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Watson TSQ Module 1.0 User Guide Version A

1. Configure your instruments You cannot configure your instruments while the TSQ Module application is running 2 Double click the TSQ Module application icon on your desktop or go to Start gt All Programs gt Thermo Watson TSQ Module gt Watson TSQ Module The Thermo Watson TSQ Module login screen opens Thermo Watson TSQ Module Login Name Password Database Exit Watson TSQ Module Table 6 Login screen parameters Parameter Description Login Name The user s Watson login name Password The user s Watson password Database The Watson environment URL or the friendly name assigned in the Environments xml file 28 Watson TSQ Module User Guide Thermo Scientific 4 TSO Module Getting Started Starting the TSO Module Application To log in to the Thermo Watson TSO Module application Each database is assigned to specific users You cannot log in to a database that is not assigned to you and you cannot log in to your assigned database unless there is at least one run assigned to you in the TSQ Module application 1 Enter your Login Name 2 Enter your Password 3 Select your Database from the menu One of the following could happen There are no databases to select from in the menu This means there are no runs in the TSQ Module Run Manager view You cannot log in to the database unless there is at least one run in the queue The database list might include databases that are not assi
2. 2009 Thermo Fisher Scientific Inc All rights reserved LCquan and TSQ Vantage are trademarks and Xcalibur and TSQ Quantum are registered trademarks of Thermo Fisher Scientific Inc in the United States Windows Excel and Windows Vista are registered trademarks of Microsoft Corporation in the United States and other countries Acrobat Flash and Acrobat Reader are registered trademarks of Adobe Systems Inc in the United States and other countries All other trademarks are the property of Thermo Fisher Scientific Inc and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This docu
3. spectrum averaging The averaging of spectral data for a number of scans stability samples An analytical run definition Used to analyze the reliability of quality control samples over time standard bracket sample type The calibration samples in a Sequence having bracket open or bracket overlapped type See also bracket open bracket overlapped standard deviation In statistics the standard deviation is a measure of the dispersion of a group of measurements For example masses times or intensities Standard deviation is calculated as follows s Varba Xn where Var Xi XN is the variance See also relative standard deviation Standard Error of the Mean SEM An analytical run definition SEM is Standard Deviation divided by the square root of n standard sample A sample with a known amount of calibration reference material standard update sample type Xcalibur adds this sample type to the calibration curve without removing previous entries The first calibration sample in a Sequence having bracket none type is a standard clear type Xcalibur clears all previous data for all calibration levels and begins a new set of calibration data Xcalibur assigns all subsequent samples in the same calibration sequence to be the Watson TSQ Module User Guide 143 Glossary Standard Update Sample Type The calibration data set consists of the data from the standard clear samples and the data from the st
4. Note To remove multiple runs from the Acquisition Queue check the check box for each of the runs in the queue and press the keyboard Delete key Thermo Scientific Watson TSO Module User Guide 57 To cancel a run in the Run Manager view You can cancel a run in the Run Manager view The TSQ Module application returns a canceled run to the Watson application and Watson users can resubmit the run to the TSQ Module application For detailed information about restarting runs see Appendix B Restarting Runs Run Manager view Acquisition Queue Canceled run Resubmitted run Pending Select the run in the Run Manager view You cannot use the Run Manager view to cancel a run that is currently in the Acquisition Queue Submitted or Acquiring Click Cancel Run The following confirmation message is displayed Thermo Watson TSQ Module You are about to cancel the run ProgTest_ShortJobStudy_5 V The canceled run will be returned to Watson Are you sure 3 To return the run to the Watson application click Yes Watson users can modify and resubmit the run or resubmit the run without changes LLL m Watson Working with Processed Runs This chapter provides information about working with runs in the Watson application that are in process or have already been processed by the TSQ Module application Contents Reviewing Runs Reintegrating Chromatograms Changing the Chromatogram Display R
5. checksum A calculated value that is used to test data integrity It is a value calculated for a given chunk of data by sequentially combining all the bytes of data with a series of arithmetic or logical operations chemical noise Signal resulting from the presence of chemical species other than the analyte chromatogram The graphical representation of a chemical separation such as liquid chromatography obtained from an analytical instrument called a chromatograph The result of plotting detector response versus time chromatographic column A chromatographic separation component A tubular column either filled with a finely divided solid impregnated with a partitioning liquid or an open tubular column with a liquid film deposited on the walls chromatography An analytical method that is used for the separation identification and determination of chemical components in a complex mixture A sample is dissolved in a mobile phase a gas or liquid and then forced through an immiscible stationary phase chromatography filter A noise reduction algorithm that smooths peak profiles at low sample concentrations in chromatographic data These peak profiles integrate more consistently than those acquired under normal data acquisition conditions See also centroid data profile data Watson TSQ Module User Guide 123 Glossary comma separated values text file A comma delimited text file The extension of a comma separated value
6. 20M 3 E 15M a z 10M E 5M i 0 Samples Analysis Type Sample Information Zoom Options Y Axis Scaling Raw Data Analysis Run Sample Sequence Number Inactive Data Point E Allow Zooming Min Y 929 609 04 i Ares labelControlt Max Y 29 282 683 50 Trend Analysis Sample Type labelControl2 f Watson Sample ID labelControt3 Update Axis Restore Defauk i Calculation of Internal Standard Limits d 1 Sample Types to Use For Mean Calculation Method Al Active Samples Mean 18 992 180 00 Print e Use Mean Offset Use Mean 5 0 o Use Range Offset O Stds Only Lower Limit as of Mean 5o save Upper Limit as of Mean 150 T Short unes NF Thermo Scientific Watson TSO Module User Guide 71 6 Watson Working with Processed Runs Reviewing Internal Standards and Performing Regression The Chart page contains the following areas Analysis type Raw Data Analysis Mean Sample Information Run Sample Sequence Number Difference Sample Type Watson sample ID Zoom options Click to allow zooming e Y Axis scaling Set the Y axis scaling To update edit the Min Y and Max Y fields and click Update Y Axis To restore defaults click Restore Defaults Calculation of Internal Standards Limits Determine the criteria for calculating internal standards Sample types to be used for mean Select the option next to the sample type to select
7. Date when samples in the run were extracted The user who created the run in the Watson application Observations Watson TSO Module User Guide The Watson application user comments Thermo Scientific LLL m Restarting Runs This appendix describes the process of restarting the acquisition of a run after it has been stopped Contents e Restarting a Run from within the TSQ Module Application Returning a Run to the Watson Application Re injecting a Run from the Watson Application For several reasons a user might remove a run from the TSQ Module application before it completes acquisition and return it to the Run Manager view or to the Watson application A run can be restarted within the TSQ Module application or returned to the Watson application From the Watson application you can modify a run that has been returned from the TSQ Module application and send the run back for re injection When a run is returned for re injection from the Watson application the TSQ Module application treats it like any other run Restarting a Run from within the TSQ Module Application For many reasons you might want to remove a run from the Acquisition Queue and later restart the run from the Run Manager view This section describes the following Restarting a Stopped Run at the Beginning e Restarting a Stopped Run at a Specific Sample Restarting a Run from the Run Manager View Workflow Thermo Scientific Watson TSQ
8. Run Edit Editing Database http 3 Drugs svc Project Test Study Study Run 2 LevellD Blank LevellD StdBracket LevellD 3 0 3 Table 14 Setup mode parameters Parameter Description Save Run Saves the edits you made to the run The Save Run command can be specified to require an electronic signature See Using E Signatures on page 25 Columns Sample Type Defines how the Watson application processes the sample data Each sample must be classified as one of the following sample types Unknown Blank QC quality control Standard Sample ID An alphanumeric string of characters that can be used to uniquely identify the sample Level The level defined for a calibration sample or quality control sample Position Sample position number in the autosampler usually provided by the Watson application This column value is editable Injection Volume uL Microliters to be injected When you have an autosampler configured the injection volume is validated against the allowable range specified by the autosampler When you do not have an autosampler configured you can enter a range of 0 1 1000 This column value is editable Comment Optional information about the sample This column value is editable Watson TSO Module User Guide 93 A TSO Module Menu and Toolbar Reference Acquire Mode Acquire Mode From the Acquire mode you can specify acquisition sett
9. linear calibration curve A linear first order polynomial least squares fit of the experimental data using slope and intercept coefficients See also calibration curve linear gradient curve A gradient curve with a constant rate of change between solvent compositions Thermo Scientific Glossary See also gradient curve liquid chromatography mass spectrometry LC MS An analytical technique that combines a high performance liquid chromatograph LC and a mass spectrometer MS Refers to either the assay methodology or a Watson application assay type list separator character The character used to separate columns of a column separated value text file of extension csv locally weighted calibration curve A calibration curve that is constructed from individual line segments At multiple points across the calibration region a weighted linear regression is performed The point slopes are then connected to form a continuous curve See also calibration curve locked workbook A copy of a workbook and its associated files that displays Locked in the title bar and in the status bar No processing or acquisition can take place in locked workbooks The only functions that are allowed are those that review data and print reports log file A text file with a log file extension that is used to store lists of information master assay Specifies the assay definition at the global system level It defines instrument i
10. sueeuuueuuuees 87 Using the Men spss pt ee e qo EY E le pde ia a ede ic dana ees 88 TSQ Application Menu Commands s eerie poc ON eas 88 Title Bar and Ribbon Commands 122a os Ete ee rcr Se uper eie 89 Status DAP c aree ehe toad iram aps tb Remeras ev pe octies s 89 Accessing TSQ Module Modes 552 EVADERE ERES ERE e 90 Select MOUE Anis dice meia o Sonia Axio auda ee Gato aed arae dep 91 Setup Mode us a aa isl die dc bo ee 93 Acque boda cid eed ibt aote s em dta area desig eee ee Gu PE D 94 Status MOS Corso dor eh Rees d Rates dd hd Rudd dd a 97 Mariage Mode wi acce por rio RO KE ECRIRE ROM Ea era 99 Thermo Scientific Thermo Scientific Contents Appendix B Restarting Runs 00e cece eee eee eee nne 101 Restarting a Run from within the TSQ Module Application 101 Restarting a Stopped Run at the Beginning 00 0000 102 Restarting a Stopped Run at a Specific Sample 1 00 0 00 000 0000 102 Restarting a Run from the Run Manager View Workflow 103 Returning a Run to the Watson Application 0 0 0 0 cee eee eee 104 Returning a Run to the Watson Application Workflow 105 Re injecting a Run from the Watson Application 0 00 0000 106 Selecting Samples to Re Ihject ioi terea Roe Mane Ae dns 106 Canceling Re injected Acquisitions 42 52 vene EX rr 107 Accepting the Analyte Results from the Standard Regression Form 107 Appendix C
11. 3 Click Yes to confirm the cancellation Ifthe run had not begun acquisition a Watson user can assign the run to a different instrument and re send the run to the TSQ Module application Ifthe run had begun acquisition a Watson user can re send the run to the TSQ Module application but it must be assigned to the same local instrument The entire run must complete acquisition on a single instrument A run returned for reinjection cannot be assigned to a different instrument To cancel multiple runs You can cancel Pending or Stopped runs and return the runs to the Watson application You cannot cancel Acquiring or Submitted runs Select the runs you want to cancel and return to the Watson application Use the Shift key to select a group of consecutive runs Use the Ctrl key to choose a group of non consecutive runs The selected rows are highlighted Run Manager Selected rows Pending http 3 Drug ProgTest_Sh_ Pending http 7 3 Drug Proglest_Sh_ F Pending http 3Drng_ ProgTest Sh Ta Pending http 3 Drug ProgTest Sh Choose Cancel Run The system confirms that you want to cancel multiple runs and return them to the Watson application The system warns that you cannot cancel Acquiring or Submitted runs Click Yes to confirm the cancellation The runs are immediately returned to the Watson application Any selected Acquiring or Submitted runs that remain in the Run Manager view are n
12. Crested Analytical Run Sample pp Sample Name 2870000007 0002 A Plasma Zh Created Analytica Run Sample Damen Sungie Nane STDI 1 Created Analyucal Run Sample mere Rezgection Testng Study Sample Name QC11 Created Analytics Run Sample er Semple Nane CONTROL BLANK Run 3 Postion 1 Watson ID 28700001 Custonld 23870000001 0001 A Pherae Oh Injections Vohame changed from mall to 2 Run 3 Postion 1 Watson ID 22700001 Caurtomld 2170000001 0001 A Pharme Oh Extemal Vial Posison changed from eral to 1 1 Run 3 Postion 2 Watson ID 22700002 Castomi4 2270000002 0001 A Plasma 1 1h Injection Vohame changed from mull to 2 Run 3 Postion 2 Watson ID 28700002 Cartomld 2170000002 0001 A Plasma Ih External Vial Posdron c from eval to 1 13 Run 3 Postion 3 Watson ID 21700003 Custom 2570000003 0001 A Plasma Zh Injection Vobame changed from mull to 2 Run 3 Postion 3 Watson ID 22700003 Custom 2270000003 0001 A Plasma 2h External Vial Powteon changed from mall to 1 25 Run 3 Postion 4 Watson ID 21700004 Curtomld 21870000004 0001 A Pharme Mh Injection Vobume changed feces mull to 2 Run 3 Postion 4 Watson ID 22700004 Custonld 2170000004 0001 A Plesme 3h External Vial Postson changed from eval to 1 37 Run 3 Postion 5 Watson ID 21700005 Castom 4 2170000005 0002 A Plasma Oh Injection Tohme changed from null to 2 Run 3 Position Watson ID 21700005 Customld 2170000005 0002 A Plasma Oh Exteenal LIC diantos steet
13. Unknowns zodone m z 0 RT 0 5 1 5 NL 2 32E4 M ms2 470 18 cid 26 00 180 07 274 08 Alprazc F c SRM 100 80 60 40 Relative Intensity 20 2 2 2 3 2 4 2 5 To view a chromatogram in the gallery 1 From the Run Review view select an analyte 2 Right click and choose View in Gallery from the menu 3 Select one of the following Analyte Only Analyte amp Int Std or Int Std Only 68 Watson TSQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Changing the Chromatogram Display Figure 17 Gallery view analyte only Nefazodone mz RT 05 15 NL 23264 F c SRM ms2 470 1833 26 00 180 07 274 08 241 f gt 1 I RT min ankle Por bom 1 Dt 4 Click Exit to close the gallery window 4 To zoom in on a chromatogram 1 Select a sample 2 Zoom in on the corresponding chromatogram by dragging the cursor 3 To reset the chromatogram right click and choose Reset Scaling Additional Run Review Features In addition to using the display features of the Run Review view you can do the following Show All Injections Accept a Run Resubmit a Run to a Different Instrument Show All Injections When the Show All Injections check box is selected all injection values that exist for all run samples are displayed When the Show All Injections check box is cleared only the last injection values for the samples in the run are displayed This has a
14. fragment mass The calculated sum of all the masses of the amino acids in the fragment full loop injection A technique that injects a sample volume into the loop that is about twice the loop volume so that the loop is completely filled FX An abbreviated form of the phrase fixed Y axis normalization mode This shortened form is used to save space in the header of the Spectrum view when the fixed Y axis normalization mode is in use for example FX 1 98e 003 1 98 x 103 G gateway Communication protocol used with the Watson application to add or remove interfaces gateway based interface Interface software is a separate application Gaussian smoothing A smoothing algorithm that averages each data point with neighboring points to give the displayed value A Gaussian smoothing uses weighting coefficients corresponding to a Gaussian peak shape GCMS gas chromatography mass spectrometry Refers to either the assay methodology or a Watson application assay type GCP Good Clinical Practices GLP Good Laboratory Practices gradient Changes in the percentage composition of two or more solvents over time Thermo Scientific Glossary gradient curve The shape of the solvent composition curve between two time lines Gradient curves are determined by specifying initial and final times and concentrations Graph view file An ASCII text file with the extension grf that a user creates to save data from the Graph view in the Tu
15. 23 24 25 26 27 28 29 30 RT min Anabyte Paroxetine Internal Standard Alprazolam d 5 ea see ee S 3TEM 62 Watson TSQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Reintegrating Chromatograms Reintegrating Chromatograms This section provides instructions for reintegrating chromatograms Reintegrate chromatograms by doing one of the following Changing the peak processing parameters E Moving the baseline Use the following procedures To change the processing parameters To configure identification parameters To configure the ICIS integration parameters To configure the ICIS advanced parameters Thermo Scientific Watson TSO Module User Guide 63 6 Watson Working with Processed Runs Reintegrating Chromatograms To change the processing parameters 1 Select a row in the top part of the window 2 Right click and choose Reintegrate gt Analyte or Int Std from the menu The Reintegrate Chromatogram view opens with the Identification page displayed Figure 13 Reintegrate Chromatogram view Identification page III Reintegration BEI Sample name New study 031150000009 0001 A Plasma 1 8h Analyte name Alprazolam d5 Percent Change 0 Original parameters Identification ICIS Integration 1CIS Advenced Detector MS Trace MassRange Mass m z 209 96 209 96 Filter c SRM ms2 314 10 cid 40 00 209 96 Smoothing points 1 Min Peak
16. Continuous update Displays the mass spectrum in the spectrum pane Continuously updates the spectrum trace to show the most current scan Manual select Display the spectrum trace of the currently selected peak User defined RT range Displays chromatograms with a time range between the times specified in the Min RT and Max RT boxes Watson TSO Module User Guide 97 A TSO Module Menu and Toolbar Reference Status Mode 98 Table 16 Status mode parameters Sheet 2 of 2 Parameter Description Min The start time of the chromatogram traces Note The Min box becomes active only when you select User defined RT range Max The end time of the chromatogram traces Note The Max box becomes active only when you select User defined RT range Apply Settings Applies the display settings to the current real time display Starts an acquisition or resume an acquisition that has been paused Pauses an acquisition after the current sample has been completely acquired Immediately stops the current acquisition Acquisition for the current sample stops and the sample is considered complete The acquisition for the run is paused Pauses the real time display during an acquisition Displays the Spectrum pane below the Chromatogram pane Stopped Submitted Pending Shortcut menu Status indicators at the bottom of the window report the number of runs for each type of status Right click the
17. Method Asso iat ion From this dialog box select the instrument group and stack defined in the Instrument Inventory dialog box Type a description in the Description box Upload Analysis Tune Analysis Method and Processing Parameters files by clicking the corresponding buttons If necessary click Clear to clear the fields Similarly you can upload or clear Startup Tune Startup Method Shutdown Tune and Shutdown Method files Click OK in the Add Instrument Method Association dialog box Click Save in the Assay view When you are in LCquan import the saved TSQTune lqn and XML files When you are in Xcalibur import the saved TSQTune meth and XML files Note You can use the Watson application to associate multiple method files with an assay or instrument by repeating these steps and saving the changes when you are finished Click the Standards tab Set the Injection Volume This field is required input for TSQ type assays This injection volume is sent to the instrument for runs using this assay Watson TSO Module User Guide 15 2 Watson Submitting Runs to the TSQ Module Working with a Watson Study Working with a Watson Study The following procedures provide instructions for working with a study in the Watson application For additional information refer to the Watson User Manual Use the following procedures To open a study To create a study To copy the
18. Thermo Scientific 7 Watson Reports and Printing Capabilities Audit Reports Generating a TSQ Module Status Audit Report This Status Audit report provides you with more detailed information about the samples in a run To generate this report follow standard Watson application processing as outlined in this section Note that in the example below TSQ Module specific data is shown The Runs are labeled as reinjection and the instrument type is Peak Integration To generate a TSO Module status or audit report 1 Create or open a TSQ Module study 2 Choose Analytical gt Analytical Run Actions The Create Sequence File Import Results and View Analytical Run view opens Figure 26 Create Sequence File Import Results and View Analytical Run view Instrument Assay Run T T 7 Biclogeal Standard Se BM oss BE Te T n d MN eli SA DUNMD l Accepted UNKNOWNS Reiyection Test Master Assay 29 Mas 2009 LCAMS MartirPealintegrason MetinPeakietegration Plasma 2 71 M 2009 LOMI Mart rPeslintegratson MartinPeskdetegration Plasma 2 3 Mw 2009 LOMI Martrf ealintegratson MwtnPeakintegration Plasma 2 Ea Choose an Analytical Aun to petom operaton on SYSTEM 3 Select a run and click Status Audit Report The Watson application generates the Status Audit Report Figure 27 Status Audit Report Anaa Run Study Sample info UNKNOWNS Reagection Test Master Assay UMIQROWNS Rewgectson Test Master Assay UNK
19. segments SIM and SRM for example scan width The width of the scan range in m z units When you use a center mass scan width input method to define the scan range the scan range is centered symmetrically about the specified center mass search window A time range or mass range to limit a search for similar scans segment A period of time during a mass spectrometer run semi automatic calibration A procedure that calibrates the MS detector automatically one or more parameters at a time See also calibration parameters sensitivity The signal obtained per amount of sample introduced Different measures of sensitivity are recommended depending on the nature of the sample and the required inlet system See also detection limit septum purge flow The flow in mL min from the septum purge line which sweeps out any residual sample after sample injection sequence The series of samples rows selected for analysis sequence file A file that you create that provides instructions about how to run a sample or list of samples 142 Watson TSO Module User Guide sequence length The number of amino acids in a peptide See also amino acid serial port An input output location channel for serial data transmission set mass The mass of interest It depends on the scan mode chosen For the Product scan mode the set mass is the parent mass For the Parent scan mode the set mass is the product mass For th
20. 3 In the Create Instrument Stack dialog box enter an Instrument Stack name 4 Optional Enter an autosampler or comment 5 Click Save To clone an instrument stack 1 Choose Options Instrument Inventory to open the Instrument Setup window 2 Select an instrument and then click Clone The Clone Instrument dialog box opens populated with the stack information Figure 2 Clone Instrument dialog box Instrument Interface Xcaibur Digtal GC MS un Test URL Locator Choose 8 Watson TSO Module User Guide Thermo Scientific Thermo Scientific 2 Watson Submitting Runs to the TSO Module Creating a Peak Integration Instrument To modify stack information click the appropriate field To test the URL click Test URL If the Watson application is unable to access the URL you receive an error message To specify a location click Choose and select a location Do one of the following To save the cloned instrument click Save Ge To exit without saving any changes click Cancel To edit an instrument stack Choose Options Instrument Inventory The Instrument Setup window opens Select an instrument stack and click Edit The Edit Instrument dialog box opens populated with the instrument information To modify instrument information click the appropriate field Doone of the following To delete save the device click Save NS To exit without making any changes cl
21. All Active Samples STDs only STDs and QCs only Calculation Method Use Mean offset Select and enter the lower limit of percentage of mean and upper limit of percentage of mean Use Mean SD Click the Number of SDs field and type a number Use Range offset Select and enter the lower limit of percentage of mean and upper limit of percentage of mean Click Update Limits to update the limits Print Print the raw data analysis e Save Save the raw data analysis Exit Exit the page Figure 19 Raw Data Analysis view Grid page 15 Area Sample Type Lent Check Included in Caks gt sa COTY 2 EY S PRS Te Int Rd review method Mean j offset SO of mn 150 of Max Lower Unt 9 296 090 00 Upper Laat 27 888 270 00 18 592 100 00 72 Watson TSQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Reviewing Internal Standards and Performing Regression To filter sample types from the run results 1 Open a study with an associated Peak Integration instrument 2 Choose Analytical gt Analytical Run Actions 3 From the run results select a run that contains results and click Review Al results are shown in the initial view You can select one sample analyte at a time from the list of samples in a run and display chromatograms and information about that analyte s peak and its associated internal standard peak When this view loads it defaults to All
22. Environment address http localhost 9001 other Host9001 SystemAudit gt lt Environment address http localhost 9002 other Host9002 gt lt Environments gt Where xm version 1 0 encoding utf 8 isa typical XML header Environments is a group or collection of Environment nodes Environment is the node type name address is the http address of the Watson application server other is the friendly name to use for that Watson application server SystemAudit optionally sends system level audit logs to this server for acquisition events Communicating with the Watson Application The TSQ Module application continuously communicates with the Watson application When you edit the sample parameters in the TSQ Module application it sends the edits to the Watson application The TSQ Module application authenticates every edit in the Run Setup view and sends an audit trail to the Watson application e As each sample completes acquisition the TSQ Module application returns the resulting data to the Watson application in XML format along with any new auditing information for the run After the TSQ Module application passes the sample data to the Watson application database and the Watson application acknowledges receipt of the data the TSQ Module application deletes any related temporary data from the local system The TSQ Module application continues to send audit records to the Watson application until the acquisi
23. Figure 32 Calibration Curve Generated by Using an Internal Standard Response ratio for 1 24 unknown sample Unknown A 0 0 T T T T Response for target compound response for ISTD 0 0 0 5 1 0 1 5 2 0 2 5 Amount of target compound A 116 Watson TSQ Module User Guide Thermo Scientific Sample Types Standards Unknowns QCs Blanks Thermo Scientific C Quantitative Analysis Overview Sample Types Each quantitative analysis consists of a number or sequence of samples The sequence represents the order of sample analysis A quantification sequence contains One or more standards One or more unknown samples For more demanding applications you can also use optional quality control QC samples and blank samples A calibration standard is a sample containing known amounts of all target components The purpose of a standard is to measure the response of the instrument to the target components so that the processing software can generate a calibration curve for each component An unknown sample is one containing unknown amounts of the target components The processing software performs quantitative analysis on any sample defined as an unknown sample A QC sample contains a known amount of one or more specific target compounds The processing software places QC samples in the sequence so that it can test quantitative analysis results for quality assurance purposes After the QC sample is analyzed The
24. Height S N Retention Time Expected min Window sec 1501 View Width min 10 75 New study 031150000009 0001 A Plasma 1 8h Alprazolam d5 m z 209 961 RT 2 295 3 045 NL 1 02E5 F c SRM ms2 314 10 cid 40 00 209 96 RT 2 654 AA 343213 255 AH 100930 975 100 Relative Intensity o co So Ss gt eo N eo 2 867 2 936 3 001 2 3 24 2 5 2 6 2 7 2 8 2 9 3 0 RT min Modified parameters Identification ICIS Integration ICIS Advenced Detector MS Trace MassRange Mass m z 209 96 209 96 Filter c SRM ms2 314 10 cid 40 00 209 96 Smoothing points 1 Min Peak Height S N 0 Retention Time Expected min 2 67 Window sec 1800 Update Chromatogram View Width min 0 75 Reset Parameters New study 031150000009 0001 A Plasma 1 8h Alprazolam d5 m z 209 961 RT 2 295 3 045 NL 1 02E5 F c SRM ms2 314 10 cid 40 00 209 96 RT 2 654 AA 343213 255 AH 100930 975 eo e eo eo o eo Relative Intensity 20 2 867 2 936 3 001 2 3 24 2 5 2 6 2 7 2 8 2 9 3 0 RT min To configure identification parameters 1 Click the Identification tab 2 Type values in the following fields in the top right view Smoothing points Enter an odd numbered value between 1 and 5 Min Peak Height S N Enter a value between 0 00 and 999 00 Retention Time Enter a value between 0 00 and 999 00 Expected min 64 Watson T
25. Instrument Figure 3 Clone Device dialog box Device Name Device Type sce Manufactures eme C S tes Save Cancel 4 Do one of the following To save the device click Save Ls To exit without cloning the device click Cancel To edit a device 1 Choose Options gt Instrument Inventory The Instrument Setup window opens 2 Select a device and click Edit The Edit Device dialog box opens populated with the device information 3 To modify the device information click the appropriate fields 4 Do one of the following To save changes to the device click Save QOr To exit without making any changes click Cancel Thermo Scientific Watson TSO Module User Guide 11 2 Watson Submitting Runs to the TSQ Module Tune Method and Processing Method Files in LCquan and Xcalibur To delete a device 1 Choose Options gt Instrument Inventory The Instrument Setup window opens 2 Select a device and click Delete A confirmation message opens 3 Do one of the following To delete the device click OK QOr To exit without making any changes click No Tune Method and Processing Method Files in LCquan and Xcalibur This section provides a list of tune method and processing method files in Xcalibur and LCquan Use the LCquan LDK software to convert the lqn or pmd file to XML format Table3 Xcalibur and LCquan tune method and processi
