Home

QuickQuan 2.1 User Guide Version A

1. Sees Drugset1_0 alibur Instrument Method Drugset1_07 alibur Raw File Drugset1_11 Xcalibur Raw File Drugset1_19 alibur Raw File Drugset1_23 Xcalibur Raw File Drugset1_27 alibur Raw File Drugset1_04 Xcalibur Result File Drugset1_08 Xcalibur Result File 157 KB Drugset1_12 Xcalibur Result File 157 KB Drugset1_16 Xcalibur Result File 157 KB Drugset1_20 Xcalibur Result File Drugset1_24 Xcalibur Result File 57 KB Xcalibur Sequence OKB ugset1_O alibur Processing Method 52 KB Drugset1_O04 Xcalibur Raw File 469 KB Drugset1_08 Xcalibur Raw File 469 KB Drugset1_12 alibur Raw File 469 KB Drugset1_16 Xcalibur Raw File 469 KB Drugset1_20 libur Raw File 469 KB Drugset1_24 Xcalibur Raw File 469 KB Drugset1_01 Xcalibur Result File 157 KB Drugset1_05 Xcalibur Result File 157 KB Drugset1_09 Xcalibur Result File 157 KB Drugsett_21 ibur Result File B Drugset1_25 calibur Result File KB ugset _061121151120 alibur Sequence KB Thermo Scientific QuickQuan User Guide 69 5 Acquiring the Sample Data Stopping an Acquisition Stopping an Acquisition To stop an acquisition before the run is finished On the QuickQuan toolbar click E Exporting the Instrument and Processing Methods You can export the generic instrument method meth and processing method pmd from the Acqu
2. 24 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Setting Up for Optimization Specifying Tune and Method Files and Optimization Settings You specify the tune and method files optimization settings and output path in the Optimization Setup view To display the Optimization Setup view In the QuickQuan navigation pane click Optimization and then il click Setup To specify method files optimization settings tune plate settings and output path 1 In the Tune and Method Files area specify the file or folder path for each of the following To select a file click the E button for the item and then select the location a In the Tune File box specify the generic tune file For an example select C Xcalibur QuickQuan Templates tune template TSQTune IMPORTANT Tune parameters are instrument parameters that affect the intensity of the ion signal You must specify a generic tune file that corresponds to the type of experiment you are performing for example ESI high flow During tune optimization QuickQuan determines additional settings such as polarity tube lens voltage parent and product ion masses Q1 peak width and collision energy These settings which maximize the ion signal for your compounds are added to the settings in the generic tune file b In the Tune Pos LC Method box specify the method file that contains the LC settings for a positive polarity tune optimization For an exam
3. The Source Type table contains the information about the compound after it has been optimized QuickQuan optimizes for a specific source type ESI APPI APCI or H ESI The compound s polarity tune file name and the source type used during the optimization are saved to this table You cannot modify the Source Type table QuickQuan updates the Source Type table whenever an optimization run has finished The Source Type table contains the following information for each tuned compound in the database Parameter Description Compound Name Name of a compound in the database Polarity The true polarity detected after optimization Tune File The tune file TSQtune named by QuickQuan that contains the optimized TSQ Tune parameters Raw File The data collected during the real time tuning PDF File A tune report stored as a PDF file and generated during the real time tuning Source Type The ion source type used for this compound during optimization where 0 untuned 1 ESI 2 APCI 3 APPI 4 H ESI Thermo Scientific QuickQuan User Guide 89 C QuickQuan Views Compounds Browse View SRM Table To view the contents of the SRM table 1 In the QuickQuan navigation pane click Compounds The Compounds Browse View appears 2 In the Table box select SRMTABLE The SRM table contains the information about the SRM transitions detected for a given compound during optimization The table can ho
4. To open the QuickQuan Help From the QuickQuan window choose Help gt QuickQuan Help To locate a particular topic use the Help Contents Index or Search panes Thermo Scientific QuickQuan User Guide vii Preface Special Notices The 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 may contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Helpful information that can make a task easier Contacting Us There are several ways to contact Thermo Scientific To contact Technical Support Phone 800 685 9535 Fax 561 688 8736 E mail TechSupport C MS thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at www mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 Web site www thermo com finnigan To suggest changes to documentation or to Help e Fill out a reader survey online at www thermo com Icms techpubs e Send an e mail message to the Technical Publications Editor at techpubs finnigan lcms thermofisher com viii QuickQuan User Guide Thermo Scientific Introduction QuickQuan can optimize the selected reaction monitoring SRM transitions and tune parameters of multiple compounds acquire chromatographic dat
5. 2007 Thermo Fisher Scientific Inc All rights reserved Microsoft Access Excel and Notepad are registered trademarks of Microsoft Corporation Adobe Acrobat and Reader are registered trademarks of Adobe Systems Incorporated Oracle is a registered trademark of Oracle Corporation 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 document 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
6. 39 Using Adobe Acrobat Reader to View the Results 0 000 39 Updating SRM Information ica ps cece e heer ied eons aebet ate es 39 Modifying SRM Information Manually 0 00 00 e ee 40 Importing SRM Information ious 2 vateane ound iat coated 41 Chapter5 Acquiring the Sample Data ccc cece e eee eee eee ees 43 Reusing Acquisition Setunngs irs s aciineed deed Aa A Oe es 43 Creating a Generic Instrument Method 00 00 c eee eee eee 44 Creating a Generic Processing Method i e 3o 08 ae ea ees ahh te eae hae ele 47 Specifying Template Options ie Gi ore ered piia wei wastes 53 Creating or Importing a Sequence 1 cee eee 55 Creating a Sequence in the Acquisition Setup View 00 55 Editing a Sequence in the Acquisition Setup View 2000 57 Copying Sequences from Excel ss vr pee bad ci aves 6 we we ele 57 Importing a Sequence e046 ews ee aea A E ee EE 58 Importing Excel and Sequence Templates nonna Aina Dats ae es 59 Creating an Excel Template for the Assays aa4 Sores aaciceitico dn yeas ees 59 Creating a Sequence Template oslo nce whe boxsets tienda ways Ba eine 61 Importing the Excel and Sequence Templates 6 0002 a ee eae wes ee 63 Saving the QuickQuan Assay ivsica es ates gates aa g aePale s dace wae e abies 64 Running an Acquisition 6 6 nis sexstiheyers negate aire eyed aoe rreren erreur 64 Stopping an Acquisition 6 0
7. Compound List 5 Sii IA Save acopy Print emai fi Search A Son buspirone caffeine 100 Wi ketoconazole reserpine Setup Quantum Tune Master Tune and Calibration iii Results from Compound Optimization for Buspirone Go Compound Optimization in MS and MS MS 20 06 Tune tube lens in positive polarity 20 06 Optimizing Tube Lens for ion 386 20 m z 20 06 Previous Setting 112 47 New Setting 99 11 20 06 Maximum Intensity 9 01le 05 20 06 28 2 Improvement 20 06 29 Tune tube lens in negative polarity 20 06 29 Optimizing Tube Lens for ion 384 20 m z 20 06 35 Previous Setting 113 93 New Setting 78 84 20 06 35 Maximum Intensity 1 45e 03 Tune Report 20 06 35 290 Improvement 20 06 36 Positive ion produces better signal 20 06 36 Optimizing collision energy at 1 5 mTorr 20 06 36 Waiting for the collision gas to stabilize 20 07 00 Finding the product ions of ion 386 2 m z 20 07 10 Constructing the breakdown curve of ion 386 2 m z 20 07 Product Ion 122 12 Maximum Intensity 4 16e 07 20 07 Product Ion 95 10 Maximum Intensity 1 73e 06 20 07 14 Collision Energy Optimization Results 20 07 14 Product Ions m z Coll Energy v 20 07 14 122542 34 20 07 14 95 10 45 20 07 15 Finish compound optimization QualBrowser Help lex 8 5 x 11 in lid 4 1 of 2 gt ro oO For Help press F1 n p NUM Thermo Scientific QuickQuan User Guide 37 4 Optimizing Your C
8. E gt Xcalibur E gt QuickQuan mr QuickQuanData List Files of Type Drives Access Databases m Y ci Network 8 In the Directories box browse to and select the QuickQuanDatabase folder By default the installation software places a QuickQuan database in the following folder C Xcalibur QuickQuan QuickQuanDatabase 9 In the Database Name list select the file QuickQuanCompounds mdb and then click OK 8 QuickQuan User Guide Thermo Scientific Thermo Scientific 2 Selecting QuickQuan Data Sources and Databases Creating a File Data Source 10 Click OK to close the ODBC Microsoft Access Setup dialog box The new data source QuickQuan appears in the Select Data Source dialog box See Figure 8 Figure 8 Select Data Source File Data Source Machine Data Source Select Data Source dialog box showing the file data source Look in Data Sources QuickQuan El QuickQuanMDB DSN Name E uickQuanMBD on your machine Select the file data source that describes the driver that you wish to connect to You can use any file data source that refers to an ODBC driver which is installed 11 Click OK to close the Select Data Source dialog box 12 Click OK to close the ODBC Microsoft Access Setup dialog box QuickQuan User Guide 9 Defining the Compounds and Drug Sets This chapter describes how to assign compounds to drug sets within the database
9. Example pmd files are in the following folder C Xcalibur QuickQuan Templates 96 QuickQuan User Guide Thermo Scientific Parameter Processing Macro Template C QuickQuan Views Acquisition Templates View Description Specifies the Microsoft Excel template file xls that was designed to invoke a macro automatically You can use macros to perform custom manipulations of the data acquisition results See Using a Macro To Perform Custom Calculations on page 83 Note In addition to selecting the processing macro template you must select the Run User Defined Macros check box in the Configuration Options dialog box to perform the data reduction Output Path Specifies the folder in which QuickQuan stores the data and template files for an acquisition for example raw meth pmd sld and PDF files QuickQuan downloads files for processing to the Xcalibur data system Internal Standard Use Internal Standard Activates the internal standard ISTD selections If you select the check box you must specify a compound for at least one of the following e Positive ISTD Default e Negative ISTD Default The ISTD lists contain all the compounds in the QuickQuan database Positive ISTD Default Specifies the compound to be used as the positive internal standard When QuickQuan creates the instrument and processing methods it uses the positive ISTD compound as a reference for drug sets that contain
10. Level RSD AMT Peak Status Response Ratio R Calc Amt Units Diff 0 997113567 1 997113567 1 6 097492218 0 219498444 5 12 35092865 0 235092865 10 31 93880305 0 596940153 20 2 54445318 0 31361133 40 97 02652714 0 212831589 80 213 784268 0 336151675 160 Equation Y 4 07058e 006 8 70927e 006 X R 2 0 9860 0 0 ojojojojo Level RSD AMT Calc Amt Units Diff 0 467934488 0 532065512 1 1 980533561 0 603893288 5 8 739912807 0 126008719 10 26 54112423 0 327056212 20 62 81690856 0 570422714 40 109 7287461 0 371609327 80 162 1387322 0 013367077 160 Equation Average Response Factor 9 7017e 008 RSD lt 37 0 0 a 0 0 a 0 Response Low 0 000712033 A 0 004744354 A 0 008298585 A 0 019431634 A 0 031143151 A 0 056425175 A 0 122786112 A Peak Status Response Ratio R Response Low 4 79057E 09 A 1 31784E 05 A 7 20477E 05 A 0 000227083 A 0 000543019 A 0 000951587 A 0 001408039 A NUM Thermo Scientific To generate an acquisition summary report 1 In the QuickQuan window choose Reports gt Acquisition Summary Report The Browse for Folder dialog box appears 2 Select the destination folder and then click OK for example QuickQuan creates a Microsoft Excel file xls that combines every Xcalibur summary report lt your_output_path_folder gt lt timestamp_folder_for_selected_acquisition gt for each sequence of the assay into a single acquisition summary report To view an acquisi
11. Report QuickQuan generates the report automatically in a Microsoft Excel file xls The report shows the compound information that was collected during the optimization of the compounds in the current tune plate See Generating an Optimization Summary Report in Excel on page 39 Acquisition Opens the Browse for Folder dialog box which you use to specify a location Summary for the acquisition summary report Report The location is lt your_output_path_directory gt lt timestamp_directory_for_selected_acquisition gt QuickQuan generates the report automatically in a Microsoft Excel file xls The report concatenates every summary report for each sequence of the assay into a single acquisition summary report See Generating and Viewing the Acquisition Summary Report on page 76 View Menu The View menu contains the following commands Command Description Toolbar Displays or hides the QuickQuan Toolbar Status Bar Displays or hides the QuickQuan Status bar 112 QuickQuan User Guide Thermo Scientific Status Bar and Toolbar Thermo Scientific D QuickQuan Menus and Toolbar Reference Status Bar and Toolbar The QuickQuan window contains a status bar which appears at the bottom left and a toolbar at the top of the window below the menus e The status bar displays a text description of the menu command or toolbar icon to which the cursor arrow is pointing If the cursor arrow is pointing to something
12. database E examples S Help Install Logs E methods params E O QuanRoot QuickQuan S aquickquantraining 20nov06 S 11212006_151117 01_Drugset2 12122006_164331 salsa sequence E O sequest O system Templates EJ amp AcrobatPro6 D E TechPubs Archive on Ussjo sanserv1 Y x a S TechPubsManuals on Ussjo sanserv1 W 8 xcalshare on Product Evaluation Secure Da S TechPubs on Ussjo sanserv1 2Z G Control Panel E 3 My Network Places we Recycle Bin lt M j fag ExcelExp_Long H Microsoft Excel Worksheet Geol 78 KB Drugset1_01 Xcalibur Raw File Xcalibur Raw File 470 KB Drugset1_21 Xcalibur Raw File 469 KB Drugset1_02 Xcalibur Result File Sis 157 KB Drugset1_06 Xcalibur Result File 157 KB Drugset1_18 Xcalibur Result File 157 KB Drugset1_22 A Pa Xcalibur Result File lkl ddal 157 KB Drugset1_26 alibur Result File 157 KB 4 tune 20nov06 TSQTune Document 17 KB Drugset1_02 libur Raw File B Drugset1_06 libur Raw File KB 469 Drugset1_10 libur File 9 KB Drugset1_14 libur Raw File 69 KB Drugset1_18 libur R 70 KB Drugset1_22 calibur Raw File Drugset1_03 Xcalibur Result File Drugset1_15 Xcalibur Result File KB Drugset1_19 Xcalibur Result File Drugset1_23 Xcalibur Result File 157 KB
13. e SRM Table on page 90 Compound Specifies SQL query commands for filtering the data To do this type an SQL statement in the Compounds box and then click Query to filter the data shown in the current table Buttons T Displays the first screen of rows in the displayed table Use the arrow buttons when the table contains many rows and you want to move around in the table without having to scroll row by row Displays the previous screen of rows in the displayed table Click this button to see the next screen of rows in the vit i displayed table 5 Click this button to see the last screen of rows in the displayed table Query Filters the data in the currently displayed table using the contents of an SQL statement in the Compound box 86 QuickQuan User Guide Thermo Scientific Compounds Table Thermo Scientific Control or Parameter C QuickQuan Views Compounds Browse View Description Add Compounds Opens the Add Compounds dialog box which you use to add and edit compound information in the database or delete compounds from the database See Defining the Compounds in the Database on page 11 Add Drug Sets Opens the Add Drug Sets dialog box which you use to add and edit drug set information in the database or delete drug sets from the database See Defining the Drug Sets in the Database on page 17 Update SRM Info Opens the Update SRM Information dialog box
14. 4 In the Database area verify that the correct database name appears for example QuickQuanCompounds mdb 5 Click OK to close the dialog box Thermo Scientific QuickQuan User Guide 5 2 Selecting QuickQuan Data Sources and Databases Creating a File Data Source Creating a File Data Source To create a new file data source 1 In the QuickQuan window choose File gt Open Database The Select Data Source dialog box appears See Figure 1 2 On the File Data Source page click New The Create New Data Source wizard appears See Figure 3 Figure 3 Create New Data Source wizard select driver list Create New Data Source Driver do Microsoft Paradox db Driver para o Microsoft Visual FoxPro Microsoft Access Treiber mdb Microsoft dBase Driver dbf Microsoft dBase YFP Driver dbf Microsoft dBase T reiber dbf Microsoft Excel Driver xls Microsoft Excel Treiber xls hdinenanth Can Den ED Meinar 1 ABET lt lt O E E Advanced Back Cancel 3 Select Microsoft Access Driver mdb from the list of drivers and then click Next Note If your site uses an Oracle database select an appropriate Oracle driver Contact your local Oracle administrator for details on how to configure QuickQuan for an Oracle database 6 QuickQuan User Guide Thermo Scientific Thermo Scientific 2 Selecting QuickQuan Data Sources and Databases Creating a File Data Source 4 In the na
15. Figure 36 shows two sequences one for Drugset1 and one for Drugset2 58 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Importing Excel and Sequence Templates Importing Excel and Sequence Templates Another way to import a sequence is to import an Excel template xls file extension and a sequence template sld file extension using the following procedures 1 Creating an Excel Template for the Assay on page 59 2 Creating a Sequence Template on page 61 3 Importing the Excel and Sequence Templates on page 63 Creating an Excel Template for the Assay The Excel template file describes the assay to be run including the drug sets to use for each sequence in the assay vial positions number of samples per sequence instrument method processing method and injection order You can use multiple plates in a single sequence and specify more than one plate type In the Excel worksheet you can specify the vial position for each sample Make sure that you name the vial positions with names that are valid for your autosampler If the autosampler supports vial validation QuickQuan automatically validates each vial position specified in the Excel worksheet at run time Figure 37 shows an example of an Excel template To create the Excel template for the assay 1 In columns 2 through 6 enter the following e Drug set name e Vial position e Sample name e Generic instrument method e Generic proces
16. name appears in the Database Drug Sets list Thermo Scientific QuickQuan User Guide 17 3 Defining the Compounds and Drug Sets Defining the Drug Sets in the Database R To add compounds to a drug set 1 In the Database Drug Sets list select the drug set name 2 In the Database Compounds list click each compound you want to add to the drug set 3 Click Add QuickQuan adds the selected compounds to the drug set 4 Click Close Figure 13 Add Drug Sets dialog box Add Drug Sets Drug Set Name Drugset2 Database Compounds Database Drug Sets Drugset1 Drugset2 reserpine 18 QuickQuan User Guide Thermo Scientific 3 Defining the Compounds and Drug Sets Defining the Drug Sets in the Database To remove compounds from a drug set In the Database Drug Sets list select the drug set name In the Database Compounds list click each compound you want to remove from the drug set Click Delete Click Close Importing Drug Sets Using a Text File Thermo Scientific You can import the drug set information from a text file txt into a QuickQuan database The text file must be in a specified format You can find an example file in the following folder Xcalibur QuickQuan ImportFiles To create a drug set file for importing Open a file in Microsoft Excel Notepad or any of the software that allows you to create a tab delimited text file txt file extension Enter
