GMSU_UserManual_2034..
Contents
1. Pe a Peake C Analyte IntemalStandard Both Peak 11 dee Select a Sample to retrieve retention data Pekt2 Sample Date Phenacetin ss Jul 08 2006 17 38 02 Apply Ret Data to Chromatogram Save this data as a C Analyte C Internal Standard Both Apply to Chromatogram Exit Figure 27 Manually Enter Peak Retention Times Users may choose to enter retention time for Analyte Internal Standard or both in the left portion of the window If desired the user may save this retention data as a new chromatographic method by clicking the Save this data button Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 35 of 40 If desired the user may use retention data from an existing saved sample by selecting the Existing Data check box located in the Obtain Retention Data from frame If the user checks this box then clicks on a sample in the Select a Sample to retrieve retention data list retention data from that sample will be automatically entered into the appropriate boxes see Figure 28 FA Peak Method Obtain Retention Data from Existing Dat Enter Expected Peak Retention Times Peak2. 21 11 6 CHOOSE DATA ACQUISITION MODE c s cccccecsesessscecececsesseeeccesccesenesesececeesseeaeseesceesesseaesecececeeseaaeseesesesenseaneeeeeeees 21 11 7 CHOOSE A RAW DATA FILE OR RAW DATA FILE 4 44444448 21 11 8 CHOOSE A SAMPLE siester ahinapi 22 12 HEPATIC CLEARANCE CALCULATOR CHROMATOGRAPHIC 23 12 1 DISPLAY CHROMATOGRAPHY cccccsccecseseseseseseseseceseseseseseseceseseseseseseseseseseseseseseseseseseseseseseseseeeseseseceseseseseseseceseeeeeeees 23 12 2 INTEGRATION PARAMETERS 25 12 3 MANUAL INTEGRATION ccccccccecesesescseseseseceseseseceseseseseseseseseseseseseseseseeeseseseseseseseceseseseseseceeececesesecesecesesesecseeeeseceeens 25 12 4 MANUAL PEAK SETTING cccccccccseseseseseseceseseseseceseseceseseseseseseseseseseseseseceseseseseseseseseseseseseseseseseseseseceseseseseseseseseneeenens 26 12 5 MANUAL PEAK RETENTION TIME ENTERING cccccccceseseseeeseseseseseseseseceseseseseseseseseseseseseseeeseceseseseseseseseseseseseseeesees 26 12 6 CHROMATOGRAPHY REVIEW DROPDOWN cccccceeeeseseeeeeseseseseseseceseseseseseseseseseseseseseteceseseseceseseseseseseseseseeeeees 26 12 7 SAVE CHROMATOGRAM
3. Enable Sample Change Warning Calibration Caco Peak Name Sets Peak Name Set 222217772 Peak Names 8 RE 60 Set204060_ 93 RE 60 5 204080 Figure 32 Permeability Calculator Calibration Tab Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 40 of 40 17 References R Cole Quantitation of Biofluids with High Speed HPLC MS MS Early Discovery Applications Invited Presentation at Early ADME and Toxicology in Drug Discovery Techniques for accelerating and Optimizing Drug Candidate Selection Berkley CA October 1998 2 Adam Brockman Donna L Hiller and Roderic Cole High Speed HPLC MS MS Analysis of Biological Fluids in Support of ADME Screens A Practical Review Current Opinion in Drug Discovery 4 3 2000 432 Janiszewski JS Rogers KJ Whalen KM Cole MJ Liston TE Duchoslav E et al A high capacity LC MS system for the bioanalysis of samples generated from plate based metabolic screening Anal Chem 2001 73 1495 1501 47 Yan J Wu L E Elvebak A Brockman Validation of a Totally Commercially Available High Throughput ADME System and Results for 60 Literature Compounds Rapid Communications in Mass Spectrometry Rapid Commun Mass Spectrom 2005 19 1191 1199 Version 6 0 July 20 2006 C GubbsIncApps GM
4. teo ceste etc cs 17 9 3 CHOOSE A BATCH TYPE OPTION FROM THE BATCH TYPE 444000 he ene ne hehehe hene ener nnns 17 9 4 ENTER SET NAME IDENTIFIER BATCH OWNER AND RAW DATA FILENAME IF BATCH TYPE IS FINAL EXPT 17 9 5 CLICK ON THE POPULATE FORM BUTTON 00000 20020 0 17 9 6 CLICK ON SUBMIT BATCH ence etes edet os eoo d eesae eau so dea saei uiv iot educ ses eavee 17 10 HEPATIC CLEARANCE CALCULATOR OVERVIEW V ee eese eese sesto aset eese sese ease eese 19 Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 3 of 40 11 HEPATIC CLEARANCE CALCULATOR INITIAL SETTINGS cscssssssccscsssssccscccccsssssssccecccsssssssccecees 20 11 1 CONSTANTS SPECIE m 20 11 2 TIME OMEN SEDE E 21 11 3 CHROM METHOD SNO TET T u 21 11 4 SAMPLE CHANGE WARNING 5 2000 n nnn nnn nne ann an n n e n n e p p nn p p e ne n p p p e 21 11 5 CHOOSE DATA ACCESS CONFIGURATION nene
5. CN 6 770738 33 40 4 7 1367595 80 Calibration Data 5 X 8 840611 61 Add gt Conc Respons Cak Bias 9 1141917 72 0 0017120145 26 2 1210 0 00 10 936279 75 Exclude 0 0021934555 29 199 2 2 12 y 11 1070944 05 lt 0 Time 12 950590 75 Remove Menuaiintegraton BE 51 TEE Figure 30 Permeability Calculator Chromatography Tab Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SZVEEz Gubbs Mass Spec Utilities 2 x x User Manual Page 38 of 40 EA Permeability Calculator Permeability Calculator Default Peak Name Set ChooseaSampe MA 21 2006 12 07 28 2 LT 55 Choose Data Acquisition Mode Enable Sample Low Throughput Acquisition Change Warning High Thoughput Acquisition Display Choose Raw Data File _ Browse Chromatography Exit C Analyst Data Projects AA Caco_20060306 New 20060221_Caco2_CC00107_ML00649843 wiff Cancel Chromatography Results Calibration w S HB gt OSE Eno Receiver Side DA gt RB gt gt Bol Save 251 E 20060221 Caco2 001071 Results Saved i 8 320687 0 93715C 10 18931 PA i 15 21964 1 356442 17 49847 15 3550 Comments lt 250 characters p RTime Anal 17 76814 1 7704 20 88117 17 67270 30 24637 1 pesi
6. Gubbs Mass Spec Utilities 2 x x User Manual Page 33 of 40 Note Samples that have a Last Point Remaining value of greater then the CutOff value will display in the Report special text values specific to a species and experiment all configured by an administrator in the Configuration Utility For example if a sample is has a Last Point Remaining of greater than 90 and the species experiment is Rat Microsome the Intrinsic Hepatic Clearance Predicted Hepatic Clearance and Eh values would be lt 0 85 lt 0 68 and lt 0 21 or some other configured text values The CutOff value is configured as Last Point Remaining Value in the Hepatic Clearance Calculator window see Section Error Reference source not found of the Configuration Utility 15 Hepatic Clearance Calculator Additional Functions Additional Hepatic Clearance Calculator functions are found under the menu Menu The following sections describe these functions Ba Hepatic Clearance Calculator Menu Accept All Chromatograms Change Data File Path Copy Peak Integrations to Clipboard Generate Reports Peak Area Text File Manually Enter Peak Retention Times Print Enter LT Retention Time Analyte Enter LT Retention Time Int Std Display Multiple Results Figure 26 Menu Items 15 1 Accept All Chromatograms The Accept All Chromatograms function will batch process and save all Chromatographi
7. 183 185 250 213 664 250 230 263 250 30 LC Sync tcsync ML00028208 001 D ML00028208 001 D PLdam UJ w w ML00028318 001 F ML00008818 003 C ML00059447 004 A ML00028318 001 F_PI dam ML00008818 003 C_PI dam ML00059447 004 A_PI dam CN 248 326 249 30 LC Sync 234 343 251 30 LC Sync 253 269 250 30 LC Sync 249 339 391 30 LC Sync 334 394 252 30 LC Sync ara EY PN p w w Figure 4 After clicking the Populate Form button 5 4 Enter appropriate information in the Enter New Default Parameters box 5 5 Click on Generate Method PI acquisition methods with the Proposed Method File Name will be created that have parameters shown in the Default Parameters box If the method already exists that method will be overwritten 6 MRM Method Generator Utility The Multiple Reaction Monitoring MRM Method Generator utility performs several functions e Allows users to quickly view Total Ion Current TIC and mass spectra contained in acquired wiff files that contain an M 1 positive ion experiment and an M 1 negative ion PI experiment e Determines the most appropriate MRM experiment to generate based on user configurable criteria e Flags wiff files whose experiments do not meet criteria e Generates MRM methods for non flagged experiments using parameters set by the user The utility will determine and record the most abundant daughter ions obtain
8. amp Sample ID blank methods ignored File Name 1 17 136 001 36 001 4_MRM dam 20050318 wiff 1 001 41 001 A MRM dam 175 489 75 489 MRM dam 28 001 28 001 F_MRM dam 47 001 0 47 001 D_MRM dam 63 001 63 001 C MRM dam 19 001 C 13 001 MRM dam 114 001 14 001 F_MRM dam 23 001 C 23 001 C_MRM dam j68 001 G 68 001 G_MRM dam 62 001 62 001 08 001 0 08 001 D_MRM dam 13 13 318 001 F 18 001 F MRM dam 118 003 18 003 C MRM dam 15 15 147 004 A 47 004 MRM dam 20050318 wiff 16 16 39 003 C 39 003 C_MRM dam 20050318 wiff 17 17 311 001 11 001 MRM dam 20050318 wiff 18 18 114 001 14 001 G_MRM dam 20050318 wiff 19 19 374 046 74 046 4_MRM dam 20050318 wiff 20 20 322 003 E 22 003 E_MRM dam 20050318 wiff 21 21 543 001 43 001 F_MRM dam 20050318 wiff 22 22 52 001 D 52 001 D_MRM dam 20050318 wiff 23 23 331 003 E 31 003 E_MRM dam 20050318 wiff Figure 14 Populate Form Final Expt Experiment 10 Hepatic Clearance Calculator Overview The Hepatic Clearance Calculator consists of three panes see Figure Figure 15 Users use the top pane Section 11 to choose data files configure default constants choose samples and choose Warning settings Users use the bottom left pane Section 12 to review and optimize chromatographic integration Users use the bottom right pane Section 13 to process and optimize Hepatic Clearance results