26. Kevins Sagebrush Kenns Sagebrush Fiasma 14 Subeutted to TSQ Modde UNKNOWNS AP testi 01 May 2009 LCMS Kevins Sagebrush Kenns Sagebrush Fiasma 15 In Process 1 of 13 Acquaed UNKNOWNS AP testi 01 May 2009 LCMS Kevins Sagebrush Kenns Sagebrush Plasma 16 Completed UNKNOWNS AP_test 11 May 2009 LCMS Kevins Sagebrush Kenns Sagebrush Plasma 17 Completed 11 May 2009 LCMS Kevins Sagebrush Kevins Sagebrush Plasms 18 Submated to TIQ Module 11 May 2009 LCMS Kevins Sagebrush Kenns Sagebrush Plasma LCMS Kevins Sagebrush Kenns Sagebrush Plasma LCAMS Kewvins Sagebrush Kevins Sagebrush Plasms Run Status Definitions The following is a list of common run statuses when working with runs that are submitted to or processed by the TSQ Module application For a complete list of run statuses refer to the Watson User Manual Submitted to TSQ Module The run has been submitted to the TSQ Module application for processing Completed The run has been processed and is now complete Created The run has been created but has not yet been submitted for processing Canceled by Notification that the run has been canceled and where the cancellation occurred In Process The run is currently being acquired Thermo Scientific Watson TSO Module User Guide 61 6 Watson Working with Processed Runs Reviewing Runs To view an ongoing or incomplete run 1 Select a run labeled as In Process 2 Click Review Run results appear Completed runs are l
27. OK The Method Exporter application remains open You can export additional files to the common folder 7 When you have finished exporting method files click Exit The Method Exporter application closes Thermo Watson TSO Module Method Exporter x Thermo Watson TSQ Module Method Exporter 1 0 0 93 Source files Xcalibur pmd or LCquan lgn filename aved Method Files Method Files for ExportsLCquan method amp lqn Instrument Method meth filename aved_Method_Files Method_Files_for_Export LCquan_Accela meth Tune TSQ Tune filename Data Saved_Method Files Method Files_for_Export TSQ TSQTune Target folder path for all exported files Table 4 Thermo Watson TSO Module Method Exporter parameters Sheet 1 of 2 Parameter Description Source files Xcalibur pmd or Path to the Xcalibur or LCquan processing file to convert to LCquan lqn filename XML format and export to a common folder 22 Watson TSQ Module User Guide Thermo Scientific 3 TSO Module System Administration Exporting Method Files to a Common Folder Table 4 Thermo Watson TSQ Module Method Exporter parameters Sheet 2 of 2 Parameter continued Description Instrument Method Path to the instrument method file to export to a common meth filename folder Tune TSQTune filename Path to the tune file to export to a common folder Target folder for all Path to the common folder in which exported files are saved
28. Ready if no run is acquiring and the number of runs that have the status Pending Submitted or Stopped Acquiring Test_Study 31 Stopped 2 Submitted 1 Pending 1 Thermo Scientific Watson TSO Module User Guide 89 A TSO Module Menu and Toolbar Reference Accessing TSO Module Modes Accessing TSQ Module Modes The TSQ Module application uses five functional modes Select Setup Acquire Status and Manage Access the Select mode from the TSQ Module application menu see TSQ Application Menu Commands on page 88 Access the other modes from the navigation 90 pane Mode Select Description The Select mode is the first mode you see when you log in to the TSQ Module application In the Select mode you can select a run for acquisition Setup From the Setup mode you can edit the Position Injection Volume or Comment values for a sample Acquire From the Acquire mode you can specify acquisition settings and start the acquisition of a run Status Manage Watson TSQ Module User Guide From the Status mode you can start stop or pause an acquisition monitor the run manager and instrument status monitor the Acquisition Queue or control the real time display From the Manage mode you can monitor the status of the runs cancel a run and return it to the Watson application or select a run for acquisition Thermo Scientific A TSO Module Menu and Toolbar Reference Select
29. Scientific Watson TSO Module User Guide 49 5 TSO Module Acquiring Data Monitoring the Run Status To immediately stop the current acquisition click Acquisition for the current sample stops and the sample is considered complete The acquisition for the run is paused To pause the real time display during an acquisition click 8 The acquisition continues only the display is paused To resume the real time display click again To display the Spectrum pane below the Chromatogram pane click To hide the Spectrum pane click again For a detailed explanation of how pausing stopping or canceling runs is managed refer to Pausing Stopping Canceling Runs on page 55 Run Status The Run Status page on the Run Status view displays information about the run currently being acquired Figure 7 Run Status page p lt Run Status Acquisition Queue B Run Manager Acquiring Sample ID 1 Position 2 B Simulation MS Running Run Name Test Study 21 Table 10 Run Status parameters Sheet 1 of 2 Parameter Run Manager Description state Reports the current status of the system Run Name Displays the run currently being acquired Sample ID Displays a unique alphanumeric name assigned to each sample The assigned name can be up to 50 characters long Position Displays the position including a tray name when applicable 50 Watson TSQ Module User Gu
30. a protein or peptide into smaller fragments of amino acids by use of the enzyme trypsin See also digest fragments trypsin TSQ mass spectrometer See triple stage quadrupole TSQ mass spectrometer 146 Watson TSO Module User Guide Tune Method A defined set of mass spectrometer tune parameters for the ion source and mass analyzer Tune methods are defined by using the Tune Plus LCQ Series LXQ and LTQ or Tune Master TSQ Quantum window and saved as the file type LCQTune LTQTune or TSQTune respectively A tune method stores tune parameters only Calibration parameters are stored separately not with the tune method tune parameters Instrument parameters whose values vary with the type of experiment tune plate A plate of compounds separated into different wells vials Each well represents compounds grouped together as a drug set tune mass spectrometer Tuning the mass spectrometer involves optimizing voltages currents flows and so on for the ion source parameters to achieve optimal mass spectral sensitivity and proper resolution tune MS detector automatic A procedure that automatically tunes the mass spectrometer See also tune MS detector manual tune MS detector semi automatic tune MS detector manual A process that lets you manually tune the mass spectrometer one parameter at a time See also tune MS detector manual tune MS detector semi automatic tune MS detector semi a
31. autosampler an error message shows you the correct syntax to use Enter a value for the first row in the fill down sequence Observe that this row is highlighted as the selected row You can begin the sequence from any row in the column Right click outside this cell but still in the Position column and choose Auto Fill Down The column values are incremented starting with the value in the selected row and ending with the last row in the run The TSQ Module application knows the number of positions configured in your autosampler and numbers the positions accordingly See Example 1 You can repeatedly use the Auto Fill Down command to create multiple sequences See Example 2 Fositi Auto Fill Down AAI 3 4 42 Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data Editing a Run Example 1 The TSQ Module application knows sequential order of the positions configured in your autosampler and numbers the positions accordingly AAI AA AAI AAA AAB AAG AA AAB A A9 A A10 AAT A A12 A B1 A B2 Example 2 You can repeatedly use the Auto Fill Down command to create multiple sequences AAT A A2 A B1 A B2 To automatically enter Injection Volume column values Right click the Injection Volume column and choose Auto Copy Down The first row value is copied to all rows Auto Copy Down Thermo Scientific Watson TSO Module User Guide 43 5 TSO Module Acquiring Data Editing a Run Se
32. by the database project and study to which it belongs A study contains design information about the subject treatment sampling times and planning of analytic runs The project and study names are displayed in the Run Name columns of the TSQ Module application queues The assay method for a run is defined in the Watson application The creation date of the assay is displayed in the Assay Date columns of the TSQ Module application queues For detailed information about setting up runs in the Watson application see Chapter 2 Watson Submitting Runs to the TSQ Module Starting the TSQ Module Application Follow these instructions to install and start the TSQ Module application Use the following procedures e To set up and install the TSQ Module application To start the TSQ Module application To log in to the Thermo Watson TSQ Module application To set up and install the TSO Module application 1 To install the Xcalibur 2 1 application and your TSQ instrument driver follow the instructions on the included CDs 2 Install the driver for your LC pump and autosampler Thermo Scientific Watson TSO Module User Guide 27 4 TSO Module Getting Started Starting the TSO Module Application 3 Insert the Watson TSQ Module CD in the drive and follow the on screen instructions If the install windows don t automatically appear navigate to the Xinstall exe file and launch it 1 To start the TSQ Module application
33. currently acquiring Acquiring The run has progressed to the top of the Acquisition Queue and is currently acquiring e Paused The run was assigned to an instrument and was acquiring but has been paused and is waiting between samples Stopped The run was assigned to an instrument and was acquiring but was removed from the Acquisition Queue Completed The run has completed acquisition Note Completed runs might not always be observed in the Run Manager view When the TSQ Module application finishes sending the results of the last completed sample to the Watson application it marks the run as Completed and quickly removes the run from the Run Manager view To add or remove columns 1 Click the Column Selector icon in the upper left corner of the view The Column Selector dialog box opens Column Selector 2 v ue 2 Check the box before a field name to display that column or uncheck the box before a field name to remove that column from the display This action is immediately implemented in your display and retained throughout your session but the column choices are not saved when you exit the TSQ Module application 3 When you are finished adding or removing columns click the red X in the upper right corner to close the Column Selector dialog box Thermo Scientific Watson TSO Module User Guide 35 5 TSO Module Acquiring Data Managing a Run 36 The Run Manager view in
34. exported files Export Converts the pmd or Iqn file to XML format and copies all specified files to the target folder Exit Closes the Thermo Watson TSQ Module Method Exporter application without exporting any files Help Opens the Thermo Watson TSQ Module Method Exporter Help Exported LCquan Parameters Thermo Scientific When you export an LCquan lqn processing method the following parameters are included for each component in the exported file Component name Detector type Smoothing points Number of mass ranges Mass ranges Trace type Mass range or TIC Base peak is converted to mass range if present or TIC Filter Adjust expected RT User entered RT Search window Display width Peak detection algorithm ICIS only Baseline window Area noise factor Peak noise factor ICIS Constrain peak width ICIS Peak height percentage ICIS tailing factor Peak identification Locate method or peak detection index ICIS noise method ICIS calculate noise as RMS ICIS Minimum peak width ICIS Multiplet resolution ICIS Area tail extension ICIS Area scan window Watson TSO Module User Guide 23 3 TSO Module System Administration Auditing Auditing The TSQ Module application immediately transmits system level audit records such as instrument errors to the Watson application The application collects and packages run level audit records with run result or run complete XML data for a particular run Au
35. for the external trigger feature predicted digest fragments Sequence fragments calculated in Pepmap Predicted digest fragments are the theoretical sequence fragment obtained by performing a hypothetical digest on the entered sequence privilege One specific assigned security element Thermo Scientific processing filter A filter that defines the characteristics of a spectrum displayed in the MS Browser These filters are displayed in the MS page of the Info bar in the Qual Browser window There are two types of processing filters Composite Spectrum processing filter and Average Spectrum processing filter processing method A defined set of parameters that provide Xcalibur and LCquan with a recipe for automatic quantitation and report generation Each method can define single or multiple target compounds single or multiple internal standards and one or more undefined components Multiple internal calibration levels or QC levels can be defined for target compounds Processing Sequence A defined set of processing settings for a single sample or list of samples A Processing Sequence can contain unknown samples calibration standard samples quality control QC samples and blank samples product spectrum Displays the product spectrum for the selected parent in the Spectrum pane This spectrum consists of all of the products from the parent in the data that is the closest to the selected parent mass coordinate profile da
36. instances and databases Re injecting samples without creating a new run in the Watson application Watson TSO Module User Guide Thermo Scientific 1 Introduction Watson LCquan Xcalibur TSQ Module Workflow Watson LCquan Xcalibur TSQ Module Workflow Method development method development analysis processing method instrument method Watson and TSQ Module C E et epi eh c T T M T M e em a Select Peak Integration Create a Enter internal Select an instrument and configure master assay standards ISTD ISTD for the instrument stack Master Assay Form Int Standards tab Each Analyte Log in to Watson Add Instrument Enter analyte name Enter n Method Association and select standards sample Enter QCs o nini Save the Tune file method file concentration units information QC tab Master Assay processing parameters Analyte tab Standards tab Instruments tab Copy Master Assay to Study Assay Create or open study Add samples to study Review real time run status Submit run to TSO Module Create a sequence file Review ISTD Report Modify samples if appropriate Initial data processing is done peak integration reintegration Watson stores the data file Run complete Perform standard regression View audit trail LLL Watson top level LLL Watson sub step TSO Module ENS LCquan Xcalibur Thermo Sc
37. is the first run in the queue the acquisition begins and the status of the run is reported as Acquiring in the Run Manager view f there are other runs in the queue the run is added to the queue and the status of the run is reported as Submitted in the Run Manager view Watson TSO Module User Guide 45 5 TSO Module Acquiring Data Acquiring a Run When acquisition for a run is complete the run is removed from the Run Manager view and the results are returned to the Watson application For detailed information about monitoring a run as it acquires see Monitoring the Run Status on page 48 Acquire Options T Acquire Acquire samples d Priority Run Additional comment Instrument Method a lal System power scheme 0n Standby L Off Table 9 Acquire options parameters Sheet 1 of 2 Parameter Description Acquire samples Displays the first and last samples to acquire Available only for a previously Stopped run Priority Run Inserts this run into the Acquisition Queue ahead of all submitted non acquiring runs Additional comment A comment that is returned to the Watson application in the run report Instrument Method Startup Method Specifies that the TSQ Module application runs the startup method specified in the run data before the run starts No data is acquired by this method and no autosampler injection takes place This feature is not available for all devices 46 Watson
38. master assay to the study assay To create a new run with the study assay To add samples to the work list To review the Plate Report page when planning an analytical run To create a sequence file To send the run to the TSQ Module application To open a study From the Watson application main menu choose File Study The Study dialog box opens Use this dialog box to create a new study or to work with an existing study within a project You can also work with any recent studies listed at the end of the File menu Select a study For more information refer to the File Menu chapter in the Watson User Manual To create a study From the Watson application main menu choose File Study The Study dialog box opens Click Create Enter values in the fields and assign the study to the correct project If you have not created the project for this study click Cancel and create the project by choosing File Project Click Save to save the study information The Assign Many Users to a Single Study Form opens Assign appropriate users to the study by selecting them and then clicking gt right arrow button 16 Watson TSQ Module User Guide Thermo Scientific Thermo Scientific 2 Watson Submitting Runs to the TSO Module Working with a Watson Study 6 Click Save For more information refer to the Study Actions chapter in the Watson User Manual From the Design menu do the following a C
39. normal scan types Scan types that are full and SIM Normal scan types all have the same scan rate and provide unit resolution normalization A data analysis procedure where all peaks are reported with heights relative to the highest peak height or area in the chromatogram spectrum or map See also fixed Y axis normalization mode normalize Y axis normalization mode normalize spectra The action of normalizing spectra to a common base peak intensity instead of using the raw intensities from the raw file before it generates correlation results Normalizing the spectra corrects for intensity discrimination in the correlation results that can occur if spectra with significantly different absolute peak intensities are used normalize Y axis normalization mode A display mode which is available for the Spectrum view that sets the vertical scale equal to the height of the largest peak in a mass spectrum In the normalize display mode the software always displays the largest peak in the spectrum at full scale See also fixed Y axis normalization mode nucleic acid Biologically occurring poly nucleotides showing the nucleotide residues linked in a specific sequence by phosphodiester bonds for example DNA and RNA Watson TSQ Module User Guide 133 Glossary nucleotide Any of several compounds that consist of a ribose or deoxyribose sugar joined to a purine or pyrimidine base and to a phosphate group and that are the basic st
40. of the measurement depends on the quality and to a lesser extent the quantity of the calibration data Mass Spectrometry Principles and Applications de Hoffman E Charette J Stroobant V Wiley New York 1996 p 162 Watson TSQ Module User Guide 113 C Quantitative Analysis Overview Quantitative Analysis Techniques The detection limit of the quantitative analysis method is the lowest concentration of analyte in a sample that can be detected but not necessarily quantitated as an exact value The lower and upper quantification limits are the lowest and highest concentrations of analytes in a sample that can be measured with an acceptable level of accuracy and precision In an analytical method the highest concentration calibration standard defines the upper quantification limit The quantitative analysis technique you use determines the manner in which the response is calculated both for generating the calibration curves and for subsequent quantitative analysis The two basic methods are described in these topics Using External Standards for Quantitative Analysis Using Internal Standards for Quantitative Analysis Using External Standards for Quantitative Analysis An external standard is a separate sample that contains the compound of interest at a known concentration in solution In the quantitative analysis that uses external standards a series of standards are analyzed and a calibration curve is constructed by pl
41. or amount of an ISTD in any standard or unknown sample remains constant Because quantitative mass spectrometric analysis usually involves multiple steps the total error in the analysis results from the accumulation of the errors at each step In general sample handling errors account for a larger fraction of the total error than do mass spectrometer errors Fortunately the internal standard method can reduce both sources of error For example internal standards can correct for variations in a components peak area that are caused by the following Injection irreproducibility Changes in analyte solution volume Matrix and coeluter interference both suppression and enhancement System instability Variations in the source conditions For maximum precision add the ISTD component as early as possible to the start of the sample work up particularly in those quantitative methods that require sample manipulations such as extraction cleanup and dilution Because the ISTD and non ISTD components are analyzed together the internal standard quantitative analysis approach has the advantage that it corrects for injection and other sample handling errors The ISTD must behave chemically in an identical or similar manner to the target compound through the extraction cleanup and analytical processes You can also add the ISTD component as the last step of sample preparation prior to the sample s use to compensate for fluctuations in the
42. p scores equal to or better than what was observed simply by chance Low expectation values represent better matches than high expectation values because they are less likely to include false positives expected amount The amount entered for each calibration level based on the calculated amount from analytical measurement and subsequent dilution See also calibration level expected RT The expected retention time RT ofa component See also retention time RT expected width A valley detection parameter that defines the minimum allowable time in minutes between the peak apex and a valley Valley detection must be enabled for this parameter to be active See also rise percentage valley detection Extensible Markup Language See XML Extensible Markup Language external standard A component not added to the target sample used to correct for instrument detection errors See also external standard calibration internal standard ISTD 128 Watson TSO Module User Guide external standard calibration A calibration that analyzes a range of known amounts of an external standard Xcalibur plots the component amounts and their corresponding response values to create a calibration curve See also calibration Extensible Markup Language internal standard ISTD calibration external wash The passing of solvent through the syringe needle while the needle is inserted in the wash station ex vivo In an artificial env
43. salts and contaminants in the eluate Specifically you must ensure that what goes into the inlet of the mass spectrometer does not suppress ionization of the compound of interest Salt concentrations above 10 mM and strong acids and bases damage the LC column Modifier concentrations greater than 10 mM are not usually necessary for chromatographic stability and can suppress ionization of other compounds For best results whenever possible use volatile modifiers Volatile modifiers include the following e Acetic acid Ammonium acetate Ammonium formate Ammonium hydroxide Formic acid Trifluoroacetic acid Your analyte solution can contain neutral particles or ions If the solution contains ions the ions can carry a single charge or multiple charges The number of charges depends on the structure of the analyte and the composition and pH of the mobile phase Solvent systems are generally composed of organic solvents water and volatile modifiers The ionization characteristics of your analyte influence your decisions about the optimum pH of your solvent system and the type of probe to use at the interface of the LC and the mass spectrometer Thermo Scientific Watson TSQ Module User Guide 111 C Quantitative Analysis Overview Considering the Variables of Quantitative Analysis by LC MS MS 112 With the TSQ Quantum series LTQ series or LCQ series instruments you can use either the H ESI probe the ESI probe the APCI probe or
44. screen 28 Run Manager view 40 dataset 125 de novo sequencing 126 deconvolution 125 delay 125 Delta Cn 125 delta retention time 126 Description parameter 40 detection limit defined 126 overview 114 device s 126 digest fragments 126 digital 126 digital DM PK 126 dilution factor 126 display range 126 dose 126 draw speed 126 driver 126 drug set 126 duplicate entries 126 duplicate sample 126 DWP 126 dynamic nanospray probe assembly 126 dynamic NSI probe assembly 126 E early expiration 126 edge type 127 eject speed 127 electronic signatures 25 end bracket sample type 127 End Time 127 environment 127 Environments xml file 19 enzyme 127 enzyme digest 127 EQB 127 error log 127 ESI probe 112 event 127 event list 127 event time 127 ex vivo 128 exact mass 127 exception peak 127 Thermo Scientific Index E exclusion mass 128 expectation value e value 128 expected amount 128 expected retention time RT 128 expected width 128 Export command 23 external standard calibration 128 external standards defined 128 overview 114 external wash 128 Extraction Date parameter 40 F F 128 FDA 128 file based 128 Filter rise time 128 firmware 128 fixed Y axis normalization mode 128 flag 129 flush volume 129 fragment length 129 fragment mass 129 FTP directory 129 full loop injection 129 G gain 129 gateway 129 gateway based interface 129 Gaussian smoothing 129 GCMS 129 GCP 129 GLP 129 g
45. shaded area and its raw areas height It displays a descriptive header footer that contains the following information Design info Subject Treatment Group Nominal Day Nominal Hour Nominal Minute Split Watson Sample ID Watson Custom ID Mass data Q1 m z Q3 m z Method and Tune information Thermo Scientific Watson TSO Module User Guide 71 7 Watson Reports and Printing Capabilities Study level and Sample level Integration Reports Chromatogram data for example peak area peak height retention time acquisition date time in currently supported Watson date and time formats acquisition instrument info Watson information for example Study Run Position in run plate position injection volume Edit info for example date time and person last edited for reintegrations Multi Level Approval or eSig info of analytical run and individual chromatograms Figure 22 Study Level Integration report 4 29 2000 Instrument Serial Processing Param 3 Druas Wodbook lan Project Name Study Name Run Component Name Sample Type Actual RT erin Iniection Index Acqui sition interna Std Response Actual RT min 78 Watson TSQ Module User Guide Martin SBTett Arch ed amp Renamed 19 Nefazodote ac 2423 59943 4362015223 0 1670273069006704X 1 Martin SBTest Arch ed Renamed QC1 1 Alprazolamds 3563565 0554003410 0 Analysis Method Sim MS100 met A
46. the keyboard Delete key 56 Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data Monitoring the Run Status o VES All Runs Test_Study_20 Sample ID 1 Sample ID 2 Sample ID 3 The currently acquiring sample immediately stops and the run is removed from the Acquisition Queue The status of the run in the Run Manager view is Stopped When there are other runs in the Acquisition Queue the pause button is red indicating that it is ready to start the next queued run 2 To begin acquisition of the next run in the Acquisition Queue click Pause To remove a non acquiring run from the Acquisition Queue You can remove a run from the Acquisition Queue and resubmit it later For detailed information about restarting runs see Appendix B Restarting Runs When you remove an non acquiring run from the Acquisition Queue the run returns to the Run Manager view and its status returns to Pending When you resubmit this run to the Acquisition Queue it begins acquiring at the first sample Run Manager view Acquisition Queue Pending Run removed from queue Resubmitted run Begins at sample 1 1 To remove a non acquiring run from the Acquisition Queue check the run check box and press the keyboard Delete key Sj Test_Study_19 Sample ID 1 Sample ID 2 Sample ID 3 The run is immediately removed from the Acquisition Queue and the run returns to the Run Manager view as Pending
47. trace Displays the mass spectrum in the spectrum pane Continuous update Continuously updates the spectrum trace to show the most current scan Manual select Display the spectrum trace of the currently selected peak User defined RT range Displays chromatograms with a time range between the times specified in the Min RT and Max RT boxes Min The start time of the chromatogram traces Note The Min box becomes active only when you select User defined RT range 54 Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data Monitoring the Run Status Table 11 Status mode parameters Sheet 2 of 2 Parameters Description Max The end time of the chromatogram traces Note The Max box becomes active only when you select User defined RT range Apply Settings Applies the display settings to the current real time display Shortcut menu Right click the chromatogram to display the menu Reset Scaling Resets the X axis and Y axis ranges in the Chromatogram pane or the Spectrum pane to their default values Pausing Stopping Canceling Runs A run submitted by the Watson application enters the TSQ Module Run Manager view with the status Pending From the Run Manager view you can submit a run to the Acquisition Queue or cancel the run sending it back to the Watson application When you submit a run for acquisition the run moves to the Acquisition Queue and the status in the Run Manager view is Acquir
48. turned off nor does it indicate that all heated components are at room temperature To perform maintenance on an instrument refer to the hardware manual for your instrument Function buttons Run Starts the acquisition for the currently selected run and opens the Status view Thermo Scientific Watson TSO Module User Guide 95 A TSO Module Menu and Toolbar Reference Acquire Mode 96 Table 15 Acquire mode parameters Sheet 3 of 3 Command Columns Description Column values are not editable in the Acquire mode Sample Type Defines how the Watson application processes the sample data Each sample must be classified as one of the following sample types Unknown Blank QC quality control Standard Sample ID An alphanumeric string of characters that can be used to uniquely identify the sample Level The level defined for a calibration sample or quality control sample Position Sample position number in the autosampler usually provided by the Watson application Injection Volume Comment Watson TSQ Module User Guide Microliters to be injected When you have an autosampler configured the injection volume is validated against the allowable range specified by the autosampler When you do not have an autosampler configured you can enter a range of 0 1 1000 Optional information about the sample Thermo Scientific Status Mode bk Status Method
49. 0 Pp Pending Test Study 8 Thursday July 09 200 2 Pending Test Study 9 Thursday July 09 200 Use the following procedures To select a run To monitor the run status To add or remove columns To select a run In the Run Select view double click anywhere in the row of the run The Run Edit view in the Setup mode opens Setup Run Edit Editing Database http 3 Drugs svc Project Test Save Run LevellD 1 Blank LevellD 2 StdBracket 3 LevellD 3 0 3 The Sample Type Sample ID and Level are not editable columns as indicated by the blue background The Position Injection Volume and Comment columns are editable From the Run Edit view you can modify the editable parameters before you submit the run for acquisition Refer to Editing a Run on page 41 Tip To return to the Run Select view from any other view click the application button in the upper left corner and choose Select from the menu To monitor the run status Until a run completes and is returned to the Watson application you can monitor the status in the Run Select view The status can be any of the following Pending The run arrived from the Watson application and is assigned to the instrument at this workstation 34 Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data Selecting a Run Submitted A TSQ Module application user has submitted this run to the Acquisition Queue but is not