17. 20n0v06 4 CQUIRE COLUMN1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMMN1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth Drugset1 CStk1 02 14 Unknown C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMMN1 meth Drugset1 CStk1 02 15 Unknown C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMMN1 meth Drugset1 CStk1 02 16 Unknown C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMMN1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth End of Assay _ gt Creating a Sequence Template The sequence template sld file is a generic sequence to be run for the entire assay The sequence template must correspond to the Excel template You create the sequence template in the Xcalibur Home Page window Sequence Setup view See the Xcalibur Help for details on how to create the sequence in the Sequence Setup view The sequence template specifies the following e Sample injection type e Injection volume used for each sample e Arrangement of sample types standards QCs blanks and unknowns Thermo Scientific QuickQuan User Guide 61 5 Acquiring the Sample Data Importing Excel and Sequence Templates At run time QuickQuan replaces the
18. 28 Update SRM Information dialog box Update SRM Information Compound Information Compound Name ketoconazole lon Source ESI v Polarity Pos v Parent Mass 531 31 Instrument detected parent mass Tune File C Xcalibur QuickQuan T emplates tune template TSQT une Tune PDF File C caliburquick quantraining 20nov06 ketoconazole pdf Tune RAW File C Xcaliburquick quantraining 20nov06 ketoconazole raw Compound SRM Information 0 2 1140000 0 2 1790000 o2 t0s0000 3 In the Compound Name box select a compound 4 In the Compound SRM Information table edit the information as required 5 Click Update to update the SRM information 6 Click Close 40 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Updating SRM Information Importing SRM Information You can import the SRM information from a text file txt into a QuickQuan database The text file must be in a specified format QuickQuan includes an example text file in the following folder Xcalibur QuickQuan ImportFiles To create an SRM information file for importing 1 Open a file in Microsoft Excel Notepad or any of the software that allows you to create a tab delimited text file txt file extension 2 Enter the following string in the first row of a text file SRM_DATABASE_INFORMATION_v1 3 Optional To include a comment in the file use a double forward slash at the star
19. A drug set can contain one or several compounds depending on the assay being run You can create a multicompound drug set to facilitate simultaneous optimization and analysis of several analytes in the same sample A cassette dosing experiment is one example of an assay where multicomponent drug sets are helpful Contents e Defining the Compounds in the Database e Defining the Drug Sets in the Database e Viewing Compound and Drug Set Data Defining the Compounds in the Database The QuickQuan database must contain the compound information for the compounds in your QuickQuan experiments You use the Add Compounds dialog box to manage the compound information stored in the database To open the Add Compounds dialog box In the QuickQuan navigation pane click Compounds and then click Add Compounds The Add Compounds dialog box appears See Figure 9 and Figure 10 Use the following procedures to manage the compound information e Manually Adding or Editing Compounds on page 14 e Importing Compounds Using a Text File on page 14 e Deleting Compounds on page 17 Thermo Scientific QuickQuan User Guide 11 3 Defining the Compounds and Drug Sets Defining the Compounds in the Database Figure 9 Opening the Add Compounds dialog box Click Compounds and then click Add Compounds a QuickQuan Untitled File Acquisition Reports Yiew Help Development Doe gt Compounds Browse View
20. Data Reduction template file contains two sheets e Sheet 1 in the template is a blank report e Sheet 2 is the Calculations page Figure 49 shows an example Figure 49 Example of the Calculations page EJ Microsoft Excel Data_Reduction xls DER i File Edit View Insert Format Tools Data RoboPDF Window Help Adobe PDF Type a question for help P X B2 amp F3 A User Defined Columns User Defined Vales CMP_VALUE 50 ool AREA 2 00 Average HEIGHT RETENTION TIME PERCENT REMAINING 3 4 S 6 SIGNAL noise 8 a M 4 gt a Sheeti Calculations Ready The processing macro Excel file must implement a macro named RunUserMacro which QuickQuan calls during the data reduction At a minimum this macro must recalculate the Calculations page Setting up the data reduction in this way allows QuickQuan to provide your custom results in real time To use the macro for post processing calculations you must do both of the following Select the Run User Defined Macros check box when you specify the configuration settings See Running an Acquisition on page 64 e Select the processing macro template when you select the template files See Specifying Template Options on page 53 QuickQuan saves the data reduction results in the output path directory QuickQuan User Guide 83 QuickQuan Views This appendix describes the primary views that you can display in the QuickQuan window Contents e C
21. INTSID Int Std File view Options GoTo Help Identification Detection Calibration Levels System Suitability z omponents Component type Target compounds istd Tegetcompond SU E C ISTD Weightin Calibration curve Linear X Ic 1 Units C 1 2 Origin C 14 Ignore r Response IC 12 C Force Area C 1482 Include Height Reports Eh Cancel Save s Default Flags Help Programs 9 On the Detection page Figure 34 enter the detection settings For more details click Help 10 Choose File gt Save As Type a new file name pmd file extension and then click Save Thermo Scientific QuickQuan User Guide 51 5 Acquiring the Sample Data Creating a Generic Processing Method Figure 34 Processing Setup Quan view Detection page Processing Setup Quan Detection INTSTD Int Std No raw file open 52 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Specifying Template Options Specifying Template Options Thermo Scientific The template options include the location of the generic instrument and processing methods which internal standards ISTDs to use and the output folder You specify the template options in the Acquisition Templates view To open Acquisition Templates view In the QuickQuan navigation pane click Acquisition and then click Templates See Figure 35 To specify template options 1 In the G
22. Optimization Only 6 In the Instrument Settings area specify the following e TSQ Quantum LC pump and autosampler are in use Yes appears in the In Use column e Autosampler is set to start Yes appears in the Start Instrument column 7 Click OK Thermo Scientific QuickQuan User Guide 79 A Configuration Procedures Configuring and Setting Up Instruments for Aria Configuring and Setting Up Instruments for Aria If you have Aria OS installed you can use the following procedure to configure and set up the instruments for optimization For more information on running QuickQuan with Aria see the QuickQuan and Aria Quick Start To configure and set up the instruments for the Aria workflow 1 Open the Instrument Configuration and Settings dialog box as follows In the QuickQuan navigation pane click Optimization and then Lx click Instrument 2 In the Instrument Settings area verify the following e Only the TSQ Quantum LC pump and autosampler are configured The In Use column displays Yes for each instrument e The autosampler is set to start The Start Instrument column displays Yes e The Status column displays Ready to Download for each instrument If the instrument settings are correct click OK Otherwise continue with step 3 3 To reconfigure the instruments do the following IMPORTANT Before starting Instrument Configuration verify that Aria Quantum Tune and Xcalibur are closed a In
23. Plate graphic Specifies the layout of the tune plate Click any well position in this graphic and then use the Drug Set Selector to associate a drug set with the well The selected well positions on the Tune Plate graphic are color coded e Green Compounds in the drug set have been tuned for this ion source e Yellow Compounds in the drug set have been tuned for an ion source other than the currently selected ion source e Red At least one compound in the drug set has not been tuned Clear Plate Clears all wells in the plate of their drug sets Thermo Scientific Clears the selected well of its drug set QuickQuan User Guide 93 C QuickQuan Views Optimization Setup View Parameter Description Displays the Open dialog box which you use to import a drug set information file txt file See Importing Drug Sets Using a Text File on page 19 TEE Opens the Losses Adducts dialog box which you use to specify that QuickQuan does the following e Disallows product ion losses that are not very specific The choices are H2O NH3 CH3 and two user definable losses e Selects adducts The choices are M H M Na M NH4 and three user definable adducts for positive ions M H M COO and three user definable adducts for negative ions Drug Set Selector Current Well Displays the position of the well you selected in the Tune Plate graphic If the drug set contains only one compound then the compound
24. Terms and Conditions of Sale shall govern all conflicting information between the two documents Revision History Revision A January 2007 Revision B April 2007 Revision C July 2007 Software Requirements QuickQuan 2 1 Xcalibur 2 0 6 or 2 0 7 TSQ Quantum 1 5 Quan Devices 2 0 LC Devices 2 0 2 includes Thermo PAL Microsoft XP Service Pack 2 Microsoft Office 2003 or2007 For Research Use Only Not regulated for medical or veterinary diagnostic use by U S Federal Drug Administration or other competent authorities Contents Chapter 1 Chapter 2 Chapter 3 Chapter 4 Thermo Scientific Pietate a rer ere er eer vii About This Gude i cces cient ae eee ed RO eee hie chee nad Oo vii Related Documentation secu cans n diaow nace dor aces Kewanee sabelsad vii Special NGUCES cite ranana aa enw dee eens Oe hee ee aes viii Contacting Us nc cdae sauna ie dew Sia ods Daa ae Hees OA viii C0 oe er ee ee ee re ree rrr 1 QuickQuan Features i ius bead da ink Was cba ee BL Pe eee eee ee 1 QuickQuan Workflow 0 0 0 ccc tenet een eens 2 Selecting QuickQuan Data Sources and Databases 055 3 About the QuickQuan Database 6 cee teens 3 About the Data Source venerei si nL Mee kaha tae et ead epee eee 4 Selecting a File Data Source ci coe ieee eh eee Rhee et 4 Creating a File DataSource dnc viiivors chu ieders coed stad Menu ee a 6 Defining the Compounds and Drug Sets 00ceeeeee cece eees 11 Defini
25. a method see Creating a Generic Instrument Method on page 44 Vial Position 100 QuickQuan User Guide Specifies the position in the autosampler To change the position type the new position in the table cell Thermo Scientific Thermo Scientific Parameter Injection Volume C QuickQuan Views Acquisition Setup View Description Specifies the injection volume in microliters of sample to be injected To change the volume type the new volume in the table cell If you are using an autosampler you can set the default injection volume in the Autosampler dialog box in the Instrument Setup window The minimum and maximum injection volumes that you can use depends upon the autosampler you select The usable range is dependent upon the injection mode and can be smaller than the range displayed in the status bar For more details consult your autosampler manual Comment Dilution Factor Displays any comments that you have entered about the sample Type in the table cell to enter more comments Displays the dilution factor that was used to prepare the sample To change this factor double click the table cell and type the correct factor Valid range 0 001 to 1000 000 If you have specified a processing method for the current Sequence Xcalibur automatically enters the Dil Factor value from the processing method settings QuickQuan User Guide 101 C QuickQuan Views Acquisition Setup View 10
26. define which compounds to use for each sequence of samples in an assay or which compounds to optimize Each database contains tables of information about the compounds and drug sets QuickQuan automatically writes the optimization data polarity parent and product ion masses collision energy and Q1 peak width for each optimized compound to the database For a high throughput acquisition run QuickQuan uses the information stored in the specified database to build methods to analyze and process the data and to provide reports on the analysis Note QuickQuan automatically opens the last used database If you want to use this database you can skip this chapter and go on to Chapter 3 Defining the Compounds and Drug Sets Note To register the QuickQuan database refer to the QuickQuan Installation Guide Thermo Scientific QuickQuan User Guide 3 4 2 Selecting QuickQuan Data Sources and Databases About the Data Source About the Data Source A data source is a connection to a database Typically you create a separate data source connection for each database A data source name DSN is the logical name that the Open Database Connectivity ODBC uses to refer to the drive and other information that are required to access data Databases can have several general configurations The QuickQuan database is typically configured as a file data source This is the most flexible format for the database and can be used on a single c
27. dialog box select the tmt file and then click Open Note By default the AS and LC methods are stored in the Aria Data folder LC Method Specifies a method to override the default LC method for the sequence To specify an override click the table cell In the Open dialog box select the htc file and then click Open LC1 to LC4 Specifies the LC systems for each sequence To change the LC systems for a sequence select or clear the LC check boxes in the corresponding row C QuickQuan Views Acquisition Results Summary View Acquisition Results Summary View Use the Acquisition Results Summary view to display and review the quantitation results See Reviewing Quantitation Results on page 73 To display the Acquisition Results Summary view In the QuickQuan navigation pane click Acquisition and then mg click Results Summary Ko The Acquisition Results Summary view has the following parameters Parameter Description Results Root Specifies the folder that contains the results for example Directory lt your_output_path_directory gt lt timestamp_directory_for_selected_acquisition gt Combined Creates an acquisition sequence sld file that combines all sequences Sequence drug sets in the assay Refresh Refreshes the Results table Qual Starts Xcalibur Qual Browser and loads the raw data collected in the Browser acquisition Quan Starts Xcalibur Quan Browser and
28. drug set name vial position instrument method processing method and sample name with the information specified in the Excel template for each sequence in the assay IMPORTANT The number of samples in the selected sequence template sld file must match the number of samples in each sequence of the selected Excel assay layout template xls file The number of samples in the selected sequence template must match the number of samples in each sequence of the Excel template file selected For example the sequence template file shown in Figure 39 corresponds to the Excel template shown in Figure 37 In this example 27 samples must be defined in the sequence template because the Excel template has 27 samples per drug set This sequence is specified only once and QuickQuan refers back to it multiple times Figure 39 Sequence template corresponding to the Excel template in Figure 37 X XCALIBURSEQUENCE Open Sequence Setup Home Page File Edit Change Actions View GoTo Help 62 QuickQuan User Guide Dict S Bs GB Selk gt mela Sample Type InjVol Proc Meth Level Status Acquisition Queue 1 Blank 10 00 C calibur quickquantraining 20nov0B INTSTD Run Manager EA Std Bracket 10 00 C Xcaliburquickquantraining 20nov06 INTSTD 1 Check Devices 3 Std Bracket 10 00 C caliburquickquantraining 20nov0B INTSTD 5 Sequence 4 Std Bracket 10 00 C caliburquickquantraining 20nov0B INTSTD 1
29. ec eee eee 70 Exporting the Instrument and Processing Methods 020005 70 Chapter6 Reviewing the Results 0 cece eee eee eee eee eee ee eee ees 73 Reviewing Quantitation Results sscewe dee uaed ae eh andes eae es 73 Generating and Viewing the Acquisition Summary Report 76 How QuickQuan Performs Post Processing 0 0 c cece eee eee 78 Appendix A Configuration Procedures 0 eeeeee cence eee e eee eens 79 Configuring and Setting Up Instruments 0 00 000 eee eee 79 Configuring and Setting Up Instruments for Aria 0 0 0000000000 80 Bypassing the LC Column and the Dual Pump Dual Column Configuration 81 Appendix B Using a Macro To Perform Custom Calculations 0005 83 Appendix QuickQuan Views 0c cece eee eee eee eens 85 Compounds Browse VIGW eas tig lake dale ted alae tee a el elated a elles 85 Compounds Table saad ances ao ated a 8 ada ane nee ees 87 Driug Set Names Vablevs cots wea awicews t ace ew ed conned wettest 88 S rce Type Table sekeres ona baie beh be ohh hes ees 89 SRM Tabler 204d heen Ban A ae oars cease A TE mallee wh 90 iv QuickQuan User Guide Thermo Scientific Thermo Scientific Appendix D Contents Optimization Setup View 0 0 ee cece eee eee 91 Optimization Tune Report View secs acces ayes a hese prion a nets dea a wintecn Sie dines 95 Acquisition Templates View aii ice
30. generic selecting 54 LC 25 selecting 26 Microsoft Access selecting database 6 minimum intensity threshold setting 26 number of products ions selecting 14 0 optimization about 23 Optimization Setup view 26 optimized settings 23 reviewing results 36 running 32 Optimization Setup view 26 Oracle database 6 output directory 69 output path 53 P PDF files acquisition output folder figure 67 location 69 output path 26 53 peak detection settings 52 polarity selecting 35 65 116 QuickQuan User Guide Post processing after acquisition 78 processing methods creating 47 generic selecting 54 product ions selecting number 14 Q Quan Browser view 75 raw data files acquisition 43 acquisition output folder figure 67 location 69 output path 26 output path acquisition 53 path 25 reports acquisition summary 73 acquisition summary viewing 76 optimization summary 39 results acquisition displaying 73 results summary 73 S selected reaction monitoring SRM 39 sequences copying from Excel 57 creating 55 creating sequence template 61 example figure 56 Excel template 59 Excel template figure 60 importing 55 importing Excel template 59 importing sequence template 59 sequence template figure 62 SRM information importing 41 T text files compounds 15 16 drug sets 19 tune plate information 31 Thermo PAL autosampler 24 threshold percent setting 65 Thermo Scientific Index U tune