9. ll 3 094531 0 36098 30 0360 2 0 74781 745121 0 878837 2223 4 1 Select an Assay Time Point Set Default Select a Papp Constant Set Default 6 758287 22 4051 67 77764 90 36175 i i 118 4731 18 4731 peeo Poona 57777 47805 5 E ummary an gt Donor Side Values DB M ERE Condition Calc Conc Dx 0 1288785 1580217 Gag an s 107 0 1 4 Calc Conc Dx 60 1074196 1835 502 Conc uM 1 5384615 1 534615 24 E pe Calc nmole Dx 0 3350841 2 4651385 Calc nmole Dx 60 27929096 2 8633831 Figure 31 Permeability Calculator Results Tab Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 39 of 40 PA Permeability Calculator Menu Choose a Sample Permeability Calculator Default Peak Name set Caco2_LT_55 Choose Data Acquisition Mode Low Throughput Acquisition High Thoughput Acquisition Display Choose Raw Data File Browse Analyst Data Projects AA Caco_20060306 New 20060221_Caco2_CC0010 7 wif Chromatography Chromatography Calibration Values Apply to Chromatography Enter Number of Calibration Points Concentrations Time Point Set Set_204060 306090120 Caco Calibration Values Time Points z
10. Automaton Exists column row is populated with No e the Proposed dam column row is populated with the new proposed filename though this will have no effect on the next actions PA Automaton File Converter Utility Automaton File Converter Utility Populate Execute Clear Form Form Name Change Choose Automaton Text File Choose SubProject Automaton Name Automaton dam Exists Proposed dam Changed 1 6 25 plate _MRM dam Yes yte 001 001 A MRM dam 2 2 6 25 plate MRM dam Yes yte 002 001 A MRM dam 3 3 6 25 plate MRM dam Yes yte 003 489 A MRM dam 4 4 6C2S plate MRM dam Yes yte 004 001 F_MRM dam 5 5 6 25 plate _MRM dam Yes yte 005 001 D_MRM dam 6 6 6 25 plate _MRM dam Yes yte 006 001 C_MRM dam 7 7 6 25 plate MRM dam yte 007 001 C_MRM dam 8 8 6C2S plate _MRM dam Yes yte 008 001 F MRM dam 9 9 6 25 plate MRM dam Yes yte 009 001 C_MRM dam 10 10 6 25 plate _MRM dam Yes jte 010 001 G MRM dam 11 11 6 25 plate MRM dam Yes jte 011 001 F MRM dam 12 12 6 25 plate MRM dam Yes jte 012 001 D MRM dam 13 13 6 25 MRM dam nalyte 013 001 F MRM dam te 014 003 C MRM dam 16116 6C2S plate pum te 016 003 C_MRM dam 18 6C25 plate MRM dam Yes _ Analyte 018 001 G_MRM dam 19 6 25 plate MRM dam ves 019 046 20 6025 plat mmdan ves araye o20003E edam O 21 6 25 plate MRM dam Analyte 021 001 F_
11. In addition Hepatic Clearance Calculator allows users to generate reports Section 0 and perform additional functions Section 15 e g copy peak integration data to the clipboard The following sections describe the procedures for using the Hepatic Clearance Calculator Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 20 of 40 11 Hepatic Clearance Calculator Initial Settings The initial state of the Hepatic Clearance Calculator is a screen lacking any data Figure Figure 15 Users first must set default constants then choose a data file for processing The following describes the steps for performing these actions Hepatic Clearance Calculator Menu Hepatic Clearance Calculator Choose a Sample Expand Choose Data Access Configuration Choose Data Acquisition Mode Data based on a single data file C Low Throughput Acquisition Enable Sample Change Warning Data based on data files within a directory High Thoughput Acquisition Chromatography I Enable Sample Change Warning Browse Choose a data file Results Cancel Exit BF Smooths AT Point to Point Chromatogr Review Time Point Set Microsome X 2 Peaks LH Drop to baseline Chrom Method None No Dats Results Pane Constants 10 0 Comments lt 250 characters Species 8 0 g of Liver Weight
12. Menu Hepatic Clearance Calculator Expand henace Phe Jul 08 2006 172 Choose Data Access Configuration Choose Data Acquisition Mode T F am Data based on a single data file Low Throughput Acquisition Enable Sample Change Warning Data based on data files within a directory High Thoughput Acquisition Chromatoaraphy Dextromethorphan Dextromethorphan Testosterone Testosterone 7 ethoxycoumarin ethoxycoumarin Jul 08 2006 18 Enable Sample Change Warning I Results Cancel Exit BF Smooths NT AT Chromatogr Review Analyte Time Point Set Microsome 2 2 70 34 351 7 Fi Peaks 12 Phenacetin No Flag El chrom Method Tene XIC of MRM 2 pairs 181 1 111 1 Max 1 0e4 ops 7 Results Pane Constants Comments lt 250 characters Species Rat Microsome Browse Choose data C Projects 00004 20060710_HepCIHTProb Data 20060708_Km_Vmax wiff 5 33 08 7 60 1 00e4 B37 8000 00 No comments g of Liver Weight Kg Body Wt 45 a eun ne mg Microsomal Protein ml Incubation ro mg Microsomal Protein g Liver 45 2 4000 00 HepaticBloodFiow 3 3 Not Reviewed z Results t 1 24 Intrinsic Hep Clearance L hr kg 1 49 Predicted Hep Clearance rk 103 Results Saved and Locked Eh 31 Last Point Remaining Y 0 0026643 X 1 9169 2 026135 Chrom Data Used for Results 30 0 0836693021
13. Method CP Clear Form Dwell Duration Collision Source Time min Energy Temp isting Parameter Values Dwell Source Time ation g Figure 8Choose Internal Standard Method File Source 7 7 Click on Populate Form to preview data A populated window is displayed see Figure 9 If a method of the type chosen is not found then the Method File field for that analyte will be blank and ignored when the Modify Method button is clicked The existing parameters of the existing methods are shown in Existing Parameter Values columns If the method already contains an internal standard it will be replaced with the Internal Standard information chosen when the Modify Method button is clicked PA Modify Methods Utility Modify Methods Utility ee Choose SubProject Form 7 All Methods of the chosen Expt Type Modify Expt Type Choose Assay Request File View File Method CP pound gt MAM dear rom Enter New Default Parameters Dwell Duration Collision Source EN a HOM ting Parameter Values LpH 55 MRM dam LpH 65 MRM dam pH 74 MRM dam Figure 9Populated Modify Methods Window bd Dwell Dur Coll Source me ation Energ True 47 LC Sync LC Sync Pe 70 16 47 Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_
14. ccccscsssessssscssssssscsescscscscscssscssesessscssssusesusesesesesesusssesesuseeesesesesesesesesusuausesusesesesuseseauaeaeanees 26 12 8 BATCH ACCEPT ALL CHROMATOGRAMS cccccseseeesesesesesesesesesesesececeseseseseseseseseseseseseseseseseseseseceseseceseseseseseeeseseseeeeees 26 13 HEPATIC CLEARANCE CALCULATOR RESULTS ccccccsssssssssccccsssscssscccccsssssssceccccsesssssscccescessssssscececees 26 13 1 OVERVIEW eue ML 27 13 2 ERARA OI AHO EIAI T nicae Een M MIL 28 13 3 PLOT OPTION FRAME ii onere eee te rtr tees iere levels 29 13 4 CONSTANTS 5 0 due Erde eue De 29 13 5 EXCLUDE DATA POINTS eno eerte ere kino ceeds ia eye ie tutae cha eid ue bu teo doe 30 13 6 RESTORE DATA POINTS 30 13 7 COMMENTS e ero ia eb epe Weide a ted p cue ans Ea eee AR N 30 13 8 REVIEW MP 30 13 9 SAVE RESULTS sees cc 31 14 HEPATIC CLEARANCE CALCULATOR REPORTS cccccsssssscsscscscsssscssccccccessssssceccccscesscecesccsscssssccccseces 31 15 HEPATIC CLEARANCE CALCULATOR ADDITIONAL FUNCTIONS 41 1 2 40 2 1 74 4 33 15 1 ACCEPT ALL CHROMATOGRAMS ccccccseeeeeessesesesesesesesesesesecesesesesesesesesesesese
15. 11 11 I 62 001 F 62 0D1 F PL dam 62 001 PI O01 wiff 12 12 I 108 001 D 08 001 D_PI dam 08 001 0 PI DD1 wiff 13 13 I 318 001 F 18 001 PL dam 18 001 PI DD1 wiff 318 003 C 18 003 C 18 003 C_PI_O01 wiff 47 004 47 004 47 004 PI DOL wiff 39 003 39 003 C PI dam 39 003 PI DD1 wiff 17 17 I 311 001 11 001 _ 1 11 001 A_PI_001 wiff 18 18 I 14 001 G 114 001 G 14 001 PI OD1 wiff 19 19 I 174 046 174 046 74 046 PI DD1 wiff 20 20 i 122 003 E 22 003 22 003 PI 001 wiff 21 21 i 343 001 43 001 F_Pl dam 43 001 F_PL_OO1 wiff 22 22 I 52 001 D 52 001 D 52 001 0 PI DO1 wiff 23 23 i 131 003 E 31 003 PL dam 31 003 E_PI_001 wiff Y Figure 13 Populate Form PI MRM Experiment Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SZVEEi Gubbs Mass Spec Utilities 2 x x User Manual Batch Queue Submission Utility Batch Queue Submission Utility Load a Saved Batch Save the Batch Choose Assay Request File ViewFile Choose SubProject Populate Submit Form Batch Clear Form Page 19 of 40 Batch Type CP Enter Default Parameters MRM wiff File Set Name Identifier Batch Owner wiff File Name FinalEspt ow Lary Method File