50. 3 051 Deactivate AP test Cal 05 1 1 Nefazodone 15728 582 None 55653 266 i AP pee celts eo for Reassay 1 Nefazodone 32446 721 None 112833 561 Re i AP test Cal 07 1 1 Nefazodone 32690 259 None 111882 535 ApplyjEdi Comment rds QCs Blanks View In Gallery gt Reintegrate gt Reintegration History Reinject Sample s 03 1 Netazodon t 124 NL 1 66E4 AP test Cal 03 1 Alprazolam d5 mz 209 i ms2 470 18Q cid Z6 UUT T80 U7 274 U8 F c SRM ms2 314 10 cid 40 00 209 96 5 Right click and choose Reinject Sample from the menu The sample is marked as Pending in the Injection column This step can be repeated for additional samples 6 Click Save to submit the sample to the TSQ Module application for processing 7 Click Exit to close the form The Run Status in the Run Review view is Submitted to TSQ Module 106 Watson TSQ Module User Guide Thermo Scientific B Restarting Runs Re injecting a Run from the Watson Application Canceling Re injected Acquisitions To cancel a re injected acquisition Click a sample to select it Right click and choose Cancel Re injection from the menu This prevents the sample from being transmitted to the TSQ Module application To review and accept re acquired chromatograms The Watson application enforces the acceptance of QCs Unknowns or STDs or prevents run review prior to completion as was specified in the Configuration form Access the Run Review
51. 4 Priority Run 46 Reason 26 Receive Date 40 Run Name 40 Sample ID 44 Sample Type 44 Samples 40 Show spectrum trace 54 Shutdown Method 47 Startup Method 46 Status 40 System power scheme 47 Target folder for all exported files 23 Tune TSQTune filename 23 User Name 26 User defined RT range 54 Xcalibur pmd or LCquan Iqn filename 22 parent drug 134 parity 134 153 Watson TSO Module User Guide partial loop injection 134 Password parameter Electronic Signature 26 Login screen 28 Paused status run management 6 Run Manager view 36 Run Select view 35 PCP 134 peak apex 134 apex detection 134 area 135 base 135 defined 134 detection 135 edge detection 135 end 135 height 135 height threshold relative 139 integration 135 noise factor 135 number 135 S N cutoff 135 start 135 symmetry 135 tailing 135 threshold 135 width 135 width constrain 136 peaks integrated illustrated 113 peak to peak resolution threshold 135 Pending status run management 6 Run Manager view 36 Run Select view 34 percent bias 136 percent difference 136 percent theoretical 136 plate position based 136 point to point calibration curve 136 point to point plotting style 136 polymorphism 136 polypropylene glycol PPG 136 polytyrosine 136 Position parameter 44 post processing 136 P P resolution 135 PPG 136 ppm 136 predefined user labels 136 predicted digest fragments 137 Thermo Scientific Index Q Prio
52. 5 and O 15 994915 mzData An XML based data format for storing peak list information such as that contained in DTAs The mzData format facilitates the comparison and exchange of peak list data among different platforms The mzData format is developed by the PSI MS Mass Spectrometry Standards Working Group N C Quadratic not calculable using quadratic regression It is not possible to calculate using quadratic regression process to find the equation ofa parabola for a set of data N C non calculable A general catch all when Watson cannot determine a value and one of the more specialized messages does not apply N C Wagner Not calculable using Wagner regression NCA Non compartmental analysis Thermo Scientific N D no data Data is not in Watson needle draw position offset The difference in the distance of the needle from the bottom of the vial from its default position negative peak A peak characterized by signal levels that drop below the baseline level of the detector neighboring amino acid The amino acids on either side of the cleaved amino acid NL An abbreviated form of the words normalized level This shortened form is used to save space in the header for example NL 1 98e 003 1 98 x 103 nominal sample time Protocol definition The theoretical relative time a sample was taken from a subject after a treatment administration non serial subject sparse sampling composite profile Prot
53. CIS Integration ICIS Advenced Mr Mn Baieine window M Baseine Weio O Asea Nowe F acto r Area Nowe F actor Ss Peak Nowe F actor fc Peak Nowe Factor Ro Ma Mn F Conan Peak Width Conatan Peak Width Peak Hex po Peak Hesghit X Bo T s ng F actor nm Ting Factor Ro update Chomatogram gt Nefazodone NL 232 Mefarodone NL 23264 F c SRM ms2 470 S06 20 00 100 07 270 00 F c SRM ms2 470 18 cid 26 00 180 07 274 08 241 100 100 E 8 59 4 d A 60 6 i EK 40 0 4 1 1 20 204 j 248 227 A 251 0 M Mg 22 23 24 25 RT min 66 Watson TSQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Reintegrating Chromatograms To configure the ICIS advanced parameters 1 Click the ICIS Advanced tab 2 Complete the following fields in the top right pane Noise Method Select Incos Noise or Repetitive Noise RMS Click to activate Min Peak Width Minimum number of scans in a peak 0 to 100 units 1 Multiplet Resolution Minimum separation in scans between two peaks 0 to 500 units 1 Area Tail Extension Number of scans past endpoint to use in averaging intensity 0 to 100 units 1 Area Scan Window Number of scans to either side of the apex allowed in a peak Use 0 to include all 0 to 100 units 1 3 Click Update Chromatogram to save your changes 4 When you have made all parameter changes apply them to the selected sample Appl
54. Data Monitoring the Run Status Real time Display The Run Status view lets you observe real time display during an acquisition The displayed time windows correspond to the time segments defined in the instrument method Figure 8 Chromatogram display 3 RT 0 00 4 00 P ti NL 5 84E3 aroxetine T Accu 100 i 330 13 cid 20 00 70 15 192 07 50 0 Nefazodone NL 1 60E4 c SRM ms2 470 18 cid 26 00 180 07 274 08 100 on eo Relative Intensity 0 Alprazolam d5 poete 100 2 d 314 10 cid 40 00 209 96 50 279 3 20 0 NL 2 91E3 Alprazolam PSP Wd 100 2 69 309 07 cid 42 00 205 02 50 3027 329 3 66 0 0 0 0 5 1 0 1 5 2 0 2 5 3 0 3 5 4 0 Time min 52 Watson TSQ Module User Guide Thermo Scientific Display Options Thermo Scientific 5 TSO Module Acquiring Data Monitoring the Run Status Figure 9 Spectrum trace display 1 437 RT 2 55 NL 4 85E1 F c SRM ms2 470 18 cid 26 00 180 07 274 08 100 246 0 o t 274 4 9 50 E 180 1 vo 180 070 246 050 274 080 m z m Z m z On the Status mode display options pane you can specify display options for the current real time display The settings for these options remain each time you log in to the TSQ Module application To specify display settings You can change the display settings at any time while an acquisition is running 1 To display the chromatograms for all compounds select Method defined traces 2 To display the sp
55. LCquan or Xcalibur methods ICIS is the only integration type allowed and MS is the only detector allowed To open the Watson TSQ Module Method Exporter application Choose Start gt Programs gt Thermo Watson TSQ Module gt Watson TSQ Module Method Exporter The Watson TSQ Module Method Exporter opens See Thermo Watson TSQ Module Method Exporter on page 22 To export files to a common folder The Watson application requires each of these files but you can export any combination of method files in a single session 1 In the Method Exporter application browse to the Xcalibur or LCquan processing method file that you want to export and click Open Browse to the instrument method file you want to export and click Open Browse to the tune file that you want to export and click Open A WW N Browse to the folder where you want the exported files to be written and click Open 5 When you have identified all the files you want to export click Export The Method Exporter application converts the processing method files to XML format and writes all the specified method files to the target folder A confirmation box lists all the files that were exported Watson TSO Module User Guide 21 3 TSO Module System Administration Exporting Method Files to a Common Folder Thermo TSQ Module Exporter x Files exported C Thermo TSQ TSQTune C Thermo LCquan_Accela meth C Thermo LCquan_methoda xml 6 Click
56. Mode Select Mode The Select mode is the first mode you see when you log in to the TSQ Module application The Run Select view displays all the runs assigned to you for the current database In the Run Select view you can select a run for acquisition Run Select a Stopped Test_Study_3 Monday June 01 2009 3 01 34 PM o Submitted Test Study 4 Monday June 01 2009 3 01 40 PM F Pending Test_Study 5 Monday June 01 2009 3 01 45 PM E Pending Test Study 2 Monday June 01 2009 3 00 47 PM Stopped 1 Submitted 1 Pending 2 Table 13 Run Select view parameters Sheet 1 of 2 Parameter Description Column Selector Opens the Column Selector where you can add or remove columns from the grid display Column choices are immediately implemented in your grid display but the column choices are not saved when you exit the TSQ Module application Stopped Submitted Status indicators at the bottom of the window report the number of Pending runs for each type of status Thermo Scientific Watson TSO Module User Guide 91 A TSO Module Menu and Toolbar Reference Select Mode Table 13 Run Select view parameters Sheet 2 of 2 Parameter Description Columns Status Status of each run Pending Submitted Acquiring Paused Stopped or Completed Pending The run arrived from the Watson application and awaits acquisition This run could have been submitted to the Acquisition Queue and returned to the Run Manager
57. Module User Guide 101 B Restarting Runs Restarting a Run from within the TSQ Module Application Restarting a Stopped Run at the Beginning For many reasons you might want to stop a submitted or acquiring run To correct a minor problem with the instrument To fix a leak replace a worn out column or correct any other minor maintenance task You can send the run from the Acquisition Queue back to the Run Manager view perform some offline injections and resubmit the run to the Acquisition Queue Example scenario 1 You initially pause the run and then decide that the problem is more serious than anticipated 2 You remove the run sending it back to the Run Manager view 3 After correcting the problem you might perform system suitability runs in the Xcalibur or LCquan applications to confirm that the system is working 4 Finally you resubmit the run for acquisition For detailed information about pausing and stopping a run see Pausing Stopping Canceling Runs on page 55 For detailed information about resubmitting a run see Acquiring a Run on page 45 Restarting a Stopped Run at a Specific Sample For many reasons you might want to stop a submitted or acquiring run You see a flat line on the real time plot where you expect to see a signal and realize that recent acquisitions in the run are not useful You see a physical problem with the instrument and want to fix it and then restart the run Yo
58. Processing Setup window An expected amount is entered for each calibration level See also calibration level expected amount calculated amount The amount present in the sample as determined using the calibration curve and the response ratio See also response ratio calibration The process of adjusting a measurement system to deliver results consistent with a known reference calibration compound mass calibration A compound whose mass spectrum is used to tune and calibrate a mass spectrometer A calibration compound generally has a well characterized mass spectrum calibration curve A calibration of sample concentration with a series of chemical standards at known concentration used as a reference point The calibration curve is given with area or height response on the Y axis and concentration on the X axis See also calibration internal standard ISTD calibration weighting w calibration level A user specified name for all of the target compounds in a given calibration step The individual amounts need not be the same for all components calibration mode The procedure LCquan uses for calibration See also update calibration mode Thermo Scientific calibration parameters Instrument parameters whose values do not vary with the type of experiment The instrument parameters that are stored in the calibration file See also tune parameters calibration replicates Multiple injections of the calibra
59. Quantitative Analysis Overview ssseeeeeeeeeeeeneen 109 About Quantitative Analysis o s ithe ons ance eh deba o hate IA a 109 Considering the Variables of Quantitative Analysis by LC MS MS 110 Using LC for Analyte Separations sis verbes e lta Uae a Rer DAR 110 Using MS MS for Analyte Detection i4 2 2 odie cash ie RERO Rd 111 Quantitative Analysis Techniques ie Oi neat ea age E Eon RA AR at 113 Using External Standards for Quantitative Analysis lesse 114 Using Internal Standards for Quantitative Analysis sees 115 Sample Types CETT 117 Standards has ee ie s e as ak RR EE 117 Unknowns Come oes ead aah iaee a acca e i telo a Se 117 o0 436 ah EEE SEE E DE E E NA E e e PE 117 Blanks trestania inn ay n ne e aye bns OR E nE bn ine 117 Glossary MEE DE 119 MINDEN qe RR 149 Watson TSQ Module User Guide V LL m Preface The Watson TSQ Module application is part of the Thermo mass spectrometry data system This user guide describes how to use the Watson application features to create and send a run to the TSQ Module application and perform data review on results files sent from the TSQ Module application This user guide also describes how to use the TSQ Module application features to accept a run request from the Watson application acquire samples and return the acquired data to the Watson data storage Contents Related Documentation Special Notices System Requirements C
60. S system responds to different compounds Quantitative calibration involves designing a processing method and performing calibration experiments with calibration standards containing known quantities of analyte R R squared A goodness of fit calculated for calibration curves A goodness of fit of 1 0 indicates that the calibration curve passes through each data point exactly The closer the goodness of fit value is to 1 0 the better the calibration curve fits the data ramp The rate of change from one temperature pressure or flow to the next raw amount The unadjusted amount of a component as determined from a quantitation analysis or by the application of a response factor raw data Uncorrected liquid chromatograph and mass spectrometer data obtained during an acquisition Xcalibur and Xcalibur based software store this data in a file that has a raw file extension raw instrument response An analytical run definition The value either direct from instrument or Thermo Scientific derived which is used to perform the regression Examples of instrument responses include peak area peak height ratio of peak Areas ratio of peak heights real time A data acquisition method that generates and displays the mass spectra as the experiment is in progress real time plot A plot of a mass spectrum or chromatogram that displays the data as it is generated by the mass spectrometer See also real time reference comp
61. SNP 143 solute 143 SOPS 143 Sp 143 Thermo Scientific Index T spectral trees 143 spectrum averaging 143 stability samples 143 standard bracket 143 standard deviation 143 Standard Error of the Mean SEM 143 standard sample 143 standard update sample 143 standards described 113 external standards 114 internal standards 115 start bracket sample 144 start delay 144 Start S 144 start time 144 Startup Method 144 Startup Method parameter 46 static modification 144 static NSI probe assembly 144 Status parameter 40 stick plotting style 144 stop bits 144 Stopped status run management 6 Run Manager view 36 Run Select view 35 structure elucidation 144 study 144 study Watson 144 study assay 145 study sample 145 study samples database 145 subject 145 subject group 145 Submitted status run management 6 Run Manager view 36 Run Select view 35 summary 145 Swiss Prot 145 System power scheme parameter 47 system requirements ix T tailing factor 145 target compound 145 Target folder for all exported files parameter 25 tension 145 Watson TSO Module User Guide 155 Index U T Half 145 threshold 145 threshold base peak 145 time function programming 145 time offset 145 time programming 145 timed event 145 tolerance 146 total composite spectrum 146 trace 146 tray temperature control unit 146 treatment treatment administration 146 treatment group 146 treatment site 146 triple play 146 triple stage quadr
62. SO Module User Guide intensity relative to base peak The ratio of intensity of a particular peak in a mass spectrum to the intensity of the mass peak of the greatest intensity This ratio is generally equated to the normalized ratio of the heights of the respective peaks in the mass spectrum with the height of the base peak being taken as 100 Interactive Chemical Information System ICIS The computer software used by the Finnigan XSQ product line when running in a UNIX environment You can use data obtained with ICIS software with Xcalibur ICIS files have the dat extension internal standard ISTD A component added to a sample to correct for injection errors and sample preparation errors It is assumed that the ratio of the target compound to the internal standard compound is constant for a given calibration standard The concentration or amount of an internal standard in any solution used in quantitation remains constant See also Extensible Markup Language internal standard ISTD calibration internal standard ISTD response ratio target compound internal standard ISTD calibration A calibration where known amounts of standard components are added to the sample to be analyzed See also external standard calibration internal standard ISTD response ratio The ratio of the signal response of an unknown peak to the response of the corresponding internal calibration peak at a specified calibration level inters
63. SQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Reintegrating Chromatograms e Window sec View Width min 3 Click Update Chromatogram to save your changes The Chromatogram on the right side is updated so you can compare it with the original Thermo Scientific Watson TSO Module User Guide 65 6 Watson Working with Processed Runs Reintegrating Chromatograms To configure the ICIS integration parameters 1 Click the ICIS Integration tab 2 Complete the following fields in the top right pane Baseline Window The number of scans over which to look for a local minima 1 to 500 Units 1 Area Noise Factor Noise level multiplier used to determine the potential peak signal threshold 1 1000 Units 1 Constrain Peak Width Selecting this check box constrains peak width Peak Height 96 Constrain peak edges to a percentage of Peak Apex Height 0 00 to 100 0 Tailing Factor Constrain peak edges to a ratio of the trailing and leading edges 0 5 to 9 0 3 Click Update Chromatogram to save your changes The Chromatogram on the right side is updated so you can compare it with the original Figure 14 Reintegrate Chromatogram view ICIS Integration page Reintegration orn A Sample name 99 1 orig Cal 04 1 Analyte name Nefazodone Change Percent 0 Original parameters Configure parameters Identification ICES Integration ICTS Advenced Identification I
64. TSQ Module User Guide Thermo Scientific Thermo Scientific 5 TSO Module Acquiring Data Acquiring a Run Table 9 Acquire options parameters Sheet 2 of 2 Parameter Shutdown Method Description Specifies that the TSQ Module application runs the shutdown method specified in the run data after the run has completed No data is acquired by this method and no autosampler injection takes place This feature is not available for all devices System power scheme On Keeps the system in the On state when the current run is completed When On is selected you can begin another run without waiting All power and flows are maintained at operational levels Default On Standby Keeps the system in the Standby state when the current run is completed When you select Standby you can begin another run with only a short delay between runs Some devices do not have a Standby feature For devices with this feature a power saving or consumable saving mode is entered and the devices can be switched back on in approximately 15 minutes or less Depending the instrument this state turns gas and liquid flows to Off but maintains heaters and other subsystems in an On state so that there is no warm up time required when you change from Standby to On Off Function buttons Keeps the system in the Off state when the current run is completed The Off state indicates that all power to the instrument which can be controlled by
65. Variables of Quantitati ve Analysis by LC MS MS Analyzing the samples Reviewing the results This documentation does not describe sample preparation and chromatographic method development This documentation assumes that you have met these important prerequisites to achieving high quality quantitative analysis For guidance in these areas refer to the documentation for your autosampler LC pump or MS pump and mass spectrometer Considering the Variables of Quantitative Analysis by LC MS MS The combination of liquid chromatography LC and mass spectroscopy MS sets up a unique set of considerations If you are familiar with quantitative analysis using one or the other of these analytical tools the information in the following topics will prove useful Using LC for Analyte Using LC for Analyte Separation Using MS MS for Analyte Detection Separation When working with LC systems you become accustomed to developing methods for analytes of interest These methods take into account a variety of parameters Consider the following LC parameters for optimum separation of compounds Composition of stationary phase Column diameter Column length Column usability over time Solvent s or composition of mobile phase Flow rates Isocratic or gradient ramped solvent compositions Often the only measurable result of optical detectors that you can use to identify an analyte is the retention time at a specified wavelength To
66. Watson application identifies different users of the application An account contains the formal name for the User This name will be used for all reports generated by the system The account also contains the name and password the user will use when logging into the application Thermo Scientific Glossary V valley detection A chromatogram peak edge detection method used to integrate unresolved peaks Xcalibur and LCquan drop a vertical line from the apex of the valley between unresolved peaks to the baseline The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak See also expected width rise percentage variance A statistical variance of a data set is used to calculate standard deviation and relative standard deviation Variance is calculated 1 5v Varli Xa Sfx XY x24 X where N is the number of samples Xi is the value of each individual sample and Y is the mean of the sample value See also mean relative standard deviation standard deviation v Version vial list A list that contains the vial number sample type level sample ID and sample name for each vial in a sequence The list is organized by ascending vial number vial position The vial position in the autosampler tray of the current sample Also called the vial number view width The duration of time in minutes that Xcalibur or LCquan displays for a c
67. When you use an autosampler you must select a tray name with which to validate the vial or well position Positions are usually provided by the Watson application Tray Name 96 Well Microplate Short Microwell Carrier 1 8 ml Vial 5 trays 40 vials each 96 Well Microplate Tall Microwell Carrier 96 Well Microplate Short Microwell Carrier Riser Plate 96 Well PCR Plate Cooling Adapter Short Microwell Carier Riser Plate 384 Well Microplate Tall Microwell Carrier 384 Well Microplate Short Microwell Carrier Riser Plate 3 To edit the Position column click the current position value and type a new value If you specify an incorrect position an error message shows you the correct syntax to use Watson TSO Module User Guide 41 5 TSO Module Acquiring Data Editing a Run 4 To edit the Injection Volume column click the current injection volume value and type a new value 5 To edit the Comment column click in the column and type a comment This field is limited to 100 characters 6 To save the edits click Save Run KD The Save Run button is enabled only after you edit a column value in the run Note The Save Run command can be specified to require an electronic signature See Using E Signatures on page 25 To automatically enter Position column values gt To use this feature you must have an autosampler configured If you specify an incorrect position for your configured
68. XOWNWS Rewection Test Master Assay Fauspectim Test Master Assay Wewpecten Test Master Assay Reagection Test Master Assay T Rewpectaon Test Martes Assay For more information refer to the Analytical Menu chapter in the Watson User Manual Thermo Scientific Watson TSO Module User Guide 83 7 Watson Reports and Printing Capabilities Printing Capabilities Printing Capabilities Printing capabilities in Watson include Printing chromatograms or saving them to a fully locked PDF or open PDF file The on screen display and the printed version of text numerical values and graphics chromatograms and charts graphs are identical Printing a Chromatogram To print a chromatogram 1 Click the Print icon The Print dialog box opens 2 Select the check boxes to print Analyte Chromatogram Internal Standard Chromatogram or Result Data 3 Click OK The Preview window shows the selected analyte chromatogram Information such as peak area height retention time Q1 and Q3 mass and analyte name is displayed 4 Click Print to print the chromatogram 5 Save the chromatogram to a PDF file by clicking the Export Document icon document with diskette You can print the chromatogram save it to a PDF file or both What you see is identical to what is printed 6 Close the Preview window Another Preview window is displayed The window displays the internal standard chromatogram Information such as peak area heigh
69. a significant length of time In these instances the duration of administration is usually recorded RT An abbreviated form of the phrase retention time RT This shortened form is used to save space when the retention time in minutes is displayed in a header for example RT 0 00 3 75 See also retention time RT Thermo Scientific S S An abbreviated form of the phrase scan number This shortened form is used to save space when the scan number is displayed in a header for example S 234 See also scan number sample A quantity of material for example plasma sample data type Protocol definition Meaning of the sample type that can be one of two values either point or interval A blood sample is considered a point sample data type because the analyzed value from a blood sample corresponds to drug concentration in the blood at a particular point in time A urine sample is considered an interval sample data type because the analyzed value form the sample must be considered in terms of the sample volume and the time between samples to accurately represent elimination of an analyte sample handling Defined as those activities that relate to handling of actual samples extracted from subjects as part of the study s protocol at the experimental site sample ID An alphanumeric string of characters that uniquely identifies a sample Sample IDs are entered using the Sequence window sample ID based Specifies how
70. abeled as such in the run queue These runs are submitted to the TSQ Module application from the Watson application processed in the TSQ Module application and then sent back to the Watson application To view the run after data acquisition is complete 1 Select a completed run and click Review Run results appear 2 To navigate between sample analytes click the tabs at the top of the view Figure 12 Sample analytes Sample analytes Ll yx Perowetne Alrazolam I Nel acodone Sequence Sample Type Iroection Acte Aeahte Hek Analyte Height Ratus Anahite rea Analyte Area Stab Analyte Peak Rete 1 AP test CONTROL BLANK I 1 2 APotes CONTRO BLANK Blank 1 Paroxetine 194 888 None 228 615 3 MP test Ca 01 1 anie d 1 Parovetine 5612 77 None 17138 799 4 M tet Cee Rarded 1 Paroxetine 5218 426 None 16565 568 5 AP test C03 1 Stant d 1 Paroxetine 4442 522 None 14481 451 6 MP test Ca 1 Rarderd 1 Paroxetre 6425 75 None 18596 579 7 MP test Cast Started 1 Paroxetine 455 27 None 17722 552 8 AP test Ca 06 1 Rarded 1 Parowetine 100 5 305 None 3Xx31 98 9 AP test Ca 07 1 Stantoed 1 Paroxetine 8752 804 None 38281 74 lt j Peara co Show Ad Injectors AP tes CONTROL BLANK Paroxetine m z 19207 RT 1808 2192 F c SRM ms 330 13Q cid 20 00 70 15 192 07 AP tes CONTROL BLANK Alprazolam 35 F c SRM ms2 314 100 cid 40 00 209 96 RT 3 AA 359257 mir 20996 RT 2733 3267 27 283 296 0
71. andard update samples See also bracket none start bracket sample type The first of a set of calibration samples in a Sequence having bracket open or bracket overlapped type Each set of calibration samples contains the standard levels defined in the active Processing Method Blank samples are often located in the Sequence before and after calibration samples See also bracket open bracket overlapped start delay A time delay in minutes before the start of acquisition Start S An abbreviated form of the phrase start scan number which is the mass spectrometer scan number that occurs at the selected chromatogram range start time This shortened form is used to save space in the header of the Spectrum view For example if the selected chromatogram range includes start time 0 00 minutes this is displayed Start S 1 See also End S start time The time in minutes corresponding to the beginning of the selected chromatogram range This phrase is used when the start time is displayed in a header For example if the selected chromatogram range starts at time 0 0 minutes this is displayed Start Time 0 0 See also End Time Start S startup method An Instrument Method that is run by LCquan Xcalibur before it runs the first sample in an acquisition You create Startup Methods in the Instrument Setup window 144 Watson TSO Module User Guide static nanospray A device that performs continuous analy
72. apable of 1280x1024 resolution XGA 75 GB on the C drive NTFS format Instrument TSQ Quantum Or e TSQ Vantage Software e Microsoft Windows XP Professional with Service Pack 3 Optional Xcalibur 2 1 0 Adobe Acrobat 9 0 TSQ 2 1 0 LC Devices 2 2 1 Watson 7 4 Foundation 1 0 1 available on the Xcalibur 2 1 0 CD Optional LCquan required to create lqn method files Watson TSQ Module User Guide ix Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 532 4752 Fax 561 688 8736 E mail us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 E mail us customer support analyze thermofisher com Web site www thermo com ms To copy manuals from the Internet Go to mssupport thermo com and click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help Fill out a reader survey online at www thermo com lcms techpubs Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com LLL m Introduction This chapter describes the general features and workflows of the TSQ Module application and the TSQ Module specific features of the Watson applicat
73. ation level See also calibration curve calibration level 136 Watson TSO Module User Guide point to point plotting style Style of plotting a spectrum that plots each intensity peak connected together 9478 5756 615 7 polymorphism Genetic variation occurring within plant and animal species where different forms exist together in the same population polypropylene glycol PPG A mixture of polypropylene glycols of different chain lengths used for high mass range calibration and tuning A mixture of PPG 2000 and PPG 2700 provides ESI peaks suitable for calibrating over the 2000 to 4000 mass range polytyrosine Polytyrosine 1 3 6 and Polytyrosine 1 3 6 9 are the factory calibration compounds provided for TSQ Quantum The polytyrosine mixtures contain the amino acid tyrosine and two or three polytyrosines respectively post processing Procedures automatically performed by Xcalibur or its layered applications after an LC MS run as defined in the predefined Processing Method Procedures include peak detection peak integration component identification quantitation data storage and report generation ppm Abbreviation for parts per million predefined user labels for Sequence Setup Allows you to specify the values of specific parameters on a per sample basis in a Sequence row These parameters are used for activation masses and reject masses for data dependent scans and for activation masses and reject masses
