MSM_AdminUserManual_..
Contents
1. ee ee ee ee ee ee ee ee ee ee ee ee ee ee ER ee ee ee ee ee ee 3 4 CONFIGURE LOCATIONS 3 3 istis Ge esiti ioci iie iiir ee 3 5 ASSIGN LOCATIONS TO NEWLY RECORDED MASS SPEC INSTRUMENTS ee ee ee ee ee ee ee ees 4 MSM SER VUC OE EE EE EE EE N EE ses 5 MSM FEATURES CONFIGURATION eee ee ee ee ee se se se ee ee ee ee Ge Ge Ge ee ee Ge ee ee ee 5 1 CONFIGURATION GLOBAL ee ee ee ee ee RE EE RE EE EE RE EE EE EE ER ener ER ER ER ER EE 5 2 CONFIGURATION LOCATION LABELS cccccccsccseseseeeseseseseseseseseseceseseseseseseseseeeseseeeeees 5 3 CONFIGURATION POLLING LOCATIONS cc0cccccseseseseseseseseseseseserecesesesesesesereseseseseeeeees 6 CONFIGURATION LOCATION cssscccsssscssssscccssssccccssseccesssccscssssccesssccscssssccesssnees 6 1 ADD IOEATION PR Ee do ee Ge oe De ee E oe ee ie 6 2 DELETE Pere WHERE T ee ee ee oe eg ee Se De ee EE ee i 6 3 CONFIGURE THE LOCATION ees ee ee ee ee ee ee ee ee ee ee RR RR RR RR Re Ee EE ee EE ER ee ee ee ee ee RR RE Re Ee 7 MASS SPEC INSTRUMENTS eere ee se se ee sesse se se Ge naso see testa Ge Ge Ge Ge Ge Ge ee Ge Ge Ge ee ee ee 7 1 EDITABLE ee EON NER T 7 2 INSTRUMENT ACTIVATION DEACTIVATION ee ee ee ee ee ee ee hehehe ee ee ee ee ee ee ee ee RR ee Ee ee 7 3 ASSIGNING LOCATIONS TO MASS SPEC INSTRUMENTS ee ee ee ee ee ee ee ee ee ee hene nn nnne 8 DA TA EIEES er 8 1 FALTER FOR MS e2. 00014 U18230703 MS00014 AB 00015 8810110811 MS00015 AB coos V21340711 MSO0016 AB 00017 VOST6050B MS00017 AB 00018 UD16870608 MS00018 AB 00003 1200110 MS00019 AB 00020 AG21630801 MS00020 AB 00021 AGOT1650512 MSODO21 AB 00022 AGO12530606 MS00022 AB Item Country Site Building Laboratory Bench Figure 15 Mass Spec Instruments Window The different mass spec instruments retrieved from the polled raw data files are recorded in a database table called TBLSN In the MSM Viewer application users are able to filter data by mass spec instrument and mass spec instrument location This window allows the user to assign locations to mass spec instruments 7 1 Editable columns The contents of the following columns may be edited by the user MS Name default is MS H H Description Status e g Archived Not In Use Decommissioned etc 7 2 Instrument Activation Deactivation Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 21 of 28 7 3 The information retrieved by MSM is viewed by MSM Viewer In MSM Viewer users have the choice of viewing data All Active or Deactivated mass spec instruments The state of the instrument is defined by clicking either the Activate or Deactivate buttons For example if mass spec instrument MS00001 is to be deactivated
3. ASSUMPTIONS lt is assumed that all samples contained within a data file were acquired on a single MS instrument SUPPORTED TESTED DATABASES Microsoft Access 2000 2003 2007 Microsoft SQLServer 2003 Oracle 10g Figure21 Requirements Window The system requirements of MSM are shown in this window Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 27 of 28 12 Monitor Polling Status 3 616 ke PGR ea ena cnet ae 25 364 KB 18 600 KB 24 008 KB Retrieving information from 50 780 KB Z MSMTesting Folder03 Projects Sciexi4AlDatal 2 48com human wiff 1 of 100 files 2A Gubbs Mass Spe Sample 30 of 54 samples Gubbs Mass Spec Metrics Polling Application Edit Save Cancel Exit About Configuration Configuration Location Mass Spec Instruments Data Files Mass Spec Entries View Logs Requirements Monitor Polling Status fit appears that MSM Polling is not responding check it s Status by clicking the Check Status button If Check Status responds with Not Responding then click the Kill Analyst Service button MSM Polling should begin responding in a few moments If MSM Polling still does not begin responding then click Kill MSM Folling to end MSM Polling Check Status Kill MSM Patina narre Last Status Check 3 23 2010 5 01 47 AM MSM Polling Status MSM Poll