16. C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 9 of 40 Product lon Method Generator Product Ion Method Generator Choose SubProject Choose Assay Request File View File Dwell Method does not exist Populate Generate Form Method Clear Form Enter New Default Parameters Duration Collision Energy LC Sync 250 3 30 csm If method exists it will be overwritten when executing Generate Method DoR Sample ID Proposed Method File Name MW Existing Parameter Values Dwell Time Dur ation LC Sync ML00304936 001 A ML00304936 001 A_PI dam 303 293 ML00275841 001 A ML00059375 489 A ML00028428 001 F ML00275841 001 A PLdam ML00059375 489 A PLdam 345 421 289 375 25 w w tcsync 30 LC Sync 100013547 001 0 ML00059463 001 C ML00008113 001 C ML00013547 001 D PLdam ML00059463 001 C PLdam ML00008113 001 C PLdam ML00028428 001 F PLldam 425 920 252 324 424 250 285 362 249 30 LC Sync ics nc 30 LC Sync ML00028714 001 F ML00028714 001 F PLdam Ww Jw w 30 LC Sync 1 2 3 4 6 7 8 9 ML00059423 001 C ML00028668 001 G ML00028262 001 F ML00059423 001 C PLdam ML00028668 001 G PLdam ML00028262 001 F_PI dam 277 266 250
17. Exists Proposed dam Changed E d No Analyte 00 1 001 4_MRM dam Yes 2 No Ana yte 002 001 A MRM dam Yes 3 No yte 003 489 4_MRM dam Yes 4 No Ana yte 004 001 F_MRM dam Yes No yte 005 001 D_MRM dam Yes 6 No Ana yte 006 001 C_MRM dam Yes y No Ana yte 007 001 C_MRM dam Yes 8 No Ana yte 008 001 F MRM dam Yes 9 No Ana yte 009 001 C MRM dam Yes No Ana yte 010 001 G MRM dam Yes No Ana yte 011 001 F MRM dam Yes No Ana yte 012 001 D MRM dam Yes No Ana yte 013 001 F MRM dam Yes No Ana yte 014 003 C MRM dam Yes No Analyte 015 004 4_MRM dam Yes No Analyte 016 003 C_MRM dam Yes Anayte 00 001 A MRMdam Anayte 018 00t G MRMdam 8 __ 019 046 Yes 20 Ne aayt 020 005E MRMdam Yes 2 5 5 5 5 5 021 001 MRMdam Yes 2 Aamaym 022 001D 23 5 5 Amaye 023 003E MRMdam 4 __ 024 035 84 Amaye 026 003 MRMdam o Yes z 1 Yes 71 0 aa DKA dara SE Figure 12 Changed Automaton Filenames Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 17 of 40 9 Batch Queue Submission Utility The Batch Queue Submission Uti
18. Kg Body Wty mg Microsomal Protein ml Incubation mg Microsomal Protein g Liver Wty 40 ResdinRevicu Hepatic Blood Flow v Results 20 z 20 Intrinsic Hep Clearance L hr kg 9 2 4 6 8 Predicted Hep Clearance L hr kg 4 Results Saved and Locked eee Last Point Remaining 3E kk DG Data Used for Results Drop to baseline Analyte w IS Peaks No Dats 10 0 8 0 6 0 40 20 0 0 9 2 4 6 8 10 s 0 2 4 Plot Reset GA Nudge 8 10 i Figure 15 Hepatic Clearance Calculator 11 1 Constants Species Ensure the appropriate species specific experiment constant set is displayed here Constants Sets are created and configured in the Hepatic Clearance Calculator Configuration Settings tab of the Configuration Utility The default constant is retrieved from the Hepatic Clearance Calculator Configuration Settings in the Configuration Utility Note If a dataset contains mixed species experiments the user later can change the assigned constants by changing the contents of the Species dropdown box after the dataset has been loaded Version 6 0 July 20 2006 C GubbsIncApps GMSU UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 21 of 40 11 2 T
19. Std R Andreas 10 8 Andreas 12 Andreas 14 5 so 900 10 86 10 86 12 83 12 83 Apply Ret Data to Chromatogram Savethisdatlaasa 13 68 13 68 C Analyte Chromatographic C Internal Standard Both Apply to Chromatogram Exit Figure 29 Use peaks from an existing chromatographic method After retention data has been entered e the user clicks on the Apply to Chromatogram button e the retention data is entered into the appropriate chromatographic data grids e the GMSU integration algorithm is called to calculate peak areas 15 7 Print The print function will print the entire window as shown This function is not available at this time 15 8 Enter LT Retention Time Analyte This function is used to set the expected retention time of the analyte for LT data Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 37 of 40 15 9 Enter LT Retention Time Int Std This function is used to set the expected retention time of the internal standard for HT data 15 10 Display Multiple Results This function will use MS Excel to plot and print regression results of several analytes on one regression plot This function is not available at this time 16 Permeability Calculator The Permeability Calculator section is under construction At this time figures will be shown fa Permeability
20. Temp LC Sync Is NA yr Method File Coll Source 15 Time ation LC Sync Parameter Values Sample ID blank methods ignored Polarity Figure 7 Modify Methods Utility 7 1 Choose Populate Form option either Assay Request File or All Methods of the chosen Expt Type If All Methods of the chosen Expt Type is chosen then the Choose Assay Request File dropbox becomes disabled and is unneeded 7 2 Choose an Experiment Type option from the Expt Type frame If Product Ion PI is chosen then IS checkbox is hidden and is not available 7 3 Choose subproject 7 4 Choose Assay Request File from the dropbox 7 5 Enter values for desired variables 7 6 If an Internal Standard is to be added select the IS checkbox Two dropdown boxes will appear for Internal Standard method file source configuration Both dropdowns must be completed see Figure 8 Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 13 of 40 Modify Methods Utility Modify Methods Utility Choose SubProject c analyst data Projects AA AA AAA Choose Assay Request File View File CompoundList 0059 xls z Enter New Default Parameters DoR Populate Assay Request File Form All Methods of the chosen Expt Type X Modify Expt Type
21. individual replicates Reps option The individual replicates view is useful to identify individual outliers Display Average Replicate Points Display Individual Replicate Points Y 0 038603 X 1 9779 R2 0 97847 Peak Area Ratio _00 4 5 0 5 10 15 20 25 30 Time Minutes Add gt Exclude lt Y 0 038603 X 1 9779 R2 0 97847 Peak Area Ratio Log A I9 0 5 10 15 20 25 30 Time Minutes Figure 21 Plot Frame Options 13 4 Constants Dropdown Hepatic Clearance value calculations contain constants that are specific to species and assay These constant values are configured by an administrator in Configuration Utility The constants set for each sample is chosen by the user If a user changes the species constant set the Hepatic Clearance Values will update automatically Results with Rat Microsome Results with Mouse Microsome Constants Species RatMicrosome x g of Liver Weight Kg Wty 45 mg Microsomal Protein ml Incubation 05 mg Microsomal Protein g Liver Wt 45 Hepatic Blood Flow tij2 780 Intrinsic Hep Clearance L hr kg 216 Predicted Hep Clearance L hr kg 2 86 Eh 0 867 Last Point Remaining 99 6 5 Results Constants Species g of Liver Weight Kg Body wt 875 mg Microsomal Protein ml Incubation mg Microsomal Protein g Liver wey 45 Hepatic Blood Flow 54 C12 Intrinsic Hep Cl
22. te 2000 00 0 00 2 4 Time min 8 1 ga Reset Smooths NT 2H 245 01 1225 03 2 AU Peaks xic ct MRM 2 pairs 272 0 156 1 Max 1 2 5 ant Std 106376 57 0 077037724 5 23 608 6 84 30 115685 92 20 0 062221397 ns 230 3 05 05 110607 77 3 0 07495451 T 116674 23 5 0 066222946 8 800 4 56 110547 18 8 0 079871546 600 44 080 33 129291 60 0 074914873 4 0064 124179 48 3 0 0724383050 Ed 132234 32 5 3 0 072640811 59 123204 57 o 0 110993204 0 00 77971 08 0 5 10 15 2 2 30 0 0 0896476279 2 4 2 8 82471 34 Minutes Time min Reset Yes Ave LT EF Figure 16 Loaded raw data file data 11 8 Choose a Sample Users may choose a sample in the Choose a Sample grid either by selecting with the mouse or using the arrow keys when the Choose a Sample grid has focus If chromatograms and or results have not been saved when the user scrolls through samples the user will be prompted with warning messages to choose to save chromatograms or results These warnings may be turned off be de selecting the appropriate checkboxes located to the right of the Choose a Sample grid see Section 11 2 If a sample is of incorrect format or if data file is of incorrect format an error message will be displayed Version 6 0 July 20 2006 C GubbsIncApps GMS U U
23. 33 39 172 58 834 5 0e5 100028739 003 001 wiff Pos 372 87 175 93 405262 Pos 2 4065 ML00028739 003 C MRM dam Neg 370 87 120 35 2 834 ME 100275611 001 PI 001 wiff 154 14 8 20 5 5 ML00002014 001 G PI 001 wiff Pos 271 35 0 00 e ML00002014 001 G MRM dam eg 269 35 170 02 5 668 6 375 91 100059374 046 MRM dam Neg 373 91 0 00 0 7 100028322 003 PI 001 wiff Pos 455 61 165 00 600 808 Pos WH sz 238 39 Exp 2 1 244 mi Max 8 2e4 ops ML00028322 003 E MRM dam Neg 453 61 340 15 2 834 100028643 001 PI 001 wiff Pos 243 70 0 00 100028643 001 MRM dam 241 70 0 00 0 so 9 100028752 001 0 PI 001 wiff Pos 279 31 180 95 22672 Flag ML00028752 001 D_MRM dam Neg 277 31 0 00 0 10 100028331 003 PI 001 wiff Pos 480 53 314 99 651 820 Pos ae 2 0 4 165 6 s 100 150 200 250 amu Figure 6 After clicking Populate Form button 6 5 Inspect results Users should inspect the results by ensuring that the Accepted Pos or Neg ion is the desired daughter ion to be used when generating the MRM method Users can view the mass spectra for each analyte by selecting it in the table Users have perform the following functions e Manual Accept Users may manually accept a Positive or Negative ion by selecting the appropriate row and clicking on the Manual Accept button e Manual Flag Users may manually flag an analyte by