74. between the observed fragment list and a sequence as by chance It is a measure of confidence in the validity of a match A low p score means that the probability of obtaining at least this many fragments matching a sequence is low so it is unlikely that random chance is the cause of the association protocol Represents an overall plan of action for a study It is defined as a set of treatments applied to groups of subjects where typically each group of subjects may receive only one or a subset of all possible treatments In association with each treatment the protocol also defines a schedule of samples to be extracted from the subjects after treatment and set of tests to be performed on those samples There is only one protocol for a study Watson TSQ Module User Guide 137 Glossary Q quadratic calibration curve A calibration curve where Xcalibur calculates a quadratic second order polynomial least squares fit of the experimental data using the following mathematical form Y AX2 BX C where A B and C are the polynomial coefficients See also calibration curve quadratic limit If B2 4 A C Response 0 there is only one root for the equation That is conc B 2 A quadratic log log calibration curve A calibration curve that calculates a quadratic second order polynomial least squares fit of the experimental data See also calibration curve qualitative analysis Chemical analysis designed to deter
75. bstance is given as a ratio of its original volume to its new volume after applying a specified pressure See also compressibility concentration Refers to an analytical measurement reported as mass per volume or mass per mass Examples are g mL uM or ug g Certain the Watson application interfaces allow importation of concentration values from the external software This occurs when a calibration curve has been regressed in the external software yielding back calculated concentration values conditioning The process used to remove surface contaminants from a chromatographic column consecutive reaction monitoring CRM scan type A scan type with three or more stages of mass analysis and where a particular multi step reaction path is monitored constrain peak width A chromatogram peak edge detection method used to integrate a peak that displays tailing Xcalibur constrains the width of a component during peak integration using the specified peak height percentage and tailing factor parameters A set of peak integration settings that constrains the peak width of an asymmetric chromatogram peak by excluding all or part of the peak See also peak height tailing factor control file A raw file that can be compared to an experimental raw file during the following Background subtraction to correct for the background signal caused by chemical noise or matrix effects Component detection to identify which components a
76. cal trial you might be seeking the maximum possible accuracy from your measurements Time and cost of analysis are less important than achieving the highest possible standards in precision and accuracy This process of measuring the amount of a particular component in a sample is called quantitative analysis In other applications such as in trace analysis you might only want to estimate the quantity of a component It might be sufficient to know that the component is present at a level either significantly higher or significantly lower than a defined threshold For example knowing whether a patient has overdosed 15 or 20 times above a prescribed limit is generally not as important as simply knowing that the limit has been exceeded Such cases would require a rapid measurement rather than a precise one This form of measurement is generally called semi quantitative analysis Quantitative analysis consists of the following steps Preparing samples Developing a suitable chromatographic method Calibrating the mass spectrometer s response For further information about the principles of quantitative analysis refer to Mass Spectrometry Principles and Applications de Hoffman E Charette J Stroobant V Wiley New York 1996 and Introduction to Mass Spectrometry 3rd ed Watson J T Lippincott Raven Philadelphia PA 1997 Thermo Scientific Watson TSQ Module User Guide 109 C Quantitative Analysis Overview Considering the
77. chromatogram to display the menu Reset Scaling Resets the X axis and Y axis ranges in the Chromatogram pane or the Spectrum pane to their default values Stopped Submitted Status indicators at the bottom of the window report the number Pending of runs for each type of status Watson TSQ Module User Guide Thermo Scientific Manage Mode 5 Manage Select Run Cancel Run Thermo Scientific A TSO Module Menu and Toolbar Reference Manage Mode From the Manage mode you can monitor the status of the runs cancel a run and return it to the Watson application or select a run for acquisition Run Manager Stopped http 3 Drugs svc Submitted http 3 Drugs svc Pending Pending _ http 3 Drugs svc Test Study 3 3 Monday June 01 2009 3 01 34 PM Test Study 4 3 Monday June 01 2009 3 01 40 PM Test_Study 5 3 Monday June 01 2009 3 01 45 PM Test_Study 2 3 Monday June 01 2009 3 00 47 PM _ _ _ _ _ _ _ _ Stopped 1 Submitted 1 Pending 2 Table 17 Manage mode parameters Sheet 1 of 2 Command Function buttons Description Select Run Opens the Setup view for the highlighted run Cancel Run Removes the highlighted run from the list and returns the run to the Watson application Columns Status Status of each run Pending Submitted Acquiring Paused Stopped or Completed Pending The run arrived from the Watson application and is assi
78. ctures in the absorbance spectrum and for high concentrations Use a wide slit to detect very low concentrations smoothing The application of a smoothing algorithm to the data to improve the graphical appearance of data by reducing the level of noise and or to improve peak detection Xcalibur provides the following types of data smoothing boxcar smoothing and Gaussian smoothing improves the graphical appearance of data by reducing the level of noise and or to improve peak detection smoothing points The odd integers from 1 number of points to 15 used in a weighted average to reduce the level of noise in the data consequently improving peak detection and the graphical appearance of the data See also smoothing SNP A single nucleotide polymorphism which is a small genetic change or variation that can occur within a DNA sequence solute A dissolved substance The dissolved component of a mixture that is to be separated in a chromatographic column Also called the sample or analyte SOP Standard Operating Procedure Sp Abbreviation for the preliminary score of the top candidate peptide or protein for a given input data file Thermo Scientific Glossary spectral trees A representation of the data structure of MS spectra A tree which is like a structural fingerprint reflects the hierarchical spectra dependencies in MS experiments For more details on spectral trees see the Help in Mass Frontier
79. d it back to the Watson application You want to rebalance the workload to another instrument so you want to send all pending runs back to the Watson application The local instrument requires maintenance and you want to move all runs to another instrument The local instrument has the wrong column or other mismatch other than the device stack that was discovered after the run was submitted so you want to send all pending and acquiring runs back to the Watson application You can send the run from the Acquisition Queue back to the Run Manager view and then back to the Watson application A Watson user can then reassign the run to a different instrument and resubmit it to another the TSQ Module application Example scenario 1 You initially pause the run and then decide that the problem is more serious than anticipated 2 You remove the run sending it back to the Run Manager view 3 You discover that the problem with the instrument is serious enough that the run cannot be restarted 4 Finally you cancel the run in the Run Manager view sending the run back to the Watson application For detailed information about pausing stopping and canceling a run see Pausing Stopping Canceling Runs on page 55 104 Watson TSO Module User Guide Thermo Scientific Returning a Run to the Watson Application Workflow Thermo Scientific Run request Canceled run from Watson Select Run Select view Manag
80. database 139 resolution chromatographic 140 response factor defined 140 overview 113 response ratio 140 response value 140 restarting a run workflow 105 result file 140 Results Table 140 retention reference 140 retention time 140 retention time shift 140 RF 140 RIA radio immuno assay 140 rise percentage 140 rise time 140 rod driver voltage 140 role 140 route of administration 140 RSD 139 RT 140 Run Name parameter 40 run status defined 5 S S N ratio 142 S N threshold 143 Thermo Scientific sample 141 sample handling 141 sample ID 141 Sample ID parameter 44 sample ID based 141 sampleloop 141 sample type 141 Sample Type parameter 44 sample types defined 117 sample volume 141 Samples parameter 40 Sat Saturation 141 Save Run command 44 SB 141 scan description 141 scan event 141 scan filter 141 scan number 141 scan power 141 scan range 141 scan rate 142 scan time 142 scan width 142 search window 142 segment 142 Select Run command 39 semi automatic calibration 142 semi quantitative analysis definition 109 sensitivity 142 septum purge flow 142 sequence 142 sequence length 142 serial port 142 set mass 142 set point 142 shipment sheet 142 shotgun annotation 142 Show spectrum trace parameter 54 shutdown method 142 Shutdown Method parameter 47 signal to noise ratio 142 signal to noise ratio threshold 143 sites 143 slit width 143 smoothing 143 smoothing points 143
81. defined traces Show spectrum trace Continuous update Manual select User defined RT range min Apply Settings Eg Manage Acquiring Test_Study 2 Thermo Scientific A TSO Module Menu and Toolbar Reference Status Mode From the Status mode you can start stop or pause an acquisition monitor the run manager and instrument status monitor the Acquisition Queue or control the real time display Run Status Run Status Acquisition Queue E amp DE All Runs amp Jf Test Study 2 C Sample ID 1 Sample ID 2 Sample ID 3 OOOO T p NL 4 52E2 Paroxetine 0 SRM ms2 100 0 87 330 13 eid 20 00 ae 70 15 192 07 021 0 61 4 UU 209 NL 1 94E2 Nefazodone 4c SRM ms2 2100 2 53 470 18 eid 26 00 180 07 274 08 5 50 2 40 2 28 7 g NL 1 0965 Alprazolam d5 4c SRM ms2 160 2 66 314 10 cid 40 00 209 96 50 2 81 0 NL 1 64E2 Alprazolam c SRM ms2 309 07 eid 42 00 100 2 63 205 02 50 0 0 0 0 5 1 0 15 2 0 25 3 0 3 5 4 0 Time min 100 210 0 2 S 50 s o r4 0 209 9600 209 9605 209 9610 209 9615 m z Stopped 1 Pending 1 Table 16 Status mode parameters Sheet 1 of 2 Parameter Method defined traces Description Displays real time chromatograms corresponding to the components defined in the processing method When the component traces are turned off the total ion current TIC trace is displayed Show spectrum trace
82. dit records are delayed until a result or run complete package is transmitted to the Watson application A run must be in acquisition or canceled and returned to the Watson application before the TSQ Module application transmits the XML packages and audit records to the Watson application When there is no network connection to the Watson application the TSQ Module server locally buffers system level result run complete audit packages for later transmission when the network is restored User permissions facilitate auditing and are set on the Watson application side The TSQ Module user has permissions at both the system level and the run level Audit Trail The TSQ Module application creates an audit trail for the following actions User actions Expired sessions or logoffs Successful and unsuccessful logins Successful and unsuccessful E signatures Activities on locked accounts Updates to sample injection volume position or comments Updates to run observation Runs submitted for acquisition Runs paused stopped or restarted in the Acquisition Queue Runs canceled in the Run Manager view System events nstrument errors e System level audits sent to the Watson application URLs 24 Watson TSQ Module User Guide Thermo Scientific User Permissions 3 TSO Module System Administration Using E Signatures The TSQ Module user has permissions at both the system level and the run level The TSQ Module application use
83. e Run Manager view Setup Run Edit view Acquire Run Edit view Status Run Status view Removed run B Restarting Runs Returning a Run to the Watson Application Watson TSQ Module User Guide 105 B Restarting Runs Re injecting a Run from the Watson Application Re injecting a Run from the Watson Application In the Watson application you can select one or more samples within the same run to re inject The ability to do this is limited to a specified time frame Samples that are selected to be re injected are submitted to the TSQ Module application where they are processed and submitted back to the Watson application to be reviewed and accepted as part of the run review After a run is accepted samples can no longer be re injected Selecting Samples to Re inject The Watson application and the TSQ Module application process re injected samples in groups When selecting samples to re inject you can select some samples but not others until the first set is in the queue To select samples to re inject 1 Access the run queue 2 Choose Analytical gt Analytical Run Actions 3 Select a completed run and click Review The Run Review form opens 4 Click a sample to select it Figure 29 Right mouse menu AP test Cal 02 1 Standard 1 Nefazodone 16461 831 None 59079 501 AP test Cal 03 1 1 16419 449 None Activate AP test Cal 04 1 1 Nefazodone 13279 834 None 5138
84. e Neutral Loss scan mode the set mass is the neutral loss mass set point The set of a mass to charge ratio and its associated value such as a voltage used to define a tuning table for a device A set point is created by having TSQ Quantum optimize a device for a specific mass shipment sheet Sample Handling definition The document the accompanies a sample shipment It describes the samples in the shipment shotgun annotation The overpopulation of a database by all combinations of all known modifications to a protein s basic sequence Shotgun annotation calculates all possible combinations of known post translational modifications PTMs onto each protein sequence shutdown method An Instrument Method that is run by Xcalibur or LCquan after it runs the last sample in an acquisition You create Shutdown Methods in the Instrument Setup view signal to noise ratio S N The ratio of the signal height S to the noise height N The signal height is the baseline corrected peak height The noise height is the peak to peak height of the baseline noise See also signal to noise ratio threshold Thermo Scientific signal to noise ratio threshold A user specified chromatogram peak edge detection criterion used for peak integration sites Specific amino acids that are attacked by the enzyme listed slit width The width of the variable slit at the entrance of the spectograph Use a narrow slit for analytes with very fine stru
85. ectrum trace select Show spectrum trace 3 Choose one of the following spectrum trace options To continuously update the spectrum trace of the most current scan select Continuous update E To display the spectrum trace of the selected peak select Manual select After you apply these settings click on a peak in the real time display 4 To specify the range for the real time display do the following a Select User defined RT range min b Enter a value for the beginning of the range c Enter a value for the end of the range 5 To update the current display with your settings click Apply Settings The changes are immediately applied Watson TSO Module User Guide 53 5 TSO Module Acquiring Data Monitoring the Run Status To zoom in on the real time display 1 Drag your cursor in the chromatogram or spectrum trace panes to define a region to zoom in 2 To return to the original display right click and choose Reset Scaling from the menu Status Mode Display Options Status Method defined traces Show spectrumtrace Continuous update L Manual select User defined RT range min Apply Settings Table 11 Status mode parameters Sheet 1 of 2 Parameters Description Method defined traces Displays real time chromatograms corresponding to the components defined in the processing method When the component traces are turned off the total ion current TIC trace is displayed Show spectrum
86. ein or peptide database duplicate sample A second independent sample A separate reportable result is expected for each duplicate sample DWP deep well plate Ninety six wells per plate dynamic NSI probe assembly The assembly that fits into the NSI body assembly and includes a snap in tip mounting device a fused silica emitter a snap in nut a MicroTee mounting block and a fused silica transfer line E early expiration Removes peaks from the dynamic exclusion list if the number of times counts that the peak s intensity falls below a specified signal to noise S N threshold exceeds a specified number of counts The number of counts is determined during the full scan on which the data dependent scans are based Thermo Scientific edge type The criteria by which the left or right edge of a peak is detected eject speed The speed at which the metering unit ejects sample or solvent A faster eject speed shortens the time required to run the injector program end bracket sample type The second of a set of calibration samples in a sequence having bracket type open or non overlapped Each set of calibration samples contains the standard levels defined in the active Processing Method Blank samples are often located in the sequence before and after calibration samples See also bracket open bracket overlapped End S An abbreviated form of the phrase end scan number This is the number of the last scan that occ
87. er defined samples Double check volumes aliquot dilution factors or both Make sure the work list is in the order you want to inject the samples When you are finished click Save From the Analytical Runs dialog box click Exit To review the Plate Report page when planning an analytical run Click the Plate Report tab The Plate Report page lists the samples with their sequence and identifier It also shows the well positions in the plate map These are carried to the TSQ Module application with run submittal To create a sequence file Choose Analytical Analytical Run Actions Select the analytical run to use for creating the sequence file Click Sequence File The Windows File dialog box opens Select the appropriate file path and name of the sequence file to be created To send the run to the TSO Module application Choose Analytical Analytical Run Actions From the list click the run you want to send Click Submit Run The Select Instrument to Run dialog box opens Select the instrument and click OK For more information refer to the Analytical Menu chapter in the Watson User Manual LLL ERN TSQ Module System Administration This chapter describes the TSQ Module tools and functions used primarily by system administrators how the TSQ Module application communicates with the Watson application and the types of actions that are audited Contents Managing the Environme
88. etection and baseline noise calculation This test is performed based on a user defined peak signal to noise cutoff threshold This test assumes an edge of a peak is found when the baseline adjusted height of the edge is less then the ratio of the baseline adjusted apex height and the peak signal to noise cutoff ratio according to the expression peak start The start of a chromatograph peak occurs whenever the detection signal increases to a value greater than the current threshold criteria peak symmetry The degree to which a chromatographic peak exhibits a peak symmetry characteristic of an ideal Gaussian peak See also peak tailing peak tailing Distortion of chromatographic peaks from ideal Gaussian shape seen as an extension of the end of the signal A tailing peak has the T flag set JA JL 4s See also peak symmetry peak threshold The minimum number of intensity counts per sampling interval that is required before a signal is recorded peak to peak resolution threshold Controls how much peak overlap can be present before two or more adjacent peaks are recognized as a peak cluster Instead of valley to valley baselines peak clusters have baseline drops The baseline drop of a peak cluster is specified as a percent of peak height overlap peak width The distance across a peak measured at a selected peak height level in minutes or mass units The peak height level is usually specified as a percentage of the maxim
89. eviewing Internal Standards and Performing Regression Reviewing Runs You can continuously monitor the status of runs even while they are being processed in the TSQ Module application You can configure the Watson application to require the review and acceptance of particular sample types In the Watson application you can review a run that is incomplete or ongoing Use this feature to review a set of chromatograms while the LC MS is acquiring additional samples If a problem occurs in the run you can see how far back in the sequence the problem occurred while the acquisition is taking place Use the following procedures To review the list of runs To configure run review requirements To view the run queue in the Watson application To view an ongoing or incomplete run To view the run after data acquisition is complete Thermo Scientific Watson TSO Module User Guide 59 6 Watson Working with Processed Runs Reviewing Runs KD M d 1 To review the list of runs Choose Analytical gt Analytical Run Actions The Run Queue opens listing recent runs From this queue you can monitor the status of runs You can also access the Run Review view that provides detailed information To review a run select it and click Run Review To configure run review requirements Create or open a study in the Watson application Choose Study Actions Configuration The Configuration dialog box opens Figure 10 Configurati
90. ference component tref corrected for the void time RRT t tvoid tref tvoid See also corrected relative retention time void time relative scaling Displays a chromatogram trace or spectrum so that the height of the Y axis scale adjusts to the peak heights of the data currently displayed relative standard deviation A measure of the dispersion of a group of measurements relative to the mean of the group Relative standard deviation is expressed as a percentage of the average value The percent relative standard deviation is calculated as RSD 100 S where S is the standard deviation and is the sample mean See also standard deviation repetitive noise A multiple pass algorithm that determines the noise level The software uses the noise level data to determine which peaks to label during area calculations and to determine the peak start and peak end See also INCOS noise replicate An aliquot of the same sample only a single reportable result is expected for replicate samples RESID database A database of annotations and structures for protein modifications Watson TSO Module User Guide 139 Glossary reservoir vial With a 12 mL capacity the reservoir vial is used to hold solvent reagent or diluent Up to four of these large vials can be fitted behind the wash station A reservoir vial is approximately the same height as a sample vial resolution chromatographic A measure of
91. fic TSQ Module Menu and Toolbar Reference This appendix provides a reference to the Watson TSQ Module menus icon bars and status bars Contents Using the Menu TSQ Application Menu Commands Title Bar and Ribbon Commands Status Dar Select Mode Setup Mode Acquire Mode Status Mode Manage Mode Thermo Scientific Watson TSO Module User Guide 87 A TSO Module Menu and Toolbar Reference Using the Menu Using the Menu The application menu in the upper left corner of the TSQ Module window includes commands to open the Select mode save changes to a run log out of or exit the application or display Help To use the keyboard to activate a menu command 1 Click the application icon to display the TSQ Module application main menu 2 Type the first character of the command in the menu title such as S in Select If you do not choose a command you can close the menu by pressing the ESC key TSO Application Menu Commands The application menu in the upper left corner of the TSQ Module application window includes commands to open the Select mode save changes to a run log out of or exit the application or display Help Click the application icon in the ribbon to display the TSQ Module application main menu Menu command Description Select Displays the Select mode Save Saves changes to a run Position Injection Volume or Comment Logout Closes the TSQ Module application and pre
92. form Click on the tabs to view All samples Standards Blanks QCs or Unknowns Click Accept Review to accept You receive the following message This will save any changes made and accept all chromatograms for this run It will also prevent any future reintegrations and re injections 4 Click OK Accepting the Analyte Results from the Standard Regression Form Thermo Scientific Analyte results can be accepted from the Standard Regression form it v l To accept analyte results from the Standard Regression form Access the Standard Regression form by selecting Analytical Standard Regression The Standard Regression form opens Click the run to select it Click Regression If the Run Review has not yet been marked as accepted an alert appears Click OK The Standard Regression form opens with the Standard and QC tab displaying To accept or reject the results of the analyte select an analyte and then click Accept or Reject Click Cancel to close the form Watson TSQ Module User Guide 107 ee i Quantitative Analysis Overview This appendix describes some of the basic principles and terminology of quantitative analysis and contains the following topics Contents About Quantitative Analysis Considering the Variables of Quantitative Analysis by LC MS MS Quantitative Analysis Techniques Sample Types About Quantitative Analysis In some applications such as a clini
93. fying DEVICE uua iate Senta deu cule nag MR dur dolo d uror died 10 Tune Method and Processing Method Files in LCquan and Xcalibur 12 Setting up the Master Assay sis uo nie eye idee eke ee Kees Mew 13 Working with a Watson Study asas se y sw er ewe Fe 16 TSQ Module System Administration 00 ccc eee eee eee eee ee 19 Managing the Environments xml File 19 Communicating with the Watson Application 0 00 cece eee ee 20 Exporting Method Files to a Common Folder 21 Exported LCquan Parameters 41 2343 p xd tacto cia noes cae cee AGE pees 23 PUM oe duce oC ob ASEM Kew eno hh whee eee Ka ba EDR b 24 Audit Trail 0 5 da iab pacis fedi i Race cce Vibe eee seeks qid 24 User P rmisstons aee eer hire eae ER CRURA ey 25 Using E Signatures ssssics edi risa eie urtat e EARE eee eens 25 TSO Module Getting Started a an annann 27 Setting up in the Watson Application 0 eee 27 Starting the TSQ Module Application viii arr RR es 27 Watson TSQ Module User Guide iii Contents iv Chapter 5 Chapter 6 Chapter 7 Appendix A Watson TSQ Module User Guide TSO Module Acquiring Data 0 cece eee eee eens 31 Lhe Baste Workflow i cal etia dee adole wea HD c D Rod kik bien dom st ohn 32 basic Workflow Vid o zo aset ie xe e Du we etra EE toad NEN d 23 Selecting a BUE 2D rez Apa eap ad d axes ated EE P acea antes dan la 34 Ma nagtupa Run s perik et ryn ESSERE ORE PREGA p
94. g A file that provides a chronological listing of all errors that are detected while processing a sample or list of samples event A parameter that has a time value or an assigned initial value which the Avalon Peak Detection algorithm uses to detect chromatogram peaks You can add change or delete events in an event list event list To detect peaks Avalon uses the settings for initial events and user defined timed events in the event list To calculate values for initial events open a raw file and then make the chromatogram view active event time The time when an external device is turned on or off The time when there is a change in the heater temperature or valve position exact mass The monoisotopic mass of a given compound The exact mass is calculated by use of the most abundant isotopes of the constituent elements for example C 12 0000 N 14 00307 H 1 007825 exception peak In spectra from high resolution analyses a peak E from an internal reference compound that has a known mass but is not a reference peak See also reference peak Watson TSQ Module User Guide 127 Glossary exclusion mass A mass that is added to the dynamic exclusion list after the mass spectrometer obtains a sufficient amount of data on it Masses in the dynamic exclusion list are ignored with respect to triggering a data dependent scan expectation value e value The number of sequences in a database that are expected to have
95. g errors in binary coded data Parity must be agreed on by the sending and receiving devices before transmission can take place See also full loop injection partial loop injection A technique that meters a specified amount of sample into the sample loop rather than overfilling the sample loop The sample is smaller than half the total volume of the sample loop PCP Personal computer peak A maximum in a graph of intensity versus time or intensity versus mass The position of the maximum is said to be the position of the peak peakapex The highest point ofa peak peak apex detection For advanced component and chromatogram peak detection the values specified for rise percentage and valley signal to noise ratio S N serve another purpose besides valley detection These values are also used during peak detection to determine whether or not the apex of a peak has been found In this case the tests are employed in the inverse of the valley detection process Xcalibur uses the valley S N value to test a possible apex then applies the rise percentage value to confirm that the values on both sides are lower This has the effect of treating a high measurement which is a possible peak apex as the crest of a hill Therefore the measurements must be lower on both sides of the crest when adjusted for noise See also rise percentage signal to noise ratio S N Thermo Scientific peak area The area obtained by integrating peak
96. gned to the instrument at this workstation Submitted A TSQ Module application user has submitted this run to the Acquisition Queue but is not currently acquiring Acquiring The run has progressed to the top of the Acquisition Queue and is currently acquiring Paused The run has been assigned to an instrument and is currently acquiring but has been paused and is waiting between samples Stopped The run has been assigned to an instrument and was acquiring but was removed from the Acquisition Queue Completed The run has completed acquisition Completed runs might not always be observed in the Run Manager view When the TSQ Module application finishes sending the results of the last completed sample to the Watson application it marks the run as Completed and quickly removes the run from the Run Manager view Watson TSO Module User Guide 99 A TSO Module Menu and Toolbar Reference Manage Mode 100 Table 17 Manage mode parameters Sheet 2 of 2 Command Database Description The the Watson application database or the friendly name assigned in the Environments xml file Run Name A combination of the project study and run ID as defined in the Watson application Samples Number of samples in the run Receive Date Timestamp when run was received Assay Date Date when assay method was created Description Watson user comments Extraction Date Analyst
97. gned to you If you select one of these databases you get the following error message Thermo Watson TSO Module o Login name and password are invalid For the selected database Re enter your login name and password and confirm vou have selected the correct database If the problem persists contact the system administrator For assistance To correct the problem click OK in the error message and do one of the following Ifyou think you made a mistake in your login or password re enter them If you made a mistake in the database you selected select another database Ifyou think you should have access to the database you chose contact your system administrator 4 When you have correctly specified a login name password and database click OK The Run Select view opens See Run Select View on page 30 You are ready to begin managing and acquiring your assigned runs For detailed information about starting an acquisition from the Run Select view see Selecting a Run on page 34 Thermo Scientific Watson TSO Module User Guide 29 Run Select View Thermo Watson TSQ Module Database http 3 Drugs svc Run Select Pending Test_Study_32 Pending Test_Study_30 Pending Test_Study_29 Logout useri 9 Help Wednesday June 10 2009 Friday June 19 2009 1 06 4 Friday June 19 2009 1 09 Pending 3 ee i TSQ Module Acquiring Data This chapter describes the functions of the TSQ Mod
98. hoose Design Study b Specify the Subject Groups Subject Treatments Biological Matrices and Nominal Times necessary for the study c Click Accept when finished d Choose Subjects e Complete your updates and click Save f Choose Treatments g Complete your updates and click Save For more information refer to the Design Menu chapter in the Watson User Manual Choose Tracking Sample Entry The Sample Entry dialog box opens Select samples and click Save when complete You may use only samples whose Sample Condition is OK in an Analytical Run For more information refer to the Tracking Menu chapter in the Watson User Manual To copy the master assay to the study assay Choose Analytical Copy Master Assay Select one or more assays to be used for this study from the list of master assays If the appropriate assay has not been set up for this project exit and create a new master assay by choosing File Master Assay Select Save to copy the master assay to this study Copy the master assay to the study assay To create a new run with the study assay Choose Analytical Plan Analytical Run The Analytical Runs dialog box opens Click Create On the Analytical Run Info page specify the type of run and the assay to be used Watson TSO Module User Guide 17 ana A uU To add samples to the work list Click the Worklist tab Add assay samples study samples and us