31. gt Save QuickQuan saves the tune plate information in an aq file Figure 22 Tune Plate graphic with samples in positions A1 and B1 Running the Optimization After you set up the optimization you can do either of the following e Run only the optimization per the following procedure e Acquire the data for an assay with real time compound optimization In this case see Acquiring the Sample Data on page 43 In either case you can choose to use the information in the database or to force the optimization of the compounds to update the database 32 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Running the Optimization To display the Configuration Options dialog box In the QuickQuan navigation pane click Optimization and then click Go id gt Torun the optimization only 1 In the Configuration Options dialog box select the Tune Optimization Only option See Figure 23 2 Optional To use optimization information that is already in the database select the Use Optimization Database for Existing Compounds check box QuickQuan optimizes the compounds in the tune plate that have not been optimized If the check box is cleared QuickQuan optimizes all compounds that are in the tune plate 3 In the Instrument Settings area verify the following a The Instrument column lists only the required instruments If the required instruments do not appear update the Xcalibur instrumen
32. positive compounds Negative ISTD Default Thermo Scientific Specifies the compound to be used as the negative internal standard When QuickQuan creates the instrument and processing methods it uses the negative ISTD compound as a reference for drug sets that contain negative compounds QuickQuan User Guide 97 C QuickQuan Views Acquisition Templates View Parameter Description Additional Internal Standards Specifies any target compound for which you want to use an ISTD reference that is different from the negative and positive ISTD defaults e Target Compound Specifies the compound for which you want to use an ISTD reference that is different from the defaults e ISTD Reference Specifies the ISTD compound to be used as a reference for the corresponding target compound To specify a compound or ISTD click the table cell and then select the compound from the list When QuickQuan creates the instrument and processing methods it uses each additional ISTD compound as a reference for the corresponding target compound specified in the table If a positive or negative ISTD default is not specified QuickQuan uses the first ISTD from the Additional Internal Standards table as the default 98 QuickQuan User Guide Thermo Scientific C QuickQuan Views Acquisition Setup View Acquisition Setup View Use the Acquisition Setup view to create an acquisition sequence containing unknown samples calibration standard
33. retrieves the information for each ISTD from the database and inserts it in the instrument method e The generic target component is modified in the same manner as the generic ISTD component The mass range is set to be the product mass range and the scan filter is set to SRM After the acquisition the software does further refining of the processing method The generic processing method requires the following e Components An external standard method must specify only one component which is named target An internal standard ISTD method must specify two components which are named target and istd e Calibration level and QC names and amounts e Calibration curve settings e Detection settings Thermo Scientific QuickQuan User Guide 47 5 Acquiring the Sample Data Creating a Generic Processing Method To create a generic processing method 1 Start Xcalibur Processing Setup a Display the Acquisition Templates view In the QuickQuan navigation pane click Acquisition and then click the Templates button b On the Acquisition Templates view click Proc Setup The Xcalibur Processing Setup view appears Figure 31 shows the Processing Setup view 2 Optional To use an example file as the basis for your processing method choose File gt Open and then select a pmd file QuickQuan includes the following examples Xcalibur QuickQuan Templates Thermo_template_ExtStd pmd method for external standards Xcalibur QuickQu
34. system overrides for the individual sequences To display the Aria Configuration view In the QuickQuan navigation pane click Acquisition and then 4 click Aria The Aria Configuration view contains the following controls Control Description Default AS Method Specifies the AS method tmt file extension for Aria OS to use if no AS method is specified To specify method click E In the Open dialog box select the tmt file and then click Open Default LC Method Specifies the LC method htc file extension for Aria OS to use if no LC method is specified To specify method click E In the Open dialog box select the htc file and then click Open Available LC Systems Displays the status of the LC Systems If a system is unavailable the label appears grayed To change the availability of an LC System see the Aria OS User Guide Use Batch Overrides Activates the Batch Overrides table If activated the software uses the specified overrides for the methods and LC systems If not activated the software uses the defaults Thermo Scientific QuickQuan User Guide 105 Control Batch Overrides Table Description Drug Set Displays the drug set name for each sequence The sequence row number from the Acquisition Setup View on page 99 also appears AS Method Specifies a method to override the default AS method for the sequence To specify an override click the table cell In the Open
35. the Instrument Configuration and Settings dialog box click Instrument Configuration The Instrument Configuration software starts b In the Instrument Configuration window reconfigure the instruments and click Done c In Instrument Configuration and Settings dialog box click Refresh d In the Instrument Settings area click the In Use or the Start Instrument cell to toggle on or off the Yes for an instrument e Wait for the Status column to display Ready to Download Make sure the instruments have been turned on From Xcalibur Home Page choose Actions gt Devices On 4 In the Instrument Configuration and Settings dialog box click OK 80 QuickQuan User Guide Thermo Scientific A Configuration Procedures Bypassing the LC Column and the Dual Pump Dual Column Configuration Bypassing the LC Column and the Dual Pump Dual Column Configuration You can bypass the chromatography column during optimization and have the samples infused directly into the ion source This option requires a Thermo Pal autosampler with multiple injection ports multiple valves and a stream selector To increase throughput for a gradient analysis you can set up your LC MS system in a dual pump dual column configuration and equilibrate one column while performing sample elution with the other column Figure 48 shows the required configuration To alternate columns between consecutive injections you must use two instrument methods In the first
36. type to determine how the compounds will be scanned Enter the following mass spectrometer settings e MS acquire time min e Tune method not optimized See the following example method Xcalibur examples QuickQuan SampleSet tune template TSQTune Click the Divert Valve tab and then enter the divert valve settings on the Divert Valve page Choose File gt Save As Type a new file name meth file extension and then click Save QuickQuan User Guide 45 5 Acquiring the Sample Data Creating a Generic Instrument Method Figure 30 Instrument Setup view E ACQUIRE COLUMN1 meth Instrument Setup File Quantum Help ECCE RE Scan Editor Syringe Pump Divert Valve Method Summary Calibration Correction Method r Run Settings T50 Quantum d MS Acquire Time min jo 0 Segments fi e Current Segment 1 To display a chromatogram here use Quantum Open Raw File 0 00 0 01 0 02 0 03 0 04 Retention Time min 0 06 0 07 0 08 0 09 r Segment 1 Settings 4 Segment Time min fo 10 Tune Method C Xcalibur quick quantraining 20nov06 tune 20nov06 TSQTune H of Thermo Pal A Scan Events zz Chrom Filter Peak Width sk IV fio at Collision Gas Pressure mT orr ns a m Scan Event 1 Polarity FullScan SIM SRM Positive C Negative Same value for all SAMs Data Type i fi 000 E i il Scan Width m z T 1004 000 1000 000 1 000 m 10 070 0o70 o Centroid C Pr
37. 0 Sample Name E5 Std Bracket 10 00 C caliburquickquantraining 20nov06 INTSTD 20 Working On 6 Std Bracket 10 00 C Xcaliburquickquantraining 20nov0B INTSTD 40 Position 7 Std Bracket 10 00 C caliburquickquantraining 20nov0BINTSTD 80 Raw File 8 Std Bracket 10 00 C caliburquickquantraining 20nov0B INTSTD 160 Inst Method 9 Std Bracket 10 00 C Xcalibur quickquantraining 20nov06 INTSTD 320 TSQ Quantum 10 Std Bracket 10 00 C Xcaliburquickquantraining 20nov0B INTSTD 1600 Not Connected 11 Blank 10 00 C Xcalibur quickquantraining 20nov06 INTSTD LT XL MS 12 Blank 10 00 C 4Xcalibur quickquantraining 20novOB INTSTD T Not Connected 13 Blank 10 00 C Xcaliburquick quantraining 20nov0BINTSTD ee oa 5 14 Joc 10 00 C Xcalibur quickquantraining 20novO6 INTSTD act 15 ac 10 00 C Xcalibur quickquantraining 20nov06 INTSTD acl 16 QC 10 00 C caliburquickquantraining 20nov06 INTSTD Qc2 17 ac 10 00 C Xcaliburquickquantraining 20nov0BINTSTD Qc2 18 oc 10 00 C Xcaliburquickquantraining 20nov06 INTSTD Qc3 19 jac 10 00 C Xcaliburquickquantraining 20nov0BINTSTD Qc3 20 Blank 10 00 C Xcalibur quickquantraining 20nov06 INTSTD 21 Blank 10 00 C caliburquickquantraining 20nov0B INTSTD 22 Blank 10 00 C Xcaliburquickquantraining 20nov0BINTSTD 23 Unknown 10 00 C calibur quickquantraining 20nov0B INTSTD 24 Unknown 10 00 C Xcaliburquickquantraining 20nov06 INTSTD 25 Unknown 10 00 C lt caliburquickquantraining 20nov06 INTSTD 26 Blank 10 00 C caliburqu
38. 0 611 0 2 9999 c xcalibur Temp etes TSsoTune TSQ_CALB_TUNE TSQTune c xcalibur system programs LCquantutorial pdf c xcalibur syst em programs BG_030718_33 RAW To import the SRM information file In the QuickQuan navigation pane click Compounds In the Compounds Browse view click Update SRM Info The Update SRM Information dialog box appears Click Import Click Yes when the confirmation message appears In the Open dialog box select the file you want to import and then click Open QuickQuan imports the compounds and SRM transitions into the database Click Update and then click Close Thermo Scientific Acquiring the Sample Data This chapter describes how to set up and run a high throughput acquisition using QuickQuan Contents e Reusing Acquisition Settings e Creating a Generic Instrument Method e Creating a Generic Processing Method e Specifying Template Options e Creating or Importing a Sequence e Importing Excel and Sequence Templates e Saving the QuickQuan Assay e Running an Acquisition e Stopping an Acquisition e Exporting the Instrument and Processing Methods Reusing Acquisition Settings You can reuse the settings from an acquisition aql file that you have already created in QuickQuan The aq file contains the configuration settings acquisition settings compound optimization information assay layout and template information To reuse the settings in an aq file
39. 006 09 30 14 921 Q STATUS Downloading 2 sequences please wait Templates 42 14 2006 09 30 15 968 0 STATUS In Acquisition for sequence C xcalibur pecl3 12142006_093011 01_mMickey mMickey sld 12 14 2006 23 42 40 00 0 STATUS Acquisition complete 12 14 2006 23 42 40 46 Q STATUS Reprocessing sequence 12 14 2006 23 42 40 234 Q SUCCESS Reprocessing sequence complete 12 14 2006 23 42 40 234 Q STATUS In Acquisition for sequence C xcalibur Decl3 12142006_093011 02_mMickey Mickey sld Results Summary 12 15 2006 01 36 31 250 0 STATUS Acquisition complete For Help press F1 68 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Running an Acquisition Figure 43 Time and date stamped folder location of raw files result files and Excel acquisition file S C Xcalibur quickquantraining 20nov06 1 121 2006_151117 02_Drugset1 Eile Edit Q sax 6 JO Search Fetes View Favorites Tools Help Address C Xcalibur quickquantraining 2Onow06 11212006_151117 02_Drugset1 v Bo Folders E E Administrator S Al Users S robert heather Cookies Desktop E ve Favorites E My Documents Sapworkbir S Start Menu E Programs amp UserData O wnoows E ROBERT 1 HEA mor O drivers B O FM6 Files a O i386 E ProductCenter E e Program Files E Robert Email a O wInpows amp xcalibur data
40. 06 4CQUIRE COLUMM1 meth C Kcaliburtquickquantraining 20nov06UNTSTD pmd Drugset2 Std Bracket C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth C Kcaliburtquickquantraining 20n0v06YNTSTD pmd Drugset2 Std Bracket C Xcaliburtquickquantraining 20nov06 4CQUIRE COLUMM1 meth C KXcaliburtquickquantraining 20n0v06YUNTSTD pmd Drugset2 Blank C Xcaliburtquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth C Xcaliburtquickquantraining 20nov06YNTSTD pmd Drugset2 Blank C Xcaliburtquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth C Xcaliburtquickquantraining 20nov06UNTSTD pmd Drugset2 Blank C Xcaliburiquickquantraining 20n0v06 ACQUIRE COLUMM1 meth C Xcaliburtquickquantraining 20no0vO6YNTSTD pmd Drugset2 ac C Xcaliburiquickquantraining 20n0v06 ACQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20n0vO6YNTSTD pmd Drugset2 ac C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20n0vO6YNTSTD pm Drugset2 ac C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20no0vOBYNTSTD pmd Drugset2 ac C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20no0vOBYNTSTD pmd Drugset2 ac C Xcaliburiquickquantraining 20novO6 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20no0vOBYNTSTD pmd Drugset2 ac C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20no0vOBYNTSTD pmd Drugset2 Blank C Xcaliburi
41. 1 In the QuickQuan window choose File gt Open 2 In the Open dialog box select the aql file and then click Open For an example open the following Xcalibur examples QuickQuan SampleSet acquire template aql 3 In the QuickQuan navigation pane click Acquisition Verify the acquisition settings in the following views Click Templates to view the settings in the Acquisition Templates view To edit the template settings see Specifying Template Options on page 53 Thermo Scientific QuickQuan User Guide 43 5 Acquiring the Sample Data Creating a Generic Instrument Method Click Setup to view the sequence settings in the Acquisition Setup view ij i To edit the sequence settings see Creating or Importing a Sequence on amb page 55 Creating a Generic Instrument Method You specify certain settings for the mass spectrometer autosampler and LC pump in a generic instrument method meth file which you create in Xcalibur Instrument Setup QuickQuan uses the generic instrument method and the optimized settings that it determines during compound optimization to build the complete instrument method for the assay QuickQuan alters the masses and mass ranges specified in the scan event of the generic instrument method based on the information retrieved from the database for each compound QuickQuan makes the following adjustments to the instrument method file for the mass spectrometer e Creates the parent product trans
42. 2 QuickQuan User Guide Parameter ISTD Correction Amount Description Specifies the correction amount for the internal standard If the value is not 0 000 the value is used in an algorithm to correct for the case in which the ISTD amounts in the active processing method are correct but the ISTD amount in one or more samples is different from the specified amount This correction eliminates the necessity of remaking the samples to the internal standard concentrations or amounts specified in the processing method and re running the samples For each component defined as an ISTD a bulk adjustment factor may be applied to the base response of each ISTD defined in the processing method e Ifno correction is required confirm that a value of 0 000 is entered in the ISTD Corr Amt cell e Ifa correction is required enter the sum of all ISTD amounts or concentrations actually in the sample into the ISTD Corr Amt cell requiring adjustment The value entered should use the same units as specified in the processing method Do not type the units for example type 20 not 20 ng Sample Volume Displays the volume of a component that has been placed in the sample The unit for this volume is specified in the Processing Setup window and is only included in Xcalibur reports Xcalibur does not convert units To change the sample volume double click the table cell and type the correct value If you have specified a processing method f
43. 4 20 0 7 74 3 59500000 Positive ESI TUNED A 195 01 109 94 23 0 7 74 3 11600000 Positive ESI TUNED 5 195 01 82 93 2z 0 7 74 3 3380000 Positive ESI TUNED 6 Drugset1 Al ketoconazole 531 31 243 82 33 0 7 106 37 1790000 Positive ESI TUNED E 531 31 176 88 42 0 7 106 37 1050000 Positive ESI TUNED 8 531 31 134 79 41 0 7 106 37 1140000 Positive ESI TUNED _9 Drugsett Al reserpine 609 01 194 89 38 0 7 123 63 30200000 Positive ESI TUNED 10 609 01 173 92 39 0 7 123 63 20300000 Positive ESI TUNED 11 609 01 397 08 28 0 7 123 63 15200000 Positive ESI TUNED 12 Using Adobe Acrobat Reader to View the Results The Adobe Acrobat Reader software can be installed from the QuickQuan software CD To view the tune results report using Adobe Acrobat Reader 1 Start Adobe Acrobat Reader 2 Open the PDF files for the tune results for example caffeine pdf Updating SRM Information You can update the SRM transitions that QuickQuan found during optimization See one of the following procedures e Modifying SRM Information Manually on page 40 e Importing SRM Information on page 41 Thermo Scientific QuickQuan User Guide 39 4 Optimizing Your Compounds Updating SRM Information Modifying SRM Information Manually To modify SRM information 1 In the QuickQuan navigation pane click Compounds 2 In the Compounds Browse view click Update SRM Info The Update SRM Information dialog box appears See Figure 28 Figure
44. 58 F c ESI cid 27 00 KE 856 173 956 134 822 194 922 397 026 397 126 MS ICIS Drugset1 03 451 178 2 08 24i 3 10 3 31 3 60 25 3 0 Time min Thermo Scientific Area Ratio 1 2 1 0 0 8 0 6 0 4 0 2 0 0 Y reserpine 0 00187465 0 000685972 xX R 2 0 9851 W 17X NUM 12 12 2006 5 22PM 7 QuickQuan User Guide 75 6 Reviewing the Results Generating and Viewing the Acquisition Summary Report Generating and Viewing the Acquisition Summary Report QuickQuan compiles the individual sample acquisition reports into a summary report xls file that you can open using Excel The Acquisition Summary Report contains the following data e File name e Sample type name and ID e Expected and calculated amount e Units e Diff e Level e RSD e Peak status e Response e Area e Height e ISTD area and height e Retention time RT Rel RT Del RT e Signal to noise ratio S N e Start and end time e Start and end height e Integ code e Search window e Threshold e Smoothing e Acquisition date e Duration e Exp method e PMD method e Vial e Injection volume e Sample weight and volume e ISTD base amount and calc amt e Dilution factor Figure 47 shows an example of an acquisition summary report 76 QuickQuan User Guide Thermo Scientific Figure 47 Excel acquisition summary report Ej Microsoft Excel Book1 15 Component Name 16 caffeine 18 File
45. IRE COLUMM1 meth Drugset1 CStk1 02 3 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMMN1 meth Drugset1 CStk1 02 4 Std Bracket C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth Drugset1 Cstk1 02 5 Std Bracket C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMMN1 meth Drugset1 CStk1 02 6 Std Bracket C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth Drugset1 CStk1 02 7 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMMN1 meth Drugset1 CStk1 02 8 Std Bracket C Xcaliburquickquantraining 20n0v06 4CQUIRE COLUMM1 meth Drugset1 CStk1 02 9 Std Bracket Cc Xcaliburiquickquantraining 20nov06 ACQUIRE COLUMN1 meth Drugset1 CStk1 02 10 Std Bracket C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMMN1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMN1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20nov06 ACQUIRE COLUMN1 meth Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth Drugset1 CStk1 02 11 QC C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth Drugset1 CStk1 02 11 QC C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth Drugset1 CStk1 02 12 QC C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth Drugset1 CStk1 02 12 QC C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMN1 meth Drugset1 CStk1 02 13 QC C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMMN1 meth Drugset1 CStk1 02 13 QC C Xcaliburiquickquantraining