24. 6 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 6 of 40 3 Console The GMSU Console is the module from which users navigate to other modules The Console contents may differ slightly from what is shown PA GMSU Console Gubbs Mass Spec Utilities Home Li Acquisition Method Generator Utilities gl Batch Queue Submission Utility Im Hepatic Clearance Calculator Permeability Calculator Configuration Utility product of Gubbs Inc Figure 1 GMSU Console Users click on the appropriate buttons either to open a utility or to navigate to an additional hierarchical level Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 7 of 40 4 Acquisition Method Generator Utilities The Acquisition Method Generator Utilities are a suite of utilities that are focused on specific tasks involved in acquisition method generation The available Method Generator Utilities are described as follows PA GMSU Console Gubbs Mass Spec Utilities Home ni PI Method Generator Utility Acquisition MRM Method Generator Utility Method Generator Modify Methods Utility Utilities Automaton File Converter product of Gubbs Inc Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SQVEBin Gubbs Mass Spec Utilities 2 x
25. 6 doc SZVEEi Gubbs Mass Spec Utilities 2 x x User Manual Page 24 of 40 2A Hepatic Clearance Calculator Menu Hepatic Clearance Calculator Choose a Sample Expand i Tolbutamide Tolbutamide Jul 08 2006 17 Choose Data Access Configuration Choose Data Acquisition Mode Mephenytoin Mephenytoin Jul 08 2006 17 Data based single data file C Low Throughput Acquisition Dextromethorphan Dextromethorphan Jul08 2006 18 Enable Sample Change Warning Data based on data files within a directory High Thoughput Acquisition 1 108 2006 18 Chromatography SA Is ne u Enable Sample Change Waring 7 l e b 1 Results Browse Choose data file C Projects 00004 20060710_HepCIHTProb Data 20060708_Km_Vmax wiff Cancel Exit BF Smooths AT Chromatogr Review Analyte Time Point Set Microsome m 2 amp 2 155 11 775 57 c Fi Peaks 12 7 ethoxycoumarin No Flag Y rom Method XIC of MRM 2 pairs 191 2 107 3 7 2 4 Analyte 9 79 224109 T 1594 98 Results Pane Constants i 2036 35 Comments 250 characters Species Rat Microsome 1 5e4 7391 90 16108 36 g of Liver Weight Kg Body wt a 1 004 4 58 16601 54 mg Microsomal Protein ml Incubation o 5 35 25956 25 mg Microsomal Protein g Liver 45 i 33 ee C
26. 72815 5 6737088509 7 1266231098 9 7279537428 0 11 4320234857 8 0665093622 9 7279537428 11 4320234857 v ln Bo IMM O Peak Area Ratio Log A IS 0 5 10 15 20 25 Time Minutes 10 15 20 Pu 30 Time Minutes Use IS Plot Reset Yes C ave C No Reps Use 15 Plot Reset Yes C Ave C No Reps Figure 23 13 6 13 7 13 8 Excluding Points Note Users may exclude as many data points as desired given that two points are remaining to generate a regression Restore Data Points Similar to the Exclude procedure users may restore excluded data points by selecting the data point to restore then clicking on Add button Results will be updated automatically Comments Users may enter comments about the sample The comments field may be selected for display in a user defined report see Section 0 Review After optimization of Results data users may classify the results by choosing a value for Results Review dropdown box The contents of the dropdown box include Not Reviewed Acceptable and Unacceptable Selecting the proper review value is important with respect to Reports Users are allowed to filter Reports based on the Review field contents Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manu
27. Analyte RT Int Std AT Chromatographic Method Peak 1 0 80 0 80 c Pes 456 456 Peaks 586 amp 08 C Analyte IntemalStandard Both Select a Sample to retrieve retention data Phenacetin Apply Ret Data to Chromatogram Save this data as a Analyte Groner C Internal Standard Bath Apply to Chromatogram Exit Figure 28 Use peaks from an existing sample Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc AVE Gubbs Mass Spec Utilities 2 x x User Manual Page 36 of 40 Alternatively the user may wish to apply retention data from an existing chromatographic method by selecting the Chromatographic Method check box located in the Obtain Retention Data from frame If the user checks this box then clicks on a method in the Select a Method to use list retention data from that sample will be automatically entered into the appropriate boxes see Figure 29 PA Peak Method Obtain Retention Data from i C Existing Dat Enter Expected Peak Retention Times ungue Peak Analyte RT Int Std RT amp Chromatographic Method Peak 1 418 418 Create Method Parameters Enter Expected Number of Get Retention Data from 12 Peaks or Excel File Peak 5 7 96 7 96 Peak6 900 so Ped 885 Ue Ret Doi C Analyte Intemal Standard Both Select a Method to use Method Name Analyte RT Int
28. Calculator Menu Permeability Calculator DefaultPeak Name Set Choseasee 2 LT 55 7 Choose Data Acquisition Mode v Enable Sample Low Throughput Acquisition Change Warning High Thoughput Acquisition ae 4 isplay Choose a Raw Data File _ Browse Chromatography Exit IC Analyst Data Projects AA Caco_20060306 New 20060221_Caco2_CC0010 y 3 wiff Cancel Chromatography Rests Calibration Smooths ido Chromatogr Review anay Comments 250 characters Ts Cel ES seine No Flag m 55 save Peak Name Set XIC of Furm 2 pairs 496 2 380 1 Max 5830 0 ceslA Std 3 1689 47 r erem Caco2 LT 55 1142 09 2H cm 1231 73 Normalize Y C No 020 5 206612 78 Intensity cps 10 1364 68 184332 70 157432 36 08 10 12 181184 11 Weighting Y 0 00013032 0 0017038 134094 76 none R2 0 95830 Remove Manual Integration Use IS Yes BF Smooths Synchronize C No ss 3058 aseline Analyte w IS Peaks 55 A Std 3 1 754931 80 XIC of MRM 2 pairs 272 0 156 1 8 4 5 cos g 5 o Int Std 2 516656 85 XIC 3 719462 36 8 0e4 4 81418111 E Normalize Y IET 0 200 400 600 200 1000 a 60 4 Yes Reset
29. E DROPBOX 1 2 04 440 2 000000000000000000000000000000000000 0 12 7 5 ENTER VALUES FOR DESIRED 5 12 7 6 IF AN INTERNAL STANDARD IS TO BE ADDED SELECT THE IS CHECKBOX 12 7 7 CLICK ON POPULATE FORM TO PREVIEW DATA ccccccesseeeseseseseseseseseseseseseseseseseseseseseseceseseceeeseseseseseseceseseseseeeseseeeeees 13 7 8 CLICK THE MODIFY METHOD BUTTON ccccssceeseeeseeeseseseseseeecevesereserecereseseceseseseseseseresereseeeceseseeecereseeeseresereserens 14 8 AUTOMATON FILE CONVERTER UTILITY 00 csssscscsssccessscccsssccscnsccccssscccssscessesssccscessecesessscecsssssccesenees 14 8 1 CHOOSE AN AUTOMATON TEXT PILE 14 8 2 CHOOSE A SUBPROJECT 14 8 3 POPULATE HORM 14 8 4 CLICK ON EXECUTE NAME CHANGE BUTTON cccc0cccseeeseeeseseseseseseceseseseseseseseseseceseseseseseseseseseseseseseseseseseseseseeesees 16 9 BATCH QUEUE SUBMISSION UTILITY 0u ssssscscssscccssscccsssscccecssccccssssccsessccccscssceccessacesessseccsesscscessasecessnees 17 9 1 CHOOSE AN ASSAY REQUEST FILE c cccccccccssssssecceececsesssaececececsenssaecesececeesssaesecececeeseseaeseeeeeeseneaeceeeceesesseaeeeeeeeeeeeas 17 9 2 CHOOSE
30. ENERATOR 9 6 1 505 440 10 6 2 CHOOSE AN ASSAY REQUEST FILE cc cccccccccssssssecceececsesssaececccecsenesaecesececsessaesesececeesesaeaeseeecseseaaeceeeeeesessaaseeeeeeceeees 10 6 3 MODIFY THE ACCEPTANCE CRITERIA AS 4000 000 10 6 4 CLICK ON POPULATE FORM ccccccceceeeseseseseseseseceseseseseceseseceseseseseseseseseseseseseseseseseseseseseseseseseseceseseseseseseseseseseseeseesens 10 6 5 INSPECT ird SUBE ROTE 11 6 6 ENTER APPROPRIATE INFORMATION IN THE ENTER DEFAULT PARAMETERS 11 6 7 CLICK ON GENERATE METHODS cccccceeeeeeseseceseseceseseseseceseseseseseseseseseseseseseseseseseseseseseseseseseseseseceseceseseseeeseeeeeeesees 11 7 MODIFY METHODS UTILITY 12 7 1 CHOOSE A POPULATE FORM OPTION EITHER ASSAY REQUEST FILE ALL METHODS OF THE CHOSEN EXPT EEEn 12 7 2 CHOOSE AN EXPERIMENT TYPE OPTION FROM THE EXPT FRAME 01 12 7 3 CHOOSE SUBPROJEGT rods soayoedeseavelueesevosuess 12 7 4 CHOOSE ASSAY REQUEST FILE FROM TH