99. hromatogram view A view width can be specified for each component void time The time after injection that it takes an unretained compound to elute from the LC column This time is subtracted from the elution time for a retained compound to obtain the corrected relative retention time for the elution of each compound Watson TSQ Module User Guide 147 Glossary W W An abbreviated form of the word weighting W This shortened form is used to save space in the header of the Spectrum view when the calibration curve data weighting factor is displayed For example W xxxx where xxxx is the weighting option selected and stored in the Processing Method See also weighting w weight In Xcalibur and layered applications this is equivalent to mass weighting w The mathematical assignment of significance weight to specific points during a least squares regression analysis calculation A weighting of one indicates equal weighting and treats each point the same in the regression calculation window size The number of scans in the window used during peak identification by the spectrum method WME Windows Meta File workbook A folder in an LCquan study that contains Instrument Methods Sequences Processing Methods and raw files for an acquisition Each Workbook contains folders named Exports Imports and Raw files See also locked workbook study LCquan workgroup A set of users assigned to specific roles wor
100. ic system baseline noise rejection factor This factor is applied to the baseline peak to peak noise band during the peak detection process See also baseline noise baseline type The baseline approximation method used for LC chromatogram peak integration Xcalibur and LCquan baseline window The number of scans for searching local minima baud rate A measure of the number of events or signal changes that occur in 1 second blank sample type A sample type that contains no target components Internal standard components can be added to calibration blanks iBLQ Result is below the limit of quantitation A user defines the limit BMV FDA Bioanalytical method validation guideline 2001 bracket A sequence of samples where calibration samples are processed before and after Unknown and or QC Samples All Calibration Samples from the same bracket are used for the quantitation of the unknown and QC samples in the bracket Watson TSQ Module User Guide 121 Glossary bracket none A bracket type that can combine the calibration standards from the current sample set with previous calibration information stored in a calibration file bracket non overlapped A bracket type where the unknown samples are broken into groups Each group is quantified against separated sets of calibration standard samples All standards are run before and after each group and standards are not shared between groups bracket open A bracke
101. ick Cancel To delete an instrument stack Choose Options Instrument Inventory The Instrument Setup window opens Select an instrument stack and click Delete A confirmation message opens Do one of the following To delete the instrument stack click OK Ore To exit without making any changes click No Watson TSO Module User Guide 9 2 Watson Submitting Runs to the TSQ Module Creating a Peak Integration Instrument Specifying Devices Use the following procedures To create a device To clone a device To edit a device To delete a device To create a device Choose Options gt Instrument Inventory to open the Instrument Setup window Select the Peak Integration instrument Click Add at the bottom of the Devices pane The Create Device dialog box opens Enter a Device Name and Device Type Optional Type the Manufacturer Model Serial Number and Barcode Do one of the following e To save the device click Save Dp To exit without creating a device click Cancel To clone a device Choose Options Instrument Inventory The Instrument Setup window opens Select a device and then click Clone The Clone Devices dialog box opens populated with the device information To modify device information click the appropriate fields 10 Watson TSQ Module User Guide Thermo Scientific 2 Watson Submitting Runs to the TSQ Module Creating a Peak Integration
102. ide in the autosampler tray of the current sample This readback value is displayed only if your LC provides this information under direct control This value is not displayed if your LC is under contact closure control Thermo Scientific 5 TSO Module Acquiring Data Monitoring the Run Status Table 10 Run Status parameters Sheet 2 of 2 Parameter Description Instruments The readback state of each configured instrument appears on the Run Status page Shortcut Menu Right click to display the instrument s shortcut menu Turn Device On Puts an instrument in the On state Turn Device Standby Puts an instrument in the Standby state Turn Device Off Puts an instrument in the Off state Instrument Status Each instrument sends its own status information to the Run Status view This is an example of a simulator status Status Status Scanning Scan speed x 1 First scan 1 Last scan 1145 Scan number 43 Start time min 0 251667 Real time elapsed min 0 251817 Repeat count 0 Ho Acquisition Queue The Acquisition Queue page on the Run Status view displays information about all the runs in the Acquisition Queue Run Status Acquisition Queue a LES All Runs SL JES Test_Study_21 E Sample ID 1 acquisition complete Sample ID 2 currently acquiring Sample ID 3 waiting for acquisition Thermo Scientific Watson TSO Module User Guide 51 5 TSO Module Acquiring
103. ie plea o Caen alee 36 Editing d Pollo d sore us o Eds ar See eit Exo es eee deed 41 Aeque d Rune ostiis Kae Geet eaaet Canta poro ete pae Raten vae 45 Monitoring the Run Status 1o ote e GO e SEE arbe PR e atcp E 48 Run Status View Control Buttons ss aisi Lo ertet rk e ora nas 49 RUG StAtUs ens kh ee ue nd ee s bt d E UR Pedes 50 Instrument Status 6 ce eee teenies 51 Acquisition Queue i e e 51 Real time Displays iui we aces oo aiu eed epe sic ea Ried tede 52 Watson Working with Processed Runs suuueeeeeeese 59 Reviewing Runs 20s serere te aeree Rhet re reos eer s ERE 59 Reintegrating Chromatograms 12323 apo opa Ip eh Mavs RR TE Rie a 63 Changing the Chromatogram Display 6o coe aat bea acs 68 Additional Run Review Features 2 ohh wie y e HERRERA 69 Reviewing Internal Standards and Performing Regression 71 Watson Reports and Printing Capabilities aaa 71 Study level and Sample level Integration Reports lessen 77 SXudit REPOT aame Wisk P orbs Ae ial eras eM aaa E a Sind A e tel died s ur f 80 Generating a Watson Audit Report sia oor Qo woes X surrer 80 Generating a TSQ Module Status Audit Report 0 000000 83 Printing Capabilities o osos oes toco loca cii etc RR te Sd EA o ac ate 84 Printing a Chromatogtatua ix 222r S VERE 1 3 ale EHE O RPG Rete 84 Printing Capabllies iot isse ad bee CR IRR d 85 TSQ Module Menu and Toolbar Reference
104. ientific Watson TSO Module User Guide 3 1 Introduction Watson LCquan Xcalibur TSO Module Sequence of Steps Watson LCquan Xcalibur TSQ Module Sequence of Steps The following table outlines user specific steps using the Watson application the Xcalibur application and the TSQ Module application Table 1 Watson Xcalibur TSQ Module key steps Step Create a peak integration instrument interface Instructions Completed by the System Manager For more information refer to the TSQ Module System Managers Guide Create or clone the instrument stack See Creating an Instrument Stack on page 7 Create the tune method and processing parameters files Completed externally to the Watson application in the LCquan or Xcalibur applications For more information refer to the LCqguan User Guide or the Xcalibur documentation set Setup the master assay See Setting up the Master Assay on page 13 Create or open a Watson study See Working with a Watson Study on page 16 Copy the master assay to the study assay Create a new run with the study assay and add samples to the work list See Working with a Watson Study on page 16 See Working with a Watson Study on page 16 Create a sequence file See Working with a Watson Study on page 16 Send the run to the TSQ Module application When necessary modify the run parameters injection volume or positio
105. ile In both cases you must take into account the baseline of the detected peak Instrument response is generally measured with several samples commonly called standards or calibration standards These standards must cover a suitably wide range of concentrations or amounts and must bracket the range of expected concentrations in the unknown Responses to these standards are plotted in a graph called a calibration curve Ideally this curve corresponds to the equation of a straight line to ensure the highest degree of precision Fitting an equation to the calibration curve with a user specified method for example a least squares regression provides a response factor a comparative measure of the response of the mass spectrometer to a component It is based on the amount of sample injected and the resulting peak area or peak height The response factor gives an intuitive and quantitative measure of how responsive or sensitive the mass spectrometer is to a certain component Figure 30 Integrated Chromatographic Peak 10 80 604 A N e Relative Intensity 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 1 0 Time min To perform quantitative analysis of samples containing unknown amounts of the target component calculate the peak area or height and compute and apply the appropriate response to the equation derived from the calibration curve These steps provide an estimate of the amount of the target component in the samples The precision
106. ing From the Acquisition Queue you can pause a run and resume it stop the currently acquiring sample and continue to the next sample or remove a run from the Acquisition Queue sending it back to the Run Manager view Use the following procedures To stop an acquiring sample To pause a run To remove a currently acquiring run from the Acquisition Queue To remove a non acquiring run from the Acquisition Queue To cancel a run in the Run Manager view To stop an acquiring sample You can stop acquisition of an individual sample in the Acquisition Queue When a sample is stopped the system considers it complete and the XML data is packaged and returned to the Watson application You cannot resume a stopped sample 1 To stop the acquisition of the current sample click Stop The acquisition stops for the currently acquiring sample and the run pauses The run status in the status in the Run Manager view is Paused The pause button is red indicating that it is ready to resume with the next queued sample Thermo Scientific Watson TSO Module User Guide 55 5 TSO Module Acquiring Data Monitoring the Run Status If the currently acquiring sample is the last sample in the run the run is marked Completed and sent to the Watson application 2 To resume the acquisition for the next sample in the run click Pause e When you resume acquisition the system begins with the next sample in the run If you stopped the final sam
107. ings and start the acquisition of a run rd Li EE Acquire Run Edit Editing Database http 3 Drugs svc Project Test Study Study Run 5 Acquire samples Blank Priority Run StdBracket Additional comment Instrument Method System power scheme O 0n L Standby Off LevellD LevellD LevellD Table 15 Acquire mode parameters Sheet 1 of 3 Command Acquire samples Description Displays the first and last samples to acquire Available only for a previously Stopped run Priority Run Inserts this run into the Acquisition Queue ahead of all submitted non acquiring runs Additional comment A comment that is returned to the Watson application in the run report Instrument Method Startup Method Specifies that the TSQ Module application runs the startup method specified in the run data before the run starts No data is acquired by this method and no autosampler injection takes place This feature is not available for all devices Shutdown Method 94 Watson TSQ Module User Guide Specifies that the TSQ Module application runs the shutdown method specified in the run data after the run has completed No data is acquired by this method and no autosampler injection takes place This feature is not available for all devices Thermo Scientific A TSO Module Menu and Toolbar Reference Acquire Mode Table 15 Acquire mode parameters Sheet 2 of 3 Command Desc
108. intensities from the start to the end of the peak peak base An interpolation of the baseline between the extremities of the peak peak detection The process of finding the locations and amplitudes of local maxima and minima in a signal that satisfies certain properties See also peak end peak start peak edge detection A chromatogram peak detection criteria that uses the peak signal to noise S N cutoff value to assist in the detection of a peak edge This test assumes an edge of a peak is found when the baseline adjusted height of the edge is less than the ratio of the baseline adjusted apex height and the peak signal to noise cutoff ratio See also peak S N cutoff peak end The end of a chromatographic peak occurs whenever the detection signal decreases to a value less than the current threshold criteria See also peak start peak height peak dimension The distance from the peak maximum to the peak base measured perpendicular to the ordinate See also constrain peak width tailing factor peak integration In this analysis of a chromatogram the area of each peak is determined peak noise factor The noise level multiplier used to determine the signal threshold of a possible peak peak number An identification number assigned by Xcalibur to each peak in an analytical run Thermo Scientific Glossary peak S N cutoff A peak edge detection advanced parameter used in conjunction with the influence of valley d
109. ion Contents Watson Feature Summary TSQ Module Feature Summary e Watson LCquan Xcalibur TSQ Module Workflow e Watson LCquan Xcalibur TSQ Module Sequence of Steps e Watson TSQ Module Watson Run Management Watson Feature Summary The TSQ Module application is designed for routine tandem liquid chromatography mass spectrometry LC MS bioanalysis of samples The TSQ Module application can be used with Thermo Fisher triple quadrupole LC MS systems such as the Quantum and Vantage LC MS products After an analytical method has been developed the TSQ Module application can be used to validate the method and perform routine bioanalysis of samples The TSQ Module specific features within the Watson application include The Watson work list tuning tun and method meth files are directly exported to the TSQ Module application The LC MS tuning tun and method meth files are stored inside the Watson application database The LC MS peak processing parameters are stored inside the Watson application database Raw data is stored inside the Watson application database Chromatogram review re injection selection and submission and peak integration and re integration occur within the Watson application Real time run peak review occurs in the TSC Module application Real time run status is obtained in the Watson application Thermo Scientific Watson TSO Module User Guide 1 1 Introduction TSQ Module Feature S
110. ironment outside of a living body F F An abbreviated form of the phrase scan filter This shortened form is used to save space when the scan filter is displayed in a header The selected scan filter is displayed using the scan filter format FDA US Food and Drug Administration file based Data received from or sent to an instrument is in ASCII or Excel file formats Filter rise time A detector parameter that controls its response time The rise time is inversely proportional to the amount of baseline noise the longer the rise time the less noise detected However excessively long rise times can result in broader peaks with shorter peak heights firmware Software routines stored in read only memory Startup routines and low level input output instructions are stored in firmware fixed Y axis normalization mode A display mode available for the Spectrum view showing the height of the vertical scale set as equal to the height of the largest peak in the current mass spectrum The height of the vertical scale is fixed when the fixed display mode is invoked Thermo Scientific flag Letters above chromatogram and spectrum peaks that provide supplemental information about the peak data For example if a peak is saturated Xcalibur displays an S above the peak flush volume The volume of solvent used to flush the lines sample loop and syringe s between injections fragment length The number of amino acids in the fragment
111. is bounded by the time baseline and the relative abundance trace Chromatogram peak areas are reported in units of count seconds where the relative abundance is measured in counts and the time baseline is measured in seconds A R assay method A plan for determining desired test values from a subject sample The plan includes definition of regression approach method Std QC concentrations replicates weightings analytes internal standards instrument to be used concentration units for reporting precision of results for reporting and so on 120 Watson TSO Module User Guide assay sample An analytical run definition A sample used in an analytical run that is used to determine a representative value from a study sample ASCII American Standard Code for Information Interchange AUC Area under the curve audit log Provides a chronological listing of all auditable software application events that the user initiated auto Dta An auxiliary application that produces dta files automatic processing The post acquisition off line batch non interactive processing of data collected from the instrument Automatic processing involves the use of all the methods specified in the Sequence for the sample s to be processed autosampler The device used to inject samples automatically into the inlet of a chromatograph autozero time The time at which the UV detector performs an automatic zero of the baseline average molecula
112. ither built in or gateway digital DM PK Drug metabolism and pharmacokinetics dilution factor A factor that specifies how much a sample was diluted during preparation This factor is used to calculate the amount or concentration in the original undiluted sample display range The portion of the graph spectrum or chromatogram that is currently displayed 126 Watson TSO Module User Guide dose Protocol Definition The numeric amount and units of measure which corresponds to the level or concentration of a drug which is to be administered via the specified route of administration draw speed The speed at which the metering unit draws sample out of the vial The draw speed may have an influence on the injection volume precision when using viscous samplers If the draw speed is too high air bubbles may form in the sample plug affecting precision driver A device specific control program that enables a computer to work with a particular device droplines A mathematically constructed vertical line from the valley between the peaks to the baseline drug set A group of compounds associated under a common name QuickQuan uses drug set names to distinguish which compounds to use for each sequence in an assay or which compounds to tune in a tune plate Using drug sets allows you to place multiple compounds in a vial or microplate well for both tuning and acquisition duplicate entries Similar entries in a non redundant prot
113. k list A set of samples to be submitted to the instrument work list based specifies how the data in the results file are matched to the Watson application s analytical run The sample in the results file is uniquely identified by the sample s position in the Watson application worklist 148 Watson TSO Module User Guide X XCorr Abbreviation for the raw cross correlation score of the top candidate peptide or protein for a given input data file XML Extensible Markup Language A general purpose markup language that is used to facilitate the sharing of data across different information systems particularly via the Internet Thermo Scientific LLL m ie Index Symbols qn file exporter 21 meth file exporter 21 pmd file exporter 21 TSQTune file exporter 21 96CV PK 136 A A R assay method 120 absolute scaling 119 Acquire samples parameter 46 Acquiring status run management 6 Run Manager view 36 Run Select view 35 acquisition sequence 119 Additional comment parameter 46 adjusted retention time 119 AIC A 119 ALQ 119 ambiguous roots 119 amino acid 119 119 amino acid modification 119 amino acid residue 119 amplifier temperature 119 Analyst parameter 40 analyte 119 analyte detection using mass spectrometry 111 Analytical Data Interchange protocol 119 analytical run 119 analytical run assay 120 ANDI 119 ANOVA 120 APCI probe 112 APCI APPI probe 112 apex RT 120 Apply Settings command 55 area chromatogram
114. le analyte and choose Tag for Reassay from the menu Do one of the following To save the tag click Save EQ To exit without saving any changes click Exit To flag a sample or sample analyte with a text comment From the run results right click the sample or sample analyte and choose Apply Edit comment from the menu The Sample Comment dialog box opens HE Sample Comment OF x Enter Sample Comment Please choose or enter sample comment a OK Cancel Enter a comment or choose one from the list Click OK To deactivate or reactivate a sample analyte for regression Right click the sample analyte and choose either Activate to activate the sample analyte or Deactivate to deactivate it Do one of the following To save the change click Save EQ To exit without saving any changes click Exit To save to the database Click Save on the Run Review view 74 Watson TSQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Reviewing Internal Standards and Performing Regression To perform a standard regression 1 Choose Analytical gt Standard Regression The Standard Regression dialog box opens with two grids The top grid contains a list of each Analytical Run for which Raw Data has been imported The lower grid is a list of analytes associated with the specified Analytical Run with analyte status regression data LLQ ULQ and who performed the regre
115. libration mass spectrometer 123 Cancel Run command 39 canceling runs 37 cassette dosing experiment 123 centroid data 123 centroiding 123 CFR 123 Check calibration 123 checksum 123 chemical noise 123 chromatogram 123 chromatographic column 123 chromatographic resolution 140 chromatography 123 chromatography filter 123 chromatography flags Thermo Scientific Index baseline clipping B 121 retention time shift 140 Column Selector dialog box Run Edit view 35 column chromatographic 123 commands Apply Settings 55 Cancel Run 39 Export 23 Reset Scaling 55 Save Run 44 Select Run 39 comma separated values text file 124 Comment parameter 44 compensation voltage 124 Complete Digest 124 Completed status run management 6 Run Manager view 36 Run Select view 35 component 124 component amount calculated 124 component amount measured 124 component detection 124 component name 124 composite spectrum 124 compressibility 124 compressibility ratio 124 concentration 124 conditioning 124 consecutive reaction monitoring scan type 124 constrain peak width 124 Continuous update parameter 54 control file 124 control matrix 125 convex gradient curve 125 convolute 125 corrected relative retention time 125 CR 125 CRM scan type 124 CRO 125 cross correlation factor 125 cryo cooling 125 CV 125 data acquisition 125 data bits 125 data rate 125 database 125 Watson TSO Module User Guide 150 Database parameter Login
116. ment interfacing types and styles calibration curve and QC samples options and other assay related parameters The Study Assay is copied from the master Assay study sample An analytical run definition A sample from a subject at a treatment site that is based on the study s protocol study samples database The sample by sample representation of the study Every sample in this database must be represented individually or as part of a group in the study subject Protocol definition A living biological entity that can be administered a dose of a drug and subsequently sampled for purposed of analyzing drug activity subject group Protocol definition A set of subjects which have a common set of treatment administrations applied to them summary Specifies the number of results files available for each analytical run One results file is created for all samples in the analytical run Swiss Prot Part of the UniProt database an annotated protein sequence database maintained by the Swiss Institute for Bioinformatics SIB and the European Bioinformatics Institute EBI The Swiss Prot database consists of protein sequence entries T T Time T Half Half life tailing factor A peak integration parameter that constrains the peak width of an asymmetric chromatogram peak that has a tailing trace See also constrain peak width peak height Thermo Scientific Glossary tangent skim A timed event that you can specify in the eve
117. ment is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A August 2009 Minimum software requirements Xcalibur 2 1 0 TSQ 2 0 5 Microsoft Windows XP Professional SP 3 optional LC Devices 2 2 1 For Research Use Only Not for use in diagnostic procedures Thermo Scientific Chapter 1 Chapter 2 Chapter 3 Chapter 4 Prelate uiae deese d ULM VC ENTE RA qa eR qa ql Inn an Re vii Related Documentation 2244 are d rr RE Ee ERE OR EORR E viii Special IMODOBE LL sesecaides ew saebws bes easet aetna esos e Vea doit Ia ope viii System Requirements cesses he nn ix Contacting US cede ade ais eb ies whe pres oe ree e a e eda es x INPOONCNON usos iure Pu acd PAD Aa Edd M d AU add daraus dard 1 Watson Feature Summary 1 1 cia ena eee 1 TSQ Module Feature Summary 06 0 eects 2 Watson LCquan Xcalibur TSQ Module Workflow 02 eee ee 3 Watson LCquan Xcalibur TSQ Module Sequence of Steps suu 4 Watson TSQ Module Watson Run Management 0 0 eee eee 5 Watson Submitting Runs to the TSQ Module 7 Creating a Peak Integration Instrument secu rer ete pro Ea 7 Creating an Instrument Stack cassa dace dob Roos aor ate d a 7 Speci
118. mine the identity of the components of a substance See also quantitative analysis quality control QC A quality management program that includes procedures designed to ensure a specified level of process quality Calibrations duplicate or replicate analyses spiked samples and blanks are quality control activities The accuracy and precision of QC sample results are used to indicate the accuracy of the quantitation of unknown samples See also quality control QC sample type unknown sample type quality control QC sample type A sample that contains known amounts of known components QC samples are placed in the sequence so that quantitation results can be compared with known component amounts or concentrations for quality assurance purposes See also quality control QC 138 Watson TSO Module User Guide quantitation The process of determining the amount of a component in a sample quantitation mass A specific mass to charge ratio for example m z 502 or range of mass to charge ratios to be used when determining the peak area and peak height of a compound Usually a quantitation mass quan mass is chosen that is characteristic of the compound See also peak area peak height quantitative analysis Chemical analysis designed to determine the quantity or concentration of a specific substance in a sample See also qualitative analysis Quantitative calibration The process of determining how the LC M
119. n See Working with a Watson Study on page 16 See Editing a Run on page 41 Start data acquisition See Acquiring a Run on page 45 Monitor peaks in real time in the TSQ Module application See Monitoring the Run Status on page 48 Monitor run status in real time in the Watson application See Reviewing Runs on page 59 Review the run See Reviewing Runs on page 59 Change the peak processing parameters See Reintegrating Chromatograms on page 63 Review internal standards Watson TSO Module User Guide See Reviewing Internal Standards and Performing Regression on page 71 Thermo Scientific 1 Introduction Watson TSQ Module Watson Run Management Step Instructions Filter sample types See Reviewing Internal Standards and Performing Regression on page 71 When necessary select runs to reinject See Re injecting a Run from the Watson Application on page 106 Review and accept the results of the See Reviewing Internal Standards and reinjected run Performing Regression on page 71 Accept the run See Reviewing Internal Standards and Performing Regression on page 71 Perform standard regression See Reviewing Internal Standards and Performing Regression on page 71 Generate and print reports See Printing Capabilities on page 84 Review the audit trail See Audit Reports on
120. n and is removed from the Run Manager view While in the Acquisition Queue you can remove a run and return it to the Run Manager view with a Stopped or Pending status To move a run from the Acquisition Queue and return it to the Watson application you must first return the run to the Run Manager view and then cancel it from there Table 2 Run Manager view status Status Pending Description The run arrived from the Watson application and awaits acquisition This run could have been submitted to the Acquisition Queue and returned to the Run Manager view before it began acquiring Submitted Acquiring The run is assigned for acquisition but is not currently acquiring The run is in the Acquisition Queue The run has progressed to the top of the Acquisition Queue and is currently acquiring Completed The acquisition has finished running and the run data was returned to the Watson application Completed runs might not always be observed in the Run Manager view When the TSQ Module application finishes sending the results of the last completed sample to the Watson application it marks the run as Completed and quickly removes the run from the queue Paused The run is assigned to an instrument and is currently acquiring but has been paused and waits between samples Stopped 6 Watson TSO Module User Guide The run was assigned to an instrument and was acquiring but was removed from the Acquisi
121. n application audit trail records the date time and user credentials Watson TSO Module User Guide 25 3 TSO Module System Administration Using E Signatures Electronic Signature dialog box Electronic Signature The following operation requires an electronic signature Edit samples User Credentials UserName Ral Password Reason Edit samples Table 5 Electronic Signature parameters Parameter The following operation Description Lists the operation that requires an electronic signature This requirements is specified in the run XML data User Credentials User Name The Watson login name for the user Password The Watson password for the user Reason Explanation for the action Default is the same as the attempted operation OK Approves the user name and password closes the Electronic Signature dialog box completes the requested operation and places an entry in the audit trail Cancel Closes the Electronic Signature dialog box without 26 Watson TSQ Module User Guide completing the requested operation and places an entry in the audit trail Thermo Scientific oo M TSQ Module Getting Started This chapter describes how to set up the TSQ Module application and log in to a session Contents e Setting up in the Watson Application e Starting the TSQ Module Application Setting up in the Watson Application Each run is identified
122. n impact on the Run Review view Thermo Scientific Watson TSO Module User Guide 69 6 Watson Working with Processed Runs Changing the Chromatogram Display Accept a Run Using the Watson application you can review analytes IS mass chromatograms and peak detection results and reintegrate the results before accepting the run To accept a run click Accept Review on the Run Review view Resubmit a Run to a Different Instrument You can cancel a run that has been submitted to the TSQ Module application and resubmit it to an alternate instrument stack or an alternate instrument only if no data has already been acquired 70 Watson TSQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Reviewing Internal Standards and Performing Regression Reviewing Internal Standards and Performing Regression Use the following procedures To review internal standards To filter sample types from the run results To flag a sample or sample analyte with a Reassay tag To flag a sample or sample analyte with a text comment To deactivate or reactivate a sample analyte for regression To save to the database To perform a standard regression To review internal standards From the Run Review view click Internal Standards Review The Raw Data Analysis view opens with the Chart page displayed Figure 18 Raw Data Analysis view Chart page ile E3 Chet Gad Raw Data Analysis Internal Standard 25M
