Plate Sensor Sample SamplelD Group Binding Rate Known Conc pg ml 4 v Ag Ag Unknown 1 25982 v B9 B9 Unknown 1 29901 A Standard Sample Alerts A 5 o o Unknown 1 25149 ype Threshold B v pg D9 Unknown 1 25400 O M Mois s Unknown 1 20833 ienesa Bis R irom a O eanNintsraMerRenaal D cae H Dion 7 H9 H9 Unknown 1 22959 E 7 A0 A0 Unknown 1 25482 F v B10 B10 Unknown 1 27917 Save Analysis Settings 7 cio cto Unknown 1 26345 COOOOSOOOOOODOOD a iow ov Urkon 125091 H 0 0000000 2 Slee Figure 4 7 Editing Processing Parameters in the Results Window Defining Replicate Groups The Replicate Group feature enables data to be organized into custom groups during anal ysis see Figure 4 8 Replicates can be de
188. page 98 Chapter 5 Basic Kinetics Analysis I ForteBio Data Analysis 7 0 Kinetics higG ProA Kinetics File Help O Data Selection 2 Processing Analysis Step 1 Data Selection Raw Data View 7 Sensor Selection A Sensors to be Analyzed Al B1 110420 11 12 ws c1 D1 4 E1 Fl Step 2 E Subtraction Reference Wells Parallel Reference Sensors Double Reference Average Reference Sensors Step 3 V Align Y Axis Range sec 0 2 To 04 E Edit Sensor Properties Copy To Clipboard aaa a ggg 868460008 rOn moO UW HE Step 4 F Inter step Correction Align to Dissociation Align to Baseline Step 5 Process Savitzky Golay Filtering Process Data kl Ligand Sensor Empty Buffer M Load Sample Reference Well Empty Step 6 View Results Processed Results Sensor Summary Well Well Sensor Sensor Report Points Number Location Type Info B3__ Ligand Sensor SA Streptavidin 110420018 fd E 1 Al Buffer Kinetics Buffer 1X Kinetics Sensor File Name gig Sse pps we Save Descript Step 7 Save Results Save Processed Data Save Prec Pamens fi PU C3 Ligand Sensor SA Streptavidin 110420_019frd Kinetics Buffer 1X Kinetics D3 _ Ligand Se
189. pboard menu 97 copying binding chart 113 sample plate map 97 sensor tray map 97 creating kinetic Settings_DataAnalysis ini file 119 kinetic Settings_Tablelnfo xml file 120 kinetic Settings_Welllnfo xml file 120 new constant 184 new project 181 new user account 174 new user group 179 Settings_DataAnalysis ini file 68 curve display customizing 108 curve fitting analysis 80 curve fitting kinetics analysis options Fitting Global Full 114 Fitting Local 114 Steps to Analyze 114 Curve fitting kinetic analysis type 113 custom reports 140 customizing binding curve appearance 56 86 curve display 108 graph appearance 56 86 graph display 108 Cycle kinetic analysis result 130 D data excluding from analysis 116 exporting 71 Data Acquisition User Guide opening online version 26 Data Acquisition icon 6 data analysis session using 44 76 Data Analysis User Guide menu 26 Data Analysis icon 6 data color setting by category 136 data export options Copy Table to Clipboard 141 Octet System Data Analsyis User Guide Release 7 1 page 194 described 140 Export Fitting Results 141 Export Table to csv File 141 in the Analysis window figure 140 listed 141 Data Options view option 126 data processing 106 applying reference subtraction 99 reference subtraction methods 100 Data Selection tab 48 Data Selection tab figure 44 Data Selection window displaying experiment summary information figure 78 edi
190. pe Size gt J DataAcquisition7 3 FBServer exe 12 3 2010 3 53 PM Application 2 966 KB gt DataAnalysis7 FBServerConfig exe 12 3 2010 3 53 PM Application 7 821 KB JL FBServer7 3 FBServerMonitor exe 12 3 2010 3 54PM Application 6 909 KB fat ForteBio 2 10 2011 6 20 PM Internet Shortcut 1KB e Globe ico 12 1 2010 4 21 PM Icon 25 KB 6 uninst exe 2 10 2011 6 20 PM Application 54 KB ma Figure B 49 ForteBio GxP Server Module Installed on a Network Location Ifthe GxP Server module is installed on a local host computer Double click the ForteBio GxP Server desktop icon Figure B 50 ForteBio GxP Server Figure B 50 ForteBio GxP Server Desktop Icon The ForteBio GxP Server Configuration window displays Figure B 51 Octet System Data Analsyis User Guide Release 7 1 page 188 Chapter B 21 CFR Part 11 Software Administrator Options Connection to clients Localhost Port 20002 Support UDP ping for discovery Default onfiguration 7 0 0 1 Users Groups Projects Constants Events PSmith JBlack RBrown Login Name Full Name Administrator Administrator Paul Smith John Black Group Privileges Password Age Info Administrator admin review change plate 4 days 00 47 57 Default administrator user Lab User run 2 days 02 45 25 Developer change plate run 1 day 04 34 45 Richard Brown Supervisor review 2 days 01 43 06 Figure
191. play features Octet System Data Analsyis User Guide Release 7 1 Save Repos cor Tae Kinetics Analysis Results page 127 IF ForteBio Data Analysis 7 0 Kinetics higG Prod Kinetics Lo ad File Help 7 Data Selection Feats View Y Ave Scaling Repos Poires i tb PE Racked Coed pem Ato Scale Time gec 100 Addo Tobie Sawe Associaton Oriy h m s Options Reesh Reiesh Full Seale Ure 20 Pont Average _ Remove Al Losd Dissociston Only Assacimon and Cisssciaton Come nM 167 Model i Fena Graph leg ne end speci ra Ponsi fied in the O atana i d Group By Rmax Linked Legen Sensor Rmax Unlinked By n amp as by op OOF l D Copan tions setin Window of interest From Stat of Step the Association 0 lo S995 secs Grouped Dusociston 0 to 899 secs View Op Use Entre Step Temes i tions dialog 001200 box Fa Curved Time sec Steady Rate Ansiyus Requibeurn Response X ide E tog Y Responsa Heme fone e e E aa m a Index Response o o L a Data Export a a Tae 03 D4 EAA 03 E G4 Gs Save Data Anaiyss Parameters Click a graph to highlight the data in the analysis results Figure 5 49 Fitting View Grouped Option Selecting Data for Viewing The following options are available for selecting data for viewing To view specific biosensor data select the rows in the analysis results table e To select ad
192. ple Information No Data Available Figure 4 5 Excluding Samples from Analysis Octet System Data Analsyis User Guide Release 7 1 page 48 Chapter 4 Quantitative Analysis Editing Standard Concentration or Well Information To edit standard concentration or well information 1 Click the Data Selection tab 2 Inthe results table click a Conc or Well Info cell and enter the desired information To access a shortcut menu of editing commands right click the cell EF ForteBio Data Analysis 7 0 Quantitation higG ProA Kinetics cja Fle Help O Oxa Selecton EJ Rents i Looded Dwa higG ProA Kinescs 16 Sensors from 1 E Krets ference Sabbacton Average i j Gap View E 06 27 11 IK ProAhigG Ank Ole d IF Fip Data Show Al Traces pe Ocm REDS Ee DD NGG Prod Krnencs 0 J kro emn n lies wher loaders Guareesncn t 0427 11 384 Ohigs Banding Curve Geng 04 27 2011 384 hy 240 _ ee 210 See 180 150 yon s F 120 pe o a 060 00 o 0 BD V W WO W 20 BO 2 XW 3 W WO 40 4 400 SIO SO SO GO aS a Select samples from the table or Plate below to display the data P 4 2 3 4 5 g 7 2 s won 1 T Sepie Sapio Type Repeat Known Conc Olktion ffermate ASOOO0OOO0008 x rE E ee Sa 1 B S O000 a Svan r WA Right to left Reading order WA Show Unicode control characters Insert Unicode control character 00000000000 k L x Open IME Recorwersion