46. In the QuickQuan navigation pane click Compounds and then click Add Drug Sets The Add Drug Sets dialog box appears In the Database Drug Set List click the drug set and then click Delete Repeat this step for any other drug set you want to delete When you have finished deleting drug sets click Close Viewing Compound and Drug Set Data QuickQuan User Guide Use the Compounds Browse view to view the contents of the database tables for the currently opened QuickQuan database You can also enter SQL query commands to filter the data in the tables For more details on the Compounds Browse view see Compounds Browse View on page 85 To view compounds with the Compound Browse view Click Compounds to display the Compounds Browse view In the Table box select COMPOUNDS The Compounds table appears See Figure 15 Optional If the table contains many rows and you want to move around in the table without having to scroll row by row click the _ a gt J and buttons to change the view in the table Optional To use an SQL statement to filter the data type the SQL statement in the Compound box and then click Query to filter the data Thermo Scientific 3 Defining the Compounds and Drug Sets Viewing Compound and Drug Set Data Figure 15 Compounds Browse view showing the compounds table QuickQuan acquire 20nov06 Compounds Browse View add or modify Compounds and Drug
47. O Drugset2 Std Bracket Std Update 160 data06 1 C Xcaliburiquickquantraining 20 3 aia Drugset2 Std Bracket Std Update 320 idataQ6 1 C Xcaliburiquickquantraining 20 oO Drugset2 Std Bracket Std Update 1600 data06 1 C Xcaliburiquickquantraining 20 iii gt oO Drugset2 Blank Blank NA data07 1 C Xcalibur quickquantraining 20 oO Drugset2 Blank Blank INA data07 4 C Xcaliburiquickquantraining 20 Go 13 F Drugset2 Blank Blank NA data08 1 od Xcaliburiquickquantraining 20 F Drugset2 ac ac act data09 1 C Xcaliburiquickquantraining 20 15 oO Drugset2 ac ac act data9 1 C Xcaliburiquickquantraining 20 o Drugset2 ac ac Qc2 data09 1 C Kcaliburiquickquantraining 20 E Drugset2 ac ac QC2 idataOg 1 C Xcaliburiquickquantraining 20 oO Drugset2 ac ac acs data09 1 C Xcaliburiquickquantraining 20 Status N Drugset2 QC lec laca data10 1 C Xcaliburiquickquantraining 20 EL oO Drugset2 Blank Blank INA data11 1 C Xcaliburiquickquantraining 20 Em fai Drugset2 Blank Blank INA datat1 1 C Xcaliburiquickquantraining 20 cies Ey Ej Drugset2 Blank Blank NA data12 1 C Xcalilsuriquickquantraining 20 23 oO Drugset2 Unknown Unknown INA data12 1 Xcaliburiquickquantraining 20 Results Summary oO Drugset2 Unknown Unknown INA data13 1 C Xcaliburiquickquantraining 20 25 Fi Drugset2 Unknown Unknown INA idatal4 1 C Xcaliburiquickquantraining 20 26 oO Drugset2 Blank Blank INA data15 1 C Xcaliburiquickquantraining 20 oO Drugset2 Blank Blank NA id
48. See Updating SRM Information on page 39 To view the contents of the Compounds table 1 In the QuickQuan navigation pane click Compounds The Compounds Browse View appears 2 In the Table box select COMPOUNDS The Compounds table contains information about how to tune each compound in the QuickQuan database To modify the Compounds table use the Add Compounds dialog box See Defining the Compounds in the Database on page 11 The Compounds table contains the following information for each compound in the database Parameter Compound Name Description Name of a compound in the database To add or delete a compound name use the Add Compounds dialog box Parent Mass Monoisotopic mass for the compound To specify the parent mass for a compound use the Add Compounds dialog box Polarity Polarity of the compound positive negative or both QuickQuan determines the best polarity during optimization unless you specify a particular polarity in the Configuration Options dialog box Charge State Charge state for the compound 1 10 To select the charge state for a compound use the Add Compounds dialog box QuickQuan User Guide 87 C QuickQuan Views Compounds Browse View Parameter Num Products Description Number of product ions to be acquired for the compound 1 10 To select the number of product ions for a compound use the Add Compounds dialog box Source Type Dru
49. Sets Compound Browser Compound ParentMass Polarity ChargeState NumProducts SourceType buspirone 195 0 lt NULL gt 1 3 0 caffeine 195 0 lt NULL gt 1 3 0 ketoconazole 531 31 lt NULL gt 1 3 0 1 3 0 reserpine 609 01 lt NULL gt Browse Table COMPOUNDS Compound Add Compounds i Add Drug Sets Update SRM Info For Help press F1 Thermo Scientific QuickQuan User Guide 21 22 3 Defining the Compounds and Drug Sets Viewing Compound and Drug Set Data R To view drug sets with the Compounds Browse view 1 In the Table box select DRUGSETNAME The Drug Set table appears See Figure 16 2 Optional If the table contains many rows and you want to move around in the table without having to scroll row by row click the _ E gt and buttons to change the view in the table Figure 16 Compounds Browse view showing the Drug Set table E acquire 20nov06 File Acquisition Reports View Help Daa gt Compounds Compounds Browse Optimization Compound Browser Acquisition Compound Compound1 Compound2 Compound3 Compound4 Compound5 Compound Drugsetl buspirone caffeine reserpine lt NULL gt lt NULL gt lt NULL gt Drugset2 buspirone caffeine ketoconazole lt NULL gt lt NULL gt lt NULL gt x ih Browse QuickQuan User Guide Thermo Scientific Optimizing Your Compounds This chapter describes how to automatically o
50. Shortcut New Populates the QuickQuan views with Cul N the default settings which you can use to create a QuickQuan assay file aql Open Displays the Open dialog box which Ctrl O you can use to open a saved QuickQuan assay file aql Save Saves any changes to the current open Ctrl S QuickQuan assay file aql Save As Opens the Save As dialog box which you can use to save a new or changed QuickQuan assay file aql with a new file name Open Database Opens the Select Data Source dialog box which you use to create or choose file data sources and machine data sources See Selecting QuickQuan Data Sources and Databases on page 3 Import Acquisition Sequence From File Displays the Open dialog box which you use to import an acquisition sequence as a sequence file sld or a text file txt or csv See Importing a Sequence on page 58 Import Acquisition Sequence From Template 110 QuickQuan User Guide Opens the Import Sequence Templates dialog box which you can use to import an acquisition sequence as a sequence template sld plus an Excel template xls See Importing Excel and Sequence Templates on page 59 Thermo Scientific Help Menu Thermo Scientific Command Export Methods D QuickQuan Menus and Toolbar Reference Help Menu Keyboard Description Shortcut Opens the Export Methods dialog box which you can use to export methods for use with other app
51. Z Workspace is also selected The TSQ Quantum adjusts the parent mass to the resolution of the mass spectrometer This adjustment might result in a different parent mass being stored in the QuickQuan database than the one you originally specified for the compound Clear this check box to specify tuning for unit resolution precursor ion peak width 0 7 amu Thermo Scientific Parameter Use Autosampler Infusion During Optimization Inj Volume ul C QuickQuan Views Optimization Setup View Description Specifies that a flow injection infusion of a single sample be used for optimization See Bypassing the LC Column and the Dual Pump Dual Column Configuration on page 81 Clear this check box default if you want multiple injections of the same sample Injections are made for positive and negative polarities tube lens offsets product ion masses and collision energies Tip Selecting the check box can provide faster optimization times Use Autosampler Infusion During Optimization option only Specifies the sample amount to inject for each compound being optimized The flow rate for the infusion with the Inj Volume determines how long the infusion sample is present during the tuning session Range 0 500 uL Plate Setup Plate Type Specifies either the 96 well or 384 well plate type Autosampler Tray Name Specifies the autosampler tray that contains the compounds to be optimized Tune
52. a and generate quantitative results in a single analytical run QuickQuan stores the compound optimization parameters in a database so you can analyze the same compounds in multiple assays You can use the database information to automatically generate the acquisition and post acquisition methods for multiple analytical runs Contents e QuickQuan Features e QuickQuan Workflow QuickQuan Features QuickQuan does the following Thermo Scientific Automates compound optimization and enables high throughput compound optimization and acquisition Provides a graphical interface for the layout of tune plates for compound optimization Supports the importing of compound information and acquisition sequences Uses a central database that supports access by local acquisition workstations and remote analysis workstations The QuickQuan database can also support multiple instruments which allows you to separate the optimization and the acquisition Uses a Microsoft Excel worksheet to drive the acquisition processing and reporting of quantitative sequences using standard methods Enables using an Excel macro to automatically generate custom calculations based on the post acquisition results Requires minimal input for rerunning complex assays Enables you to bypass the chromatography column during optimization and inject the samples directly into the ion source which can speed up the optimization process Thermo PAL
53. a tab to separate each field in the row compound name formula F or mass M index compound molecular weight or molecular formula charge state number of product ions to detect 5 Save the compound file as a txt file Figure 12 shows the file format for importing compounds with both molecular weights and formulas Figure 12 Compound file with both molecular weights and formulas DE ImportCompoundsWithFormulas Notepad File Edit Format View Help COMPOUND_DATABASE_INFO RMATION_v2 ffImport compounds template file fcompound name fF formula M mass f fparent mass molecular weight fcharge state ies of product ions buspirone M 385 50 1 3 caffeine F C8HLON4O2 1 3 ketoconazole M 531 44 1 3 reserpine M 608 68 1 3 Importing the Compounds Text File To import the compound file to the QuickQuan database 1 In the QuickQuan navigation pane click Compounds and then click Add Compounds The Add Compounds dialog box appears Figure 10 2 Click Import 3 Click Yes when the confirmation message appears 4 In the Open dialog box select the file you want to import and then click Open The compounds appear in the Database Compound List 5 Click Close 16 QuickQuan User Guide Thermo Scientific 3 Defining the Compounds and Drug Sets Defining the Drug Sets in the Database Deleting Compounds To delete compounds from a QuickQuan database 1 In the QuickQuan navigation pane click Com
54. add or modify Compounds and Drug Sets Compound Browser Compound ParentMass Polarity ChargeState NumProducts SourceType buspirone 386 21 Positive 1 1 1 caffeine 195 009 Positive 1 1 1 ketoconazole 531 309 Positive 1 1 1 PolyTyrosine 182 009 Positive 1 1 1 Browse PolyTyrosine 508 309 Positive 1 1 1 PolyTyrosine 997 41 Positive 1 1 1 reserpine 609 01 Positive 1 1 1 a lt gt ree Table COMPOUNDS w Compound Query Add Compounds Add Drug Sets Update SRM Info For Help press F1 12 QuickQuan User Guide Thermo Scientific 3 Defining the Compounds and Drug Sets Defining the Compounds in the Database Figure 10 Add Compounds dialog box Add Compounds Thermo Scientific QuickQuan User Guide 13 3 Defining the Compounds and Drug Sets Defining the Compounds in the Database Manually Adding or Editing Compounds To add the compound information in the Add Compounds dialog box add the information manually using the following procedure or see Importing Compounds Using a Text File on page 14 To add or edit compounds in a QuickQuan database 1 In the QuickQuan navigation pane click Compounds and then click Add Compounds The Add Compounds dialog box appears 2 In the Compound Name box type the new compound name If you are editing a compound select the compound in the Database Compound List 3 In the Charge State box select a charge state 4 In the Num Products box select the num
55. an Templates Thermo_template_IntStd pmd method for internal standards If you use one of these examples go to step 5 to edit the example 3 On the Identification page create a component named target as follows a In the Name list select New b Type target using lowercase letters c Click OK The target component appears in the Components list 4 ISTD only Create a component named istd as follows a In the Name list select New b Type istd using lowercase letters c Click OK The istd component appears in the Components list 48 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Creating a Generic Processing Method Figure 31 Processing Setup Quan view Identification page amp Processing Setup Quan Identification Untitled Int Std File view Zoom Options GoTo Help oleme a 141 4lo 4 2 Identification Detection Calibration Levels System Suitability Peak Purity Components EM Retention time istd Name target zl Expected min 1 00 Window sec 30 00 Detector type Ms Peak Detect jicis eneee eIn os Fiter En Trace Tic Mass m z Save As Default Help Programs No raw file open NOT SAVED 4 5 On the Levels page enter the calibration levels a Inthe components list select target b Enter the calibration and QC level names and amounts for your standards external or internal and QCs c Cl
56. and then press CTRL C 2 In the Excel file position the pointer in the grid and then press CTRL V Tip You can also copy portions of the sequence grid from the Acquisition Setup view and paste the copy into an Excel file To do this highlight the columns and rows in the Acquisition Setup view and then press CTRL C In the Excel file position the pointer in the grid and then press CTRL V Importing a Sequence You can import a sequence sld txt or csv file that you created previously in Xcalibur Sequence Setup See Acquisition Setup View on page 99 for a description of the sequence columns You can import the information for all the columns in the QuickQuan sequence grid except the New Sequence and Drug Set columns Tip Instead of importing a sequence you can copy the sequence from a Microsoft Excel file to the Acquisition Setup view The copy can contain all columns that appear in the Acquisition Setup view including the Drug Set column See Copying Sequences from Excel on page 57 To display the Acquisition Setup view In the QuickQuan navigation pane click Acquisition and then iW i click Setup To import a sequence 1 In the Acquisition Setup view click Import 2 In the Open dialog box select a sequence file sld csv or txt file to import and then click Open QuickQuan imports the sequence into the sequence grid 3 Optional Edit the sequence to specify a drug set for each sample
57. and ISTD Reference table specify any additional compounds to override the defaults specified in step b Click the table cell to display the list of compounds QuickQuan User Guide 53 5 Acquiring the Sample Data Specifying Template Options QuickQuan includes the default ISTD compounds as separate components in each new processing method The positive compounds reference the default positive ISTD and the negative compounds reference the default negative ISTD unless you specify additional ISTDs in the table Each ISTD in the table is also included in the processing method and references the target compound specified in the table Figure 35 shows the Acquisition Templates view that uses the processing method and instrument method that were created earlier Figure 35 Acquisition Templates view a QuickQuan acquire template aql File Acquisition Reports Yiew Help oe gt ow Acquisition Templates Template Information Generic Instrument Method C Xcalibur examples QuickGQuan SampleS et ACQUIRE COLUMN1 meth amp Generic Processing Method C Xcalibur examples QuickQuan S ampleS et INTSTD pmd Templates Processing Macro Template Output Path C Xcalibur examples QuickQuan ampleS et Internal Standard Use Internal Standard Positive ISTD Default caffeine Negative ISTD Default chloramphenicol Additional Internal Standards and Reference Selections chlorpromazine D3 oy Zz R
58. ata16 1 C Xcaliburiquickquantraining 20 Ea Drugset1 Blank Blank NA data01 1 C Xcaliburiquickquantraining 20 29 e Drugset1 Std Bracket Std Update 4 data02 1 C Xcalibur quickquantraining 20 amm fF Drugsetl Std Bracket StdUpdate 5 ldatao3 1 C iXcalibur quickquantraining 20 a oO Drugset1 Std Bracket Std Update 10 data04 1 C Xcalibur quickquantraining 20 oO Drugset1 Std Bracket Std Update 20 data05 1 C Xcaliburiquickquantraining 20 Ena E Drugset1 Std Bracket Std Update 40 Idata06 1 C Xcalibur quickquantraining 20 E Drugset1 Std Bracket Std Update 80 data06 1 C Kcaliburiquickquantraining 20 fe Fj Drugset1 Std Bracket Std Update 160 data06 1 C Xcaliburiquickquantraining 20 36 P Drugset1 Std Bracket Std Update 1320 data06 1 C Xcaliburiquickquantraining 20 im Drugset1 Std Bracket Std Update 1600 data06 1 C Xcaliburiquickquantraining 20 38 E Drugset1 Blank Blank NA data07 1 C Xcaliburiquickquantraining 20 3a Fi Nriinseti Alank Alank M Astan 4 AX ealihiirianinkanantrainina 2N 56 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Creating or Importing a Sequence Editing a Sequence in the Acquisition Setup View You can edit the sequence in the Acquisition Setup view For a description of each column in the sequence grid see Acquisition Setup View on page 99 To fill down the entries from one row to a contiguous range of rows 1 Click the row that you want to copy right click the table and the
59. autosampler systems only QuickQuan User Guide 1 1 Introduction QuickQuan Workflow QuickQuan Workflow The first time you use QuickQuan perform the following procedures On subsequent uses you can skip some of the steps if you plan to reuse the previous settings 1 Selecting QuickQuan Data Sources and Databases on page 3 2 Defining the Compounds and Drug Sets on page 11 3 Optimizing Your Compounds on page 23 and Viewing the Optimization Results on page 36 4 Acquiring the Sample Data on page 43 5 Reviewing the Results on page 73 Note See the QuickQuan 2 0 Installation Guide for a description of how to install QuickQuan and register an ODBC database 2 QuickQuan User Guide Thermo Scientific Selecting QuickQuan Data Sources and Databases This chapter describes how to connect to the QuickQuan database via a data source Contents e About the QuickQuan Database e About the Data Source e Selecting a File Data Source e Creating a File Data Source About the QuickQuan Database QuickQuan stores compound information used for both compound optimization and data acquisition in a central database that supports access by local acquisition workstations and remote analysis workstations The QuickQuan database can also support multiple instruments which allows you to separate the optimization and the acquisition QuickQuan uses drug sets which are groups of one or more compounds to