123. n score XCorr between the top candidate and the current candidate for a given input data file For example the Delta Cn for the fourth hit would be Xcorr1 Xcorr4 Xcorrl where Xcorr1 is the Xcorr of the first hit and Xcorr4 is the Xcorr of the fourth hit See also XCorr Watson TSQ Module User Guide 125 Glossary delta retention time The difference in time between when a peak is expected to elute according to previous run data and when it actually elutes expressed as a percentage de novo sequencing The derivation of a peptide sequence from its MS MS spectrum without relying on protein databases for identification detection limit The point at which the signal and noise become statistically indistinguishable In practice this is often taken as the point at which the amplitude of a peak is only two to three times the amplitude of the average baseline noise See also sensitivity device s A single item or items within an instrument for example pump digest fragments The set of smaller compounds formed by the action of an enzyme on a larger compound For example the digest resulting from the action of the enzyme trypsin on a protein is a set of peptides and protein fragments See also enzyme trypsin tryptic digestion digital Data to from an instrument is through either API calls or direct connection this transfer type can be uni or bi directional the Watson application s digital interfaces may be e
124. nalysis Tune fake tune RT 2 10 2 54NL 1 6064 ceSRM m2 470 18 Gi 420 00 190 07 274 08 p D LX E e Uu RT 2 56 4NL 16064 SRM ms2 314 10 62 i4 40 00 209 961 sors Thermo Scientific Thermo Scientific 7 Watson Reports and Printing Capabilities Study level and Sample level Integration Reports Figure 23 Sample Level Integration report Instrument Serial Analysis Method Sim MS100 meth Processing Param 3 Druas Wo amp book lan Analysis Tune fake tune Project Name Study Name MartinSBTestt Arch RT 0 01 2 16 NL 45262 edi Renamed cSRM m2 330 130i4 20 00 70 15 192 07 Ruy 19 QAeem iaa Tug ES Component Name Paroxetine Dni sul 1 L Sample Type UNKNOWN wl Actual RTjmen 873 i Response 33 6085046001506 i m j 5 Ratio 000014285360206 0 a niection index 1 gt we LI a T Ll Acquisition AM JU n Med se d XL A es 15 ae Semele MartinSBTett Archiv ed amp Renamed 0120000002 0001 At Plasma 1 Gh internal St AlprazolamdS RT 2 46 4NL 452E2 cSRM m2 314 10 2ci4 40 00 209 96 Response 373598 27524900900 Apes OT ORE Actual RT min O ie a P rv mentem om hy Watson TSO Module User Guide 79 7 Watson Reports and Printing Capabilities Audit Reports Audit Reports Use the Watson application to create view and print system or study level audit reports for the TSQ Module application You can print a basic audit report from the Watson File menu
125. ne Plus or Tune Master window This file contains 7 columns of information about a particular graph Graph view files can be imported into Microsoft Excel for display and manipulation group scan The number of intermediate MS MS scans between two MS MS scans that have the same precursor m z value H header information Data stored in each data file that summarizes the information contained in the file HPLC high performance liquid chromatography Refers to either the assay methodology or a Watson application assay type ICIS Interactive Chemical Information System ICP MS inductively coupled plasma mass spectrometry Refers to either the assay methodology or a Watson assay type ID or Id Identification Unique identifier incomplete digest The digest type where not every possible digest site is digested For example if an incomplete digest is done with trypsin every combination of digested not digested Lysine K and Arginine R will be considered INCOS noise A single pass algorithm that determines the noise level The noise level data is used to determine which peaks to label during area calculations and to determine peak start and peak end See also repetitive noise Watson TSQ Module User Guide 129 Glossary indexed database A database created with the Database Manager or the FASTA Database Indexer to speed up searches individual Specifies the number of results files available for each sample One resul
126. ng parameter files File extension File description Xcalibur pmd Processing QC levels Stds component names and integration parameters TSQTune Tune parameters mass spec amount of gas amount of heat and so on meth Instrument method file LC parameters autosampler A S settings pump settings mass spec transitions SRMs LCquan qn Combination of pmd and meth files TSQTune Tune parameters mass spec settings amount of gas amount of heat Note The Tune and Method files are closely associated with each other and form a matched pair In LCquan export the TSQTune and lqn files QOr In Xcalibur export the TSQTune meth and pmd files 12 Watson TSQ Module User Guide Thermo Scientific 2 Watson Submitting Runs to the TSQ Module Setting up the Master Assay Setting up the Master Assay Thermo Scientific This section provides the steps required when setting up the master assay For more information about the master assay refer to the Watson User Manual While many steps follow the standard Watson application workflow for runs to be submitted to the TSQ Module application there are some differences For example the Instrument page is available only when you configure a Peak Integration instrument Use the Instrument page to submit the run to the TSQ Module application Use the following procedures To set up the Instruments page in the Assay view To add instrument method ass
127. nt list shown with the Avalon Peak Detection algorithm Tangent skim identifies the tallest peak in a cluster and detects peaks on either side or both sides of the tallest peak Tangent skim resets automatically at the end of a peak cluster target compound A compound that you want to identify or quantitate or that a specific protocol for example an EPA method requires that you look for Target compounds are also called analytes or target analytes tension Controls how closely the baseline follows the overall shape of a chromatogram A low tension traces the baseline closely to follow changes in the chromatogram A high tension follows the baseline loosely and over longer time intervals See also baseline threshold A value above which something will take place For example if a peak height is above the indicated peak label threshold that peak is labeled threshold base peak Indicates that peaks below this percentage of the base peak will not be plotted time function TF programming The process of turning external devices such as column switching valves and fraction collectors on or off at preset times during your run To create a time program fill in the Time Events table time offset The value that adjusts for fluctuating retention times when comparing data between the experimental source raw file and the control background file time programming The process of changing the heater temperature or valve position at
128. nterfacing types and styles calibration curve and QC samples options and other assay related parameters A Master Assay is associated with a project so that multiple studies within a project may use it master assay method An analytical method that is specified as part of a project It is handled separately from an actual study but is available to be associated with any study A Master Assay method may be associated with multiple studies Watson TSO Module User Guide 131 Glossary mass An abbreviated form of the phrase mass range This shortened form is used to save space when the selected mass range in mass to charge ratio units is displayed in a header for example Mass 150 375 massmap params file Stores the parameters used for the Peptide Mapping application You can edit this file in a text editor mass step size Size of the plotting or calculating interval For example a mass step size of 10 u would result in a calculation occurring at a point every 10 u along the baseline of the spectrum matrix The material that contains the compound of interest for example blood mean The average of a group of measurements for example masses times or intensities The mean is used to calculate variance and relative standard deviation See also relative standard deviation variance metabolic modifications Changes that occur to metabolites while in the body metabolite A chemical intermediate or product due to metab
129. ntrol Buttons Run Status Instrument Status Acquisition Queue Display Options Pausing Stopping Canceling Runs Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data Monitoring the Run Status Figure 6 Run Status view in the Status mode Display options Control buttons atson TSQ Module Database http 3 Drugs svc Logout useri o Help 2 RT 0 00 4 00 Method defined traces P NL 1 13E2 Show spectrumtrace Acquisition Queue pri c SRM ms2 330 13 eid 20 00 Continuous update a LIES All Runs 100 1 16 4 4p i 70 15 192 07 Manual select JES Test Study 26 0 Sample ID 1 gt Nefazodone NL 0 c SRM ms2 User defined RT range min SamplellD 2 z 100 470 18 eid 26 00 t 180 07 274 08 EN 2 Alprazolam d5 NLO E c SRM ms2 c 314 10 eid 40 00 209 96 e NL 0 c SRMms2 309 07 cid 42 00 205 02 Alprazolam 0 1 2 3 4 Time min 151 0 702 192 1 E Manage 70 150 151 010 192 070 m z m z m z Acquisition Queue Chromatogram display Spectrum display Run Status View Control Buttons The control buttons on the Status view let you control the acquisition process To start stop or pause an acquisition To start an acquisition or resume an acquisition that has been paused click 9 To pause an acquisition after the current sample has been completely acquired click To resume the acquisition click f again Thermo
130. nts xml File Communicating with the Watson Application Exporting Method Files to a Common Folder Auditing Using E Signatures Managing the Environments xml File In the Environments xml file the administrator assigns user friendly names to the Watson application Web addresses When a user logs onto the TSQ Module application the system queries for available databases When the administrator assigns a name to a Watson application Web address in the Environments xml file the user friendly name is displayed in the logon screen Database menu When the administrator does not assign a name in the to the Watson application Web address in the Environments xml file the complete URL is displayed in the logon screen Database menu The Environments xml file is located in the following directory C Documents and Settings All Users Application DataNWatson TSQ Module Thermo Scientific Watson TSO Module User Guide 19 3 TSO Module System Administration Communicating with the Watson Application Any new installation of the TSQ Module application preserves the edits to the Environments xml file Changes to the Environments xml file are not apparent in the logon screen until you restart your computer and the TSQ Module application The following is a sample Environments xml file lt xml version 1 0 encoding utf 8 lt Environments gt Environment address http localhost 9000 other Host9000 SystemAudit 1 gt lt
131. o longer selected To select a run for acquisition Select a run and click Select Run or double click in the run row The Run Edit view opens and displays each sample in the run From this view you can edit the run before you submit it for acquisition For detailed information about editing the run before you submit it see Editing a Run on page 41 38 Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data Managing a Run 2 To submit the run click Acquire The Run Edit view in the Acquire mode displays the samples for the run You cannot edit the samples from the Acquire mode The Acquire options in the Acquire mode provide parameters for submitting a run for acquisition For details about using the Acquire options to submit a run see Acquiring a Run on page 45 Manage Mode Manage Run Manager Select Run 2 Pending http 3DDrug ProgTest_Sh_ o Pending http 3 Drug ProgTest_Sh_ a Pending http 3 Drug__ ProgTest_Sh_ Cancel Run Table 7 Manage mode parameters Sheet 1 of 2 Command Description Function buttons Select Run Opens the Setup view for the highlighted run Cancel Run Removes the highlighted run from the view and returns the run to the Watson application Thermo Scientific Watson TSO Module User Guide 39 5 TSO Module Acquiring Data Managing a Run Table 7 Manage mode parameters Sheet 2 of 2 Command Run Manager columns Descripti
132. ociations To set up the Instruments page in the Assay view Complete the following process in the Master or Study Assay so that the definition is copied for each run assay 1 Click the Assay tab 2 Select LC MS as the Assay type 3 Click the Details tab 4 Select Peak Integration as the Instrument type The Instrument tab is activated in the Assay view Watson TSO Module User Guide 13 2 Watson Submitting Runs to the TSO Module Setting up the Master Assay Figure 4 Instruments page in the Assay view FA Path UIIE TEST Sve CA Sagebrath natsfbe DOCcCD0 ESL math Usee TESTSVR E C ASagebrush nstrf les DOC COXO0HESE 104 This page contains three panes Top untitled Instrument Files and Processing Method Details 5 In the Processing Method Details pane use the Analyte IS Name row to associate a parameter component with an analyte Each cell contains a list of analytes and internal standards defined in the assay from which you select the analyte that matches the identified component column header To add instrument method associations 1 From the Master Assay click the Instrument tab 2 In the top section click Add to open the Add Instrument Method Association dialog box 14 Watson TSQ Module User Guide Thermo Scientific Thermo Scientific 2 Watson Submitting Runs to the TSQ Module Setting up the Master Assay Figure 5 Add Instrument Method Association dialog box Badd instrument
133. ocol definition A group of subjects that can be sampled only once or a limited number of times after treatment administration It is not possible to study a subject s time vs concentration profile To create a time vs concentration response profile for a treatment a subject group dosed at the same time are divided into subsets of subjects that are sampled at different time points Sample concentrations at the same time point are averaged together and then the averages at the time increments are combined to form the time vs concentration profile no peak Not calculable No data was returned from the instrument for the sample or the Watson application is unable to calculate a solution for the regression Not Reportable user definable string User assigned flag no sites Amino acids in a sequence that follow an amino acid listed are not susceptible to digestion For example trypsin_k digests at Lysine K but if the K follows a Proline P in the sequence it will not be digested Thermo Scientific Glossary no waste injection A technique that injects the exact amount of sample requested Of the three injection modes the no waste injection mode uses the least amount of sample but it is also the least precise Use this injection mode to conserve sample nominal molecular weight The calculated mass of a molecule based on the integer mass number of the most abundant isotope of each element for example C 12 H 1 andO 16
134. olic reactions method A file containing commands that are interpreted by Xcalibur Xcalibur uses the following methods to run a sample Tune Instrument and Processing The file extensions of these methods are LCQtune or TSQTune meth and pmd respectively Xcalibur helps you to create edit save and use methods See also instrument method processing method Tune Method minimum number of scans in baseline An advanced parameter used to calculate a component baseline See also baseline 132 Watson TSO Module User Guide minimum peak width The value in scans required to identify that a peak exists To be included in the list of found peaks a peak must be larger than the minimum value missing component A component that is included in the calibration data but is not found during the analysis of a chromatogram modification A chemical or structural alteration ofa molecule such as oxidation or methylation modification mass The mass increment associated with an amino acid which you can specify to limit the size of a database you create molecular weight The mass of a molecule calculated for a given molecular formula as the sum of the atomic weights of the constituent atoms monoisotopic molecular weight The calculated mass of a molecule based on the exact mass of the most abundant isotope of each element Use the monoisotopic molecular weight for all data field entries for example C 12 000000 H 1 00782
135. on Status Status of each run Pending Submitted Acquiring Paused Stopped or Completed Pending The run arrived from the Watson application and awaits acquisition This run could have been submitted to the Acquisition Queue and returned to the Run Manager view before it began acquiring Submitted The run is assigned for acquisition but is not currently acquiring The run is in the Acquisition Queue Acquiring The run has progressed to the top of the Acquisition Queue and is currently acquiring e Paused The run has been assigned to an instrument and is currently acquiring but has been paused and is waiting between samples Stopped The run was assigned for acquisition and was acquiring but a user action moved it back to the Run Manager view Completed The run has completed acquisition Completed runs might not always be observed in the Run Manager view When the TSQ Module application finishes sending the results of the last completed sample to the Watson application it marks the run as Completed and quickly removes the run from the Run Manager view Database The Watson database or the friendly name assigned in the Environments xml file Run Name A combination of the project study and run ID as defined in the Watson application Samples Number of samples in the run Receive Date Timestamp when run was received Assay Date Timestamp when as
136. on dialog box Misc 1 page Stndwdlew Rephcses Precmeon Ouput Caedaeons Mec 1 Mac 2 Emai Mating NuGeness Sign Ot Show Gridines Font Name fee Grids E Shem Gid Lines on tables sent to RIF ox Document Management System Fort Name Tenes New Roman Detagn Study Set Custom Id equal to Watson Barcode ID Ces O Peed O Week C Morth C Yew C Senece E Set Sampie Customs Id equal to Watson Barcode Delad File Type for S R Display Deactry ated Samples on Regresison Graph rn ALL Present Aboot oi D ution f actor Allow samples hom multiple sudes in one analytical run O Abyat Factor Daten Facto C Aiow sangis from multiple studies n one anaitical an Delad Sire fee en Graphs Allow changing regetion type weighing lactot dur regeesion Delad Sce C Allow change tor analytical rune of unknown and or PSAE samples r Show Tet Show Numenc Value O Show Tes ard Number C Enable eding of sampile remet comment Margna sh aches Chromstogan Run Renew wps a napaja Resto Reose OC C Peas Urkrowne 1o 13 Bee fF 3j D Prevert Run Review Pres to Completion Retegsn Pes dx ocmon Vier ma manroshy ipecty vesti decns Q Peto Atomai Repke ate Ave sonis Ure fond automated decion tee Indc ate Felatrve Nominal Tune C ideato Reisive Teme diers bom Nominal Tee to epon C 4d Preiminary to Analytical Rapat Tiles Enable E diting ol Desctrrate Reasons E Lee Dexi we Reasons to the Desctwate Restora Anno
137. onents in the same run or to calculate their relative retention times Also known as calibration reference reference component retention reference component and internal standard 140 Watson TSO Module User Guide See also relative retention time RRT retention time RT The time after injection at which a compound elutes The total time that the compound is retained on the chromatograph column retention time shift For each compound in a method there will be a predicted retention time RT for the quantitation mass peak This predicted RT will be determined by the SOP definition of predicted RT It can change from day to day or between batches because it is a function of column maintenance RF See response factor RIA radio immuno assay RIA refers to either the assay methodology or a Watson application assay type ring electrode The mass analyzer electrode that is located between the endcap electrodes rise percentage An advanced parameter used for both valley detection and peak detection rise time A parameter that controls the response time of UV Vis or PDA detector The rise time is inversely proportional to the amount of baseline noise For example the longer the rise time the less noise detected role A role is a set of assigned security privileges route of administration Protocol Definition The means by which a drug enters into a subject For certain types of administration the drug is infused over
138. ontacting Us To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the link below Thank you in advance for your help SURVEY Thermo Scientific Watson TSO Module User Guide vii Preface Related Documentation Documentation for the TSQ Module application includes Help and the TSQ Module User Guide as a PDF file To view the TSQ Module User Guide Go to Start gt All Programs gt Thermo Watson TSQ Module gt Manuals gt Watson TSQ Module User Manual To open the TSO Module Help From the TSQ Module application choose Help gt Watson TSQ Module Help To find a particular topic use the Help Contents Index or Search panes For more information including upcoming application notes visit www thermo com Special Notices This guide includes the following types of special notices IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier viii Watson TSO Module User Guide Thermo Scientific System Requirements Thermo Scientific Preface Your system must meet these minimum requirements System Requirements PC 2 GHz processor with 1 GB RAM CD ROM drive Video card and monitor c
139. otting the magnitude of the detector response as a function of the external standard concentration You analyze the unknown sample and determine the concentration by matching the magnitude of the detector response with the magnitude on the calibration curve Using external standards is advantageous when you are analyzing various components in a sample and you can assay all compounds of interest by using a single set of external standards Although this approach offers time and cost effective quantitative analysis it cannot achieve the very highest precision and accuracy Variations in analyte and solution stability injection reproducibility and matrix interference lead to lower precision levels in the external standard method than in the internal standard method Figure 31 Calibration Curve Generated by Using an External Standard 500000 Response for unknown sample 400000 gc a ee NPNTEMONOEN c 3 2 3000004 5 o o l D 200000 4 S l Amount A in S 100000 unknown sample B l S P 0 E 0 20 40 60 80 100 Amount of target compound A 114 Watson TSO Module User Guide Thermo Scientific C Quantitative Analysis Overview Quantitative Analysis Techniques Using Internal Standards for Quantitative Analysis Thermo Scientific An internal standard ISTD is a component that is added to a sample to act as a response reference for one or more non ISTD components in the sample The concentration
140. ound The internal standard for a given target compound reference mixture For internal standard calibration A solution that contains one or more internal standard ISTD and target compound For external standard calibration A solution that usually contains the target compound s See also internal standard ISTD target compound reference peak In spectra from high resolution analyses a peak R from an internal reference compound that has a known precise mass Reference peaks are used as measures of calibration accuracy See also exception peak regression calculation A least squares method of obtaining a mathematical equation that best fits a set of experimental calibration data Xcalibur and LCquan support linear quadratic and cubic regression calculations related peaks Peaks in a mass spectrum that are produced by fragments of a common compound relative intensity The ratio of the intensity of a specific peak to the intensity of the peak with the highest intensity Thermo Scientific Glossary relative peak height threshold A threshold that excludes all peaks whose height falls below a specified percentage of the height of the highest peak in the chromatogram relative retention time RRT The LC elution time of a component divided by the elution time of a reference component The ratio of the LC elution time of a retained component t corrected for the void time tvoid and the elution time of a re
141. page 80 Watson TSO Module Watson Run Management Thermo Scientific The TSQ Module application workflow moves runs between three locations the Watson application where runs originate the T Q Module Run Manager view that receives each run and the TSQ Module Acquisition Queue where runs are acquired Watson Run Manager view Acquisition Queue R R un un r3 Sample 1 n Samples 1 n Y Instrument Y XML 1 n pata 1 n Arun sent from the Watson application enters the T Q Module Run Manager view The run status is Pending When you submit the run for acquisition the run is placed in the Acquisition Queue and the status in the Run Manager view changes to Submitted If the run is the first run in the Acquisition Queue acquisition immediately begins and the status in the Run Manager view is Acquiring When the acquisition begins the status changes to Acquiring Watson TSO Module User Guide 5 1 Introduction Watson TSO Module Watson Run Management When the acquisition finishes the status for the run changes to Completed The data for the run returns to the Watson application in XML format and the run is removed from both the Run Manager view and the Acquisition Queue While in the Run Manager view you can cancel a run A canceled run returns to the Watson applicatio
142. peak 120 Thermo Scientific area or height ratio 120 area ratio 120 area scan window 120 120 area tail extension 120 120 area threshold 120 area chromatographic peak 120 ASCII 120 Assay Date parameter 40 assay sample 120 AUC 120 audit log 120 auditing 24 Auto Copy Down command 43 Auto Fill Down command 42 auto Dta 120 automatic processing 120 autosampler 120 autozero time 120 average molecular weight 120 average response factor RF calibration curve 120 curve fit type 121 defined 120 average response factor curve fit type 121 average spectrum 121 averaged scans 121 base file name 121 base peak 121 base peak chromatogram 121 base sample ID 121 baseline 121 Baseline Clipping 121 baseline noise 121 baseline noise rejection factor 121 baseline type 121 baseline window 121 Watson TSQ Module User Guide 149 baud rate 121 blank sample type defined 121 overview 117 BMV 121 bracket calibration 122 defined 122 none 122 non overlapped 122 open 122 overlapped 122 building a database 122 built in Interface 122 Bunch Factor 122 C CaCO2 122 callevel 122 calculated amount 122 calibration 122 calibration compound 122 calibration curve defined 122 overview 113 using external standard 114 using internal standard illustrated 116 calibration level 122 calibration mode 123 calibration parameters 123 calibration replicates 123 calibration sample type 123 calibration standard sample type overview 117 ca
143. ple in a run the system begins the next run in the queue For detailed information about repeating the acquisition for a stopped sample see Appendix B Restarting Runs To pause a run You can pause a run in the Acquisition Queue and resume it later Watson application Run Manager view Acquisition Queue Paused run Y Resumed run 1 To pause the acquisition of the current run click Pause After the current sample completes the acquisition for the run pauses until you resume it The run status in the Run Manager view immediately changes to Paused even if the current sample is still acquiring 2 To resume the acquisition for the next sample in the run click Pause To remove a currently acquiring run from the Acquisition Queue You can remove an acquiring run from the Acquisition Queue and resubmit it later For detailed information about restarting a run see Appendix B Restarting Runs When you remove an acquiring run from the Acquisition Queue the run returns to the Run Manager view and its status is Stopped When you resubmit a stopped run from the Run Manager view you can specify a range of sample numbers that you want to acquire It is not necessary to reacquire previously acquired samples Watson Run Manager Acquisition Stopped Run removed from queue Resubmitted run gt Resumes at specified sample 1 To remove a run from the Acquisition Queue check the run check box and press
144. preset times during your run To create a time program fill in the Time Program table timed event An instrument action triggered to occur at a specific preset time during a run or analysis Watson TSQ Module User Guide 145 Glossary tolerance The allowable range of deviation from a specified value expressed as a percentage of this nominal value total composite spectrum A spectrum that is the sum of all MS MS MS3 MS4 MS5 MS10 averaged spectra trace A record made by an instruments recording element A common term for a chromatogram See also chromatogram treatment treatment administration Protocol definition per 21 CFR Part 11 The actual event of administering a drug dose via a route of administration to a group of subjects treatment group Protocol definition The same set of subject who have been administered a treatment treatment site Sample Handling definition The location at which subjects are dosed and sampled triple stage quadrupole TSQ mass spectrometer A tandem MS MS instrument which has the first and third quadrupoles performing mass analysis and the second quadrupole operated in RF only mode functioning as an ion transmission device trypmyo01 raw A raw spectrum file of the tryptic digest of myoglobin raw See also mzData trypsin A proteolytic enzyme found in pancreatic juice and active in alkaline environments tryptic digestion The site specific breakdown of
145. processing software compares the measured quantity with the expected value and an acceptability range The quantitative analysis of a QC sample is classified as passed if the difference between the observed and expected quantities is within the user defined tolerance A QC sample is classified as failed if the difference between the observed and expected quantities is outside the defined tolerance A blank sample contains no target components but might contain an ISTD when you use the internal standard quantitative analysis technique By analyzing a blank sample you can confirm that there are no residual components in the solvent system that can cause erroneous results Watson TSQ Module User Guide 117 o NEN Glossary AB CD EFGH JK LMNOPORSTUVWXYZ A absolute scaling Displays a chromatogram trace or spectrum so that the height of the Y axis scale is equal to the height of the largest peak in the data file The height of the vertical scale is fixed for the data file even if you change the range of the display acquisition sequence A defined set of acquisition settings for a single sample or list of samples The acquisition sequence includes information on how to acquire a sample and whether and how to automatically process the sample adjusted retention time The retention time RT ofa component adjusted or normalized using a retention reference component See also retention reference retention time RT AICA Kaike
146. quantitate compounds accurately the compound peaks must be distinctly separated from each other in time By carefully optimizing the LC variables listed above you can successfully separate and detect compounds with an optical detector such as an ultraviolet UV or photodiode array PDA detector 110 Watson TSO Module User Gu ide Thermo Scientific C Quantitative Analysis Overview Considering the Variables of Quantitative Analysis by LC MS MS In contrast to optical detectors mass spectrometers can often successfully detect individual analytes even when two or more compounds coelute as a single chromatographic peak Coeluting compounds are ionized in the mass spectrometer and the parent or fragment ions specific to the analyte or analytes are detected and measured for quantitative analysis Because the mass spectrometer detection is so specific you can reduce the chromatographic resolution and shorten the run times Using MS MS for Analyte Detection To optimize detection of ions by MS MS consider the following variables when working with a mass spectrometer interfaced to an LC Solution chemistry and polarity of the analyte of interest Probe selection H ESI ESI APPI or APCI Collision energy to fragment parent ions inside the mass spectrometer optimized by experiment The LC provides a stream of analyte solution eluate into the mass spectrometer where the analyte is detected You must consider the content of modifiers