193. porting Data c5acnscden s witidawieceadeugadeewnend beste ENEAS EEEE EE EE DE ieee 71 Octet System Data Analsyis User Guide Release 7 1 page 44 Chapter 4 Quantitative Analysis WORKING WITH EXPERIMENTS A quantitation experiment enables you to determine sample concentration using a refer ence set of standards After an experiment is run start a data analysis session double click the a icon on the desktop see Analyzing Binding Data on page 57 Loading an Experiment for Analysis A data analysis session can be used to e Load and analyze an experiment e Re analyze an experiment NOTE More than one experiment can be opened during a session If multiple quantitation experiments are open the analysis includes the data from all of the biosensors that are check marked in the Results tab 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 re analyze 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 To load an experiment 1 On the desktop click the 3 icon or click the Windows Start button and select All Pro grams gt ForteBio gt Data Analysis 7 0 The Data Selection tab displays Figure 4 1 File Help O D
194. r ensure that Localhost is selected e Ifa remote machine is to be used and it is located on the same subnet de select Localhost and click Find to display a list of potential GxP server addresses Choose the desired GxP server from this list and click OK Click OK in the Authen tication Server dialog to finish The new GxP server should be listed in the Login dialog box next to Server e Ifa remote machine is to be used and it is located on a different subnet de select Localhost and enter the IP address of the machine running the GxP server Click OK to close the authentication server 3 Select your login name from the User drop down list Figure 3 6 For the first time log ging in select Administrator NOTE To start an administrator session select Administrator in the User drop down list o mx fort sio localhost 20002 Figure 3 6 Selecting Login Username Octet System Data Analsyis User Guide Release 7 1 page 34 Chapter 3 21 CFR Part 11 Compliance 4 Enter your password in the Password field Click for a password reminder if needed Figure 3 7 For the first time logging in leave the Password field blank o E E Reminder Employee number Figure 3 7 Password Reminder Option 5 Optional Select a project from the Project drop down list Figure 3 8 For the first time logging in leave as none r Login fort sio Ser
195. r 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 w rtebloa com Figure B 7 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 8 33 Data Analysis 7 0 Setup Smo Installing z Please wait while Data Analysis 7 0 is being installed Execute msiexec i C Program Files ForteBio 7 DataAnalysis7_0_0_29 Prerequisites VC90 Output folder C Program Files ForteBio 7 DataAnalysis7_0_0_29 Prerequisites Extract WindowsInstaller KB893803 v2 x86 exe Extract VC90Runtime 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 Next gt Cancel w o Qa Figure B 8 Installation Progress Octet System Data Analsyis User Guide Release 7 1 Installing the Data Analysis 7 0 21 CFR Part 11 Software page 161 The installation wizard displays the Completing the D
196. r left corner of the main screen Figure 2 1 Menu options are described in this section Figure 2 1 displays the non 21 CFR Part 11 main menu Figure 2 2 displays the main menu for the 21 CFR Part 11 Fie Security Help Figure 2 2 Main Menu 21 CFR Part 11 Version of the Data Analysis Software Octet System Data Analsyis User Guide Release 7 1 page 24 Chapter 2 Getting Started File Menu The File menu Figure 2 3 allows users to open and save re analyze work with experiments in different modes save reports and set port options File Security Help Load a Folder Quantitation Batch Mode Kinetics Batch Mode Save Report Options Exit Figure 2 3 File Menu Table 2 1 File Menu Commands Menu Command Function Load a Folder Loads an experiment method file frd Quantitation Batch Opens the Quantitation Batch Mode dialog Mode box Kinetics Batch Mode Opens the Kinetics Batch Mode dialog box Save Report Saves all open report files Options Allows you to determine the port automa tion options e TCP IP with a localhost option Serial RS 232 Exit Closes the application after prompting to save any changes NOTE When using the 21 CFR Part 11 version of the Octet System Data Analy sis software only 21 CFR Part 11 compliant experiments and re analyze gen erated using the 21 CFR Part 11 version of the software can be opened Files generated using the
197. red to unlock the program Logoff Exits the program A password is required to log in again Octet System Data Analsyis User Guide Release 7 1 page 26 Chapter 2 Getting Started Help Menu The Help menu provides access to software and instrument support information Help Data Analysis User Guide ForteBio Web Site About ForteBio Data Analysis Figure 2 5 Help Menu Table 2 3 Help Menu Commands Menu Command Function Data Analysis User Opens the online Octet System Data Analysis Software User Guide Guide ForteBio Web Site Opens a web browser and displays the ForteBio web page www fortebio com About ForteBio Data Displays software user and instrument information Analysis NOTE Clicking the ForteBio logo in the upper right corner of the main screen also displays the About window Octet System Data Analsyis User Guide Release 7 1 page 27 CHAPTER 3 21 CFR Part 11 Compliance Octet System 7 0 21 CFR Part 11 Software Overview ccc cece e eee e eee e nee ees 28 ForteBio GxP Server Module 20 2 0 ccc c cece cece nae c ene see ebbeaecesbeeececbeceseeu 29 Selecting a Server Location cece cece cece cence nen e nee ences eee eee REENA NEA 30 Starting a User Sessio s 085 cocks neater eabacs seaue erasers E E E E E TE EE 33 Compliance Features 0 0 cece ccc cece cece ene eee n ee eee een ESRA PERIS en en enenes 35 page 28 Chapter 3 21 CFR Part 11 Co
198. rel DVD MovieFactory Lenovo Edition DivX Plus Dropbox FileZilla FTP Client FileZilla Server ForteBio X ForteBio Inc www forteblo 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 When the installation is complete the installation wizard displays the Completing the Data Acquisition 7 0 Setup Wizard dialog box Figure B 4 Octet System Data Analsyis User Guide Release 7 1 page 158 Chapter B 21 CFR Part 11 Software Administrator Options i Data Acquisition 7 0 Setup CRS C 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 4 Completing the Data Analysis 7 0 Setup 6 Click Finish to complete the installation Octet System Data Analsyis User Guide Release 7 1 Installing the Data Analysis 7 0 21 CFR Part 11 Software page 159 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 5 i Data Analysis 7 0 Setup Welcome to the Data Analysis 7 0 Setup Wizard for 21 CFR pa