4. to 100 raw data files Errors can occur during raw file data retrieval resulting in the interruption of the polling event and a message box displayed to the user see Figure 1 Users have two options to proceed o The user may click the OK button on the message box which will kill the interrupted session The user then can re start the polling event by clicking the Begin Polling button o If the polling event is part of a Scheduled Event then the user may wait until the next scheduled polling event starts at which time MSM will automatically kill the interrupted session to start the new scheduled polling event Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 6 of 28 EI EP s TurboTax u MSM Polling Event Status BA d Gubbs Mass S NOTE Each polling event is limited to 100 non polled files Menu Inventorying 1 of 1 configured polling directories ZAMSMTesting Gubbs Mas Finding MS Serial Numbers for 8 of 99 ZAMSMTesting Folder08 Projects Test D ata 644003 wiff SN D12650311 Configuration Configuration Location Mass Spec Instruments Data Files Mass Spec Entries If Check Status responds with Not Responding then click the Kill View Logs Analyst Service button Requirements Monitor Polling Status If it appears that MSM Polling is not responding check it s Status
5. VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 16 of 28 5 2 Configuration Location Labels PA Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Menu Gubbs Mass Spec Metrics Polling Application Edit Save Exit pon About Configuration Confiquration Configuration Location Configuration Type Location Labels v Changes to Location Labels requires application restart to take effect a iam Instruments Parameter Setting Mass Spec Entries gt Define Location 1 Country View Logs Define Location 2 Site Requirements Monitor Polling Status Define Location 3 Building Define Location 4 Laboratory Define Location 5 Bench Define Location 5 Polling Locations Add How Delete Row Browse LastPolling Date March 21 2010 07 27 07 AM Log Item Polling 20100321 072707 000001 Allow manual path entry Label Directory ETT Eg SITE SS ZAMSMT esting Folder01 Gubbs DMPK Z MSMTesting Folder02 Figure 10 Configuration Window Location Labels Users are allowed to assign locations to the individual instruments that are inventoried The definitions for these locations are configured in this window Labels are defined in a hierarchical tree fashion see Figure 10 for an example The user must give some thought to how this hierarchical tree should be defined See Section 6 for assigning locations to mass spec instruments Version 1 0 March 23 2010 C GubbsIncApps
6. by clicking the Check Status button MSM Polling should begin responding in a few moments If MSM Polling still does not begin responding then click Kill MSM Polling to end MSM Polling Microsoft Visual C Runtime Library Check Status Buffer overrun detected Last Status Check Program C Program Files Gubbs Inc Gubbs MSM MSM_Do exe MSM Polling Status A buffer overrun has been detected which has corrupted the program s Last Polling Date internal state The program cannot safely continue execution and must now be terminated Next Polling Date Kill AnalystService Figure 1 Example of raw file data retrieval error message box 2 2 1 AB Data Retrieval Process The following is a description of the process of retrieving information from AB raw data files 2 2 1 1 FindFile Process MSM sets up a For Next loop to evaluate the directories defined in the Polling Location section of the Configuration window This process is called the FindFile process The information determined in the FindFile process is placed in memory to be written to the database at the end of the Polling Event Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 7 of 28 Looping one directory at a time MSM generates an array of files consisting of all electronic files containing the file extension wiff lo