60. ber of product ions for QuickQuan to detect 5 In the Mass Formula box type the monoisotopic mass or the molecular formula for the compound For example if you were adding reserpine the monoisotopic mass would be 607 680 instead of 608 680 6 Click Add 7 To add additional compounds repeat steps 2 to 6 8 Click Close Importing Compounds Using a Text File You can import the compound information from a text file txt instead of entering the information manually The text file must be in a specified format You can find example files in the following folder Xcalibur QuickQuan ImportFiles Creating a Text File for Importing Compounds The text file can include either of the following e Compounds with molecular weight only e Compounds with a Formula Mass index and either molecular formula or molecular weight 14 QuickQuan User Guide Thermo Scientific R kod l 5 1M 1 2 3 Thermo Scientific 3 Defining the Compounds and Drug Sets Defining the Compounds in the Database To create a compound file with molecular weights only Open a file in Microsoft Excel Notepad or any other software that allows you to create a tab delimited text file with a txt file extension In the first row of the text file type the following text string COMPOUND_DATABASE_INFORMATION_v1 Figure 11 shows the file format for importing compounds with molecular weight only no formulas Figure 11 Compound fi
61. cell displays Yes for the instrument that will initiate the run 4 In the Optimization Settings area select the following a Polarity positive negative or both b Ion source ESI APCI APPI or H ESI Thermo Scientific QuickQuan User Guide 65 5 Acquiring the Sample Data Running an Acquisition Figure 41 Configuration Options dialog box Configuration Options Run time Settings High throughput Acquisition O Tune Optimization Only Use Optimization Database for Existing Compounds Instrument Settings Instrument Start Instrument TSQ Quantum Thermo Pal Yes Optimization Settings Polarity Positive lon Source ESI Processing Settings Num Quan Masses Threshold Mass Window Width 1 C Put Instrument into Standby After Batch Do Post Processing after Acquisition Generate Excel Summary C Run User Defined Macro 66 QuickQuan User Guide Thermo Scientific Thermo Scientific 5 Acquiring the Sample Data Running an Acquisition 5 In the Num Quan Masses box type the number of masses to use for post acquisition processing The valid range is 1 to 3 6 In the Threshold box type a percentage All the Num Quan Masses selected for post processing must meet the specified percentage threshold of the highest intensity ion 7 Optional To set the devices to standby after the acquisition has finished select the Put Instrument Into Standby Mode After Batch
62. check box 8 Optional To start post processing after each sequence has been acquired select the Do Post Processing After Acquisition check box You can also select the following options a To produce a summary report for the acquisition data after post processing has completed select the Generate Excel Summary check box b To execute a custom Excel macro after data acquisition and post processing have finished select the Run User Defined Macro check box For details see Using a Macro To Perform Custom Calculations on page 83 9 Click OK to start the acquisition QuickQuan displays the Acquisition Status view See Figure 42 You can view the status of the run in the EZ Tune Real Time Plot view or in the QuickQuan Acquisition Status view or both When you run the acquisition QuickQuan creates a time and date stamped folder under the folder you specified as the output path Figure 35 on page 54 In the output path folder QuickQuan creates a folder for each drug set 01_Drugset2 and 02_Drugset1 QuickQuan puts the raw and processed data in the drug set folders See Figure 43 QuickQuan User Guide 67 5 Acquiring the Sample Data Running an Acquisition Figure 42 Acquisition Status view QuickQuan Untitled File Acquisition Reports View Help Dai gt n Acquisition Status Processing sequence 1 for drug set Mickey Processing sequence 1 for drug set mickey Processing sequence 2 for drug set Mickey 12 14 2
63. e Acquisition Setup View on page 99 You can repeat these steps to add additional sequences 3 Choose File gt Save to save the sequences to the assay aq file For a description of ways to edit the sequence grid see Editing a Sequence in the Acquisition Setup View on page 57 Thermo Scientific QuickQuan User Guide 55 5 Acquiring the Sample Data Creating or Importing a Sequence Figure 36 Acquisition Setup view showing the sequences for Drugset1 and Drugset2 2 QuickQuan acquire 20nov06 File Acquisition Reports view Help Dei gt Acquisition Setup PrevRow Row 1 Maximum Rows 100 Q C Piewseanenee orug se samote vame samote Type tevet _ Fietame sampe C Drugset2 Blank Blank data01 1 C Xcalibur gquickquantraining 20 a Oo Drugset2 Std Bracket Std Update 4 data02 1 C Kcaliburiquickquantraining 20 Templates ae jaj 7 Drugset2 Std Bracket Std Update 5 data03 4 c Xcalibur quickquantraining 20 4 oO Drugset2 Std Bracket Std Update 10 data04 4 C Xcaliburiquickquantraining 20 il 5 E Drugset2 Std Bracket Std Update 20 Idata05 1 C XXcaliburiquickquantraining 20 pi amp J O Drugset2 Std Bracket Std Update 40 data06 1 C Xcaliburiquickquantraining 20 oO Drugset2 Std Bracket Std Update 80 dataQ6 1 C Xcalibur quickquantraining 20 Setup cal o
64. e negative or both b Optional Ion source ESI APCI APPI or H ESI 5 Select the Put Instrument Into Standby Mode After Batch check box to set the devices to standby after the acquisition has finished 6 Prepare to run the optimization a Open Xcalibur to the Real Time Plot view b In Xcalibur verify that the instrument status is Ready to Download and make sure the initial system parameters are within the acceptable ranges c Verify that the vessel holding the compounds for tuning is ready and in position Verify the same for assay plates d Start Quantum EZ Tune 7 In the Configuration Options dialog box click OK QuickQuan starts the optimization and displays the Optimization Status view Tip You can also view the status of the run in the EZ Tune Real Time Plot view 8 After the optimization verify that the compounds were optimized successfully Figure 24 shows a successful optimization in the Wil Optimization Setup view gt Figure 24 Tune plate graphic showing optimized compounds Thermo Scientific QuickQuan User Guide 35 4 Optimizing Your Compounds Viewing the Optimization Results Viewing the Optimization Results Once optimization completes QuickQuan creates a tune report that includes tune status breakdown curves and MS MS spectra View the optimization results using any of the following procedures e Viewing Results in the Optimization Tune Report View on page 36 e Generating a
65. e 24 QuickQuan uses the information specified in a tune plate to optimize all the compounds within the plate The compound information is passed to the TSQ tune application in real time and QuickQuan monitors the status of each compound during the optimization The data returned from the optimization is added to the central database The optimization data for each compound stored in the QuickQuan database includes polarity tube lens offset parent ion mass product ion mass es collision energy tune status report and tune raw data Note The instrument methods for optimization can differ from the instrument methods for acquisition Tip If your system includes a Thermo PAL autosampler with multiple injection ports multiple valves and a stream selector you can speed up the optimization process See Bypassing the LC Column and the Dual Pump Dual Column Configuration on page 81 Note If you are using the LC column and the tune operation has a time out before the compounds have been tuned use a longer delay for the divert valve setting To display the Optimization Setup view In the QuickQuan navigation pane click Optimization and then il click Setup The Optimization Setup view has the following parameters Parameter Description Tune and Method Files Tune File Specifies the unoptimized TSQTune file to use for this tune plate for example C Xcalibur QuickQuan Templates Tune template TSQTune If you a
66. eneric Instrument Method box click and then select the method meth file you created in Creating a Generic Instrument Method on page 44 2 In the Generic Processing Method box click W and then select the method pmd file you created in Creating a Generic Processing Method on page 47 3 Optional In the Processing Macro Template box specify a macro to perform custom manipulations of the data acquisition results To do this click E and then select the Excel template file xls that was designed to invoke that macro automatically For more information see Using a Macro To Perform Custom Calculations on page 83 4 In the Output Path box click E and then select the folder where you want QuickQuan to create a time and date stamped folder to store the data and method files for the acquisition for example files with the file extensions raw meth pmd sld and pdf Note The sample data raw and the PDF files are stored in the QuickQuan database The raw files can be read using any Xcalibur software that supports raw data files Adobe Acrobat Reader is required to view the PDF files 5 Optional Select the positive and negative internal standards from the QuickQuan database as follows a Select the Use Internal Standard check box b In the Positive ISTD Default and Negative ISTD Default lists select the compounds you want QuickQuan to use by default c Optional In the Target Compound
67. esults Summary For Help press F1 54 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Creating or Importing a Sequence Creating or Importing a Sequence The Acquisition Setup view allows you to set up a sequential sequence containing unknown samples calibration standard samples quality control samples and blank samples One row of the sequence corresponds to one sample injection Each injection is defined by the settings in its sequence row The number of calibration levels in each calibration set is defined by the processing method that you created in Creating a Generic Processing Method on page 47 To create a sequence use one of the following procedures e Creating a Sequence in the Acquisition Setup View on page 55 e Copying Sequences from Excel on page 57 e Importing a Sequence on page 58 e Importing Excel and Sequence Templates on page 59 Creating a Sequence in the Acquisition Setup View In the Acquisition Setup view you can create multiple sequences for an assay To display the Acquisition Setup view In the QuickQuan navigation pane click Acquisition and then Wy click Setup To create sequences in the Acquisition Setup view 1 In the sequence grid select the New Sequence check box to designate the start of a new sequence See Figure 36 2 Enter the sample information in each row of the sequence For a description of each column in the sequence grid se
68. fied output path and stores the instrument method and processing method for the selected drug sets in that folder QuickQuan User Guide 71 Reviewing the Results This chapter describes how to display QuickQuan results Contents e Reviewing Quantitation Results e Generating and Viewing the Acquisition Summary Report e How QuickQuan Performs Post Processing Reviewing Quantitation Results Use the Acquisition Results Summary view to display and review the quantitation results To display the Acquisition Results Summary view In the QuickQuan navigation pane click Acquisition and then click Results Summary The Acquisition Results Summary view appears To display and review the quantitation results 1 In the Root Directory box browse to and select the time and date stamped folder that QuickQuan created for example lt your_output_path_folder gt lt timestamp_folder_for_selected_acquisition gt See Figure 45 Thermo Scientific QuickQuan User Guide 73 6 Reviewing the Results Reviewing Quantitation Results Figure 45 Acquisition Results Summary view QuickQuan Untitled Results Root Directory C Xcalibursquickquantraining 20nov06511212006_151117 Combined Sequence Templates wii gt Setup Sequence Name Date Results Path Drugset1 sld 11 28 2006 Yes 27 C Xcalibur quick quantraining 20nov06 11212006_151117 02_Drugset1 Drugset2 sld 1128 2006 Yes 27 C Xcalibur q
69. files generic selecting 25 54 path 26 tune parameters described 25 tune plate color code 29 graphic 29 information text file 31 inspecting 35 selecting drug sets 29 setting up 27 tune report Excel summary 39 figure 37 viewing 36 U Update SRM Information dialog box 40 user guides vii Thermo Scientific QuickQuan User Guide 117
70. formation Using a Text File on page 31 2 Optional To select adducts or to disallow product ion losses that are not specific enough click Losses Adducts In the Losses Adducts dialog box select the adducts to include and the product ion losses you want to disallow and then click OK Thermo Scientific QuickQuan User Guide 27 4 Optimizing Your Compounds Setting Up for Optimization Using the Tune Plate Graphic to Add Drug Sets Manually You set the injection order based on the order in which you add the drug sets to the tune plate graphic For example if you add the first compound to well position C2 and the second compound to A1 the first injection is taken from C2 and the second from A1 and so on To add drug sets using the tune plate graphic In the QuickQuan navigation pane click Optimization and then Wil click Setup os 1 In the Optimization Setup view click a well position in the tune plate graphic See Figure 18 Figure 18 Tune plate graphic esta Cio 28 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Setting Up for Optimization 2 Select a drug set in the Drug Set Selector See Figure 19 Notice that the selected well positions on the tune plate graphic are color coded as follows e Green All compounds in the well drug set have been optimized for the currently selected ion source e Yellow All compounds in the well have been optimized for an ionization so
71. g Set Names Table Ion source type for tuning the compound where 0 untuned 1 ESI 2 APCI 3 APPI 4 H ESI To specify the ion source type for tuning a compound use the Configuration Options dialog box To view the contents of the Drug Set Names table 1 In the QuickQuan navigation pane click Compounds The Compounds Browse View appears 2 In the Table box select DRUGSETNAMES The Drug Set Names table contains the drug sets that you can combine for a given sequence or tune vial You can group multiple compounds by selecting the compounds under a common drug set name You can associate up to 10 compounds with a single drug set To modify the Drug Set Names table see Defining the Drug Sets in the Database on page 17 The Drug Set Names table contains the following information for each drug set in the database Parameter Description Compound Name of the drug set in the database To add a drug set to or delete it from the database use the Add Drug Sets dialog box Compound 1 Compound 10 Compounds associated with the selected drug set To 88 QuickQuan User Guide add a compound to a drug set use the Add Drug Sets dialog box Thermo Scientific C QuickQuan Views Compounds Browse View Source Type Table To view the contents of the Source Type table 1 In the QuickQuan navigation pane click Compounds The Compounds Browse View appears 2 In the Table box select SOURCETYPETABLE
72. gset2 CStk1 01 1 Blank C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth Drugset2 CStk1 01 11 QC C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth Drugset2 CStk1 01 11 QC C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth Drugset2 CStk1 01 12 QC C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMMN1 meth Drugset2 CStk1 01 12 QC C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth Drugset2 Cstk1 01 13 QC C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMN1 meth Drugset2 CStk1 01 13 QC C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth Drugset2 Cstk1 01 1 Blank C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMMN1 meth Drugset2 Cstk1 01 1 Blank C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMMN1 meth Drugset2 Cstk1 01 1 Blank CX caliburiquickquantraining 20n0v06 4 CQUIRE COLUMN1 meth Drugset2 CStk1 01 14 Unknown C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth Drugset2 Cstk1 01 15 Unknown C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMN1 meth Drugset2 Cstk1 01 16 Unknown C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth Drugset2 Cstk1 01 1 Blank CX caliburiquickquantraining 20n0v06 4 CQUIRE COLUMMN1 meth Drugset2 CStk1 01 1 Blank C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMMN1 meth Start of New Sequ ence gt 32 Drugset1 CStk1 02 1 Blank C Xcalibur iquickquantraining 20n0v06 4 CQUIRE COLUMN1 meth Drugset1 CStk1 02 2 Std Bracket C Xcaliburiquickquantraining 20n0v06 4 CQU
73. hat you selected in the Optimization Setup View on page 91 Thermo Scientific QuickQuan User Guide 95 C QuickQuan Views Acquisition Templates View Acquisition Templates View Use the Acquisition Templates view to select the template files that QuickQuan uses to establish the starting conditions for an assay and to specify internal standards if applicable See Specifying Template Options on page 53 To display the Acquisition Templates view In the QuickQuan navigation pane click Acquisition and then D click Templates The Acquisition Templates view has the following parameters Parameter Description Template Information Generic Instrument Method Specifies the file path of the instrument method meth file for the automated analysis QuickQuan uses the generic instrument method along with optimized settings from the optimization to build the complete instrument method for the assay To create a generic instrument method see Creating a Generic Instrument Method on page 44 Example meth files are in the following folder C Xcalibur QuickQuan Templates Generic Processing Method Specifies the file path for the processing method pmd file for automated batch analysis The generic processing method contains a defined set of parameters that provide QuickQuan with a recipe for automatic quantitation To create a generic processing method see Creating a Generic Processing Method on page 47
74. he new name in the table cell Thermo Scientific QuickQuan User Guide 99 C QuickQuan Views Acquisition Setup View Parameter Sample Type Description Displays the type of sample described by the Sequence row Different sets of sample types are presented for different bracket types The sample type defines how Xcalibur processes the sample data Each sample must be classified as one of the following Xcalibur sample types e Unknown e Blank e QC quality control e Standard Clear e Standard Update To change the sample type click the cell and then select a sample type from the list Level For calibration or quality control QC samples only displays the name of the level To select a different level name click the cell and select from the list Sample ID Specifies a unique identification ID number for each sample To change the current ID number type the new ID number in the table cell Tip To edit this field after it is saved select the cell and press F2 Xcalibur places a cursor at the right side of the cell text You can then delete the old Sample ID and enter the new Sample ID Instrument Method Specifies the file path and file name of the instrument method meth file extension that defines the acquisition To select a different method double click the right end of the table cell In the Select Instrument Method dialog box select the meth file and then click Open To create