199. rking with Experiments page 47 Excluding Including Samples from Analysis To toggle sample analysis in the Results window perform one of the following tasks Inthe sample plate map select the well s right click and select Exclude Wells If the selection is already excluded from analysis select Include Wells to return include the samples to the analysis e Inthe results table to exclude wells de select the check box in the first column or right click the selected rows and select Exclude Selected Wells If the selection is already excluded from analysis click the check box for the desired rows or right click the desired rows and select Include Selected Wells T ForteBio Data Analysis 7 0 Quantitation higG ProA Kinetics 7 M Dittion C Sample Sensor T a File Help Include Selected Rows m SSS Results Exclude Selected Rows Standard Curve Equation Group View i Set Color Linear Point to Point X Options Set Color By Group Set Color By Load Standards Save Standards Size Columns by Title Use standards from loaded file i Size Columns by Data Calibrate within plate Size Columns by Both Processing Parameters Binding Rate Equation R equilibrium z Read Time 599 8 secs Zero Conc Threshold 0 0001 BR Low Conc Threshold 0 003 BR Select All Rows Invert Selection Order Columns Edit Sam
200. rresponding standard deviation and CV statistics are calculated for all samples in each replicate group automatically For kinetics experiments samples in each replicate group are identified by the same color 62 Sample Alerts The Sample Alert highlights data that fit user specified criteria Flip Data Allows acquisition data to be inverted This function is useful when the observed wavelength shift is neg ative due to use of large particles such as liposomes and phage during the assay Grouped View Displays graphs in custom groupings This feature allows you to display graphs organized into groups according to sample attribute or results category This is a highly useful feature when working with large data sets 126 X Y Graph An X Y plotting tool that graphs several important parameters such as binding rate R2 calculated concen tration and residual 138 1 2 Bivalent Analyte Model The model is intended to fit data derived from systems where two molecules of analyte solution based mole cule bind to one molecule of the immobilized ligand The model is available in the Analysis tab Kinetics mode gt Model menu 114 Octet System Data Analsyis User Guide Release 7 1 page 20 Chapter 1 welcome 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
201. rt 11 This wizard will guide you through the installation of Data Analysis 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 5 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 6 i Data Analysis 7 0 Setup lo ws 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 v Figure B 6 Choose Install Location Dialog Box Octet System Data Analsyis User Guide Release 7 1 page 160 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 7 3 Data Analysis 7 0 Setup o Choose Start Menu Folder Choose a Start Menu folder for the Data Analysis 7 0 shortcuts Select the Start Menu folde
202. s data saving 66 starting basic kinetics experiment 76 user session 33 steady state analysis 80 Steady State Analysis graph described 140 displayed figure 140 Steady state analysis kinetic analysis type 113 steady state kinetics analysis options 118 Average from 119 R equilibrium 118 Response 118 Steps to Analyze curve fitting kinetics analysis option 114 Subtraction check box 99 sum of squared deviations 130 symbols electrical hazard 20 fuse 20 heat hot 20 system artifacts 101 system drift 100 T Table Information batch mode option kinetics 122 technical support contacting 20 testing ForteBio GxP Server module 189 threshold values Do not use alerts 64 Max Residual 63 Min Sample r2 63 Sample Alert 63 Time sec Fitting view option 124 Time 1 sec 112 Time 2 sec 112 time range of the association step data to analyze 115 of the dissociation step data to analyze 115 time at which the first binding measurement is acquired 112 toggling sample analysis in the Results window 47 81 Treat Empty Cells as Match Advanced Search option 133 types of report data included by the Processing options figure 147 Octet System Data Analsyis User Guide Release 7 1 page 210 U Unweighted 59 Use Included Traces Only check box 126 Use 20 point average 111 Use Entire Step Times analysis option 115 Use one for all folders batch mode option kinetics 121 quantitation 70 Use
203. s feature can be used to edit sensor sample information after data acquisition It is useful for example if naming conventions within a project change over time and the sample information used during data acquisition requires updating or if the original plate assignment was incorrect A Settings_Tablelnfo xml file will be found in the experiment folder of any experiment after the data has been processed in the Processing tab of the Octet System Data Acquisition software and the Anal ysis tab has been activated The Settings_Tablelnfo xml file is updated after clos ing the Edit Sensor Sample Information dialog box of the Analysis tab If no xml file is specified the well information from the original data acquisition file is used 3 Select the experiments for batch analysis a Click Add Folders b In the displayed dialog box select an experiment folder and click Add Repeat to select each experiment in the batch c Optional To remove an experiment s from the batch select the folder s and click Remove Selected 4 Click Analyze Data Octet System Data Analsyis User Guide Release 7 1 Kinetics Analysis Results page 123 KINETICS ANALYSIS RESULTS Kinetics analysis results Figure 5 45 are presented in graphical and tabular formats Some viewing options in the Analysis window do not require data fitting analysis and are avail able for processed data UF Fortetio Data Analysis 7 0 Kinetics higG Prot Kinetics lo