31. MRM dam 2 6 25 plate MRM dam 022 00 0 MRMdam 23 6 25 plate MRM dam 025 00 24 6 25 plate MRM dam 77 024 035 MRMdam 25 6 25 plate MRM dam 025 003 MRMdam 26 6 25 plate MRM dam 7 026 003 mE Hx 6 plate MRM dam _Yee_ Analyte 027 O01 D yRMidam__ __ Figure11 Automaton File Converter Utility Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc AVE Gubbs Mass Spec Utilities 2 x x User Manual Page 16 of 40 8 4 Click on Execute Name Change button When the Execute Name Change button is clicked only the rows that have an entry in the Automaton column are processed The application changes the filename of the method file then checks the directory to ensure that the filename has been changed When the name change has been verified Yes will be entered in the appropriate row of the Name Changed column and the Automaton dam column row value will be cleared see Figure 12 2A Automaton File Converter Utility Automaton File Converter Utility Populate Execute Clear Form Form Name Change Choose Automaton Text File Choose SubProject Automaton Name Automaton dam
32. OD 36 FIGURE 30 PERMEABILITY CALCULATOR CHROMATOGRAPHY TAB 37 FIGURE 31 PERMEABILITY CALCULATOR RESULTS TAB 38 FIGURE 32 PERMEABILITY CALCULATOR CALIBRATION TAB 39 Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 5 of 40 1 Introduction Gubbs Mass Spec Utilities GMSU is a suite of utilities that enhance the ability of scientists to perform high volume actions in mass spectrometer data acquisition systems This is useful in laboratories engaged in high throughput studies GMSU uses either Microsoft MS Access or MS SQL Server as a datastore MS Access may be used to quickly setup a GMSU instance for user testing or production use MS SQL Server may be used if a more secure environment is desired The MS Access database can be directly upgraded to SQL Server without loss of data GMSU may be used in a multi user environment The GMSU database and acquired mass spectrometer raw data files may be stored in a common location accessible to others Multiple installations of GMSU may be configured to use the database and access the raw data files located in the common location This allows users in the analytical department to use GMSU to generate and optimize chromatographic integration acquired data Once the chromatographic integration data is approved users in the pharmacokinetics department may be notified and can i
33. S U UserManuals UserManual GMSU_UserManual_06 doc
34. TAE Gubbs Mass Spec Utilities 2 x x User Manual Page 1 of 40 Gubbs Mass Spec Utilities 2 x x GMSU 2 0 34 and earlier Supported Platforms Sciex Analyst 1 3 1 1 4 1 Users Manual Gubbs Inc 265 Blue Spruce Circle Alpharetta GA 30005 P 770 573 0169 F 508 453 1338 gubbs gubbsinc com www gubbsinc com Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc 7 Gubbs Mass Spec Utilities 2 x x User Manual Page 2 of 40 Table of Contents Section Page Number 1 INTRODUCTION 5 2 HIGH THROUGHPUT HT VS LOW THROUGHPUT LT ACQUISITION e ener ee eren 5 3 CONS OL D C 6 4 ACQUISITION METHOD GENERATOR UTILITIES eese eee ee eee 7 5 PI METHOD GENERATOR 8 5 1 CHOOSE A i 8 5 2 CHOOSE AN ASSAY REQUEST BILE heic ertet 8 5 3 CLICK ON POPULATE FORM 5 4 ENTER APPROPRIATE INFORMATION IN THE ENTER NEW DEFAULT PARAMETERS 222 2 2 9 5 5 9 6 MRM METHOD G
35. UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 14 of 40 7 8 Click the Modify Method button The method parameters are updated accordingly and are reflected in the table Methods that are identified as Pos have positive Internal Standard method transitions added while methods that are identified as Neg have negative Internal Standard method transitions added Modify Methods Utility Modify Methods Utility Amp rec Choose SubProject Form All Methods of the c analyst data ProjectsVMAVAA AAA chosen Expt Type Modify Expt Type Choose Assay Request File View File Method CP MAM Clear Form Enter New Default Parameters Dwell Duration Collision Source Pos Is Pos dam Time min Energy Temp NA 3 Neg IS aaaPrac_FinalMRM_Neg dam Parameter Values ooa Dwell Dur Source ation al Sync True 013 7 3 400 tcsync Pes zo 3 47 fucsync Figure 10 Results of Modify Method button click 8 Automaton File Converter Utility Utility for Sciex equipment only The Sciex Automaton application allows users to generate autotuned acquisition method files in batch mode based on a user inputted text file Unfortunately the Automaton utility generates files with filenames that are a combination of previously mentioned text filename and s
36. al Page 31 of 40 13 9 Save Results When the user is satisfied that Results processing is complete the user locks the Results by clicking on Save Results This disables all functions relating to chromatographic integration and results processing and the Results Saved checkbox becomes selected In addition Results data are stored in the GMSU data store If the user attempts to further process Saved Results an error message will be displayed In order to further process Saved Results the user must deselect the Results Saved checkbox 14 Hepatic Clearance Calculator Reports Users may generate Microsoft Word or Excel reports based on user defined choices The reports module may be activated from the GMSU Console see Figure 24 or from the Hepatic Clearance Calculator menu Menu Generate Reports see Section 15 1 pA GMSU Console Gubbs Mass Spec Utilities Home Hepatic Clearance Calculator Hepatic Hepatic Clearance Calculator Reports Clearance Calculator 21 product of Gubbs Inc Figure 24 GMSU Console Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc AVE Gubbs Mass Spec Utilities 2 x x User Manual Page 32 of 40 The default field displayed in a Report include e Analyte e Predicted Hepatic Clearance e Intrinsic Hepatic Clearance e Eh Additional fields that may be displayed in a Report include e Results Rev
37. ample order Therefore when a user is searching for method files to configure in an instrumental sequence the user needs to interpret with a cross reference table the name of the file to determine which method file is associated with a given analyte It would be beneficial if the method file names included the analyte name thus eliminating any ambiguity involved in determining the identity of the method file The Automaton File Converter renames Automaton generated files to a filename that includes the analyte name The following describes the procedure for using the Automaton File Converter Utility 8 1 Choose an Automaton Text File 8 2 Choose a SubProject 8 3 Click on Populate Form Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc AVE Gubbs Mass Spec Utilities 2 x x User Manual Page 15 of 40 The form is populated according to the following rules see Figure 11 If an Automaton generated method file that corresponds with the chosen Automaton text file EXISTS then e the Automaton dam column row is populated with the Automaton generated method filename e the Automaton Exists column row is populated with Yes e the Proposed dam column row is populated with the new proposed filename If an Automaton generated method file that corresponds with the chosen Automaton text file DOES NOT EXIST then e the Automaton dam column row is left blank e the
38. ane Comments lt 250 characters Constants Species Rat Microsome v of Liver Weight Kg Body Wt Microsomal Protein ml Incubation mg Microsomal Protein g Liver Wt Hepatic Blood Flow Results Review Not Reviewed Results Intrinsic Hep Clearance L hr kg Predicted Hep Clearance L hr kg Eh Last Point Remaining 20 Y 0 048113 X 1 8533 R2 0 97324 Chrom Data Used for Results 30 0 0197846117 30 0 0233722010 20 0 0691391027 20 0 0754750813 0 2373090134 Peak Area Ratio Log A IS 10 15 20 25 30 Time Minutes Replace Use IS Plot dm Yes Ave No Reps Figure 19 Hepatic Clearance Results Pane Overview Comments box allows users add comments about sample Comments may be included in Reports Results Review box allows the user to choose a Review Status Save Results button allows users to save lock the data such that it can t be changed unless manually unlocked Results Saved and Locked checkbox allows users to unlock data for further processing Species dropdown box allows users to associate samples with a specific species The regression plot shows plotted data Users may expand either axis by clicking dragging the axis The Chrom Data Used for Results shows the retention data time point and peak area or ratio data for each data point Reset button returns plot to full
39. c and Hepatic Clearance Results for all samples displayed in the Choose a Sample grid This is a quicker way to review and accept data and is useful if the user knows that chromatography was most likely sufficient 15 2 Change Data File Path 15 3 Peak Integrations to Clipboard 15 4 Generate Reports Generate Reports will display the Reports window shown in Figure 25 15 5 Peak Area Text File The Peak Area Text File function will export Analyte and Internal Standard time point and peak area data to a comma delimited text file The text file header includes Date of Report Raw Data File Path Analyte Name and Acquisition Time Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc AVE Gubbs Mass Spec Utilities 2 x x User Manual Page 34 of 40 15 6 Manually Enter Peak Retention Times There are times when the automatic peak identification algorithm of GMSU will not identify peaks properly This typically occurs when a peak or entire chromatographic signal is close to a signal noise of approximately two Users may use the Manually Enter Peak Retention Times function to manually enter the expected peak retention times or generate and apply a new chromatographic method FA Peak Method Obtain Retention Data from Enter Expected Peak Retention Times Peak Analyte RT Int Std RT e Chonotogaphic Method Pek2 Pek3