75. ick OK Figure 32 shows an example Thermo Scientific QuickQuan User Guide 49 5 Acquiring the Sample Data Creating a Generic Processing Method Figure 32 Processing Setup Quan view Levels page 2 Processing Setup Quan Levels INTSTD Int Std File view Options GoTo Help Cy ad S Identification Detection Calibration Levels System Suitability Campe Pen Units istd Cal Level Amount OCLevel Amount Test 1 1 1 000 1 Qci 80 000 20 00 2 5 5 000 2 ac2 150 000 20 00 3 10 10 000 3 Qc3 800 000 20 00 4 20 20 000 Z 0 010 0 00 5 40 40 000 6 sp 80 000 Reports T 160 160 000 Eh e Save As Default Help Programs 6 ISTD only On the Calibration page specify that istd is the internal standard as follows a Inthe Components list select istd b In the Component type area select ISTD c Click OK 7 On the Calibration page specify that target is the target compound as follows a In the Components list select target b In the Component type area select Target compound c ISTD only In the Target compounds ISTD list select istd d Click OK 8 On the Calibration page enter the settings for the calibration curve and then click OK See Figure 33 for an example 50 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Creating a Generic Processing Method Figure 33 Processing Setup Quan view Calibration page amp Processing Setup Quan Calibration
76. ickquantraining 20nov0B INTSTD 27 Blank 10 00 C caliburquickquantraining 20nov06 INTSTD 0 00 Thermo Scientific 5 Acquiring the Sample Data Importing Excel and Sequence Templates Importing the Excel and Sequence Templates 1 To import an Excel template and sequence template 1 Choose File gt Import Acquisition Sequence gt From Templates to open the Import Sequence Templates dialog box See Figure 40 Figure 40 Import Sequence Templates dialog box Import Sequence Templates Excel Template C caliburquickquantraining 20nov06 training 20nov0B xls a Sequence Template C Xcalibur quick quantraining 20nov06 xCALIBURSEQUE C Use Templates 2 Select the Excel template and sequence template 3 Click OK to close the dialog box Thermo Scientific QuickQuan User Guide 63 5 Acquiring the Sample Data Saving the QuickQuan Assay Saving the QuickQuan Assay You save the QuickQuan assay in an aql file To save the QuickQuan assay 1 Choose File gt Save As to open the Save As dialog box 2 Enter a name for the assay in the File Name box 3 Click Save to save the assay Running an Acquisition Before running an assay QuickQuan can optimize either all the compounds in the assay or only the unoptimized compounds that are not in the optimization database To prepare to run an acquisition 1 Open Xcalibur to the Real Time Plot view 2 In Xcalibur verify that de
77. idth 0 2 amu uN Optional To specify a flow injection infusion of a single sample for optimization select the Use Autosampler Infusion During Optimization check box and then type the sample amount to inject for each compound in the Inj Volume box Or to perform multiple injections of each sample for the optimization run clear the Use Autosampler Infusion During Optimization check box 5 In the Plate Type list select the autosampler plate type to be used for this optimization 6 In the Autosampler Tray Name box select the name of the autosampler tray to be used for this optimization 26 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Setting Up for Optimization Setting Up the Tune Plate for Compound Optimization QuickQuan uses the compound information specified in a drug set to optimize all the compounds within the drug set One drug set is assigned to each well of the plate The tune plate can represent hundreds of compounds at a single time each compound being optimized individually You can arrange the drug sets within the tune plate in any desired layout To set up the tune plate for compound optimization 1 Specify the drug sets in the tune plate by doing one of the following e Use the tune plate graphic to add drug sets one at a time See Using the Tune Plate Graphic to Add Drug Sets Manually e Import the tune plate information from a text file See Importing Tune Plate In
78. isition Templates view for use with other applications To export the methods 1 In the Acquisition Templates view specify the template information See Specifying Template Options on page 53 2 Choose File gt Export Methods The Export Methods dialog box appears Figure 44 Export Methods dialog box Export Methods Templates Output Path Base Filename Combine Drug Sets into single method C Database Drug Sets buspirone caffeine chloramphenicol chlorpromazine chlorpromazine D3 Drugset Drugset2 ketoconazole laurie polptyrosine J PolyT yrosine 181 PolyTyrosine 507 E PolyT yrosine 995 reserpine it ee 70 QuickQuan User Guide Thermo Scientific Thermo Scientific 5 Acquiring the Sample Data Exporting the Instrument and Processing Methods In the Output Path box specify the file path for the exported files In the Base Filename box type the file name To create a single instrument method and processing method for all the selected drug sets select the Combine Drug Sets into single method check box Clear the check box if you want to create a separate instrument method and processing method for each selected drug set In the Database Drug Sets list select the drug sets and compounds for the exported methods To select multiple drug sets press CTRL click Click Export QuickQuan creates a time stamped folder at the speci
79. ition pairs from the information it retrieves from the database for each compound e Uses this information to create and replicate as necessary scan events for the internal standard if specified and for all compounds used within the drug set for this sequence e Adds all SRM transitions for each compound to the SRM table of the scan event for the compound QuickQuan does not alter instrument methods for the autosampler LC pump or other detectors Note You can specify different LC methods for different samples within a sequence For example you might use multiple pumps within the same sequence See Bypassing the LC Column and the Dual Pump Dual Column Configuration on page 81 To create a generic instrument method 1 Start Xcalibur Instrument Setup as follows a In the QuickQuan navigation pane click Acquisition and then click Templates b In the Acquisition Templates view click Inst Setup The Xcalibur Instrument Setup view appears Figure 30 shows the Instrument Setup view 2 Optional To use an example file as the basis for a new instrument method choose File gt Open and then select a meth file from the following folder Xcalibur QuickQuan Templates 44 QuickQuan User Guide Thermo Scientific Thermo Scientific 5 Acquiring the Sample Data Creating a Generic Instrument Method Verify the following mass spectrometer settings e Segments 1 e Scan Events 1 e Scan Type SRM QuickQuan uses the scan
80. kquantraining 20nov06YNTSTD pmd Drugset1 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20nov06YNTSTD pmd Drugset1 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Xcaliburtquickquantraining 20nov06YNTSTD pmd Drugset1 CStk1 02 7 Std Bracket OC Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Kcaliburtquickquantraining 20nov06UNTSTD pmd Drugset1 CStk1 02 8 Std Bracket C Xcealiburiguickquantraining 20nov0SACQUIRE COLUMN1 meth C Kcaliburtquickquantraining 20nov06UNTSTD pmd Drugset1 CStk1 02 9 Std Bracket C Xcaliburiquickquantraining 20nov0SACQUIRE COLUMN1 meth C Xcaliburtquickquantraining 20nov06UNTSTD pmd Drugset1 CStk1 02 10 Std Bracket C Kcaliburtquickquantraining 20n0v06 4CQUIRE COLUMM1 meth C Xcaliburiguickquantraining 20nov06YNTSTD pmd Drugset1 CStk1 02 1 Blank C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20nov06YNTSTD pmd 60 QuickQuan User Guide Thermo Scientific Ej Microsoft Excel training 20nov06 y r Famat Tok Data RoboPDF Window Help Adobe PDF ee AJ Z Y v C r 5 Acquiring the Sample Data Importing Excel and Sequence Templates Figure 38 Excel template showing the start of a new sequence and the end of the assay Drugset2 CStk1 01 1 Blank C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth Dru
81. ld more than one entry for a given compound depending on the number of transitions selected QuickQuan updates the SRM table whenever an optimization run has finished To modify the SRM table see Updating SRM Information on page 39 The SRM table contains the following information for each compound in the database Parameter Compound Parent Description Name of the compound Detected mass of the parent compound Product Detected product ion mass of the parent compound Col Energy Optimal collision energy of the product ion Ql Peak width setting used during optimization Q1 is set to 0 2 for H SRM otherwise Q1 is set to 0 7 The Q1 setting is used to set the peak width for ions passed by the Q1 mass analyzer The lower the peak width setting the higher the resolution Q3 Peak width setting used during optimization Q3 is always set to 0 7 The Q3 setting is used to set the peak width for ions passed by the Q3 mass analyzer The lower the peak width setting the higher the resolution Tube Lens Optimal tube lens offset Width Scan width used during optimization Max Intensity 90 QuickQuan User Guide Maximum intensity of the product ion Thermo Scientific C QuickQuan Views Optimization Setup View Optimization Setup View Thermo Scientific You use the Optimization Setup view to set up compound optimization See Setting Up for Optimization on pag
82. le with molecular weights no formulas ED ImportCompounds Notepad File Edit Format Yiew Help COMPOUND_DATABASE_INFORMATION_V1 ffImport compounds template file fcompound name parent mass molecular weight f charge state fnumber of product ions buspirone 385 50 1 3 caffeine 194 19 1 3 ketoconazole 531 44 1 3 reserpine 608 68 1 3 Optional To include a comment in the file use a double forward slash at the start of the row The software ignores any rows that begin with In each row enter the following fields Use a separate row for each compound and use a tab to separate each field in the row compound name compound molecular weight charge state number of product ions to detect Save the compound file as a txt file To create a compound file with molecular weights and formulas Open a file in Microsoft Excel Notepad or any other software that allows you to create a tab delimited text file with a txt file extension In the first row of the file type the following text string COMPOUND_DATABASE_INFORMATION_v2 Optional To include a comment in the file use a double forward slash at the start of the row The software ignores any rows that begin with QuickQuan User Guide 15 3 Defining the Compounds and Drug Sets Defining the Compounds in the Database 4 In each row enter the following fields Use a separate row for each compound and use
83. lications You can export the generic instrument method meth and processing method pmd for any drug sets in the QuickQuan database See Exporting the Instrument and Processing Methods on page 70 Print Print Preview Opens a Print dialog box which you Ctrl P can use to print the content of the QuickQuan status view Opens a print preview that displays the first page of the QuickQuan status view in a print format Print Setup Opens the Print Setup dialog box that you can use to specify print parameters for printing the content of the QuickQuan window Recently Accessed Files List Opens the selected file Choose the file name of the recently accessed QuickQuan file aql that you want to open Exit Closes QuickQuan The Help menu contains the following commands Command Description QuickQuan Help Displays the Help topics for QuickQuan QuickQuan Glossary Opens the QuickQuan Glossary How to Use Online Help Displays information for using the Help About QuickQuan Opens the About QuickQuan dialog box which displays information about the QuickQuan version and copyright QuickQuan User Guide 111 D QuickQuan Menus and Toolbar Reference Reports Menu Reports Menu The Reports menu contains the following commands Command Description Optimization Opens the Browse for Folder dialog box which you use to specify a location Summary for the optimization summary report
84. loads the raw data collected in the Browser acquisition Results Table Sequence Lists the individual acquisition sequence files sld that make up the Name combined sequence Date Lists the date QuickQuan ran the sequences Results Lists the number of samples in a sequence that were run successfully Yes or unsuccessfully No Path Lists the output directory path in which QuickQuan stores the data and template files for the acquisition for example raw meth pmd sld and PDF files Thermo Scientific QuickQuan User Guide 107 QuickQuan Menus and Toolbar Reference This appendix provides a reference to the QuickQuan menus toolbar and status bar Contents e Acquisition Menu e File Menu e Help Menu e Reports Menu e View Menu e Status Bar and Toolbar Acquisition Menu The Acquisition menu contains the following commands Command Description Go Opens the Configuration Options dialog box which you use to start the optimization or acquisition See Running the Optimization on page 32 or Running an Acquisition on page 64 Stop Stops the run of the current optimization or acquisition Configuration Opens the Configuration Options dialog box which is where you set configuration options Thermo Scientific QuickQuan User Guide 109 D QuickQuan Menus and Toolbar Reference File Menu File Menu The File menu contains the following commands ee Keyboard Command Description
85. me box Figure 4 type your data source name for example QuickQuanMDB Click Next Figure 4 Create New Data Source wizard name data source box Create New Data Source Type the name of the file data source you want to save this connection to Or find the location to save to by clicking Browse Quick uanMDB J Figure 5 5 Verify that the file name of the new data source appears in the file data source box Figure 5 Create New Data Source Create New Data Source wizard Finish page When you click Finish you will create the data source which you have just configured The driver may prompt you for more information File Data Source Filename QuickQuanMDB Driver Microsoft Access Driver mdb QuickQuan User Guide 7 2 Selecting QuickQuan Data Sources and Databases Creating a File Data Source 6 Click Finish The software creates the file data source and then displays the ODBC Microsoft Access Setup dialog box Figure 6 Figure 6 ODBC Microsoft Access Setup dialog box ODBC Microsoft Access Setup Cancel Help Create Repair Compact Advanced System Database None C Database Options gt gt 7 Click Select The Select Database dialog box appears Figure 7 Figure 7 Select Database dialog box Select Database Database Name Directories uickQ uanCompounds mdb en Cancel QuickQuanCompounds f
86. method pump 1 produces a gradient for sample elution on the first column and pump 2 produces a gradient that re equilibrates the second column In the second method pump 1 produces a gradient for sample elution on the second column and pump 2 produces a gradient that re equilibrates the first column Using these alternating instrument methods along with valve switching allows for each injection to run through a separate column and removes the wait time for column equilibration QuickQuan also enables you to use different instrument methods for the acquisition and the optimization Thermo Scientific QuickQuan User Guide 81 A Configuration Procedures Bypassing the LC Column and the Dual Pump Dual Column Configuration Figure 48 Injection valve configuration Infusion Inlet Injection Inlet O D 1 Open Port 1 C To Waste z 2 5 3 5 Infusion Tee O C 4 N AN Pump 1 10 2 Pump 2 9 Column 1 Column 2 4 To Waste 7 6 5 gt To Waste Ds 1 Ke To Waste C 6 4 5 O 82 QuickQuan User Guide To Detector To Waste Thermo Scientific Using a Macro To Perform Custom Calculations Thermo Scientific The software includes a Microsoft Excel template file for data reduction which you can customize to perform the calculations and display the assay results that you require The location of the Data_Reduction xls file is as follows C Xcalibur QuickQuan Templates The
87. n Optimization Summary Report in Excel on page 39 e Using Adobe Acrobat Reader to View the Results on page 39 Tip Compounds that do not tune correctly appear in red and the status is NOT TUNED Viewing Results in the Optimization Tune Report View You can view the tune report in the Optimization Tune Report view The tune reports for each compound are also stored as PDF files in the PDF RAW Output Path folder that you specified in the Optimization Setup view See Specifying Tune and Method Files and Optimization Settings on page 25 You can also open the Xcalibur Qual Browser to see the display of raw data results for the selected compound KD To display the Optimization Tune Report view In the QuickQuan navigation pane click Optimization and then mig click Tune Report EP To view a tune report 1 In the Optimization Tune Report view select the compound from the list on the left side See Figure 25 and Figure 26 QuickQuan automatically displays the latest tune report for the compound 2 To display the raw sample data collected for the compound click QualBrowser Xcalibur Qual Browser opens and displays the raw data 36 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Viewing the Optimization Results Figure 25 Optimization Tune Report view page 1 8 QuickOuan Bae _Ele Acquisit Reports Yiew Help Oe poe Compounds Optimization Tune Report lt
88. n choose Fill Down from the shortcut menu 2 In the Fill Down dialog box select the columns to be duplicated select the destination rows and then click OK To insert a row in the sequence grid Right click the row below the target location and then choose Insert Rows from the shortcut menu To delete a row from the sequence grid Click the row number to highlight the entire row right click the selection and then choose Delete Rows Copying Sequences from Excel You can copy sequences or portions of a sequence from a Microsoft Excel file to the Acquisition Setup view You can also copy sequences from the Acquisition Setup view to an Excel file The copied sequence can contain all the columns that appear in the Acquisition Setup view including the drug set name To copy sequences from an Excel file to QuickQuan 1 In the Excel file verify that the column headings and column order match the columns in the Acquisition Setup view 2 Select the columns and rows of the sequence in the Excel file and then press CTRL C 3 In the Acquisition Setup view position the pointer in the sequence grid and then press CTRL V 4 Verify that the correct values appear Thermo Scientific QuickQuan User Guide 57 5 Acquiring the Sample Data Creating or Importing a Sequence To copy sequences from the Acquisition Setup view to an Excel file 1 In the Acquisition Setup view select the columns and rows that you want to copy
89. name 19 Drugset2_02 20 Drugset2_03 21 Drugset2_04 22 Drugset2_05 23 Drugset2_06 24 Drugset2_07 25 Drugset2_08 27 Component Name 28 buspirone 30 Filename 31 Drugset2_02 32 Drugset2_03 33 Drugset2_04 34 Drugset2_05 35 Drugset2_06 36 Drugset2_07 37 Drugset2_08 39 Component Name 40 ketoconazole 42 Filename 43 Drugset2_02 44 Drugset2_03 45 Drugset2_04 46 Drugset2_05 47 Drugset2_06 48 Drugset2_07 49 Drugset2_08 51 Component Name 52 caffeine Ready Drugset2 Drugset2 Drugset2 Drugset2 Drugset2 Drugset2 Drugset2 Sample Type Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Sample Type Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Sample Type Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample Std Bracket Sample CStk1 01 2 CStk1 01 3 CStk1 01 4 CStk1 01 5 CStk1 01 6 CStk1 01 7 CStk1 01 8 Curve Index Average RF HEB Ble gdt View Insert Format Tools Data RoboPDF Window Help Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Weighting Index Equal Sample Name Sample ID Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Curve Index Linea