204. s settings A Settings_DataAnalysis ini file ini is saved in the experiment folder These process ing settings are displayed the next time the experiment is loaded Step 6 Viewing Results The Octet System Data Acquisition software provides multiple display options Figure 5 33 for processed data e Processed Results on page 108 Sensor Summary e Report Points Step 6 View Results Processed Results Sensor Summary Report Points Figure 5 33 Options for Viewing Results Octet System Data Analsyis User Guide Release 7 1 page 108 Chapter 5 Basic Kinetics Analysis Processed Results e Double click a graph to display it in a separate window Figure 5 34 Hover the cursor over a curve to highlight the curve and display a tooltip of the time X axis and nmshift Y axis at that point Figure 5 34 Customize the graph by right clicking the graph for a shortcut menu of display options Figure 5 35 e Customize the curve display right click the curve for a shortcut menu of display options Figure 5 35 NOTE The same display options are also available for binding charts in the Fitting and Residual views in the Analysis tab 500 600 700 800 900 1 000 1 100 1 200 1 300 1400 1 500 Time sec Figure 5 34 Double click a Binding Chart to View it in a Separate Window Octet System
205. s with the Replicate Group names entered see Figure 4 11 Octet System Data Analsyis User Guide Release 7 1 page 52 Chapter 4 Quantitative Analysis 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 OA4 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 OD4 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 1 Kinetics Buffer H4 Association 6 Reference 1X Kinetics Buffer OAS 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 ODS Association 4 Sample 1 25 150 8 333 1X Kinetics Buffer OES Association 5 Sample 0 625 150 4 167 1X Kinetics Buffer F5 Association 6 Reference 1X Kinetics Buffer G5 Association 6 Reference 1 Kinetics Buffer H5 Association 6 Reference 1X Kinetics Buffer Figure 4 11 Replicate Groups Displayed 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
206. se the original data folder Use this folder Selected Folders Add Folders _ Remove Selected Status Folder Processing Status Analyze Data Figure 4 28 Quantitation Batch Mode Dialog Box 2 Set the batch mode options as follows e IniFile e Use the one in each folder Analyzes each experiment using the ini file found in the same experiment folder Use one for all folders Analyzes all experiments using a user selected ini file Well Information Specifies a path within the experiment folder to the Settings_Welllnfo xml file Select only a Well Information file if you modified the original well information by editing for more information see Editing Experiments on page 46 The Settings_Welllnfo xml file can be found in the experiment folder of an experiment that has been edited in the Octet Sys tem Data Acquisition software Select a well information file if the Use one for all folders option is selected Output Folder Use the original data folder Analysis results are saved in the experiment folder e Use this folder Saves the analysis results to a user selected folder 3 Click Add Folders to select the experiments for batch analysis Octet System Data Analsyis User Guide Release 7 1 Exporting Data page 71 4 Inthe displayed dialog box select an experiment folder and click Add Repeat to select each experiment in the batch 5 Option
207. select and confirm the biosensors to analyze 1 Apply Savitzky Golay filtering by clicking the Savitzky Golay Filtering check box see Figure 5 31 i ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics Ser lysi Ig File Help I Data Selection Processing lt Analysis Step 1 Data Selection Sensor Tray 1 Sample Plate Map 110420 Raw Data View vy 4 5 6 7 s 9 10 11 12 vy i 2 3 4 5 6 7 3 p 10 4 12 Sen Sento A OO OO A Onn Sensors to be Analyzed E a in el SEE afa B1 F1 ll B Jl B cgpa EDT c1 F1 a SA N N IP FP N bal SINS NS 1 1 in pa Brey OOOOOO amA OD G1 F1 i c c _ Lo lt in s P Se 2 Staton D AAAOCO D D LLT Reference Wells re a YY SY JH ae et YY YS S gt eee E Select Sensors for Analysis F m gt O A E A pea Double Reference Change Sensor Type SSS SS _ oe Nec Net Ne A O nme eee e Edit Sensor Properties Oli F oo OD cl Step 3 Z Aion Y Ads Copy To Clipboard a P lt pa s gt ame G OOO Bs ooo gt Time Range sec a z pa 2 Pa From 01 To 2998 H O OGOGO OH Booed e aa Step 4 7 Inter step Correcti Align to Dissociation Aignto Baseline Step 5 Process X Savitzky Golay Fit
208. sing the Column Name pull down menu select a column to search Using the Operator pull down menu assign an operator Enter the search term under Value If the search is case sensitive select the Case Sensitive option Optional Select the Include Excluded Traces option to include traces excluded from analysis in the search Optional Select the Treat Empty Cells as a Match option to include empty cells in the search Optional Click Add Level and repeat steps 2 4 to add additional levels to the search The set of rows selected in the table when the Advanced Search dialog box was opened can be applied to the search using ALL OR and AND operators a Select Search All to search the entire table ALL operator b Select Search All but keep current selection to search the entire table with reten tion of the selection present when the Advanced Search dialog box was opened OR operator Octet System Data Analsyis User Guide Release 7 1 page 134 Chapter 5 Basic Kinetics Analysis c Select Search only current selection to search only the rows selected when the Advanced Search dialog box was opened AND operator The search can be saved by specifying a name under Search Name and clicking Save The name of the saved search will appear in the Saved Searches list 9 Click OK to execute the search Rows that contain cells meeting the search criteria will be highlighted Editing a Search To edit a search 1 On the Ana
209. socia Unk 1 C2 c5 Associa Unk 1 D2 EN D5 Associa Unk 162 EE Unk 1 oe Figure 5 21 Results Window with Calculated Binding Rates NOTE To return to kinetics analysis mode reload the kinetics experiment data in the Loaded Data directory tree click the experiment PROCESSING KINETIC DATA The Processing window provides tools for correcting binding curves using different refer ence subtraction and alignment options The data processing steps specify how to refer ence the data and produce the final binding curves processed data Step 1 Sensor Selection When a kinetics experiment is opened for the first time the sensor tray map depicts all active biosensors as ligand biosensors biosensors with immobilized ligand If the experi ment included reference biosensors biosensors without immobilized ligand you must specify their location in the sensor tray map If the experiment included reference buffer wells to correct for system drift you must specify their location in the sample plate map Octet System Data Analsyis User Guide Release 7 1 Processing Kinetic Data page 97 Working with the Sample Tray Map and Sensor Tray Map To use the sample tray map and the sensor trap map Figure 5 22 1 Hover the cursor over a biosensor or sample to display a tooltip with information about the item 2 Click a biosensor or sample to highlight the associated row in