147. r system level permissions Log onto the Watson TSQ Module application Manage the Run Manager view The TSQ Module application user run level permissions Submit a run for acquisition Edit samples injection volume position comment Edit run information enter additional comment or change acquisition options Save an edited run e Cancel a run in the Run Manager view e Stop pause resume a run in acquisition Remove a run from the Acquisition Queue Using E Signatures Thermo Scientific You can set the TSQ Module application to request an electronic signature from a user when the run requires it The attempted action for example saving an edited run cannot be completed until the user provides a password and submits the electronic signature The requirement for an electronic signature is set in the Watson application You can require an electronic signature when a user edits samples and saves a run in the Setup mode or when a user enters an additional comment and submits a run in the Acquire mode To submit an electronic signature The end user follows these instructions 1 Enter your user credentials or ask your supervisor to enter credentials User credentials are the same as your TSQ Module login and password 2 Accept the default reason or enter your own reason for the operation 3 Click OK The requested operation is completed In addition to the type of operation and the reason for the operation the Watso
148. r weight The calculated mass of a molecule based on the average atomic weight of each element Also known as the formula weight for example C 12 01115 H 1 00797 and O 15 9994 See also molecular weight average response factor RF A calibration type where the response factor is calculated for replicates at all calibration levels and then averaged The amount in a sample can then be calculated by dividing the response by the average response factor average response factor RF calibration curve A calibration curve where the slope of the calibration curve is constructed from the average response factor RF of all levels This calibration curve always passes through the origin See also average response factor RF calibration curve Thermo Scientific average response factor RF curve fit type A calibration curve fit type where LCquan calculates a curve that shows its slope is constructed from the average response factor of all levels See also average response factor RF calibration curve calibration curve average spectrum A spectrum that is the sum of all of the microscans taken for a particular MS experiment An average spectrum can be independently displayed for MS MS MS3 MS4 MSS MS10 experiments The average spectrum is displayed normalized NL to the average base peak averaged scans The number of mass spectrometer scans that are averaged to display a spectrum from the data in a raw file ba
149. radient 129 gradient curve 129 Graph view file 129 group scan 129 H header information 129 height ratio 120 H ESI probe 112 HPLC 129 l ICIS 129 Watson TSQ Module User Guide 151 Index L ICP MS 129 ID 129 in vivo 130 incomplete digest 129 individual 130 injection status autosampler status 130 injection volume 130 Injection Volume parameter 44 input parameters files 130 instrument 130 instrument configuration 130 Instrument method 130 Instrument Method meth filename parameter 23 insulin_ms raw 130 intensity relative to base peak 130 Interactive Chemical Information System 130 internal standards calibration 130 defined 130 response ratio 130 internal standards ISTDs calibration 130 defined 130 overview 115 response ratio 130 using for quantitation 115 interstitial volume 130 isolation width 131 isotopic cluster 131 L label threshold 131 lactoglobulin pep 131 layout 131 LC MS 131 LCquan exportable processing parameters 23 level amount 131 level name 131 Level parameter 44 linear calibration curve 131 linear gradient curve 131 liquid chromatography LC analyte separation 110 list separator character 131 locally weighted calibration curve 131 locked workbook 131 log file 131 Login Name parameter 28 lower quantitation limit 114 152 Watson TSO Module User Guide Manual select parameter 54 Mass 132 calibration compound 122 mass spectrometry analyte detection 111 massmap pa
150. rams file 132 mass step size 132 master assay 131 master assay method 131 matrix 132 matrix subtraction 132 mean 132 metabolic modifications 132 metabolite 132 method 132 method file exporter 21 Method defined traces parameter 54 minimum number of scan in baseline 132 missing component 132 modification 132 modification mass 132 modifiers volatile 111 molecular weight 132 mzData 132 N C general 132 Quadratic 132 Wagner 132 N D no data 133 NCA 132 needle draw position offset 133 negative peak 133 neighboring amino acid 133 NL 133 no peak 133 no sites 133 no waste injection 133 nominal molecular weight 133 nominal sample time 133 non serial subject 133 normal scan types 133 normalization 133 normalize spectra 133 normalize Y axis normalization mode 133 nucleic acid 133 nucleotide 134 number of scans in background 134 Thermo Scientific Index 0 0 Observations parameter 40 oligonucleotide 134 one way interface 134 optimization graph 134 optimization modes 134 outlier 134 OWL database 134 P parameters Acquire samples 46 Additional comment 46 Analyst 40 Assay Date 40 Comment 44 Continuous update 54 Database Login screen 28 Run Manager view 40 Description 40 Extraction Date 40 Injection Volume 44 Instrument Method meth filename 23 Level 44 Login Name 28 Manual select 54 Method defined traces 54 Observations 40 Password Electronic Signature 26 Login screen 28 Position 4
151. re unique to the experimental raw sample file Thermo Scientific control matrix A matrix that has the same composition as the sample for example body fluid but does not have the components that are being analyzed A control matrix is used to filter out extraneous data create a background subtracted raw file and thereby simplify the analysis convex gradient curve A gradient curve that begins with a large rate of change and ends with a small rate of change See also gradient curve corrected relative retention time The time after injection that it takes for a retained compound to elute minus the time required for an unretained compound to elute void time See also retention time RT CR A shortened form of the phrase creep Y axis normalization mode This shortened form is used to save space in the header when the creep mode is in use For example CR 1 98e 003 1 98 x 103 CRO Contract Research Organization cross correlation factor MS MS cross correlation factors indicate a level of similarity between the reference MS MS spectrum from a user selected spectrum and the remaining MS MS scans within the data file cryo cooling The use of CO2 70 C or N2 90 C to achieve low temperatures cSNPs A single nucleotide polymorphism SNP that is found within a coding sequence It is a small genetic change or variation that can occur within a DNA sequence CTRL Control key on a standard computer ke
152. reproducibility of the sample injection Use ISTDs in a quantitative analysis experiment as follows 1 Analyze a series of standard solutions containing known concentrations of the target compound and ISTD and plot the ratio of the target compound and the ISTD detector responses as a function of the corresponding ratio for the two quantities present in the solution 2 Add a fixed amount of the ISTD to each sample prior to any manipulation and after preparing and analyzing the samples obtain the quantity of the target compound present in an unknown sample from the calibration curve Ideally an ISTD is closely related to the target component in terms of its physical and chemical properties It must be pure not present in the sample and inert toward the components of the sample ISTD components are typically analogs homologs or isomers of the target non ISTD component An ideal ISTD is a structural or isotopically labeled analog Watson TSQ Module User Guide 115 C Quantitative Analysis Overview Quantitative Analysis Techniques of one of the target components Stable isotope labeled ISTDs act almost identically to the analyte throughout sample manipulation and with regard to ionization tendencies and fragmentation Internal standards labeled with two or more deuterium D atoms are frequently used for LC MS There can be any number of ISTD components in a sample but each non ISTD component can be calibrated against only one ISTD
153. ring Data Acquiring a Run To submit a run From the Run Edit view in the Setup mode of the run you want to acquire click Acquire The Acquire mode opens The Run Edit view in the Acquire mode displays the samples for the run You cannot edit the samples from the Acquire mode The Acquire options in the Acquire mode provide parameters for submitting a run for acquisition See Acquire Options on page 46 Note If you made changes to the setup and did not explicitly save them a dialog box asks if you want to save the changes now If this run was previously stopped and removed from the Acquisition Queue you can specify the first and last samples you want to acquire By default all samples are acquired To insert this run into the Acquisition Queue ahead of any submitted non acquiring runs check Priority Run Note When you submit a priority run it goes into the Acquisition Queue ahead of all other submitted non acquiring priority runs Optional Add an additional comment Optional Specify an instrument startup or shutdown method To run a startup method before the run starts check Startup Method To run a shutdown method after the run is completed check Shutdown Method Specify the status of the system after data acquisition by selecting one of the system power schemes On Standby or Off The default is On To submit the run to the Acquisition Queue click Run e fthis
154. ription System power scheme On Keeps the system in the On state when the current run is completed When On is selected you can begin another run without waiting All power and flows are maintained at operational levels Default On Standby Keeps the system in the Standby state when the current run is completed When you select Standby you can begin another run with only a short delay between runs Some devices do not have a Standby feature For devices with this feature a power saving or consumable saving mode is entered and the devices can be switched back on in approximately 15 minutes or less Depending the instrument this state turns gas and liquid flows to Off but maintains heaters and other subsystems in an On state so that there is no warm up time required when you change from Standby to On Off Keeps the system in the Off state when the current run is completed The Off state indicates that all power to the instrument which can be controlled by the TSQ Module application is turned Off This includes power to all heaters and most subassemblies but in some cases not all subassemblies Some devices do not have an Off feature For devices that do have this feature a power saving or consumable saving mode is entered and you can manually switch the devices back on When several runs are queued the system power scheme of the last submitted run is used Caution The Off state does not guarantee that all voltages are
155. rity Run parameter 46 privilege 137 probes choosing 111 processing filter 137 processing method 137 processing method file exporter 21 Processing Sequence 137 product spectrum 137 profile data 137 project 137 protein 137 protein database 137 protein sequence 137 proteolysis 137 proteome 137 proteomics 137 protocol 137 protonated molecule 137 Q QC 138 QC sample type defined 138 quadratic calibration curve 138 quadratic limit 138 quadratic log log calibration curve 138 qualitative analysis 138 quality control 138 quality control sample defined 138 overview 117 quantitation 138 quantitation limits 114 quantitation mass 138 quantitative analysis defined 138 described 109 117 sources of error 115 steps of 109 techniques 113 using external standards 114 using internal standards 115 Quantitative calibration 138 queue status definitions 5 R squared 138 ramp 138 raw amount 138 154 Watson TSQ Module User Guide raw data 138 raw instrument response 139 real time 139 real time plot 139 Reason parameter 26 Receive Date parameter 40 reference compound 139 reference peak 139 reference wavelength 139 regression calculation 139 re injecting a run from Watson 106 related peaks 139 relative intensity 139 relative peak height threshold 139 relative retention time 139 relative scaling 139 relative standard deviation 139 repetitive noise 139 replicate 139 reservoir vial 140 Reset Scaling command 55 RESID
156. ructure units of nucleic acids number of scans in background An advanced background subtraction parameter used to minimize the contaminating effect of background on the peak identification process when scan information is used 0 one way interface Refers to instrument interfaces that do not export Sample ID information With one way interfaces matching of data in the results file to the Watson application worklist can be made on the basis of either the sequential Worklist position or the position on a plate oligonucleotide A short chain of usually up to 20 nucleotides See also nucleotide optimization graph The plot of mass spectrometer detector response for a specific device as generated by the calibration procedures origin The unique point on a calibration curve plot where zero response Y axis occurs at zero amount X axis This is the point at which the Y axis crosses the X axis outlier A calibration data point that does not appear to correlate to other calibration data points within experimental error OWL A nonredundant composite protein sequence database produced from the following source databases Swiss Prot PIR 1 3 GenBank translations and NRL 3D See also Swiss Prot 134 Watson TSO Module User Guide P parent drug A source compound drug providing one or more molecules or compounds See also analyte parity The state of being odd or even used as the basis of a method of detectin
157. s information criterion ALQ Result is above the limit of quantitation A user defines the limit ambiguous roots A R If B2 4 A C Response gt 0 there are two roots for the equation The Watson application decides which one is suitable If both roots seem good the Watson application reports A R and lets the user decide the root Thermo Scientific amino acid An organic compound that contains both an amino group NH2 and a carboxyl group COOH Twenty specific amino acids serve as the building blocks of peptides and proteins These are the alpha amino acids that have the amino and carboxyl groups attached to a single carbon atom the alpha carbon amino acid modification A change in the mass of an amino acid used for a calculation amino acid residue In biochemistry a residue is the portion of a molecule that remains after it has lost some of its components An amino acid residue loses a water molecule when it is joined to another amino acid amplifier temperature The temperature measured by the sensor on the RF amplifier analyte A substance or chemical constituent that is undergoing analysis for example a parent drug Analytical Data Interchange ANDI protocol A file format that allows the conversion and transfer of data between mass spectral data systems A file conversion protocol supported by the Analytical Instrument Association analyte The compound to be measured analytical run A sequence of stud
158. s text file is csv This file format can be read by a text editor program such as Microsoft Notepad or by a spreadsheet program such as Microsoft Excel complete digest Digest type where every possible digest site is digested For example if a complete digest is done with trypsin every occurrence of Lysine K and Arginine R will be digested component An identified compound in a mixture See also target compound component amount calculated The amount of a component in a solution as determined by quantitation using a calibration curve See also calibration curve calibration level component amount measured component amount measured The measured amount of a component added to a calibration solution The amount measured defines a calibration level for quantitation purposes See also calibration level component amount calculated component detection The process of identifying the chromatographic components in MS MS or MS sample data by extracting the mass spectral signals component name The user defined name of the component to be analyzed composite spectrum A spectrum that is the sum of all MS MS MS MS MS MS spectra as defined by your Instrument Method This is not Normalized Spectrum compressibility The compressibility of a substance is a measure of the reduction in its volume at a specified applied pressure 124 Watson TSO Module User Guide compressibility ratio A su
159. samples Figure 20 Run Results All Samples 1 T Q Module Study Buld 1 2 149 606 None 2 TSQ Module Shady Bul 1 67 023 Nore 3 TSQ Module Study Build 1 15849 005 None 4 TSQ Module Shady Duld 1 16441 831 None 5 TSQ Module Study Buld 1 16419 449 None TSQ Module Shady Duki 1 13279 804 None 7 TSQ Module Shady Buld 1 15728 582 None TSQ Module Study Build 1 32448 721 None 9 TSQ Module Shady Buld 1 326 0 258 None A e le TSQ Module Study Build 12 034300000013 0004 B Plasma Om Nefazodone TSQ Module Study Bulid 12 034300000013 0004 B Plasma O Alprazoiam d5 mz 27408 RT 2025 2775 NL 19482 mer 200961 RT 2295 3045 NL 1 0085 F c SRM ms2 470 18 pcid 26 00 180 07 274 08 F c SRM ms2 314 10 cid 40 00 209 96 RT 2522 RT 2658 AA 179 398 AA 359256 620 AH 169 606 AH 107238 077 2183 2276 2772 2929 2963 22 23 24 25 26 27 24 25 26 27 24 29 30 RT min RT min Analyte Nefarodone Internal Standard Alprazolam dS meenen senate we 6 C2 4 Optional Filter this view by Standards QCs Blanks and Unknowns Figure 21 Standards Filtering tabs 5 If you want to accept the review click Accept Review Thermo Scientific Watson TSO Module User Guide 73 6 Watson Working with Processed Runs Reviewing Internal Standards and Performing Regression itN 1 To flag a sample or sample analyte with a Reassay tag From the run results right click the sample or samp
160. say method was created Description Comments entered by a Watson user Extraction Date Timestamp when samples in the run were extracted Analyst The user who created the run in the Watson application Observations 40 Watson TSQ Module User Guide The Watson application user comments Thermo Scientific Editing a Run Thermo Scientific 5 TSO Module Acquiring Data Editing a Run When you edit the parameters of a run in the TSQ Module application the edits are sent back to the Watson application Every action in the Run Edit view in the Setup mode is authenticated and an audit trail is sent to the Watson application Use the following procedures To edit the samples in a run To automatically enter Position column values To automatically enter Injection Volume column values To edit the samples in a run Do one of the following to open the Run Edit view in the Setup mode From the Run Select view double click any column in the run row Ce From the Run Manager view do one of the following Double click any cell in the run row QOr Click anywhere in the run row to select it and click Select Run The Run Edit view in the Setup mode opens See Setup Mode on page 44 In this view only the Position Injection Volume and Comment columns are editable Optional To specify a tray name click Options in the ribbon above the view and select a tray name from the list
161. scan filter Created by Xcalibur from instrument method settings a scan filter specifies that processing is to be applied to a subset of the scans in a raw file In the Qual Browser window The autofilter feature can be used to display chromatogram traces for each scan filter In addition filters are automatically transferred to the target display when data is selected graphically You can also drag a filter onto a graph from a Scan Filter display scan number A number assigned to each scan that identifies the relative order when it was acquired in a mass spectrometer run scan power The power 7 in the expression MS The number of stages of mass analysis expressed as MS where 7 is the scan power For example a scan power of n 1 corresponds to an MS1 or MS scan with one stage of mass analysis A scan power of n 2 corresponds to an MS2 or MS MS scan with two stages of mass analysis A scan power of 7 3 corresponds to an MS3 scan with three stages of mass analysis and so on scan range The range of mass to charge ratios over which the mass spectrometer is scanned Watson TSQ Module User Guide 141 Glossary scan rate The rate at which the quadrupole mass spectrometer scans the specified scan range in units of u per second scan time ST The amount of time required to accomplish one scan from the lowest mass to the highest mass of a specified scan range The scan can be continuous full scan type or it can be in
162. se file name A name that Xcalibur or LCquan uses when it creates the raw file for a sequence Xcalibur or LCquan appends a two digit number 01 99 ora three digit number 100 999 to the base file name so that each sample in a sequence has a unique identification See also sequence base peak The most intense mass peak in the mass spectrum It is used as the base against which the intensities of all other peaks are normalized base peak chromatogram For this type of chromatogram the intensity of the base peak from each mass spectrum is plotted as a function of time to form a chromatogram base sample ID An alphanumeric prefix to the sample ID that Xcalibur or LCquan applies to each sample in a new sequence Xcalibur or LCquan adds a suffix to the base sample ID starting with 001 See also sample ID sequence Thermo Scientific Glossary baseline The constant signal produced by the background level of an instrument In quantitative analysis the base line represents the reference point for integration when measuring the area of any given peak baseline clipping An integrated target peak having its integration line originating or terminating in a baseline region of no noise A peak is considered to be baseline clipped if there is no signal that is it is of zero intensity on both sides of the peak within the time range baseline noise Any signal present on the base line represents the noise of the chromatograph
163. sents a new Login screen This does not stop the acquisition of runs Help Watson TSQ Module Help Opens the main Help tool How to Use Hel Opens instructions in the Help for using the online P P P g navigation features Glossary Opens the glossary in the Help tool About Watson TSQ Module Opens an about box that displays the version of the tool you are running copyright information and the end user agreement Exit Closes the TSQ Module application This does not stop the acquisition of runs 88 Watson TSQ Module User Guide Thermo Scientific A TSO Module Menu and Toolbar Reference Title Bar and Ribbon Commands Title Bar and Ribbon Commands The title bar of the window includes icons to minimize maximize or close the TSQ Module application The ribbon of the window includes icons to access the Help or log out of the TSQ Module application Logout useri e Help Command Description Collapses the TSQ Module application window to your toolbar Maximizes or minimizes the size of the application window Closes the TSQ Module application This does not stop the acquisition of runs Closes the TSQ Module application and presents a new Login Logout MM screen This does not stop the acquisition of runs Opens the Help lm ON Status Bar At the bottom of the TSQ Module application window is a status bar that reports the name of the run that is currently acquiring or reports
164. sis of small analyte solution volumes over an extended period of time static NSI probe assembly The assembly that fits into the NSI body assembly and includes the static nanospray probe tip the nose cone tip mount and the probe body assembly stick plotting style Style of plotting a spectrum that plots each intensity peak as a vertical line 9478 5756 615 7 See also point to point plotting style stop bits A bit that signals the end of a character structure elucidation A process that determines both the molecular formula the number of atoms of each type in a molecule and the molecular structure the order showing how the atoms are connected to each other The MS MS scan modes are powerful tools for elucidating the structure of organic compounds study LCquan A folder that contains one or more LCquan workbooks for a specific analytical experiment See also workbook study Watson Determines the interaction of a drug with test subjects animals or man which have been administered that test article drug Based on a plan for subject dosing followed by subject sampling The samples obtained from the subject via a variety of biological matrices are then analyzed for drug levels according to an analytical method Results of this analysis are then stored for further analysis and reporting in terms of the protocol Thermo Scientific study assay Specifies the assay definition at the study level Defines instru
165. son TSQ Module User Guide Thermo Scientific 7 Watson Reports and Printing Capabilities Audit Reports Figure 24 Select Criteria for Audit Report view Select Date Time and Audit Level _ 1 O System Level Sud Level Select Category Select Users Select Project Shady Selected Categond Selected Users Selected Shades O Al Cotegones OQ Al Users O Al Suse Or te Select one or more vues SYSTEM Thermo Scientific Watson TSO Module User Guide 81 7 Watson Reports and Printing Capabilities Audit Reports Figure 25 Audit Report 82 5 255 E E A pest eS ELI FUR Ascend Desced Scratch Seve Pre j Select Rows fedCol Ede Tithe Manage System 3M 2009 131528 Ran Semple RTS Renamed Manager System 3M ae 2009 131528 Ran Sample RTS Renamed Manager System 30 Mae 2009 1315 2 Ran Sample RTS Renamed Manages System 30 Mae 2009 131528 Run Sampie RTS Renamed Manager System 30 Mw 2009 13 1528 Ran Sampie RTS Renamed Manager System 30 Me 2009 13 1528 Run Sample RTS Renamed Manager System 30 Mar 2009 131528 Ran Sample RTS Renamed Manager System 30 Me 2009 13 1528 Run Sample RTS Renamed Manager System 30 Mee 2009 131528 Run Semple RTS Renamed Manager System 30 Mae 2009 131528 Run Sample RTS Renamed Manager System 30 Mae 2009 131522 Run Semple RTS Renamed Manages System 3 Mae 2000 131528 Ran Sampie RTS Renamed Manages System 30 M e 2009 13 1522 Run Sample Watson TSQ Module User Guide
166. ssion 2 Click Regression The Watson application performs a standard regression on the specified analyte associated with the specified Analytical Run 3 After regression is complete click the appropriate button to accept reject or save the results For more information refer to the Analytical Menu chapter in the Watson User Manual Thermo Scientific Watson TSO Module User Guide 75 LLL m Watson Reports and Printing Capabilities Use the Watson application to generate several types of reports including integration reports at the study and sample levels audit reports and several Crystal reports You can then print reports using extended printing capabilities available within the Watson application Contents e Study level and Sample level Integration Reports Audit Reports Printing Capabilities Study level and Sample level Integration Reports This section provides information about study level and sample level integration reports To view study level and sample level reports 1 Access the Run Review view 2 From the Select Report Type list select either Study Level Integration Report or Sample Level Integration Report See Study Level Integration report on page 78 or Sample Level Integration report on page 79 You can subdivide each report into Master Report ICIS Report or Reinjection Report by selecting the appropriate options on the top of the view The reports show the integrated peak as a
167. t retention time Q1 and Q3 mass and IS name is displayed 7 Click Print to print the chromatogram 8 Save the chromatogram to a PDF file by clicking the Export Document icon You can print the chromatogram save it to a PDF file or both 9 Close the Preview window A new Preview window opens This window displays results data which you can print The print display and printout are identical 10 Close the Preview window for the results data 84 Watson TSQ Module User Guide Thermo Scientific 7 Watson Reports and Printing Capabilities Printing Capabilities Printing Capabilities The Watson application lets you preview reports before printing or modify page layout orientation or paper dimensions When viewing a report a print menu appears at the top of the window The print menu lets you navigate between pages of the report locate text zoom and print Figure 28 Print menu d amp G f2 78 M 4 M amp M R Table 12 Print menu icons Icon Description Export report Print report C Refresh S Toggle group tree 7a BIB Go to first page M Go to previous page 4 Go to next page gt Go to last page M Go to page Close current view Thermo Scientific Watson TSO Module User Guide 85 7 Watson Reports and Printing Capabilities Printing Capabilities Table 12 Print menu icons Icon Description Find in page M Zoom iN 86 Watson TSQ Module User Guide Thermo Scienti
168. t type showing that all unknown samples in the sequence are quantified against all standard samples of the sequence regardless of the ordering of the sequence bracket overlapped A bracket type showing the unknown samples broken into groups which are each quantified against separate sets of calibration standard samples All standards are run before and after each group and standard samples between the groups are used to form the calibration curve for both groups bracket calibration A calibration that runs standards before and after unknown samples are run Both sets of calibration standard data results are included in the calibration curve building a database The action of creating a subset database from a larger database and either creating it separately or appending it to an existing database built in Interface Interface software that is written into the Watson application code Bunch Factor The Bunch Factor is the number of points grouped together during peak detection It controls the bunching of chromatographic points during integration and does not affect the final area calculation of the peak C CaCO2 Refers to a the Watson application assay type Caco 2 is also a technique used to measure the permeability of test compounds through a membrane or barrier 122 Watson TSO Module User Guide cal level The alphanumeric name assigned to the calibration level when it is created in the Component Calibration view of the
169. ta Data representing mass spectral peaks as point to point plots with each point having an associated intensity value project Houses studies Each project generally has It The drug or drugs used within the studies are often the same When used at a CRO it may be appropriate to associate sets of Studies Sponsors together as a project protein A macromolecule composed of one or more polypeptide chains each with a characteristic sequence of amino acids linked by peptide bonds protein database A database consisting of protein sequences See also protein sequence Thermo Scientific Glossary protein sequence The sequence of amino acids making up a protein See also protein proteolysis The hydrolytic breakdown of proteins into simpler soluble substances such as peptides and amino acids by proteases or intramolecular digestion proteome The protein complement expressed by an organism s genome proteome warehouse A relational database consisting of a collection of proteome databases and a small amount of metadata Proteome databases contain the shotgun annotation of all possible combinations of PTMs on each basic sequence in the proteome The proteome warehouse stores PTM information and the sequence information used to identify and characterize proteins proteomics The study of the proteome the protein complement expressed by an organism s genome p score The probability of obtaining at least as good a match
170. tation Allow Adding Hot Recerved Samples to werh bst D Aloo ading Not Recened samples to veoddet of analytical run hady Tithe Presentation O Said Delouk P Piste Innerton Method Columneuse Allow Piepa shon S amples Vabdeton Runt C Allow Preparation Samples n V alitahon Aura Save Cancel Path lor Sequence and inport and Report Files Sequence Fle Path murem Report Fie Pah 3 To require QCs Unknowns or STDs select the appropriate parameter in the Chromatogram Run Review section 4 To prevent users from reviewing a run before the run completes select Prevent Run Review Prior to Completion in the Chromatogram Run Review section 60 Watson TSQ Module User Guide Thermo Scientific 6 Watson Working with Processed Runs Reviewing Runs To view the run queue in the Watson application 1 Open a study with an associated Peak Integration instrument 2 Choose Analytical Analytical Run Actions The Run Queue opens From this window you can view the run status in real time All runs are date and time stamped Figure 11 Run queue Run Status column 2 Completed 3 Completed 4 Completed 5 Completed 6 Completed 7 Completed 3 Completed 9 Completed 10 Completed 11 Completed 12 Submatted to TQ Module UNKNOWNS AP test 01 May 2009 LCMS Kevins Sagebrush Kevins Sagebrush Plasma 13 Subeutted to T9Q Modde UNKNOWNS AP testi 01 May 2009 LCMS