7. event is limited to 100 total non polled raw data files The very first time MSM is run on a system it is highly probable that the total number of non polled files could reach into the thousands Therefore it is recommended that the following procedure be used when performing the initial polling event on AB data Configure the Automated Polling Frequency hours see Section 5 1 2 parameter to 0 5 Click Begin Polling Choose Scheduled event when prompted Allow MSM to proceed Check the status of polling completion by inspecting the logs see Section 10 o Ifthe 6 item reads Polling limit of 100 files then the Polling Location has not been completely polled Configuration View Logs Configuration Location Copy to Include logs after Saturday March 13 2010 x Mass Spec Instruments Clipboard Select Log yyyymmdd hhmmss Poling 20100323 100828 Q00001 Data Files Mass Spec Entries Polling event began 3 23 2010 5 56 46 AM Polling event ended 3 23 2010 6 12 18 AM Polling 20100323 100825 000001 R Number of new data files inventoried scroll down to Inventoried Data Files section 100 Polling 20100323 100333 000001 equirements Number of new mass spec instruments found scroll down to New Mass Spec Instruments section 4 Monitor Polling Status Number of problems experienced 13 in 5 180 data extraction events Polling limit of 100 files was reached Polling action must be repeated t
8. the Edit button If the user wishes to cancel all changes made during an edit action then he she may click the Cancel button Once all editing actions are complete the changes must be saved by clicking the Save button AB Analyst Data The MSM polling event is limited to 100 total non polled raw data files see discussion below The very first time MSM is run on a system it is highly probable that the total number of non polled files could reach into the thousands Therefore it is recommended that the procedure defined in Section 3 2 1 1 be followed for the initial polling event of data MSM relies on the robustness of the AB Analyst dll s in order to reliably retrieve the needed information for database storage The act of opening the raw data file retrieving information then closing the raw data file is defined by MSM as polling The polling even involves rapid open and closing of raw data files It seems some of the objects within the AB Analyst dll s are not designed to work reliably with such rapid opening closing events resulting in occasional non trappable errors most commonly buffer overrun errors that interrupt the polling event The following are notes about MSM features in place to resolve the robustness issues of the AB Analyst dll s It has been found that the probability of error increases when the number of raw data files polled in a single polling event is greater than 100 Therefore polling events are limited
9. the user would select the row and click the Deactivate button The user may filter the mass spec instruments for All Activated or Deactivated mass spec instruments by choosing the appropriate entry in the Show dropdown box Assigning Locations to Mass Spec instruments Users may assign a location to a mass spec instrument in two ways 7 3 1 Apply a defined location A location that has been defined in the Configuration Location window see Section 6 may be applied to a mass spec instrument by selecting the appropriate row in the MS Instrument table the MS Locations Apply Location a Gubbs Georgia Gubbs German MS Location Item Country Site Building Laboratory Bench Figure 16 Apply Location 7 3 2 Manually enter a location MS Locations MS Location Item Country Site Building Laboratory Bench Apply Location M Label USA Alpharetta 1 1 The user may manually enter locations in the Label column Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc VER Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 22 of 28 8 Data Files PA Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Configuration f Mass Spec hatuments teel ruere Data Files Mass Spec Entries B Data File ere vi Z MSMTesting Folder01 Projects 44 050 ct200