210. standards from loaded file check box 60 Use the one in each folder batch mode option kinetics 121 quantitative 70 Use the original data folder batch mode option 70 Use this folder batch mode option 70 Use__Point Average Fitting view option 125 user account creating 174 deleting 176 user account password changing 177 user account settings changing 176 viewing 176 user group creating new 179 deleting 180 user password changing 41 user session changing projects during 40 ending 42 locking 41 starting 33 user selected results changing color figure 135 user specified ligand biosensor information 111 notes about the wells 63 standard concentration 63 using data analysis session 44 sample tray map 97 sensor tray map 97 V Value Advanced Search option 132 Verify Digital Signature dialog box figure 36 Verify Document menu 25 verifying digital signatures 36 View Audit Trail menu 25 Octet System Data Analsyis User Guide Release 7 1 page 211 viewing Audit Trail 38 binding curves basic kinetic analysis 84 quantitative analysis 53 constants 184 events for a specific project or computer 39 events for a specific user account project or computer 186 group settings 180 project settings 182 raw data 88 results options 107 shortcut menu of display options 131 specific biosensor data 127 user account settings 176 viewing options basic kinetics analysis Align X 85 E
211. started 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 ForteBio GxP Server module To restart the ForteBio GxP Server module choose one of the following two options Ifthe ForteBio GxP Server module is installed on a network location Double click the FBServer exe file in the FBServer7 folder from the installed location Figure B 54 File Edit View Tools Help Organize Include in library Share with Burn New folder fie 4 ForteBio Name Date modified Type Size JL DataAcquisition7 z J 58 FBServer exe 12 3 2010 3 53 PM Application 2 966 KB JL DataAnalysis7 eis PP B FBServerConfig exe 12 3 2010 3 53 PM Application 7 821 KB J FBServer7 i 2 FBServerMonitor exe 12 3 2010 3 54 PM Application 6 909 KB ForteBio 2 10 2011 6 20PM __Internet Shortcut 1KB Globe ico 12 1 2010 4 21 PM Icon 25 KB Se uninst exe 2 10 2011 6 20 PM Application 54 KB Figure B 54 ForteBio GxP Server Module Installed on a Network Location Ifthe GxP Server module is installed on a local computer Double click the Restart Server desktop icon Figure B 55 Restart Server Figure B 55 Restart Server Desktop Icon The Restart Server console display momentarily as the ForteBio GxP Server module restarts Figure B 56 Octet System Data Analsyis User Guide R
212. sults 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 Octet System Data Analsyis User Guide Release 7 1 What s New in the Octet System Data Analysis Software Release 7 1 page 7 WHAT S NEW IN THE OCTET SYSTEM DATA ANALYSIS SOFTWARE RELEASE 7 1 The following features are new for the Octet Data Analysis software Release 7 1 1 The Kinetics Analysis tab 2 Align to Association is added to the Step 5 Inter step Correction option list Figure 1 1 Step 4 Inter step Correction Align to Association Align to Dissociation Align to Baseline Figure 1 1 Align to Association Option 2 For the Quantitation analysis the interactive binding graph and Group View have been implemented These features simplify data visualization and add consistency to the existing user interface Figure 1 2 Select from the binding graph sample plate map result table X Y graph or Group View corresponding wells are highlighted respectively in all views tandard 1 Fitting Curve Inknown amp Contr Q lected Standard Fitting C Unknown amp Control O Sek 0 170 0 160 0 150 0 140 0 130 0 120 0 110 0 100 0 030 0 080 0 070 0 060 0 050 0 040 0 030 0 020 0 010 0 000 Binding Rate 10 20 30 40 50 60 70 8
213. t click the cell to access a shortcut menu of edit commands The modified parameters are saved in the Settings_DataAnalysis ini file and are auto matically loaded when the data is analyzed again If a new data set is loaded the default parameters are restored Octet System Data Analsyis User Guide Release 7 1 page 84 Chapter 5 Basic Kinetics Analysis G Data Selection O Results Standard Curve Equation Linear Paint to Point x Standards Fiting Curve Unknowns amp Contros Load Standards Save Standards Ta Use standards from loaded file 1 200 v Calibrate within plate 1 000 Processing Parameters 2 Binding Rate Equation 0 800 Initial Slope v O J Read Time sere do Zero Cone Threshold TN i Low Conc Threshold oog Cet Copy Paste Delete 0 200 400 600 800 1 000 1 200 1 400 1 600 1 800 2 000 Calculate Binding Rate Concentration pg ml Select All Data Export PEPE Save Report Plate Sensor Sample Sample ID Group Binding Rate Known Cone pg m Ag Ag Unknown 1 25982 B9 Bg Unknown 1 29901 a ca ca Unknown 1 25149 D9 pg Unknown 1 25400 E9 E9 Unknown 1 20833 F9 Fg Unknown 1 21404 G9 G9 Unknown 1 21071 H9 H9 Unknown 1 22959 A0 A10 Unknown 1 25482 B10 B10 Unknown 1 27917 c0 cto Unknown 1 26345 Dio D10 Unknown 1 25091 000 AAI I 1 1 1010
214. t highlights data that fit user specified criteria To apply sample alerts 1 Set the thresholds for r2 max residual or both Figure 4 22 Standard Sample Alerts Type Threshold s Sample Alert Do not use alerts Save Analysis Settings Figure 4 22 Sample Alerts 2 Alternatively set either a positive or negative threshold on the standard deviation of either the binding rate or the calculated well concentration Figure 4 23 all Sample Alert Sensor Type Protein G x Alert based on Negative Threshold gt Average n SD Positive Threshold lt Average n SD n 2 SD Standard Deviation of Binding Rate Well Concentration ox canca Figure 4 23 Sample Alert Dialog Box Rows that match criteria specified in the Sample Alert are highlighted in the results table of the quantiation experiment Figure 4 24 File Help Data Selection Resutts Standard Curve Equation E Group View Scale Linear Point to Point x Options Ato Full Jota Load Standards Save Standards Standard Fitting Curve Use standards from loaded file Calibrate within plate Processing Parameters Ringing Rate Fruistinn 0 320 Figure 4 24 Sample Alert Results Octet System Data Analsyis User Guide Release 7 1 page 66 Chapter 4 Quantitative Analysis The highlight