40. ceseseseseeesesesesesesesesesecesececeseseceseseseseseeeeens 33 15 2 CHANGE DATA FILE PATH 0 0 0 0sesscovessvesssevevevevesscosspenevevevsveseoeessvsvevsvesonssveveseosvesbessssvsesvossesesvovnssvsvosnesbavssussoesssess 33 15 3 COPY PEAK INTEGRATIONS TO CLIPBOARD ccccccceseeesesesesesesesesesecesesesesesesesesesecesesesesesesesesesecesesececeseseseseseseseseeeeees 33 15 4 GENERATE REPORTS dgnnsseveinveosbaadydsnvaabusoutdadudeeveisvessidesydswvasnusebiencdsavereys 33 15 5 PEAK AREA TEXT 33 15 6 MANUALLY ENTER PEAK RETENTION TIMES c0ccccceseseseseseseseseseseceseseseseseseseeeseseseseseseseceseseseseseseseseseseseseseseeeeees 34 15 7 PRN DE E 36 15 8 ENTER LT RETENTION TIME ANALYTE cccccccccceceseseseseseceseseseseseseseeeseseseeeseseseseseseseseseseseceseseseseseseseseseseseeeseeeeees 36 15 9 ENTER LT RETENTION TIME INT STD c ccccccccceeeseseseseseseseseseseseceeeseseseseseseseseseseeesesesesesesesesesereseseseseeeseseseseseeesees 37 15 10 DISPLAY MULTIPLE 5 2 ese s esse ess ses ese esee sse seses esee sees esee esee essen 37 16 PERMEABILITY CALCULATOR ei eecs esas eser ora e ea lera eR Ee ao urea ee 37 17 REFERENCES 40 Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManual
41. d in Section 9 4 see Figure 14 9 6 Click on Submit Batch When the user is ready to submit the batch to the queue the Submit Batch button is pushed Note Rows that have blank entries in the Method File column will be ignored and not submitted Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SZVEBi Gubbs Mass Spec Utilities 2 x x User Manual Page 18 of 40 Batch Queue Submission Utility Batch Queue Submission Utility Save the Batch Populate Submit Form Batch Clear Form Choose Assay Request File Yiew File Choose SubProject PS Batch Type G Enter Default Parameters C MRM wiff File Set Name Identifier Batch Owner Final Expt Set 1 001 Larry Method File s Sample ID blank methods ignored wiff File Name 3 1 1 136 001 A 136 001 36 001 A PI DO1 wiff 41 001 41 001 PLdam 41 001 A_PI_OO1 wiff 175 489 175 489 75 489 DO1 wiff 28 001 F 28 001 PL dam 28 001 PI 001 wiff 47 001 0 147 001 0 47 001 D PI DD1 wiff ls 6 i 163 001 C 663 001 PL dam 63 001 PI DOL wiff 13 001 C 13 001 C_PI dam 13 001 C_PL_OOL wiff 714 001 14 001 PL dam 14 001 PI DOL wiff 9 123 001 C 23 001 C_Pl dam 23 001 PI DD1 wiff j68 001 G 168 001 6 68 001 G PI DD1 wiff
42. earance Lihr kg 42 0 Predicted Hep Clearance 4 78 Eh 0 886 Last Point Remaining 9 6 5 Results Figure 22 Species Constants Settings Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 30 of 40 13 5 Exclude Data Points Users may exclude data points if desired by selecting a data point to exclude then clicking on the Exclude button Results will be updated automatically For example if the red 30 minute replicate in Figure 23 is to excluded the user would select the red 30 minute time point in the Chrom Data Used for Results grid and click the Exclude button Exclude Data Point Results Updated CT r Results L Results Results Review ti l 744 Results Review t 1 2 Not Reviewed Intrinsic Hep Clearance L hriko 23 6 Not Reviewed Intrinsic Hep Clearance L hr kg Save Results i Y 0 042155Y X 1 9799 R2 0 99822 Peak Area Ratio Log A IS Predicted Hep Clearance Lihr kg 2 90 Eh Last Point Remaining Qe 5 44 Chrom Data Used for Results 0 3377865382 Predicted Hep Clearance L hr kg Save Eh Results Last Point Remaining 25 Chrom Data Used for Results 0 3377865382 0 Y 0 048806 2 0205 R2 0 99444 1 1 2757549509 1 4677223497 2 9063966187 3 1064679606 4 50170
43. ed from the M 1 positive ion experiment and M 1 negative ion PI experiment The utility will then recommend the most appropriate MRM experiment to generate based on the daughter ion that is most abundant Users may manually override any decision made by the utility The following describes the procedure for using the MRM Method Generator utility Version 6 0 July 20 2006 C GubbsIncApps GMSU UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 10 of 40 Pa MRM Method Generator Utility MRM Method Generator Utility Form Methods neri Choose Assay Request File View File Choose SubProject No Data 0 Enter Default Parameters Enter Acceptance Criteria Dwell Collision Min Min Time Duration Energy Daughter Daughter View in Analyst msec min kv LC Sync m z Intensity x Manual Accept Methods will not be generated for Flagged analytes Manual Flag Daughter Parent wiff File Parent Daughter Ion Proposed MRM Acq Method Ton Intensity Wi NoData Figure5 Generator Utility 6 1 Choose a SubProject 6 2 Choose an Assay Request File Note Users may view the Assay Request File by clicking the View File button 6 3 Modify the Acceptance Criteria as needed e Min Daughter m z The minimum daughter ion m z that will be considered when evaluating mass spectra e Min Daughter Intensit
44. hrom 6 10 26895 57 niece Hepatic Blood Flow 33 6 87 38767 57 Not Reviewed Results 7 63 39244 05 tun 8x 00 8 40 71039 51 Save insi Intrinsic Hep Clearance Lhr kg 2643 26 37 28 39 40 64145 83 Results Predicted Hep Clearance L hr kg Time min ja a Eh Remove Manual Integration p m Reset Last Point Remaining 3 60 BF Smooths NT AT Y 0 048113yX 1 8533 G Synchronize Data Used for Results R2 0 97321 2 H 2 kH 257 06 1285 3 Analyte w IS Pecks 30 0 0197846117 xic ct MRM 2 pairs 272 0 156 1 12e5c95 qut Std 0 79 95886 99 30 0 0233722010 1 54 80617 20 a 20 0 069139102 3 80 2 30 106743 31 20 0 075475081 3 05 106913 45 S 0 145979546 3 30 0 148788451 2 60e4 4 58 113725 11 8 0 2402715748 5 35 109377 43 c 0 2373090134 4fe4 6 10 111938 21 amp 3 0 3278368958 ae 6 87 117667 11 3 0 329468192 7 63 119706 02 0 0 7613623658 00 8 40 78703 78 5 w 2 c 0 0 9026187815 37 38 40 x 9 15 84251 38 Time min 0 Time Minutes Use IS Plot Replace Remove Manual Integration Reset Reset E Exdude us Figure 17 Click on Peak 1 40 of Analyte Retention Time Peak Area table grid with Synchronize Analyte w IS selected 12 1 2 Synchronize Analyte w IS If the Synchronize Analyte w IS checkbox is selected then a selection in either Analyte or In
45. iew Acceptance Status e Sample Number e Comments e Species Experiment To generate a report e User chooses one or more Analyte specific items and clicks the Add button to add them to the print queue sers may enter an optional Print Job Description ser chooses a Results Type filter and any additional report content ser chooses a Report Format ser clicks Generate Report button 0 0 Hepatic Clearance Calculator Reports Existing Data a by Analyte by Data File bySample o Raw Data File 01 455 08 9 1 Stab all in one L yst Data P 000 dreas_HTH 01 4455 D amp Ld HTI SDF 2 C Analyst Data Projects 00004 20060710_ HepCIHTProb Data 20060708_Km_Vmax wiff Choose one or more entries in the above table Then click Add to add the entries to the print aueue Enter Print Job description Optional f 1 Sort Print Data Choose Additional Report Content Filter Choose Results Type Re Sort Choose a Report Format Acceptance Status Acceptable by Analyt Microsoft Excel Comments 7 Unacceptable by Data File C Microsoft Word Acquisition Time C Not Reviewed 5 by Sample Species Experiment All Egt Raw Data Fil Andreas_HTHep Data 01 4455 _06Ld_HTI_SDF _pos wiff Figure 25 Hepatic Clearance Calculator Reports Module Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc
46. ime Point Set The Time Point Set contains assay time points to be applied to the chosen data file Ensure an appropriate Time Point Set is displayed here Time Point Sets are created and configured in the Hepatic Clearance Calculator Configuration Settings tab of the Configuration Utility The default Time Point Set is retrieved from the Hepatic Clearance Calculator Configuration Settings in the Configuration Utility 11 3 Chrom Method Note This field is optional for HT acquisition and not applicable to LT acquisition The Chrom Method chromatography method is a chromatographic method containing expected chromatographic retention times to be applied to the chosen data file This method may be applied to the data file if the GMSU automatic peak identification algorithm is not successful for e g data files with low signal Ensure an appropriate Time Point Set is displayed here None if not used The default Chrom Method is retrieved from the Hepatic Clearance Calculator Configuration Settings in the Configuration Utility Chrom Methods are created and configured in the Hepatic Clearance Module via the Menu Manually Enter Peak Retention Times feature see Section 11 4 Sample Change Warning boxes If the user attempts to select a new sample but hasn t saved the Chromatograms or Results two warnings are displayed These warnings may become annoying if initial data review is all that is desired By deselecting one or bo