10. 1 then AD 1 nDur Else AD 2 cAD Endif If Count 1 then nADur nDur Else nADur AD 2 AD 1 AD 1 AD 2 Endif AlInfo GetAdditionalInfo function Save data to memory Next Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 9 of 28 2 2 1 3 2 3 Thermo Data Not yet available 2 4 Waters Data Not yet available 2 2 1 2 2 Parameter A Yes In this logic the wiff file is evaluated to determine the number of samples in the wiff file If the number of samples is equal to 1 it is assumed that it is a single injection and that all the wiff files within a single directory are from the same sequence intR number of wiff files in a directory cAD acquisition date time of the one sample within the wiff file AD 1 acquisition date time AD 2 acquisition date time nDur duration of current sample as defined in data acquisition method DAM file in minutes nADur duration of current sample as defined by AD pAD in minutes AInfo Sample specific additional information For Count 1 to intR If Count 1 then AD 1 cAD Else AD 2 cAD Endif If Count 1 then nADur nDur Else nADur AD 2 AD 1 AD 1 AD 2 Endif AInfo GetAdditionalInfo function Save data to memory Next Database Writing Process After the Retrieve Data Proc
11. 5CacoN050828 CACO2 CCOO86 DOT wiff Monitor Polling Status Z MSMTesting Folder01 Projects 44 050 ct2005Caco D ata 050928_CACO2_CCO086_001 wiff Z MSMTesting Folder01 Projects 44 44 4444041014_Vinita_Humna_Batch02 7 Ethoxycoumarin_MRM_0O01 wiff Z MSMTesting Folder01 Projects 44 44 4444041014_Vinita_Rat_Batch01 7 Ethoxycoumarin_MRM_OO1 wiff Z MSMTesting Folder01 Projects AAAA AAA B atch incubation_2 wiff Z MSMTesting Folder01 Projects 4A NAA AAAND ataME2 48com human wiff Z MSMTesting Folder01 Projects A AA AAAD ata 3 24H 24R wiff Z MSMTesting Folder01 Projects 44 44 444 D ata 041014_Vinita_Humna_Batch02 7 E thoxycoumarin_MRM_001 wiff Z MSMT esting Folder01 Projects A4 44 444 D ataX20041020 R 58 wiff Z MSMTesting Folder01 Projects 44 44 4 44 D ataX28J UL Human mic32 wilf Z MSMTesting Folder01 Projects AA AA AAASD atas 28JUL Human microsomeSET1 Second time wiff Z MSMTesting Folder01 Projects A4 44 444 D ata 28JUL Human microsomeSE T1 wiff Z MSMTesting Folder01 Projects A4 A4 A44 D ataX28J LR at mic 32 wiff Z MSMTesting Folder01 Projects AA A4 A44 D ataX28JLILNRat microsomeSE T 1 wiff Z MSMTesting Folder01 Projects AA A4 AAA D ata 3_48 com H R wiff Z MSMTesting Folder01 Projects 44 44 A44 Data 48 cps H R wiff Z MSMTesting Folder01 Projects A4 44 444 D ata D ata wilf Z MSMTesting Folder01 Projects A4 44 444 D ata incubation_2 wiff Z MSMTesting Folder01 Projects A4 A4 444 D ata lS test wiff Z MSM
12. AdminUserManual_01 doc T RE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 18 of 28 6 Configuration Location Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Menu Gubbs Mass Spec Metrics Polling Application Edit Save Cancel Exit jeu Polling About Configuration Location Configuration Configuration Location Mass Spec Instruments Add Location Data Files Delete Locati Mass Spec Entries SSS View Logs Location Item Label Requirements gt Gubbs Georgia Country USA Monitor Polling Status Si Alph ite pharetta Building 1 Laboratory 1 Figure 12 Configuration Location Window Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 19 of 28 Users are allowed to assign locations to the individual instruments that are inventoried The definitions of the locations are configured in this window the contents of Item Column are configured in the Configuration Location Labels window see Section 5 2 6 1 Add Location Users may add a Location by clicking the Add Location button entering a Location Name then clicking the OK button New Location Name Enter a new Location Set Name Gubbs Germany Figure 13 Add Location dialog box 6 2 Delete Location Users may delete a location by selecting the row in the Location t