171. that contains TSQ Module specific information alone or in combination with all other categories In addition you can view and print detailed audit reports from the Create Sequence File Import Results and View Analytical Run views Generating a Watson Audit Report Generating a TSQ Module Status Audit Report Generating a Watson Audit Report This process is similar to existing Watson application workflows with the exception of selecting TSQ Module as the category of information to be viewed t bd 1 To view audit reports for TSQ Module data Choose File gt Audit Report The Select Criteria for Audit Report view opens See Select Criteria for Audit Report view on page 81 From this view enter or select the following criteria Date Time and Audit Level Date and time range System or Study Audit Level your level of access is established by the system administrator Category For TSQ Module information only select TSQ Module Forall information select All Categories User Select the user or role Project Study Select at least one study from the list that appears in this column 3 After entering and selecting the report criteria do one of the following Click OK to generate the audit report See Audit Report on page 82 Nam Click Exit to close the view without generating the report For more information refer to the File Menu chapter in the Watson User Manual Wat
172. the APCI APPI probe at the interface of the LC The choice of probe depends on the class of compound that you want to analyze and to a small extent on the flow rate of your experiment In general the APCI and the APCI APPI probes accommodate higher flow rates and molecules of a less polar nature than does the ESI probe Refer to the introduction in the documentation for your mass spectrometer for what factors might influence your decision about flow rates and what probe to use for optimum transfer of ions into the mass spectrometer After the ions are inside the mass spectrometer and the parent ions are isolated collision energy is applied to dissociate the parent ions into product ions MS MS The relative collision energy for a particular analysis depends on the structure of the compound that you are analyzing For this reason you optimize the collision energy on your analyte of interest in a tuning experiment Refer to the documentation for your mass spectrometer for the tuning procedure that describes how to optimize the collision energy Watson TSQ Module User Guide Thermo Scientific C Quantitative Analysis Overview Quantitative Analysis Techniques Quantitative Analysis Techniques Thermo Scientific To carry out quantitative analysis you must evaluate the instrument s response to known amounts of the target component Response is based on either the height of the chromatogram peak or more commonly the area under the peak s prof
173. the Manage mode displays all runs sent from the Watson application Use the following procedures To display the Run Manager view To monitor the run status To add or remove columns To cancel a run and return it to the Watson application To cancel multiple runs To select a run for acquisition To display the Run Manager view From any view click Manage The Run Manager view in the Manage mode displays all runs sent from the Watson application but only the runs assigned to your database are available to you See Manage Mode on page 39 To monitor the run status Until a run completes and is returned to the Watson application you can monitor the status in the TSQ Module Run Manager view The status can be any of the following Pending The run arrived from the Watson application and is assigned to the instrument at this workstation Submitted A TSQ Module application user has submitted this run to the Acquisition Queue but is not currently acquiring Acquiring The run has progressed to the top of the Acquisition Queue and is currently acquiring Paused The run has been assigned to an instrument and is currently acquiring but has been paused and is waiting between samples Stopped The run has been assigned to an instrument and was acquiring but was removed from the Acquisition Queue Completed The run has completed acquisition Note Completed runs might not always be observed in the R
174. the TSQ Module application is turned Off This includes power to all heaters and most subassemblies but in some cases not all subassemblies Some devices do not have an Off feature For devices that do have this feature a power saving or consumable saving mode is entered and you can manually switch the devices back on When several runs are queued the system power scheme of the last submitted run is used Caution The Off state does not guarantee that all voltages are turned off nor does it indicate that all heated components are at room temperature To perform maintenance on an instrument refer to the hardware manual for your instrument Run Starts the acquisition for the currently selected run and opens the Status view Watson TSO Module User Guide 47 5 TSO Module Acquiring Data Monitoring the Run Status Monitoring the Run Status 48 When you begin acquisition for a run from the Acquire mode the Run Status view in the Status mode is displayed You can return to the Status mode at any time as long as there are runs in the Acquisition Queue t bd Start stop or pause an acquisition Monitor the run manager and instrument status This section contains information about the following To return to the Status mode To return to the Status mode click Status From the Run Status view in the Status mode you can Monitor the Acquisition Queue Control the real time display Run Status View Co
175. the ability of a chromatography column to separate components during a chromatographic experiment response factor A calculation coefficient that corrects for the different response of the instrument to different compounds The response factor is used in quantitation to convert peak areas to numbers proportional to the weight of sample response ratio The numerical value of the Response ISTD Response If the Response is specified as Area in the processing method then the units of both Response and ISTD Response are counts sec If the Response is specified Height in the processing method then units of both Response and ISTD Response are counts See also calculated amount response value The signal from the mass spectrometer detection of a component peak as it elutes from an LC column Xcalibur and LCquan can use either the peak area or peak height to record the response to a specific component result file The file containing the data that resulted from the analysis of a raw data file Each analyzed run has both a raw data file of type raw and a result data file of type rst Results Table The name given to the table of data in the DeNovo and Peptide Mapping applications DeNovo contains the list of candidate sequences and scores Peptide Mapping contains the list of results from the Peptide Mapping search retention reference A calibration standard whose retention time is used to adjust the retention time of other comp
176. the data in the results file are matched to the Watson application s analytical run The sample in the results file is uniquely identified by the sample s unique ID that is generated by the Watson application sample loop A loop of calibrated volume that is used to perform flow injection analysis sample type Protocol definition Any tissue or biological fluid taken from a subject for analytical testing in order to determine the effects of a drug treatment Every different kind of sample will be assigned a biological matrix type A sample category tells Xcalibur or LCquan how the data for a particular sample is to be processed Thermo Scientific Glossary sample volume The Sample Volume column of a sequence is used to calculate concentrations from amounts or amounts from concentrations saturation sat A measure of the purity of the hue As saturation is decreased the hue becomes more gray A saturation of zero results in a grayscale value SB An abbreviated form of the phrase subtract background This shortened form is used to save space in the header when indicating the number of background scans subtracted from a Spectrum display for example SB 30 scan description A symbolic code used to describe the scan event settings for a specific scan event scan event A mass spectrometer scan that is defined by choosing the necessary scan parameter settings Multiple scan events can be defined for each segment of time
177. tion Queue Thermo Scientific LLL m Watson Submitting Runs to the TSQ Module This chapter provides information about setting up a run and submitting it to the TSQ Module application Contents Creating a Peak Integration Instrument Tune Method and Processing Method Files in LCquan and Xcalibur Setting up the Master Assay Working with a Watson Study Creating a Peak Integration Instrument The system manager sets up the peak integration instrument that is part of the Watson TSQ Module application configuration process This section describes the following tasks Creating an Instrument Stack Specifying Devices Creating an Instrument Stack The following procedures provide instructions to create clone edit or delete an instrument stack Use the following procedures To create the instrument stack To clone an instrument stack To edit an instrument stack To delete an instrument stack Thermo Scientific Watson TSO Module User Guide 7 2 Watson Submitting Runs to the TSQ Module Creating a Peak Integration Instrument To create the instrument stack 1 Choose Options gt Instrument Inventory The Instrument Setup window opens 2 From the Instrument Setup window click the Peak Integration instrument and then click Add to create define the stack The Create Instrument Stack dialog box opens Figure 1 Create Instrument Stack dialog box Instrument Stack un es Coenenert
178. tion mixture at the same calibration level or amount See also calibration level calibration sample type One of several types that are used for quantification The specific types available depend on the bracket type used Examples include standard bracket standard update standard clear Blank Unknown and so on calibration mass spectrometer A compound that has a well known mass spectrum used as a reference See also calibration cassette dosing experiment A high throughput screening procedure sometimes used in drug discovery to speed up assessment of pharmokinetic properties of compounds Multiple compounds are grouped together and given to an animal Samples are drawn and then the multiple compounds in each sample are assayed simultaneously See also drug set centroid data Data used to represent mass spectral peaks in terms of two parameters the centroid the weighted center of mass and the intensity The data is displayed as a bar graph The normalized area of the peak provides the mass intensity data See also centroiding centroiding A method used to improve mass spectral data quality get better mass assignments and reduce data file size Profile data is converted into centroid data by a data compression algorithm Thermo Scientific Glossary See also centroid data profile data CFR Code of Federal Regulations Check calibration A procedure that checks the MS detector calibration automatically
179. tion service reports that the run is complete When the acquisition service reports that the run is finished the TSQ Module application sends a final notification to the Watson application This notification includes the Completed status of the run the completion time and any audit items that occurred after the last sample completed 20 Watson TSQ Module User Guide Thermo Scientific 3 TSO Module System Administration Exporting Method Files to a Common Folder Exporting Method Files to a Common Folder Thermo Scientific Use the Watson TSQ Module Method Exporter application Method Exporter to convert processing parameters from an Xcalibur processing method pmd or an LCquan workbook lqn to XML format and export the parameters to a common folder where Watson users can access them You can use the Method Exporter application on any system to export Xcalibur pmd files To export LCquan lqn files first install the LCquan software including the LCquan Development Kit LDK The Method Exporter application exports all required LCquan parameters See Exported LCquan Parameters on page 23 You can use the Method Exporter application to export instrument method meth files and tune TSQTune files You can also use the Method Exporter application to group instrument method and tune files in a single directory with the exported processing file This simplifies uploading the files to the Watson application Note For exported
180. titial volume LC Another name for void volume The total volume of mobile phase within the length of the LC column The void volume consists of the intraparticle volume inside the packing material itself and interparticle volume between the packing particles The remainder of the volume of the column consists of the packing material in vivo In the living body of a plant or an animal Thermo Scientific isotopic cluster A group of peaks that differ in m z because they incorporate different isotopes of their component elements isotope search For the analysis of unknown drugs an isotope search finds extra chromatograms for each ion that has an intensity above a particular threshold isolation width The baseline width of a window for a mass peak or peak cluster of interest for an MS MS or MS scan L label threshold The percent intensity value of the highest peak that a peak height must exceed to be labeled lactoglobulin pep Thermo Scientific supplied peptide sequence file of lactoglobulin layout An arrangement of views and data displays that can be saved and opened as a file in the Qual Browser window Layout files can be identified by their file extension lyt level amount The amount of a component injected for a specific calibration level See also calibration level level name A user assigned name for a calibration level See also calibration level LIMS Laboratory Information Management System
181. ts file is created for each individual sample in the analytical run initial temperature The temperature of the oven or injector to be applied as soon as the GC receives the Start signal injection status autosampler status Indicates whether or not the current sample has or has not been injected injection volume The actual volume in microliters uL of a sample injected by the autosampler into the chromatograph The minimum and maximum injection volumes that you can use depend on the autosampler you selected input parameter files Text files that store the settings used in dialog boxes Whereas most of the settings in the input parameters files can be changed in the dialog boxes within the BioWorks Browser some can be changed only by altering the contents of the input parameters file in a text editor instrument Set of physical items that comprise an LC MS system instrument configuration A set of user defined hardware and software options Xcalibur provides configuration options for the following mass spectrometer fonts HPLC autosampler inlet analog inputs and Ethernet instrument method A set of experiment parameters that define Xcalibur operating settings for the autosampler liquid chromatograph LC mass spectrometer divert valve syringe pump and so on Instrument methods are saved as file type meth insulin_ms raw The raw spectrum of insulin that is provided with the BioWorks Browser program 130 Watson T
182. tup Mode Run Edit Editing Database http 3 Drugs svc Project Test Blank StdBracket LevellD LevellD 3 LevellD Table 8 Setup mode parameters Command Function buttons Description Save Run Saves the edits you made to the run The Save Run command can be specified to require an electronic signature See Using E Signatures on page 25 Run columns Sample Type Defines how the Watson application processes the sample data Each sample must be classified as one of the following sample types Unknown Blank QC quality control Standard Sample ID An alphanumeric string of characters that can be used to uniquely identify the sample Level The level defined for a calibration sample or quality control sample Position Sample position number in the autosampler usually provided by the Watson application Injection Volume uL Microliters to be injected When you have an autosampler configured the injection volume is validated against the allowable range specified by the autosampler When you do not have an autosampler configured you can enter a range of 0 1 1000 Comment 44 Watson TSQ Module User Guide Optional information about the sample Thermo Scientific Acquiring a Run From the Acquire mode you can start the acquisition of a run and specify the real time display settings Thermo Scientific 5 TSO Module Acqui
183. u can send the run from the Acquisition Queue back to the Run Manager view and resubmit it to the Acquisition Queue When you return the run to the Acquisition Queue you can start the acquisition from any row to reacquire samples whose acquisitions were flawed Example scenario 1 You initially pause the run and then decide that the problem is more serious than anticipated 2 You remove the run sending it back to the Run Manager view 102 Watson TSO Module User Guide Thermo Scientific B Restarting Runs Restarting a Run from within the TSO Module Application 3 After correcting the problem you perform system suitability runs in the Xcalibur application 4 Finally you resubmit the run for acquisition starting from a previous sample to ensure that all bad samples are restarted For detailed information about pausing and stopping a run see Pausing Stopping Canceling Runs on page 55 For detailed information about submitting a run see Acquiring a Run on page 45 Restarting a Run from the Run Manager View Workflow Manage Run Manager view Setup Run Edit view Acquire Run Edit view Status Run Status view Removed run Thermo Scientific Watson TSQ Module User Guide 103 B Restarting Runs Returning a Run to the Watson Application Returning a Run to the Watson Application For many reasons you might want to stop a submitted or acquiring run and sen
184. ule application selecting a run managing a run editing a run setup acquiring a run and monitoring the run status Contents The Basic Workflow Selecting a Run Managing a Run Editing a Run Acquiring a Run Monitoring the Run Status Thermo Scientific Watson TSO Module User Guide 31 5 TSO Module Acquiring Data The Basic Workflow The Basic Workflow A routine workflow uses all modes of the TSQ Module application Select Manage Setup Acquire and Status Run request from Watson Select Run Select view Manage Run Manager view l Setup Run Edit view e met Acquire Run Edit view Status l L Manage l Run Status view Run Manager view To watch a video of this basic workflow see Basic Workflow Video 32 Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data The Basic Workflow Basic Workflow Video The following video demonstrates a typical TSQ Module application session Thermo Scientific Watson TSO Module User Guide 33 5 TSO Module Acquiring Data Selecting a Run Selecting a Run When you first start the TSQ Module application the Run Select view opens All runs assigned to you within the current database are listed During this session all runs received by the TSQ Module application for your current login and database are added to the list Run Select a Pending Test_Study_ Thursday July 09 20
185. um peak height See also peak width at half height Watson TSO Module User Guide 135 Glossary peak width at half height The full width of a peak at half its maximum height sometimes abbreviated FWHM See also peak end peak width peak width constrain A chromatogram peak edge detection method used to integrate a peak that displays tailing LCquan constrains the width of a component during peak integration using a user specified peak height percentage and tailing factor See also peak height tailing factor percent bias An analytical run definition The difference from nominal and observed concentration value CV PK Pharmacokinetics percent theoretical An analytical run definition The bias plus 100 percent difference The difference between the expected value and the calculated value is determined as a percentage as follows Diff 100 x Xcalc Xexpected Xexpected where Xcalc is the calculated value of the variable X and Xexpected is the expected value of the variable X PK PD Pharmacokinetic pharmacodynamic plate position based Specifies how the data in the results file are matched to the Watson application s analytical run The sample in the results file is uniquely identified by the sample s position in the sample plate point to point calibration curve A calibration curve that averages data at each calibration level This averaging results in a single averaged data point at each calibr
186. ummary Raw data is archived within the Watson application study archive A single audit trail of data acquisition performed in the TSQ Module application and run review processing is stored in the Watson application TSO Module Feature Summary 2 The TSQ Module application is a software solution for use in bioanalytical quantitation The features of the TSQ Module application provide support for the acquisition of run requests submitted by the Watson application The TSQ Module application features include Submission of run requests to an instrument Editing of samples in a run Real time view of runs in progress or in the Acquisition Queue The ability to start stop pause and cancel an acquisition in the queues with audit messages sent to the Watson application Security provisioning against the Watson LIMS Secure and verified transmissions of the data files using a proprietary schema Run manager that holds multiple run requests from the Watson application so that users can visualize the current load on a system select the next run to acquire and when necessary send an unacquired run back to the Watson application for assignment to a different instrument A processing method exporter to extract processing information from an Xcalibur processing method or LCquan workbook and upload these parameters General purpose communication service layer between the TSC Module application and the Watson application that supports multiple
187. un Manager view When the TSQ Module application finishes sending the results of the last completed sample to the Watson application it marks the run as Completed and quickly removes the run from the Run Manager view Watson TSQ Module User Guide Thermo Scientific 5 TSO Module Acquiring Data Managing a Run To add or remove columns 1 Click the Column Selector icon in the upper left corner of the view The Column Selector dialog box opens Column Selector pepe v Be E 2 Check the box before a field name to display that column or uncheck the box before a field name to remove that column from the display This action is immediately implemented in your display and retained throughout your session but the column choices are not saved when you exit the TSQ Module application 3 When you are finished adding or removing columns click the red X in the upper right corner to close the Column Selector dialog box To cancel a run and return it to the Watson application To cancel a run the status of the run must be either Pending or Stopped 1 Click the row selection tab to select the run and enable the Cancel Run button G Manage Run Manager Select Run Cancel Hun Click here 2 Click Cancel Run The system confirms that you want to cancel the run and return it to the Watson application Thermo Scientific Watson TSO Module User Guide 37 5 TSO Module Acquiring Data Managing a Run
188. upole mass spectrometer 146 trypsin 146 tryptic digestion 146 TSQ mass spectrometer 146 Tune TSQTune filename parameter 23 tune file exporter 21 Tune Method 146 tune parameters 146 tune plate 146 tune mass spectrometer defined 146 manual 146 semiautomatic 146 tuning and calibration solution 146 two way interface 146 U undefined component 147 unidentified peak 147 uni directional interface 147 UniProt 147 unknown sample type defined 147 overview 117 unresolved peak 147 upper quantitation limit 114 User Account 147 User Name parameter 26 User defined RT range parameter 54 V v version 147 valley detection 147 variables 156 Watson TSO Module User Guide quantitation with internal standards 115 separation by LC 110 variance 147 vial list 147 vial position autosampler status 147 view width 147 void time 148 volume sample 141 W W weighting 148 weight 148 weighting 148 window size 148 WME 148 work list 148 work list based 148 workbook 148 workflow diagrams run management 5 TSQ Module basics 32 Watson LCquan XC TSQ Module 3 workgroup 148 X Xcalibur pmd or LCquan Iqn filename parameter 22 Xcalibur processing method 137 XCorr 148 XML 148 Thermo Scientific
189. urs at the selected chromatogram range end time For example if the selected chromatogram range has End Time 2 46 min this might be displayed End S 434 See also End Time Start S End Time The time in minutes corresponding to the end of the selected chromatogram range This phrase is used when the end time is displayed in a header For example if the selected chromatogram range ends at time 3 74 minutes this is displayed End Time 3 74 See also End S enzyme A biomolecule that catalyzes a specific chemical reaction The enzyme does not affect the equilibrium of the catalyzed reaction The enzyme enhances the rate of the reaction by providing a reaction path with a lower activation energy environment Refers to the whole computer system Oracle O S Citrix NET framework and so on Thermo Scientific Glossary enzyme digest The action of an enzyme such as Trypsin on a peptide The enzyme breaks up the peptide into smaller peptides Enzymes are site specific that is an enzyme always breaks a peptide at the same amino acid For example Trypsin attacks an Arginine R and Lysine K EQB exceeds quadratic bounds If B2 4 A C Response lt 0 there is no root for the equation the Watson application reports EQB for standard samples For study samples the raw value will be analyzed to determine if the result is ALQ or BLQ EQB is reported for quadratic and Wagner regressions only error lo
190. utomatic An automatic procedure that tunes the mass spectrometer one parameter at a time tuning and calibration solution In the TSQ Quantum the standard ESI tuning and calibration solutions are polytyrosine mixtures Polytyrosine 1 3 6 and Polytyrosine 1 3 6 9 two way interface Refers to instrument interfaces that export sample ID information With bidirectional interfaces matching of data in the Thermo Scientific results file or external application for a digital interface to the sample in the Watson application worklist is made on the basis of the results being tagged with the Sample ID U undefined component Any component that is not defined as a target compound or an internal standard compound This is the default component type unidentified peak A peak in an LC chromatogram or mass spectrum that is not identified Sometimes called an unknown peak uni directional interface UniProt An international repository of organisms containing all the proteins and genes that are known for a specific organism unknown sample type A sample type that is not a Calibration Sample Calibration Blank Quality Control Sample or Quality Control Blank unresolved peak A peak that overlaps the previous or next peak A peak that starts or ends at a valley above the baseline update calibration mode A calibration mode where a new data point is added to the calibration curve User Account The mechanism by which the
191. view before it began acquiring Submitted The run is assigned for acquisition but is not currently acquiring The run is in the Acquisition Queue Acquiring The run has progressed to the top of the Acquisition Queue and is currently acquiring e Paused The run is assigned to an instrument and is currently acquiring but has been paused and waits between samples Stopped The run was assigned to an instrument and was acquiring but was removed from the Acquisition Queue Completed The acquisition has finished running and the run data was returned to the Watson application Completed runs might not always be observed in the Run Manager view When the TSQ Module application finishes sending the results of the last completed sample to the Watson application it marks the run as Completed and quickly removes the run from the Run Manager view Run Name A combination of the project study and run ID as defined in the Watson application Assay Date Date when assay method was created Receive Date Timestamp when run was received 92 Watson TSQ Module User Guide Thermo Scientific Setup Mode i Setup Save Run Thermo Scientific A TSO Module Menu and Toolbar Reference Setup Mode From the Setup mode you can edit the parameters of a run in the TSQ Module application Every action you take in the Run Edit view in the Setup mode is authenticated and an audit trail is sent to the Watson application
192. y or apply to each sample in the run Apply All The new parameters are stored in the database Figure 15 Reintegrate Chromatogram view ICIS Advanced page ReintegrationForm BF Ea Sample name 99 1 orig Cal_04 1 Analyte name Nefazodone Change Percent 0 Original parameters Configure parameters Identification ICIS Integration ICIS Advenced Identification ICIS Integration ICIS Advenced Nowe Method cos Nose z Noise Method fe m Ams F AMS Min Peak Width p Min Peak Width IE Muliplet Resoluson ro Muliplet Resoluon 10 Area T ad Extension F Asea Tal Extension g Area Scan Window p Area Scan Window 9 Update Chomatogrem Nefazodone NL 2 32E4 F c SRM ms2 470 18 cid 26 00 180 07 274 08 Nefazodone NL 2 32E4 F c SRM ms2 470 18 cid 26 00 180 07 274 08 100 241 3c0 241 so so amp E p 40 40 20 20 248 251 248 251 7 0 227 0 22 22 23 24 25 22 23 24 25 RT min RT min Thermo Scientific Watson TSO Module User Guide 67 6 Watson Working with Processed Runs Changing the Chromatogram Display Changing the Chromatogram Display In the chromatogram view you can change the display Use the following procedures To move the baseline To view a chromatogram in the gallery To zoom in on a chromatogram To move the baseline Using the cursor drag the baseline in the chromatogram view Figure 16 Moving the baseline dards QCs Blanks
193. y and assay samples meant to be analyzed using an analytical instrument Watson TSQ Module User Guide 119 Glossary analytical run assay Specifies the assay definition for each analytical run It defines instrument interfacing types and styles calibration curve and QC samples options and other assay related parameters The analytical run assay is created automatically from the study assay whenever a new run is created ANOVA Analysis of variance apex RT The retention time at which the apex of a chromatographic peak is located Area or Height Ratio The ration of the area or height of the selected peak to the area or height of the internal standard peak area scan window The number of scans on each side of the peak apex that you want to include in the calculation of peak area The value 0 specifies that all scans from peak start to peak end are included in the area integration area tail extension The number of scans beyond the peak endpoint on each side of the peak ICIS uses this number to calculate an average for the intensity counts of a peak area ICIS then uses this average intensity value as the lower limit of intensity and includes the area above this limit in the integration calculation for the peak Area Threshold Controls the area cutoff automatically calculated by Avalon Any peaks with a final area less than the Area Threshold are not detected area chromatographic peak The region of a chromatogram peak that
194. yboard cubic spline calibration curve A calibration curve where a cubic polynomial curve is fit between each pair of calibration levels so that the slopes of the separate cubic polynomial curves match at common calibration curve points Thermo Scientific Glossary CV Coefficient of variation data acquisition The process of accumulating and storing data received from instrument sensors as they detect the sample Also the conversion of analog signals to digital data files database Refers to the Watson application Oracle database data bits A group of bits typically 5 6 7 or 8 bits used to represent a single character of data for transmission The number of bits used in data transmission must be agreed on by the sending and receiving parties data rate The rate of data collection by the UV detector dataset A name that binds together related files and actions in the auditing database for Xcalibur deconvolution In BIOMASS Deconvolution a process whereby an electrospray ionization mass spectral ESI MS plot of relative abundance versus m z is transformed into a plot of relative abundance versus mass delay The time difference in minutes between the UV detector and the MS detector The mass spectrometer corrects the retention time so that peaks from both the UV detector and MS detector appear at the same retention time in the data file Delta Cn Abbreviation for the difference or delta in cross correlatio

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