215. ta Acquisition software Baseline Loc Well location in the sample plate or reagent plate Octet 384 instru ments only in which the baseline was performed Assoc Sample Loc Sample well location in the sample plate Sample ID The sample ID entered during assay setup Dissoc Loc Well location in the sample plate or reagent plate Octet 384 instru ments only where the dissociation was performed Conc nM The molar concentration of the sample used in the association step The molar concentration is entered by the user or computed by the molarity calculator during experiment setup Response Response calculated from the time window entered in the Steady State Analysis section KD M Affinity constant For the 2 1 and 1 2 models the Octet System Data Acqui sition software computes two Kp values kon 1 Ms Rate of association For the 2 1 and 1 2 models the Octet System Data Acquisition software computes two kon values kon Error Standard error of the rate of association kdis 1 s Rate of dissociation For the 2 1 and 1 2 models the Octet System Data Acquisition software computes two kgis values kdis Error Standard error of the rate of dissociation Rmax The maximum response determined from the fit of the binding data Rmax Error tThe standard error of Rmax For the 2 1 and 1 2 models the Octet Sys tem Data Acquisition software computes two Rmax values Octet System Data Analsyis User Guid
216. ta sets may be processed without attended opera tion The Octet System Data Acquisition software analyzes experiment data using the data processing parameters in a designated Settings_DataAnalysis ini file The experiments in a batch can be analyzed using the same or different ini files The processed data can be saved to either the original data folder or an alternative folder Octet System Data Analsyis User Guide Release 7 1 page 68 Chapter 4 Quantitative Analysis Creating a Settings_DataAnalysis ini File NOTE The Settings_DataAnalysis ini file is also automatically saved when you click Calculate Binding Rate To create a Settings_DataAnalysis ini file 1 Load and open an experiment that will be included in the batch The Data Selection window displays Figure 4 26 I Date Setecton E gt Rents E Looded Data hG PreG Q D E Krets P Tn Tedesence Subtraction Average of Fip Dats Show Al Tocos Group View instrument Type Octet REDI ex 2011_03_01 _ mm 10 h 7 ignore eron in ties when loading Legends ero AeroGoeol Gy amp x1021 2490 002 002 E 8130 2409037 Gy 0427 11 3840 hG By 04 27 2011 384 hig Q G hG Prec a no ns 120 1235 130 p HE Desktop Te Ragiem Known Cone a 2 200 Ow wwo wo Ow w s z Oan 5 25 a 0 w on anG Fi Waza 2 5 5 6a ProtenG GI Waza 2a 25 25 7m ProtenG HI t Re 1 1 sa Prete AZ WGs Se 200 200 s 82 Preten
217. teady State Steady State Analysis 4 R 16625 167 c3 E 1 o x Index v E Log Y Response z R eguiibrium 5 k 16621 167 3 ic 2 cl a Response 6 E 1 052 8 33 D3 a 1 DI Index Response Averagefrom 585 to 595 secs 7 K 10345 8 33 03 E 2 D1 s E 1 119 417 E3 E 1 El e 9 E 10987 417 E3 E 2 El E ai w k onog 0 G3 G4 1 a z z Data Epot n g oon o0 G3 G4 2 G1 f ii 2 amp 00126 0 H3 E 1 H1 cree a o ooe 0 H3 ae u 2 Hi E H 1 n u k 26206 667 S E 1 A2 Sara Papat Copy Table to 5 R 26318 667 3 2 A2 Clipboard 6 x 2275 383 B3 E 1 B2 7 k 2218 33 B3 ky 2 B2 o qre opes eo im w oo B o_o x Index Figure 5 40 Analysis Window Octet System Data Analsyis User Guide Release 7 1 page 116 Chapter 5 Basic Kinetics Analysis Excluding Data from Analysis To exclude data from the analysis 1 In the table a Select the biosensor data rows to exclude e To select adjacent rows hold down the Shift key while you click the first and last row in the selection e To select non adjacent rows hold down the Ctrl key while you click the rows b Right click the selected row s and select Exclude Wells Figure 5 41 or press the space bar Press the space bar again to toggle the include exclude status of the curve Biosensors that will be included in the analysis have an X in the Include column excluded biosensors do not Figure 5 41 I ForteBio Data Analysis
218. tet System Data Analysis Software Release 7 0 succsee 18 Conventions and Symbols Used in This Guide 0 cece eee cence eee eee e es 20 ForteBio Technical SUPPOrt cece cece cece eee ene eee EPESA NERES NERENN SEN 20 Octet System Data Analsyis User Guide Release 7 1 page 6 Chapter 1 welcome Welcome to the Octet System Data Analsyis User Guide Release 7 1 for the ForteBio Octet sys tem This guide explains how to Start a data analysis session and load a quantitation or kinetics experiment frd View and analyze the experiment data e View the analysis results in tabular and graphical formats Export analysis results and generate reports 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 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 experiment for future use e Define custom assays Runthe experiment and acquire binding data View and save binding data to a user specified location Data Analysis e Analyze binding data and view analysis results Export or copy analysis re
219. the column header again Applying Alerts Applying Standard Alerts In the Results window you can select threshold s that are applied to the standards You can also edit the alert threshold value Min Sample r2 The threshold r value for a standard or unknown binding curve If the r value of a standard or unknown binding curve is less than the threshold value the standard or unknown sample is highlighted in the results Max Residual Specifies a threshold residual value for standards If a calculated standard concentration deviates 10 or greater from the expected concentration the standard is highlighted in the results e Sample Alert Specifies highlights data that fit user specified criteria Thresholds can be set for r2 max residual or both e Both Min r2 and Max Residual Applies both the Min Sample r2 and Max Residual thresholds to the data Octet System Data Analsyis User Guide Release 7 1 page 64 Chapter 4 Quantitative Analysis Do not use alerts Select if you do not want to apply any thresholds to the unknown or standard sample data To apply a standards alert 1 Inthe sample plate map select the type of data to display data from the drop down list 2 Select a type of alert Samples that do not meet the threshold are highlighted in the sample plate map and results table 3 Edit an alert threshold value a Select the cell and enter a new value a Right click the cell to display a short
220. ting 81 loading for analysis kinetics 76 loading for analysis quantitative 44 Export Aligned Step csv files menu 91 Export button 141 Export File Report Point Analysis feature 111 Export Fitting Results data export option 141 Export Table to csv File data export option 141 exporting raw data 91 F FBServer exe file 190 file type changing 37 Fit Curves button 116 Fitting view grouped option figure 127 individual option figure 125 stacked option figure 124 Fitting view and Residual view stacked option figure 124 Fitting view options Add to Table 125 Auto Scale 124 Full Scale 124 Grouped 124 Individual 124 listed 124 Options 124 Refresh 124 Remove All 125 Report Points 124 Stacked 124 Time sec 124 Use_ Point Average 125 Octet System Data Analsyis User Guide Release 7 1 page 197 Y Axis Scaling 124 Fitting Global Full options By Color 115 By Sensor 115 Fitting Global Full curve fitting kinetics analysis option 114 Fitting Local options Full 114 Partial 114 Fitting Local curve fitting kinetics analysis option 114 Flip Data viewing options quantitative analsys 54 85 flip analyzed data 62 ForteBio GxP Server 7 0 exe 162 ForteBio GxP Server desktop icon 173 ForteBio GxP Server module accessing 187 ForteBio GxP Server module installing 162 ForteBio technical support contacting 20 ForteBio Web Site menu 26 Full R2 kinetic analysis result 130 Full Scale F