13. Manuals MSM_AdminUserManual_01 doc T RE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 12 of 28 3 3 3 4 3 5 3 2 2 3 2 3 One time event After a One time polling event is finished MSM stops and waits for further user input Scheduled event If the user chooses this option MSM will repeat the polling process at a frequency described by Automated Polling Frequency Configuration parameter see Section 5 1 2 When the polling event is active the Begin Polling button changes to a Quit Polling button Edit Save Cancel Exit Quit Figure5 Quit Polling button Clicking this button will cancel the scheduling process and will also kill any active polling event Once a polling event has finished continue with Polling Location configuration Configure Configuration Location Labels Configure the basic tree structure of the Location labels see Section 5 2 Configure Locations Configure the different locations of the mass spec instruments see Section 6 Assign Locations to newly recorded mass spec instruments After the polling event unique mass spec instruments are shown in the Mass Spec Entries window Assign locations to these mass spec instruments The data is now ready to be viewed by the MSM Viewer Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin U
14. SM Polling button The polling event will be canceled and no changes will be made to the database 12 3 Kill AnalystService Users may manually kill AnalystService by clicking the Kill Analyst Service button though it is not anticipated that this will ever be necessary 13 MSM Viewer To be published Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc
15. SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T RE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 17 of 28 5 3 Configuration Polling Locations The directory or directories defining the location of the raw data files to be polled are configured here Users add polling locations by clicking the Add Row button A dialog box is displayed that allows the user to browse to a local mapped or network directory Browse For Folder Select the directory in which you want search and drill For raw data Files Desktop 5j My Documents j Y My Computer ee Local Disk C Ge Data D 3 Audio CD F S Gubbs08 Data on GubbsO8 2 amp E Control Panel Bl ZEN Media Explorer a My Network Places l Recycle Bin C3 Adobe Reader 9 Installer v Om j Cancel Figure 11 Polling Location Add Row Browse for Folder dialog box To modify an existing Polling Location select the row and click the Browse button The Directory column in the Polling Location table by default is read only If the user wishes to manually modify or enter the contents of Directory column the user may check the Allow manual path entry checkbox however this is not recommended as the probability of manual path entry can be hig Users may define a label in the Label Column for each polling location Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_
16. SlInfo in1 Sample is empty Z MSMTesting Folder01 Projects 00006 2008051 5Prob D ata 080416_0088 080421_ 1040 PC80501 MST M pos wiff Sample 3 000002 Problem with thew Fa GetDABSInfo Sample is probably empty or corrupt ZAMSMTestingsFolderD1 Projects OO006 20090427Problems 090403 0009 030424 1600_PC80501_MST_M _pos wiff Sample 10 000003 Problem with theWFa GetDABSInfolin1 Sample is empty Z MSMTesting Folder01 Projects 00006420091 21 0_Problem 091120_0049 091208_ 0908 PC102488 PRM M pos wiff Sample 18 000004 Problem with thewFa GetDABSInfo Sample is probably empty or corrupt Z MSMTesting Folder01 Projects O0006 Andreas_ tTHep Data 04 A455 D6Ld SDF pos wiff Sample 10 000005 Problem with thewFa GetDABSlInfo Sample is probably empty or corrupt Z MSMTesting Folder01 Projects O0006 Andreas_ LTHepiDateND7 5455 BLd SDF pos wiff Sample 2 000006 Problem with thew Fa GetDABSInfo Sample is probably empty or corrupt Z MSMTesting Folder01 Projects O0006 Andreas_LTHep Data09 A455 OELd SDF pos wiff Sample 11 000007 Problem with theWFa GetDABSInfo in1 Sample is empty Z MSM Testing Folder01 Projects O0006 Andreas_LTHep Data 12 455 O BLd SDF _pos witt Sample 3 000008 Problem with the WFa GetDABSInfofin1 Sample is empty Z MSMTesting Folder01 Projects O0006 Andreas_LTHep Data 1 4 4455 OELd SDF pos wiff Sample 12 000009 Problem with the WFa GetDABSInfo Sample is probably empt