90. name and mass are also displayed Drug Set List Displays all drug sets that you added or imported in the database Associates the selected drug set with the selected well 94 QuickQuan User Guide Thermo Scientific C QuickQuan Views Optimization Tune Report View Optimization Tune Report View You can use the Optimization Tune Report view to do the following e View a tune results report PDF file See Viewing the Optimization Results on page 36 e Open Xcalibur Qual Browser to see the display of the raw data results for the selected compound The tune report includes tune status breakdown curves and MS MS spectra To display the Optimization Tune Report view In the QuickQuan navigation pane click Optimization and then Smg click Tune Report ae The Optimization Tune Report view has the following parameters Parameter Description Compound List Specifies the compound for which you want to view tune results Tune Report text pane Read only Displays the Quantum Tune Master optimization report PDF file for the selected compound You can view save and print this report Refresh Refreshes the Tune Report text pane QuickQuan automatically updates the display Qual Browser Starts Xcalibur Qual Browser and loads the sample data raw file collected for the selected compound after the compound has been optimized The raw data file is stored in the PDF RAW output path Export Directory t
91. ne to three product ions with the greatest intensity are used in the quantification of the component QuickQuan selects these masses from the scan corresponding to the expected RT determined above The top ions are selected only from those whose intensities are greater than the user defined threshold of the intensity of the base peak for the scan 5 Instructs Xcalibur to reprocess the sequence with the new processing modifications when the component modification process is complete 78 QuickQuan User Guide Thermo Scientific Configuration Procedures This appendix includes configuration procedures that you might need to use periodically Contents e Configuring and Setting Up Instruments e Configuring and Setting Up Instruments for Aria e Bypassing the LC Column and the Dual Pump Dual Column Configuration Configuring and Setting Up Instruments If you are running QuickQuan with Aria OS see Configuring and Setting Up Instruments for Aria on page 80 To configure and set up the instruments 1 Close QuickQuan Quantum Tune and Xcalibur 2 On the Windows desktop click the Instrument Configuration shortcut to start the Instrument Configuration software 3 In the Instrument Configuration window configure the following instruments e LC pump e Autosampler e TSQ Quantum Click Done 4 Start QuickQuan In the QuickQuan window choose Acquisition gt Configuration 5 In the Configuration Options dialog box select Tune
92. ng the Compounds in the Database sd ecdews cis cand cee Saran 11 Manually Adding or Editing Compounds 00 00000004 14 Importing Compounds Using a Text Pile ciecvepncoavaes arse ne caves 14 Deleting Compounds 65 ci4 5055 lt tod top edy ones cian Meares aati ees 17 Defining the Drug Sets in the Databases 203 4ve cede oe pee eed pe wee ees 17 Adding Drug Sets Manually 42h cceedcacseatssanes beaebe deeds 17 Importing Drug Sets Using a Text File n annuau 19 Deleting Dig Sets 5 74s ci ri csr iata er E A ERT EEAS 20 Viewing Compound and Drug Set Data 00 eee eee 20 Optimizing Your Compounds 00 cece eee e eee eee eee eae 23 Understanding the Compound Optimization Process 0 0000 23 Setting Up for Optimization sas ccc ackepheeGdentea thes edaedeseieedes 24 Reusing Optimization Settings 0 0k ccc eee 24 Specifying Tune and Method Files and Optimization Settings 25 Setting Up the Tune Plate for Compound Optimization 27 Using the Tune Plate Graphic to Add Drug Sets Manually 28 Importing Tune Plate Information Using a Text File 31 Running the Optimization 6 5 0 ociauicachatesraineake rr rra rene 32 QuickQuan User Guide Contents Viewing the Optimization Results i 4cntees pen de wae 36 Viewing Results in the Optimization Tune Report View 36 Generating an Optimization Summary Report in Excel
93. ng the LC Column and the Dual Pump Dual Column Configuration on page 81 If you are using the LC column and the tune operation times out before the compounds have been tuned use a longer delay for the divert valve setting Setting Up for Optimization IMPORTANT Before you can set up for optimization you must have configured an autosampler To configure an autosampler see Configuring and Setting Up Instruments on page 79 To set up for optimization perform the following procedures e Specifying Tune and Method Files and Optimization Settings on page 25 Or you can reuse the settings from a previous optimization See Reusing Optimization Settings on page 24 e Setting Up the Tune Plate for Compound Optimization on page 27 Reusing Optimization Settings You can reuse the settings from an acquisition aql file that you have already created in QuickQuan The aq file contains the configuration settings acquisition settings compound optimization information assay layout and the template information To reuse the settings in an aq file 1 In the QuickQuan window choose File gt Open 2 In the Open dialog box select the aql file and then click Open For example open the following Xcalibur examples QuickQuan SampleSet optimization template aql 3 Verify the optimization settings in the Optimization Setup view See Specifying Tune and Method Files and Optimization Settings on page 25
94. ofile Sean Time fs foo 4 4 1004 000 1000 000 i000 0020 10 070 070 Ske Oke lt _ lt Skimmer Offset vj M E Coll Energy V I io Peak Width Qi FWHM M omn a Q3 FWHM fo 70 z Micos tans Use Tuned Tube Lens Value Copy ScanEvent Paste Sean vent Tune e E ER ERR OBER ER OR ER ERR ER oR CR ER ER ERR RR ERROR ERR ERR A AE ERR CERN CR CR ER OR RRO ER oN ORR AA E oR ER oR ER OR CR EEE E Ar A AE RR OLR RN SR AS A O RR A A AA AS AI EPA AS AS A EAE ANA ES ERR NOT SAVED 7 46 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Creating a Generic Processing Method Creating a Generic Processing Method A processing method is a defined set of parameters that provide Xcalibur and QuickQuan with a recipe for automatic quantitation You use Xcalibur Processing Setup to create a generic processing method pmd file for automated batch analysis QuickQuan uses the generic processing method as the base for creating a processing method for each drug set in each sequence in the assay QuickQuan modifies the generic method based on the component information and the data acquired To create the initial processing method QuickQuan does the following e The generic ISTD component if specified is renamed using the ISTD compound names you selected A partial scan filter is created to match the instrument method scan filter for each ISTD component QuickQuan
95. ompounds Viewing the Optimization Results Figure 26 Optimization Tune Report view page 2 B QuickOuan _ File Acquisition Reports View Help Oe po C Optimization Tune Report Compound List buspirone caffeine Select Text ketoconazole In reserpine Bookmarks N can CO EEE we MLL OES ON AO i 122117 Tune Report Signature 5 May 19 2005 08 07 16 Page 2 of 2 8 5x11in I4 4 2of2 gt Mlo 6 UNUM For Help press F1 38 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Updating SRM Information Generating an Optimization Summary Report in Excel To generate the optimization summary report in an Excel spreadsheet In the QuickQuan window choose Reports gt Optimization Summary Report Figure 27 shows an example of an optimization summary report for a tune plate Figure 27 Optimization summary report E Microsoft Excel OptimizationSummaryReport_01232007 13111 ie File Edit View Insert Format Tools Data RoboPDF Window Help MBR A BE We We MICA Oe ce Rae AR aaa eee et Arial z710 z B Z UJ Z Hi wa A Te oe A X A A ga Ce Reply with Changes End Review C16 fe A B D E F G H J K E _1_ DrugSet Name Vial Compound Name Parent Product Collision Energy Q1 Tube Lens Max Intensity Polarity Source Type Status 2 _3 Drugsett Al caffeine 195 01 137 9
96. ompounds Browse View e Optimization Setup View e Optimization Tune Report View e Acquisition Templates View e Acquisition Setup View e Acquisition Aria Configuration View e Acquisition Results Summary View Compounds Browse View Use the Compounds Browse view for the following procedures e Defining the Compounds in the Database on page 11 e Defining the Drug Sets in the Database on page 17 e Viewing Compound and Drug Set Data on page 20 e Updating SRM Information on page 39 In the Compounds Browse view you can search the compound drug set SRM and source type tables in the currently opened QuickQuan database Thermo Scientific QuickQuan User Guide 85 C QuickQuan Views Compounds Browse View To display the Compounds Browse view In the QuickQuan navigation pane click Compounds The Compounds Browse view has the following controls and parameters Control or Parameter Description Compound Browser Displays the table you select in the Table list The tables are not editable in this view To edit a table see one of the following procedures e Defining the Compounds in the Database on page 11 e Defining the Drug Sets in the Database on page 17 e Updating SRM Information on page 39 Table Specifies one of the following table types for display in the Compound Browser e Compounds Table on page 87 e Drug Set Names Table on page 88 e Source Type Table on page 89
97. omputer or by several computers over a network Selecting a File Data Source QuickQuan automatically opens the last used data source You must select a data source in the following instances e At the first use of QuickQuan on your system e Ifyou want to change the data source for the current QuickQuan session To select a file data source 1 In the QuickQuan window choose File gt Open Database The Select Data Source dialog box appears 2 On the File Data Source page select a file data source See Figure 1 QuickQuan User Guide Thermo Scientific 2 Selecting QuickQuan Data Sources and Databases Selecting a File Data Source Figure 1 Select Data Source dialog box showing the file data source Select Data Source File Data Source Machine Data Source Look in Data Sources QuickQuanDSN DSN Name QuickQuanDSN New Select the file data source that describes the driver that you wish to connect to You can use any file data source that refers to an ODBC driver which is installed on your machine Cancel Help 3 Click OK the ODBC Microsoft Access Setup dialog box appears Figure 2 ODBC Microsoft Access Setup dialog box ODBC Microsoft Access Setup IR Data Source Name OK Description Cancel Database Database C QuickQuanCompounds mdb Help J Cows ETA A System Database Advanced None O Database System Database Options gt gt
98. or your sequence Xcalibur automatically enters the units for the sample volume of the calibration and QC samples from the processing method settings Thermo Scientific Thermo Scientific Parameter Sample Weight C QuickQuan Views Acquisition Setup View Description Displays the amount of a component that has been placed in the sample The unit for this volume is specified in the Processing Setup window and is only included in Xcalibur reports Xcalibur does not convert units To change the sample weight double click the table cell and type the correct value If you have specified a processing method for your sequence Xcalibur automatically enters the sample weights of the calibration and QC samples from the processing method Processing Method Specifies the file path and file name of the processing method pmd file extension which tells QuickQuan how to process the raw data To select a different method double click the right end of the table cell In the Select Processing Method dialog box select the pmd file and then click Open To create a method see Creating a Generic Processing Method on page 47 Cal File Specifies a calibration curve file xcal rather than having QuickQuan create one To specify a calibration file double click the right end of the table cell In the Select Calibration File dialog box select the xcal file and then click Open QuickQuan User Guide 103 C Q
99. other than a command or icon for example the menu label File the Status Bar displays the text For Help press F1 e The toolbar contains shortcut buttons for the frequently used menu commands To show or hide the status bar Choose View gt Status Bar To show or hide the toolbar Choose View gt Toolbar The toolbar contains the following buttons Button Description New Populates the QuickQuan views with the default settings which you can use to create a QuickQuan assay file aql Open Displays the Open dialog box which you can use to open a saved QuickQuan assay file aq Save Opens the Save As dialog box which you can use to save a new or changed QuickQuan assay file aql with a new file name gt Start Acquisition Displays the Configuration Options dialog box which you use to start the run of the selected optimization or acquisition See Running an Acquisition on page 64 Stop Acquisition Stops the run of the current optimization or acquisition o QuickQuan User Guide 113 Index aql file saving 64 A acquiring data 43 64 acquisition results summary 73 acquisition sequences creating 55 example figure 56 Excel template figure 60 importing 55 importing Excel template 59 importing sequence template 59 running 64 acquisition status displaying 68 acquisition summary report 76 Acquisition Templates view 54 adducts selecting 27 Aria OS software vii 80 105 au
100. ple select C Xcalibur QuickQuan Templates Tune_LC_Pos meth c Inthe Tune Neg LC Method box specify the method file that contains the LC settings for a negative polarity tune optimization For an example select C Xcalibur QuickQuan Templates Tune_LC_Neg meth d Inthe PDF RAW Output Path box enter the folder path for the export folder Thermo Scientific QuickQuan User Guide 25 4 Optimizing Your Compounds Setting Up for Optimization Figure 17 Optimization Setup view 8 QuickQuan Untitled Saks Eile Acquisition Reports Yiew Help Osi gt n Optimization Setup Huge sod etal Bes Curent Welt Compound Mass Tune File fel Wi 2 an Al Tune Pos LC Method PA Setup Tune Neg LC Method m Apply PDF RAW Output Path Drug Set Selector iid Optimization Settings Go Minimum Intensity Threshhold 1000 CHSRM r 7 D ia Use Autosampler Infusion During Optimization nj Volume ul 100 Bie oO Plate Setup Plate Type 36 well plate lt Tune Report AutoSampler Tray Name Mj Clear Plate Clear Well Losses Adducts For Help press F1 NUM 2 In the Minimum Intensity Threshold box type the minimum intensity threshold for the product ions Qo Optional Select the H SRM check box to specify tuning for H SRM precursor ion peak w
101. pounds and then click Add Compounds The Add Compounds dialog box appears 2 In the Database Compound list click the compound and then click Delete Repeat this step for any other compounds you want to delete 3 When you have finished deleting compounds click Close Defining the Drug Sets in the Database In QuickQuan compounds are grouped together in drug sets The tune plate and the acquisition assay both use drug sets to define the compounds associated with one another for each tuning well or acquisition sequence If you do not specify a drug set for a compound QuickQuan adds a drug set containing just that compound to the database Note Up to 10 compounds can be associated with a single drug set Use the following procedures to manage the drug sets e Adding Drug Sets Manually on page 17 e Importing Drug Sets Using a Text File on page 19 e Deleting Drug Sets on page 20 Adding Drug Sets Manually You can create drug sets manually and edit the compounds included in a given drug set To create a drug set in a QuickQuan database 1 In the QuickQuan navigation pane click Compounds 2 In the Compounds Browse view click Add Drug Sets The Add Drug Sets dialog box appears Figure 13 3 In the Drug Set Name box type the name 4 In the Database Compounds list click each compound you want to add to the new drug set 5 Click Add QuickQuan adds the selected compounds to the drug set and the drug set
102. ptimize the tune and SRM parameters for all the compounds defined in the tune plate Contents e Understanding the Compound Optimization Process e Setting Up for Optimization e Running the Optimization e Viewing the Optimization Results e Updating SRM Information Before you set up the tune plate information add compounds and drug sets to your selected database as described in Defining the Compounds and Drug Sets on page 11 Understanding the Compound Optimization Process Thermo Scientific You assign a drug set to each well in the tune plate QuickQuan passes the compound information from the drug set to the TSQ Quantum tune application in real time and then monitors the status of each compound during the optimization The data returned from the optimization is added to the QuickQuan database The optimization data for each compound includes the following e Polarity e Precursor ion mass e Product ion masses e Collision energy e QI peak width e Tube lens voltage e Product ion intensity QuickQuan User Guide 23 4 Optimizing Your Compounds Setting Up for Optimization Tip QuickQuan uses instrument methods for optimization that differ from those for acquisition If your system includes a Thermo PAL autosampler with multiple injection ports multiple valves and a stream selector you can use QuickQuan to bypass the chromatography LC column during optimization speeding up the optimization process See Bypassi
103. quickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20novO6YNTSTD pmd Drugset2 Blank C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Xcalibur quickquantraining 20n0vOBYNTSTD pmd Drugset2 Blank C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth C Xcalibur quickquantraining 20n0v0BYNTSTD pmd Drugset2 Unknown C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20no0vOBYNTSTD pmd Drugset2 Unknown C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20no0v0BYNTSTD pmd Drugset2 Unknown C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20n0vOBYNTSTD pmd Drugset2 Blank C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20no0vO6YNTSTD pmd Drugset2 Blank C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20n0vOBYNTSTD pmd x Drugset1 Blank C Xcaliburiquickquantraining 20n0v06 4 CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20n0vOBYNTSTD pmd Drugset1 Std Bracket C Kcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Xcaliburiquickquantraining 20novO6YNTSTD pmd Drugset1 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Kcaliburiquickquantraining 20n0v06YNTSTD pmd Drugset1 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Kcaliburiquic
104. r Weighting Index UK Sample Name Sample ID Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Curve Index Linear Weighting Index 1x Sample Name Sample ID Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Curve Index Average RF Weighting Index Equal C Xcaliburiquickquantraining C Xcalibur quickquantraining 20nov06 INTSTD pmd C Xcalibur quickquantraining C Xcalibur quickquantraining 20nov06 INTSTD pmd C Xcaliburiquickquantraining C Xcalibur quickquantraining 20nov06 INTSTD pmd C Xcaliburiquickquantraining C Xcalibur quickquantraining 20nov06 INTSTD pmd C Xcalibur quickquantraining C Xcalibur quickquantraining 20nov06 INTSTD pmd C Xcaliburiquickquantraining C Xcalibur quickquantraining 20nov06 INTSTD pmd C Xcalibur quickquantraining C xcalibur quickquantraining 20nov06 INTSTD pmd Origin Index Ignore Exp Amt Origin Index Ignore Exp Amt Origin Index Ignore Exp Amt Origin Index Ignore 10 20 40 160 Equation Average Response Factor 9 7017e 008 RSD Calc Amt Units Diff NA NA NA NA NA NA NA NA NA NA NA NA NA NA Equation Y 0 00127876 0 000568364 x R 2 0 9720 6 Reviewing the Results Generating and Viewing the Acquisition Summary Report a 37 Level RSD AMT Peak Status Response Ratio R 1NA NA N 5 NA NA N 10 NA NA N 20 NA NA N 40 NA NA Ne 80 NA NA N 160 NA NA N