221. ting sample information kinetics figure 82 editing sample information quantitative figure 48 example figure 68 loading an experiment kinetics figure 77 loading an experiment quantitative figure 45 opening an experiment figure 45 viewing options table 54 data viewing options 127 DataAcquisition CFR 7_0_0_x exe 156 Define Custom Colors menu 135 defining Replicate Groups 49 Delete Constant menu 185 deleting constants 185 project 182 user account 176 user group 180 determining binding rate 63 sample concentration 44 digital signatures verifying 36 dilution factor 62 discontiguous biosensors selecting figure 91 display options viewing shortcut menu of 131 displaying graphs organized into groups 124 license information 26 Octet System Data Acquisition software properties 26 selected step data from a kinetic assay figure 93 Dissoc Loc kinetic analysis result 129 Dissociation only analysis option 114 Dissociation analysis option 115 Do not use alerts threshold value 64 Octet System Data Analsyis User Guide Release 7 1 page 195 Dose Response 4PL Default 59 Dose Response 4PL Weighted Y 59 Dose Response 4PL Weighted Y2 59 Default 59 Dose Response 5PL Unweighted 59 Dose Response 5PL Dose Response 5PL Weighted Y 59 Double Reference reference subtraction method figure 103 reference subtraction method described 102 Edit Group window
222. tion 5 D2 1 P 5 cooo Exclude Wells from Binding Rate Calculation 5 E2 1 Associa Save Analysis Settings H Edit Sample Information 5 F2 1 Associa 5 G2 1 Associa 10 N A E ey H2 1 Associa Mon 2 ea AI 1 Associa W 12 10 E B1 1 Associa TO 13 5 E c c1 1 Associa Mou 25 _ 4 D1 1 Associa X oi F r Selecting wells in the sample plate map Selecting rows in the results table Figure 5 6 Excluding Samples from Analysis Editing Standard Concentration or Well Information To edit standard concentration or well information 1 In the table of either the Data Selection or Result tab Figure 5 8 right click and select Edit Sample Information EF Fortetio Data Analysis 7 0 Quantitation higG ProA Kinetics se File Help O Dats Selecton EJ Rents SW Leaded Dus 16 Sensors from 1 D totes E 0427 11 WAK PAHS Fio Data Show Ab Traces NGG Prod Kenencs 1 J kye emn n hies wher loaders 0427 11 384 Ohi E 0427 2011 hga s WE Desktop Asosa Unknown Assocs Unknown Associa Unknown Right to left Reading order Associa Unknown Show Unicode control characters es Associa Unknown Ei nce a ue Insert Unicode control character Open IME Recorwertion Figure 5 7 Data Selection Window Editing Sample Information The Edit Sample Information dialog box displays Figure 5 8 Octet System Data Analsyis User Guide Release 7 1
223. tiple groups can be used in an experiment IMPORTANT The Octet System Data Analysis software only recognizes and groups samples that use the same Replicate Group names where spacing and capitalization must be identical For example samples assigned to Group 2 and group2 are treated as two groups Viewing Binding Curves To view binding curves in the sample plate select a well s or in the sample plate table select a row s To select non adjacent rows or wells press and hold the Ctrl key while clicking the wells or rows File Help Ome eco Rn 5 Looded Data hig PreG Q Kinetics rT S 7 7 ia L ApX Reference Subtraction Average of Re Daa Show Al Traces L Gop View Tyoe OcetREDIG Ege Ht owas a i io a EZ ignore emors in fies when Legende By 04 27 11 334 Q hG Ignore leading s D rigs Pm a Ber n Curve Graph 440 4 00 SS ee SS Ee Se 360 P n E et no 120 1 Type Rexiicat Known Con a 200 20 a Se 100 100 F So 50 50 a 70 SaS _ D W 04 27 11 384 K Prod higG Per w D 04 27 11 384 Q hig a 5 HA 04 27 2011 384 higG Q sis 25 pi So 1 1 J u Sa 200 20 a Acquisition Se 100 100 Ji Analysis S 5 50 PI hlgG Prod Kinetics Sa 2 2 D higG ProG Q Se 10 10 mji Screen Shots 3 S 5 5 ml Software v6 3 data files m eha C E s 25 E m Figure 4 13 Selecting Sample Wells or Rows to Display in the Binding Curve Graph Octet System Data Analsyis User Guide R
224. ty Reference Sensor hi Select Ligand Sensor s for Data Analysis Step 5 Process Savizky Golay Fiteang Process Data Step amp Vew Roz s Processed Resuts Senex Sumay Report Points Step 7 Save Rosts Save Processed Deta Save Raw Data J Seve Proc Parameters Sagie Piate Map 110420 1 2 a ee d 8 s wo n t i a E s O a g200907909 3 i O rommonoowrpr 0707070 oOo Lead hl E gt Buffer Load W Sample Reference Wel Empty Regel g Gamage PPILL TILT m alals arenasi 8228s T _ 4 Figure 5 28 Double Reference Subtraction Method NOTE In Figure 5 28 Al1 A3 Target biosensor A1 corrected by reference bio sensor A3 both probing reference wells B1 B3 Target biosensor B1 corrected by reference biosensor B3 for biosensor and microplate well artifacts both probing pos itive sample B1 B3 A 1 A3 Double reference subtraction fully corrects for biosen sor and microplate well artifacts and the effect of sample media Average Reference Sensors Corrects the binding data using either a single refer ence biosensor or the average signal of multiple biosensors Octet System Data Analsyis User Guide Release 7 1 page 104 Chapter 5 Basic Kinetics Analysis ForteBio Data Analysis 7 0 Kinetics higG Pro Kinetics o B gZ Fle Help E ata Selecti
225. ure 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 Analsyis User Guide Release 7 1 Installing the Data Acquisition 7 0 21 CFR Part 11 Software page 157 E3 Data Acquisition 7 0 Setup al Choose Install Location Choose the folder in which to install Data Acquisition 7 0 wee 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 accept this path location The Choose Start Menu Folder dialog box displays Figure B 3 lt 2 Data Acquisition 7 0 Setup coaja X Choose Start Menu Folder Choose a Start Menu folder for the Data Acquisition 7 0 shortcuts ie d 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 Co