47. ities 2 x x User Manual Page 26 of 40 12 4 Manual Peak Setting In some instances e g when peak heights are close to the signal to noise ratio or if integration parameters are not optimal Hepatic Clearance Calculator will not identify the correct peak The peak may be manually set by e ensuring the peak in question is selected in the appropriate Retention Time Peak Area grid e right click on the desired peak 12 5 Manual Peak Retention Time Entering In some instances several peaks cannot automatically picked or cannot be set with a right mouse click The user may manually enter retention times for the run by choosing Menu Manually Enter Peak Retention Times See Section 15 6 for further discussion 12 6 Chromatography Review Dropdown Box The user may choose from a list of choices to denote an assessment of the chromatographic results The contents of the Chromatogr Review dropdown box are configured by an administrator in the Configuration Utility 12 7 Save Chromatogram When the user is satisfied that the chromatography is acceptable the user locks the chromatogram by clicking on Save Chrom This disables all functions relating to chromatographic integration and the Chrom Saved checkbox becomes selected In addition chromatographic data are stored in the GMSU data store If the user attempts to further process a Saved Chromatogram an error message will be displayed In order to further process a Saved Ch
48. lity allows users to automatically create a batch sequence that whose samples contain existing unique data acquisition methods dam and collect the data into a single raw data file wiff This is useful in a high throughput environment in which tens to hundreds of samples are acquired in one analytical sequence The Sciex alternative to this utility requires manually entering choosing the correct method file for each sample After preparing a batch and before submitting the user may save the batch by clicking the Save the Batch button As expected the user may load this batch again at a later time The following describes the procedure for using the Batch Queue Submission Utility 9 1 Choose an Assay Request File 9 2 Choose a SubProject 9 3 Choose a Batch Type option from the Batch Type frame 9 4 Enter Set Name Identifier Batch Owner and raw data filename if Batch Type is Final Expt 9 5 Click on the Populate Form button The Method File column will be filled with the appropriate existing method files based on the contents of the Assay Request File If the expected method file does not exist the Method File column row entry will be blank If the Batch Type was PI or MRM then the wiff File Name column row entry will be created corresponding to the sample name see Figure 13 If the Batch Type was Final Expt then the wiff File Name column will be named according to the user entry describe
49. mmediately generate pharmacokinetic data GMSU data are stored in a database either MS Access MS SQL Server This data may be accessed or generated from multiple installations of GMSU System requirements and installation procedures please refer to the Gubbs Mass Spec Installation and Administration Manual 2 High Throughput HT vs Low Throughput LT Acquisition One of the salient features of GMSU is that it can process HT acquired data as well as LT acquired data Typically mass spectrometry data acquisition systems require that compound s of interest occur once in a chromatographic analysis Therefore in order to analyze a 12 point assay scientists had to acquire twelve separate samples within a data file This is referred to as LT acquisition in the GMSU system In HT acquisition users open the data acquisition window for as long as needed and inject and acquire all assay time points a single chromatographic run The benefits of HT acquisition include ability to view all chromatographic peaks simultaneously to check for possible instrumental or sample handling problems and or trends e When combined with multiple column switching techniques increases throughput by decreasing the time between sample injections and minimizes communication problems that can occur between instrument and data acquisition system Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_0
50. romatogram the user must deselect the Chrom Saved checkbox 12 8 Batch Accept Chromatograms In order to expedite the processing of a large number of samples the user may batch process and save all samples by choosing from the menu Menu Accept All Chromatograms The samples listed in the Choose a Sample grid will be processed sequentially and application optimized chromatographic data will be stored in the GMSU data store See Section 15 1 for further details 13 Hepatic Clearance Calculator Results The Hepatic Clearance Calculator Results bottom right pane allows users to perform several functions e Automatically generates Hepatic Clearance Results based on selected species specific Experiment Constants e Allows the user to optimize Hepatic Clearance Results by selecting the choice of using or not using internal standard peak area ratios e Allows the user to optimize Hepatic Clearance Results by excluding data points e Allows the user to select Results Review assignments and comments The following describes the functionality of the Hepatic Clearance Calculator Results section Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 27 of 40 13 1 Overview The right Results Pane contains functionality for users to optimize and process data to obtain Hepatic Clearance Results Results P
51. s UserManual GMSU_UserManual_06 doc 7 Gubbs Mass Spec Utilities 2 x x User Manual Page 4 of 40 Table of Figures Figure Page Number FIGURE 1 GMSU CONSOLE 6 FIGURE 2 ACQUISITION METHOD GENERATOR UTILITIES 7 FIGURE 3 PI METHOD GENERATOR STARTUP SCREEN 8 FIGURE 4 AFTER CLICKING THE POPULATE FORM BUTTON 9 FIGURE 5 MRM GENERATOR UTILITY 10 FIGURE 6 AFTER CLICKING POPULATE FORM BUTTON 11 FIGURE 7 MODIFY METHODS UTILITY 12 FIGURE 8 CHOOSE INTERNAL STANDARD METHOD FILE SOURCE 13 FIGURE 9 POPULATED MODIFY METHODS WINDOW 13 FIGURE 10 RESULTS OF MODIFY METHOD BUTTON CLICK 14 FIGURE 11 AUTOMATON FILE CONVERTER UTILITY 15 FIGURE 12 CHANGED AUTOMATON FILENAMES 16 FIGURE 13 POPULATE FORM PI MRM EXPERIMENT 18 FIGURE 14 POPULATE FORM FINAL EXPT EXPERIMENT 19 FIGURE 15 HEPATIC CLEARANCE CALCULATOR 20 FIGURE 16 LOADED RAW DATA FILE DATA 22 FIGURE 17 CLICK ON PEAK 1 40 OF ANALYTE RETENTION TIME PEAK AREA TABLE GRID WITH SYNCHRONIZE ANALYTE W IS SELECTED 24 FIGURE 18 MANUAL INTEGRATION 25 FIGURE 19 HEPATIC CLEARANCE RESULTS PANE OVERVIEW 27 FIGURE 20 USE IS FRAME OPTIONS 28 FIGURE 21 PLOT FRAME OPTIONS 29 FIGURE 22 SPECIES CONSTANTS SETTINGS 29 FIGURE 23 EXCLUDING POINTS 30 FIGURE 24 GMSU CONSOLE 31 FIGURE 25 HEPATIC CLEARANCE CALCULATOR REPORTS MODULE 32 FIGURE 26 MENU ITEMS 33 FIGURE 27 MANUALLY ENTER PEAK RETENTION TIMES 34 FIGURE 28 USE PEAKS FROM AN EXISTING SAMPLE 35 FIGURE 29 USE PEAKS FROM AN EXISTING CHROMATOGRAPHIC METH
52. scale on both axes Use IS frame allows users to choose to use Internal Standard peak area ratios or not Plot frame allows users to display average or individual replicates in the regression plot Exclude and Add buttons allow users to exclude and restore data points The following describes the functions available in the Hepatic Clearance Results pane Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 28 of 40 13 2 Use IS Option Frame Users may choose to use Yes option or not use No option internal standard area ratios by selecting the appropriate option button The y axis label will update accordingly Use Internal Standard Don t Use Internal Standard Y 0 038603 X 1 9779 R2 0 97847 Peak Area Ratio Log A I8 0 5 10 15 20 Time Minutes 25 30 Add gt Exclude lt Y 0 038539y X 2 0126 R2 0 98932 Peak Area Log A 0 5 10 15 20 25 30 Time Minutes Add gt A 15 m Figure 20 Use IS Frame Options Version 6 0 July 20 2006 C GubbsIncApps GMSU UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 29 of 40 13 3 Plot Option Frame Users may choose to display average replicate points Ave option or