105. re only acquiring data and not optimizing a tune file is not necessary QuickQuan User Guide 91 C QuickQuan Views Optimization Setup View Parameter Tune Pos LC Method Description Specifies the instrument method meth file for positive polarity for example C Xcalibur QuickQuan Templates Tune_LC_Pos meth You can select different instrument methods for positive and negative tuning when doing multiple injections Tune Neg LC Method Specifies the instrument method meth file for negative polarity for example C Xcalibur QuickQuan Templates Tune_LC_Neg meth You can select different instrument methods for positive and negative tuning when doing multiple injections PDF RAW Output Path Specifies the folder where the tune status report PDF file and tune sample data raw file are stored Optimization Settings Min Intensity Threshold Specifies the intensity thresholds for the product ions If a compound fails the threshold the system skips that compound s optimization and goes to the next compound in the list Range 500 1000000 H SRM 92 QuickQuan User Guide Activates tuning for H SRM precursor ion peak width 0 2 amu The H SRM mode is either turned on or turned off for the entire tune plate Compounds tuned in H SRM keep their H SRM parameters during data acquisition Note When H SRM is selected the Adjust Parent Mass option in the Quantum Tune Master on source E
106. s itso tae ohio i ea awn lee 96 Acquisition Setup View 0 ccc cc cee eee eens 99 Acquisition Aria Configuration View 0 000s cee cece ee eee 105 Acquisition Results Summary View sx x20 oko cdot Shoe rs ahhore bebe BESS 107 QuickQuan Menus and Toolbar Reference 00eeceeeeeeees 109 Acquisition Ment re eiiaoe a cence eee nee 109 File Ment enoksen pie hes bere hee Ree eee Mews aoe aces 110 Help Menut aed sa Bu ad a Ma eh PA Noa atts Eora A E e naan clin 111 Reports Ment Sr sce trey ite EE TE E E ara a a 112 View Mentir edits ire Bae a A E RATA ee wee wi 112 Status Bar and Toolbar eh tis a sionethtar dana a Tete eee 113 deki naurna eatin actuator taxa Sha aid R a ENNE crac ais EN EE 115 QuickQuan User Guide v Preface About This Guide This user guide describes how to use QuickQuan 2 1 to perform high throughput optimization and quantitative analysis of your compounds Related Documentation The following QuickQuan manuals are available on the QuickQuan software CD as PDF files QuickQuan Installation Guide describes how to install QuickQuan and register the database QuickQuan User Guide describes how to use QuickQuan to perform high throughput optimization and quantitative analysis of your compounds QuickQuan and Aria Quick Start describes how to use QuickQuan with the Aria OS software To view the QuickQuan manuals Go to Start gt Programs gt Xcalibur gt Manuals gt QuickQuan
107. samples quality control samples and blank samples See the following procedures e Creating a Sequence in the Acquisition Setup View on page 55 e Importing a Sequence on page 58 To display the Acquisition Setup view In the QuickQuan navigation pane click Acquisition and then Tit click Setup One row of the sequence corresponds to one sample injection Each sample is defined by the settings in the corresponding row Alternatively you can manually inject samples from the front panel injector as predefined in the sequence For quantitative analysis a sequence can be generated semi automatically based on a processing method For example Sequence Setup can divide up a large number of samples into smaller groups that are bracketed by calibration sets The number of calibration levels in each calibration set is defined by the processing method which you create in Xcalibur Processing Setup Calibration sets can be shared between brackets to make overlapping brackets if required QuickQuan supports sequences with open brackets The sequence table parameters include the following Parameter Description New Sequence Specifies the start of a new acquisition sequence Drug Set Specifies which drug set is associated with the acquisition sequence To select a different drug set click the cell and select from the list Sample Name Displays the name that you assign to your sample To change a sample name type t
108. sing method Each row corresponds to an injection 2 To indicate the start of a new sequence type an X in column 1 3 To indicate the end of the assay type an X in column 1 in the row after the last injection See Figure 38 4 Save the Excel template as an xls file Thermo Scientific QuickQuan User Guide 59 5 Acquiring the Sample Data Importing Excel and Sequence Templates Figure 37 Excel template for an assay Sequence Drug Instrument Method Processing Method Drugset2 Blank C Xcaliburiquickquantraining 20nov06 4 CQUIRE COLUMM1 meth C Xcaliburtquickquantraining 20n0v06YUNTSTD pmd Drugset2 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Kcaliburtquickquantraining 20nov06YNTSTD pmd Drugset2 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Kcaliburtquickquantraining 20nov06YNTSTD pmd Drugset2 Std Bracket C Kcaliburiquickquantraining 20no0v06 4CQUIRE COLUMMN1 meth C Xcaliburtquickquantraining 20no0vO6YNTSTD pmd Drugset2 Std Bracket C Xcaliburiquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Kcaliburtquickquantraining 20nov06YNTSTD pmd Drugset2 Std Bracket C Xcaliburtquickquantraining 20nov06 4CQUIRE COLUMM1 meth C Xcaliburtquickquantraining 20nov06YNTSTD pmd Drugset2 Std Bracket C Xcaliburiquickquantraining 20n0v06 4CQUIRE COLUMM1 meth C Kcaliburtquickquantraining 20nov06YNTSTD pmd Drugset2 Std Bracket C Xcaliburiquickquantraining 20nov
109. t of the row The software ignores any rows that begin with 4 In each row enter the following information Use a tab to separate each entry in the row compound name F formula or M mass molecular formula or nominal mass molecular wt ion source ESI 1 APCI 2 APPI 3 HESI 4 or SIM 5 polarity POS or NEG H SRM 2 or 7 product ion mass collision energy tube lens width maximum intensity tune method file tune PDF file tune raw file Figure 29 shows an example text file 5 Save the file as a txt file Thermo Scientific QuickQuan User Guide 41 4 Optimizing Your Compounds Updating SRM Information 42 QuickQuan User Guide Figure 29 Example of File for Importing SRM Information PD importSRMinfo txt Notepad File Edit Format wiew Help SRM_DATABASE_INFORMATION_v1 f Import SRM template file tf f compound name f f F FORMULA M MASS f f Molecular Formula or the Nominal mass molecular wt f jon source ESI 1 APCI 2 APPI 3 HESI 4 SIM 5 f Polarity POS NEG f H SRM 2 or 7 f product jon mass f collision energy f f tube lens f f width ff max i a f f tune method file f f tune PDF file f tune raw file ff MyImport SRMTL M 385 2 4 NEG 0 2 365 143 29 20 611 0 2 9999 c xcalibur Templetes TSsoTune TSQ_CALB_TUNE TSQTune c xcalibur system programs LCquantutorial pdf c xcalibur system programs BG_030718_33 RAW MyImport SRMTL M 385 2 4 NEG 0 2 233 123 30 12
110. t Excel Notepad or any other software that allows you to create a tab delimited text file with a txt file extension 2 In the first row of the file type the string TUNE_DATABASE_INFORMATION_v1l 3 Optional To include a comment in the file use a double forward slash at the start of the row The software ignores any rows that begin with 4 In each row type the following fields Use a separate row for each well and use a tab to separate columns Figure 21 shows an example well index polarity scan width drug set name 5 Save the tune plate information file as a txt file Figure 21 Tune plate information txt file ImportTunePlate Notepad File Edit Format Yiew Help i E_DATABASE_INFORMATION_v1 fVial Index Cal H12 fPolarity CO Positive l Negative 2 Both fscan width Vai Set Name AL 2 1 Drugsetl B1 2 al Drugset2 Thermo Scientific QuickQuan User Guide 31 4 Optimizing Your Compounds Running the Optimization Importing the Tune Plate Information File To import the tune plate information file 1 In the Optimization Setup view click Import A message asks if you want the imported file to overwrite well information for existing well positions 2 Click Yes The Open dialog box appears 3 In the Open dialog box select the tune plate information file txt and click OK Figure 22 shows the tune plate graphic after importing information for wells Al and B1 4 Choose File
111. t configuration per Configuring and Setting Up Instruments on page 79 b The In Use column displays a Yes for each instrument If necessary click the In Use cell to toggle on or off the Yes c Optional The Start Instrument column displays Yes for the instrument that you want to initiate the run Note Typically the autosampler is selected to be the start instrument because it controls when a run starts In this case the In Use column displays a Yes for all instruments to be used for the sequence submission including the autosampler This means the instruments are awaiting a contact closure event to start operation When this status has been achieved by all instruments used in the run the start instrument initiates the run Thermo Scientific QuickQuan User Guide 33 4 Optimizing Your Compounds Running the Optimization 34 QuickQuan User Guide Figure 23 Configuration Options dialog box Configuration Options Run time Settings O High throughput Acquisition Tune Optimization Only Use Optimization Database for Existing Compounds Rows To Process 1 0 Instrument Settings Instrument In Use Start Instrument TSO Quantum Yes Thermo Pal Yes Yes Optimization Settings Polarity Positive lon Source ESI Processing Settings Thermo Scientific 4 Optimizing Your Compounds Running the Optimization 4 In the Optimization Settings area select the following a Polarity positiv
112. the following string in the first row of a text file DRUGSET_DATABASE_INFORMATION_v1 Optional To include a comment in the file use a double forward slash at the start of the row The software ignores any rows that begin with In each row enter the drug set name followed by up to 10 compound names Use a separate row for each drug set and use a tab to separate each field in the row Figure 14 shows the file format for importing drug set names Save the file as a txt file Figure 14 Drug set names file created in Excel and saved to a txt file DP importDrugSets Notepad File Edit Format View Help DRUGSET_DATABASE_INFORMATION_v1 fImport drug sets template file fDrug Set Name Compound 1 Compound 2 Compound 10 Drugsetl buspirone caffeine reserpine Drugset2 buspirone caffeine ketoconazole QuickQuan User Guide 19 3 Defining the Compounds and Drug Sets Viewing Compound and Drug Set Data 20 Deleting Drug Sets To import the drug set file In the QuickQuan navigation pane click Compounds and then click Add Drug Sets The Add Drug Sets dialog box appears Figure 13 Click Import Click Yes when the confirmation message appears In the Open dialog box select the drug set file you want to import and then click Open The drug sets appear in the Database Drug Sets list Click Close to close the dialog box To delete drug sets from the QuickQuan database
113. tion summary report In Microsoft Excel open the Excel template file for the assay The file is in the folder that contains the files for the assay of interest QuickQuan User Guide 71 6 Reviewing the Results How QuickQuan Performs Post Processing How QuickQuan Performs Post Processing To obtain post processed data you must specify the configuration settings for post processing before running the acquisition If you have configured the post processing option QuickQuan does the following 1 Submits the acquired sequence to the Xcalibur data system 2 Monitors the acquisition files being generated for each sequence that is submitted and performs the back end processing that communicates with Xcalibur At the completion of each sequence QuickQuan attempts to post process the sequence using the information about each compound assigned to the drug sets for each sequence 3 Determines the required expected retention time RT for each component in the processing method QuickQuan determines this value by extracting the filtered mass chromatogram specified for each component using the most concentrated calibrant level as specified in the processing method meth file QuickQuan uses the most intense data point as the expected RT and enters it in the processing method for that component 4 Enables you to specify from one to three masses to be selected when the component specifications in the processing method are created Only the o
114. tosampler Thermo PAL 24 C calibration curves Quan Browser figure 75 settings 51 calibration levels creating 49 calibration parameters 25 charge state selecting 14 compounds Add Compounds dialog box 13 adding manually 14 compounds table 21 deleting 17 importing 14 15 16 optimization settings 23 viewing 20 Compounds Browse view 20 21 Configuration Options dialog box 35 Thermo Scientific data source selecting 4 databases about 3 Microsoft Access 6 Oracle 6 selecting data source 4 4 detection settings 52 documentation vii drug sets Add Drug Sets dialog box 18 adding manually 17 deleting 20 described 17 Drug Set Selector 29 drug set table 22 drug set text file 19 importing 19 selecting 29 tune plate 29 viewing 20 E Excel optimization summary report 39 sequence template 59 59 sequence template figure 60 tune report 39 exporting instrument and processing methods 70 H H SRM selecting 26 l importing compounds 14 drug set text file 19 SRM information 41 QuickQuan User Guide 115 Index L instrument methods creating 44 generic selecting 54 Instrument Setup view 46 Instrument Setup view 46 internal standards specifying 49 51 54 ion source selecting 35 65 L LC methods 25 levels page 50 levels creating calibration 49 losses selecting 27 macros selecting 53 manuals vii methods generic instrument method 44 54 generic processing method 47 54 generic tune method 54
115. uick quantraining 20nov06 11212006_151117401_Drugset2 Results Summary For Help press F1 74 QuickQuan User Guide Thermo Scientific 6 Reviewing the Results Reviewing Quantitation Results 2 Click Quan Browser Xcalibur Quan Browser starts and displays the data in the Quan Browser window See Figure 46 3 Select a component to display the results Figure 46 Quan Browser showing the results for reserpine Quan Browser Drugset1 sid Bracket 1 View All File view Zoom Options GoTo Help se Alm t14 t pclolole i 2 Bracket in use Bracket 1 a Calibration File Embedded Calibration 1 Drugsett _02 2 Drugsett _03 3 Drugsett _o4 Drugset1 _05 5 Drugsett _06 je Drugsett_o7 Drugset1 _08 ETI 3 Drugsett_10 Standard Standard l Standard Standard Standard Standard Standard Standard Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Std Bracket Method Settings 44868 499050340 Method Settings 588722 503110990 Method Settings 911827 516384381 Method Settings 2593850 529493066 Method Settings 7280925 562866754 Method Settings 17272748 526411309 Method Settings 53400848 512930228 Method Settings 607206125 537695952 a AN Standards QCs Blanks Unknowns l Dregset1_O3 Method Settings RT 1 44 3 31 SM 1G 100 30 Relate Abundance 1172172006 5 50 23 PM NL 2 56E7 96 58 397
116. uickQuan Views Acquisition Setup View Parameter Description File Name QuickQuan automatically creates the file names for the acquired sample data The file name is a combination of the base file name prefix assigned to a sequence and a sequential sequence number e Ifthe New File Template is used to create a sequence the base file name and the sequence starting number are defined at that time e Ifthe default sequence starting number 1 is not changed the suffix number is the same as the row number of the sequence for example 001 002 and so on e Ifthe default sequence starting number is changed to another number the first sample has the starting number and subsequent rows in the sequence increment by 001 For example if the starting number is 100 the file name for the first sample has a suffix of 100 the second sample has a suffix of 101 and so on 104 QuickQuan User Guide Thermo Scientific C QuickQuan Views Acquisition Aria Configuration View Acquisition Aria Configuration View The Aria Configuration view is available in the Acquisition section only if Aria OS is installed on the computer You can use QuickQuan with Aria OS to increase the throughput of the acquisition For an overview of how to use QuickQuan with Aria OS see the QuickQuan and Aria OS Quick Start Use the Aria Configuration view to specify the default autosampler AS methods and LC methods for the Aria system You can also specify method and LC
117. urce other than the currently selected ion source e Red At least one compound in the well has not been optimized Figure 19 Drug Set Selector and current well information Current Wel Compound Mass S Drug Set Selector Drugset1 Drugset2 Thermo Scientific QuickQuan User Guide 29 4 Optimizing Your Compounds Setting Up for Optimization 3 Click Apply to associate the drug set to the well The tune plate in Figure 20 shows well A1 is red indicating at least one unoptimized compound 4 Repeat steps 1 to 3 for each well position 5 Choose File gt Save QuickQuan saves the tune plate information in an aql file Figure 20 Tune plate graphic indicating unoptimized compounds in well position A1 Gearon 30 QuickQuan User Guide Thermo Scientific 4 Optimizing Your Compounds Setting Up for Optimization Importing Tune Plate Information Using a Text File You can import a text file txt that contains all the tune plate information that you would otherwise enter manually using the tune plate graphic in the Optimization Setup view When you import the file that contains all the tune plate information QuickQuan adds the tune plate information to the database Creating a Tune Plate Information File An example file for importing tune plate information is in the following folder Xcalibur QuickQuan ImportFiles To create a tune plate information file 1 Open a new file in Microsof
118. vices are ready and make sure the initial system parameters are within the acceptable ranges 3 Verify that the vessel holding the compounds for tuning is ready and in position Verify the same for assay plates 4 Start Quantum EZ Tune To display the Configuration Options dialog box In the QuickQuan navigation pane click Acquisition and then rrr lick Go ith click Go To set up and run the acquisition 1 In the Configuration Options dialog box Figure 41 select High Throughput Acquisition to run an analytical experiment with real time compound optimization 2 Optional To use optimization information that is already in the database select the Use Optimization Database for Existing Compounds check box QuickQuan optimizes the compounds that are in the tune plate that have not been optimized If the check box is cleared QuickQuan optimizes all compounds that are in the tune plate 64 QuickQuan User Guide Thermo Scientific 5 Acquiring the Sample Data Running an Acquisition 3 In the Instrument Settings area verify the following a The Instrument column lists only the required instruments If the required instruments do not appear see Configuring and Setting Up Instruments on page 79 You must configure the instruments before performing the following steps b The In Use column displays a Yes for each instrument Click the In Use cell to toggle on or off the Yes c Optional The Start Instrument

QuickQuan 2.1 User Guide Version A

Contents

Download Pdf Manuals

Related Search

Related Contents