226. value 63 sample alerts applying 65 sample concentration computed from the standard curve 63 defined 112 determining 44 sample designations changing kinetics analysis 81 quantatitative analysis 46 sample ID 111 sample ID entered during assay setup 129 Sample ID analyzed data 62 Sample ID kinetic analysis result 129 sample location 111 sample plate map copying 97 defined 63 sample tray map using 97 sample type changing 93 sample well location in the sample plate 129 Save All Method Files menu 24 Save Analysis Settings menu 69 Save Data Analysis Parameters button Analysis window figure 118 Save Report menu 141 Save Results options 112 saving all reports 24 analysis results for each biosensor to a separate text file 141 for selected biosensors to system clipboard 141 analysis settings 66 binding data for each biosensor to a separate text file 141 for selected biosensors to system clipboard 141 processed data 112 processing parameters 112 quantitation results report 73 raw data 71 112 Octet System Data Analsyis User Guide Release 7 1 page 207 results 112 results options 112 results table to a csv file 141 standards data 66 Savitzky Golay filtering 106 scatter plot 138 Search all but keep current selection implies OR Advanced Search option 133 Search All Advanced Search option 133 Search only current selection implies AND Advanced Search option 133 search resu
227. ve desktop icon see Figure B 15 Data Data Analysis Acquisition 7 0 CFR11 7 0 CFR11 Figure B 15 Data Acquisition or Data Analysis Software Desktop Icons The Login dialog box displays Figure B 16 n E E fort sio Figure B 16 Login Dialog Box 2 Selecta Server location by clicking browse The Authentication Server dialog box displays Figure B 17 a x Authentication ES Connection to server Server address localhost v Localhost a 20002 Figure B 17 Authentication Server Octet System Data Analsyis User Guide Release 7 1 page 166 Chapter B 21 CFR Part 11 Software Administrator Options 3 Click Default to recall the default server settings of localhost and Port 2002 Local host lf the local computer is to be used as the GxP Server module host click the Localhost check box Change the Port number if needed e 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 x More than one server was found Please choose one 192 168 1 78 JRICHARDS 192 168 1 78 JRICHARDS Figure B 18 Choose Server Address Remote host on another subnet lf the GxP
228. ved nm shift is negative due to the presence of large ana lytes such as phage cells and lipoparticles on the biosensor surface For examples of flipping data see Figure 4 14 and Figure 4 15 Grouped View Displays graphs in custom groupings Choose this option to dis play graphs organized into groups according to sample attri bute or results category This is a highly useful feature when working with large data sets e Options Click to show the Grouped View Options dia log box e Refresh Updates the graph display Octet System Data Analsyis User Guide Release 7 1 Working with Experiments page 55 Table 4 1 Viewing Options in the Data Selection Window Continued Option Description Edit Legends Select the sample information displayed in the legend Options include Sensor Sample Sample ID Group and Concentra tion higG ProG Q mee eee eee ee eee Scale nstrument Type OctetRED96 10 Sec Al Row Column J Ignore errors in files when loading Ato Full 4 00 3 50 3 00 2 50 nm 2 00 1 50 1 00 0 50 0 00 Time sec Figure 4 14 Flip Data Example of Flipping Data to Example in Figure 4 15 Figure 4 15 New Flip Data from Figure 4 14 Octet System Data Analsyis User Guide Release 7 1 page 56 Chapter 4 Quantitative Analysis Opening Binding Curve in Separ
229. ver localhost 20002 User JBlack Password eeececseece Project none Cell Culture screen Receptor Ligand screen Figure 3 8 Project Selection 6 Click OK The Data Acquisition or Data Analysis software launches and starts the user session During the session the user account and project selected at login are displayed in the Data Acquisition software status bar Octet System Data Analsyis User Guide Release 7 1 Compliance Features page 35 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 box will display and a 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 User sessions will not be locked during experi mental data acquisition NOTE To create and edit new users groups and proj ects see User Account Administration on page 174 Group Administration on page 178 and Project Administration on page 181 COMPLIANCE FEATURES You can access the 21 CFR Part 11 compliant features provided in the 21 CFR Part 11 ver sions of the Data Acquisition and Data Analysis software by selecting the Security menu from the main menu Figure 3 9 Security Help Verify Document View Audit Trail Cha
230. with the Analysis Results Table on page 131 e Rmax Unlinked option for Global Fitting When fitting data the theoretical response maximum Rmax can be calculated assuming equivalent surface capacity between biosensors Rmax linked or non equivalent surface capacity between bio sensors Rmax unlinked Window of Interest From Start of Step e Association The time range of the association step data to analyze Dissociation The time range of the dissociation step data to analyze Use Entire Step Times Analyzes the entire time duration of the selected step s 3 ForteBio Data Analysis 7 0 Kinetics hlgG ProA Kinetics een x File Help Data Selection C Processing Analysis Curve Fitting View Y Axis Scaling Report Points Seo Asie Sued Gowes mon A See Tine bec 10 ean oriy Onions fees JIA tne 20 Prt reap ene A C tam Dissociation Only Association and Dissociation Fitting View Mosa Fitina 5 Local ful Partial Global Ful Group By 5 Rmax Linked Sensor Rmax Unlinked By Color Sensor Compound 700 800 Time sec Window of Interest From Start of Step Association 0 to 599 6 secs Dissociation 0 to 900 secs wo w 0 too 13001200130 Time sec Response Conc nM Dissoc Loc Color Assoc Sample Loc Sensor Locatic XY Graph Iso Affinity S
231. xperiments 57 87 application 24 experiment 57 87 kinetics experiment figure 87 selected experiment left or all experiments right in the Quantitation or Kinetics folder figure 57 closing a kinetics experiment figure 87 COD coefficient of determination 130 coefficient of determination 130 color of the biosensor binding curve 129 Color kinetic analysis result 129 color coded analysis results enabling 131 sorted by color figure 137 color coding data 134 results by category 135 user selected results 134 Column Advanced Search option 132 compliant experiments generated 36 compliant features for 21 CFR Part 11 35 Conc nM kinetic analysis result 129 Concentration mM 112 Concentration avg analyzed data 62 Concentration CV analyzed data 62 Concentration SD analyzed data 62 concentration values setting 95 confirming biosensors to be analyzed figure 106 Reference Well is subtracted from the sample wells figure 100 connecting Octet instrument to computer 22 Connections to Clients box 189 constants administrator 183 changing 184 creating 184 deleting 185 viewing 184 Octet System Data Analsyis User Guide Release 7 1 page 193 Constants tab 182 Model 114 contacting ForteBio technical support 20 Rmax Unlinked option for Global Fitting 115 contiguous biosensors selecting figure 91 conventions used in this guide 20 Copy Table to Clipboard data export option 141 Copy to Cli

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