53. selecting either the Positive or Negative row of an analyte and clicking on Manual Flag e View in native data acquisition system If desired users may view the data in the native system by selecting the analyte and clicking on View 6 6 Enter appropriate information in the Enter Default Parameters box 6 7 Click on Generate Methods MRM acquisition methods with the Proposed Method File Name and the Accepted positive or negative transitions will be created If the method already exists that method will be overwritten Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 12 of 40 7 Modify Methods Utility The Modify Methods Utility performs several functions e Allows users to modify common method variables of existing methods in batch mode based on a user specified text Excel file or all methods within a directory e Allows users to add an Internal Standard second transition in a period to existing methods form MRM methods only The following describes the procedure for using the MRM Method Generator utility Modify Methods Utility Modify Methods Utility Populate Assay Request Fie Form All Methods of the chosen Expt Type Modify Expt Type Choose Assay Request File View File Method CP m Clear Form Enter New Default Parameters Dwell Duration Collision Source Time min Energy
54. serManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 23 of 40 12 Hepatic Clearance Calculator Chromatographic Processing The Chromatography bottom left pane allows users to perform several functions e Allows users to quickly view analytical runs generated in one or several raw data files and quickly identify possible problems in instrument operation or sample preparation e Automatically optimizes chromatographic integration parameters and picks peaks Allows the user to further optimize chromatographic integration including manual integration e View Hepatic Clearance Results on the fly as chromatography is being optimized 12 1 Display chromatography There are several ways in which chromatographic data may be displayed 12 1 1 Retention Time Peak Area table grids If the user clicks on an entry in the Retention Time Peak Area table grid located to the right of the chromatogram the corresponding chromatographic peak will be zoomed in the chromatogram For example Figure 17 shows that when peak retention time 1 40 in the Retention Time Peak Area table grid is selected the corresponding peak obtains focus in the chromatogram In the figure shown the Synchronize Analyte w IS checkbox was selected so the corresponding Internal Standard peak was also obtained focus Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_0
55. tated with an M to signify that the peak has been integrated manually Panel Panel 1 Panel 2 BF Smooths Chromatogr Review BF Smooths NT Point to Point Chromatogr Review CH CH 0 99 0 88 No Flag x Peaks 12 1 4 0 99 0 88 Drop to baseline No Flag zi Peaks _ 12 4843 1193 Max 5 9e4 IC of MRM 2 84 3 119 3 5 9e4 pairs a Analyte 360 64 Xi pairs 484 3 ax ops c t Intstd EE Std 2 09 21088 79 5 1500 1 2 76 1500 2502108 Normalize Y 21 Normalize Y 4 f L ka pe Yes 3 43 21720 85 C Yes e 1000 i C No 4 10 23134 78 1000 C No 2 i A x10 77 21429 92 10 M i 5 43 23333 98 ETT E 6 11 77819 96 E 6 77 90086 30 Ce NER 0 i 7 44 94669 63 0 gj ev 26 27 28 29 2 0 BE 8 11 90021 66 26 27 28 29 30 Time Time Reset Reset Remove Manual Integration me lt Er Remove Manual Integration lt gt Figure 18 Manual Integration The manual integration can be re manually integrated if desired The manual integration may be removed by e ensuring that the correct peak is selected in the Retention Time Peak Area grid e clicking on the Remove Manual Integration button Version 6 0 July 20 2006 C GubbsIncApps GMSU UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Util
56. ternal Standard Retention Time Peak Area table grid will result in the corresponding peak obtaining focus in both chromatograms 12 1 3 Normalize Y f Normalize Y is set to Yes then the Y axis is automatically normalized to the peak height e If Normalize Y is set to No then the Y axis remains at its most recent setting e If Normalize Y is set to x10 the Y axis is automatically magnified by a factor of 10 with respect to the peak height of the selected peak 12 14 Y Axis Scale buttons The gray arrow buttons to the right of the chromatograms increase or decrease the scale of the Y Axis Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 25 of 40 12 1 5 X Axis Shift buttons The gray arrow buttons to the bottom right of the chromatograms shift the X axis to the left or right 12 1 6 X Axis Expansion buttons The blue arrow buttons to the bottom of the chromatograms expand or contract the scale of the X axis 12 2 Integration Parameters Users may optimize integration with the following parameters Bunching Factor BF Smoothing Smooths Noise Threshhold NT Area Threshhold AT 12 3 Manual Integration Manual integration may be performed by clicking and dragging Panel 1 with the left mouse button the peak desired to be integrated The corresponding item in the Retention Time Peak Area grid will be anno
57. th of these warnings the warning messages will be disabled 11 5 Choose Data Access Configuration Users may choose to load a single wiff file or all wiff files within a directory The default setting for this frame is configured in the Hepatic Clearance Calculator Configuration Settings in the Configuration Utility If desired an administrator can make this option frame invisible 11 6 Choose Data Acquisition Mode Users must select whether the data file being loaded is LT or HT If the data file does not exist in the database users will be prompted to assign the data as LT or HT The default setting for this frame is configured in the Hepatic Clearance Calculator Configuration Settings in the Configuration Utility If desired an administrator can make this option frame invisible If the frame is invisible new data will be processed automatically according to the LT or HT setting and users will not be prompted to assign data 11 7 Choose a raw data file or raw data file directory Choose the Browse button to browse to a raw data file or raw data file directory Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc Gubbs Mass Spec Utilities 2 x x User Manual Page 22 of 40 Data will be loaded into the Choose a Sample table grid and the first sample will be processed The resulting window is shown in Figure 16 Hepatic Clearance Calculator
58. x User Manual Page 8 of 40 5 PI Method Generator Utility The PI Method Generator Utility generates Product Ion PI experiments configured with one positive ion M 1 experiment and one negative ion M 1 experiment Methods are generated based on data contained in a selected Assay Request file that contains analyte name and its corresponding molecular weight The following describes the procedure for using the PI Method Generator Pa Product lon Method Generator la Product Ion Method Generator Populate Generate Clear Form Choose SubProject Enter New Default Parameters Choose Assay Request File View File Dwell Duration Collision h Time min Energy LC Sync Method does not exist Tf method exists it wil be overwritten when executing Generate Method Proposed Method File Name Figure 3 PI Method Generator startup screen 5 1 Choose a SubProject 5 2 Choose an Assay Request File Note Users may view the Assay Request File by clicking the View File button 5 3 Click on Populate Form The form is populated with information e Ifa PI acquisition method dam file already exists its parameter information will be displayed e IfaPI dam does not exist the parameter information columns will contain asterisks If the user wishes to populate the form with information from a different Assay Request file the Clear Form button must first be clicked Version 6 0 July 20 2006
59. y Ions must be greater than this value in order to be considered as acceptable 6 4 Click on Populate Form If the user wishes to populate the form with information from a different Assay Request file the Clear Form button must first be clicked Version 6 0 July 20 2006 C GubbsIncApps GMS U UserManuals UserManual GMSU_UserManual_06 doc SQVEBi ny Gubbs Mass Spec Utilities 2 x x User Manual Page 11 of 40 PA MRM Method Generator Utility MRM Method Generator Utility Populate Generate Methods Sear Form Choose Assay Request File View File Choose SubProject Tic of MS2 240 29 CE 20 E Max 1 2 7 ops Enter Default Parameters Enter Acceptance Criteria i Dwell Collision Min Min Time Duration Energy Daughter Daughter View in Analyst msec min kv LC Sync m z Intensity bso 2 30 uc sync 70 40 000 Manual Accept 5 Methods will not be generated for Flagged analytes Neither Neg or Pos scan met Minimum Daughter lon intensity criteria Manual Flag 0 00 02 04 06 08 10 12 14 16 18 20 100008818 003 001 Pos 340 39 201 96 CEBOEER TA ML00008818 003 C MRM dam Neg 338 39 165 85 2 834 2 100059447 004 PI 001 wiff Pos 335 39 0 00 5 7e5 ML00059447 004 A_MRM dam 3
Download Pdf Manuals
Related Search
GMSU_UserManual_2034..