17. T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 1 of 28 Gubbs Mass Spec Metrics MSM MSM Polling Application 1 x and earlier MSM Viewer 1 x and earlier Supported Platforms Sciex amp Analyst M 1 3 1 1 5 x Administration and User 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 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 2 of 28 Table of Contents Section 1 OVER VIEW Gee 2 MSM USAGE NOTES 2 1 EDIT SAVE MODES 2 ees es esse esse ese De es ee ee Ee ees gs Gee Da ee ee es ee ee ea es ee ges De ee ee 2 2 AB ANALYST DATA EES ee es ese Ee EE es GEES Ee SEE ee Ge GE ee Ee Ee ee Ge DEE ee Sk oe Ee EG Ek 2 3 THERMO DATA N RR N EE ER EE EE N N Ei 2 4 WATERS DATA ie Es DERE o nEn Ee oe ee Ee oe Ee DEE Ge Ee ge Ee ee GO ee Oe GEES EE ee Ee ee ee be Ee 3 MSM PROCEDURE ies does es ees ese See Ge sl eend ogie De ee ee ee Ge co esee oe Se ee De Vae Ge oes ee ie see 3 1 CONFIGURE POLLING LOCATIONS ee ee ee ee ee ee ee ee ee ee RR RR EE RE ee Ee Ee ee ee ee ee ee ee ee ee Ee ee ee 3 2 BEGIN POLLING EE ESE EE Ee Ge GE GE EE Ee Ge GE EE Ee GE ies 33 CONFIGURE CONFIGURATION LOCATION LABELS
18. Testing Folder01 Projects A4 44 444 D ata Panos 20041020_RA_S9 wilf Z MSMTesting Folder01 Projects 4A A4 AAAND ata PracHT 48 cps H4R wiff ZAMSMT estinas Folder SProiecto dd4hd S44 NatasPracHTSHiiman mierasameSF T1 witt Figure 17 Data Files Window In this window the user may view the data files that have been inventoried 8 1 Filter for MS The user may filter the data file display by selecting choices from the Filter for MS dropdownbox To view all files polled choose Al Version 1 0 March 23 2010 CAGubbsIncAppsWSciexMetricsTool Administration Manuals MSM AdminUserManual 01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 23 of 28 Note When MSM polls the data files it sometimes happens that no information can be retrieved from the data file In this instance MSM assigns the data file to an imaginary mass spec instrument of serial number 999999 Though no data has been stored for the data file it is recorded here so that MSM doesn t unnecessarily attempt to poll it again in the next polling event gt mcm ZAMSMTestingkFoldero1 MS00002 012650311 MS00003_M0630208 Ms00004_B 4160109 ZAMSMTestingkFolder04MSO00DOS v1430304 MSO00006_ 2449903 Z MSMTesting Folder04 Projects E xample SD ata Data Files Numberoffiles 6510 Filter for MS HS sa e Num Figure 18 MS 999999 Version 1 0 March 23 2010 C Gu
19. able and clicking the Delete button 6 3 Configure the location Once a location has been added the user must configure the Location Configuration Add Location Delete Location Location Item Label Gubbs Georgia Country Germany gt Gubbs Germany Site Biberach Building AS Laboratory Lab A Figure 14 Configuration of a location Note The configuration of a location may be edited at any time Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 20 of 28 7 Mass Spec Instruments PA Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Menu Gubbs Mass Spec Metrics Polling Application Edit Save cancer Exit od About Connguraton MS Instruments Deactivate MS Locations Apply Location Configuration Location ESE SES Number of Instruments Show Active zi Activate MS Location Fi Data Files Mass Spec Entries View Logs i SEES Description Status Vendor ere mr 1 mmy ABI Monitor Polling Status 00002 D12650311 MS00002 AB 00003 M0630208 MS00003 AB 00004 B 4160109 MS00004 AB 00005 V1490304 MS00005 AB 00006 2449903 MS00006 AB 00007 MS00007 AB 00008 MOOBOTOTPT MSO0008 AB 00009 u01870405 MS00009 AB 00010 vO4820405 MS00010 AB 00011 33080204 MS00011 AB 00012 4419812 MS00012 AB 00013 AG20700706 MS00013 AB
20. bbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc VER Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 24 of 28 9 Mass Spec Entries PA Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 EE Configuration Configuration Location CTS Mass Spec Instruments MSOO0001 1 SMTesting 41020 R S 9 Start Sample S Monitor Polling Status October 20 2004 04 21 15 PM ZAMSMTesting 20041020 R S October 20 2004 04 30 21 PM ZAMSMTesting 20041020 R S 9 1 Start Sample Ducha 2 204 0550 53 PH ZuSWrea GNMEORAS S112 Slat Sones August 01 2004 11 55 33 4M Human mic32 wiff 10 Start Sample Star August 01 2004 12 15 47 PM s ing Human mic32 wiff August 01 2004 12 25 52 PM ing Human mic32 wiff 10 08 August 01 2004 01 06 03 PM 5 Human mic32 wiff 10 05 Start Sample Star August 01 2004 01 16 06 PM ing Human mic32 wiff 10 05 Start Sample Star August 01 2004 01 26 09 PM d ing Human mic32 wiff 10 05 Start Sample Star August 01 2004 01 36 12 PM 10 y ings Human mic32 wiff 10 05 Start Sample Star August 01 2004 01 56 18PM_ 12 ing Human mic32 wilf August 01 2004 02 16 24 PM 14 ing Human mic32 wiff 10 05 Start Sample Star August 01 2004 02 26 30 PM 15 ing Human mic32 wiff 10 1 Start Sample Star August 01 2004 02 36 36 PM 16 5 ing Human mic32 wiff Start Sam
21. cated in the polling location Note Because of reliability issues with the AB dll s the number of files that can be inventoried at once is limited to 100 MSM sets up a For Next loop to evaluate each file in the array of files The file is inventoried if it meets the following criteria o The file has not been inventoried previously MSM checks for the file and path information recorded in the database table TBLDATAFILE o The file creation date is greater than the date defined in the Cut Off Date parameter of the Configuration window The following file specific information is gathered generated and recorded in TBLDATAFILE o The size of the file in Mb o The creation date of the file o The date on which this database record was created o The sample number from which file creation date was retrieved The number of samples contained in the wiff file o File specific Additional Information described in Section 1 O Mass spec instrument serial numbers are then retrieved from the raw data files Because of reliability issues of the AB dll s MSM retrieves and stores the mass spec instrument serial number from the raw data files in a separate For Next loop 2212 RetrieveData Process After the FindFile process is complete MSM continues to the RetrieveData process in which the newly polled raw files are inventoried for the following information The acquisition date of each sample in the wiff file The sample inde
22. d Ee ses PRERE ED Ed ese EER Red el VOS be ees E ee eek EE EEUU Ge EUR gee Oe EO RS Ede GE AREE Te ed eis 11 IPOLEING HAS ooN le OR OE EE EN EN OE RE N EE EG 11 QUIT POLLING BUTTON AR RE OR EE OE IE OO EE eects 12 MSM MINIMIZE TO SYSTEM TRAY MENU ITEM esse se se ee ee ee ee ee ee se ee ee ee ee ee ee ee ee ee s ee ee Re ee ee ee ee Re Re ee dessen ee Re ee ee ee 13 MSM MINIMIZED TO SYSTEM TRA iss sesse Be see Ed E E ee OS Does e ese EIER ERE EEUU Ge ee be ees Oe Gee geed ee GE GE Nee eed eis 13 CONFIGURATION WINDOW GLOBAL WINDOW se se ees ee ee ee ee ee ee ee ee ee ER ee AR ee ee ee ee ER Re nnde seen ee Re snas seen 14 POLLING CHOICE WINDOW DA ER 15 CONFIGURATION WINDOW LOCATION LABELS se se ees ee ee ee ee ee ee ee ee ee ER ee ee ee ee ee Re ee ee ee RR Re ee ee ee ee Re Re ee ee 16 POLLING LOCATION ADD ROW BROWSE FOR FOLDER DIALOG BOX iese ede esse ee se ee ee ee ee ee ee ee ee ge ee ee ee ee ee Re nnn seen 17 CONFIGURATION LOCATION WINDOW ee ee ee ee se ee ee ee ee ee ER Re Re ee ee ER ER Re Re ee ee ER ER Re Re ee sese sette assess eret terea ee ee nnne 18 ADD LOCATION DIALOG BOX se Ee bebe ee Ne SG lent ee ve GER Gee De He AE GER Ee ke eg ee Ge Ge ce Eee GE De SEU Es EP 19 CONFIGURATION OF A LOCATION sccscsccccecssssssececececsesseaeeecececsesenaeseceeecsessuaeaececsceesenaeaesececseseseaaeseeseecsenseaeeeeeeeens 19 MASS SPEC INSTRUMENTS WINDOW ese sees ne che eue
23. dere ep eye aee Qe De de Ede i vue ee y cue e ie Ne b tbe ve ciet 20 APPLY LOCATION yaoi a HHL c EE Eg 21 DATA FILES WINDOW EE a E e eg ee Cas de ke beiden 22 UNE EE EE E E E N 23 MASS SPEC ENTRIES WINDOW esse onn E EE dee a ede tre beo cue e Be SE be GER Ge 24 VIEW LOGS WINDOW 3 eite e Eee Se ee ir i ERN Hebe bae due bu n Eee e e a ree ee eun di Ve E UE Re Es eave 25 REQUIREMENTS WINDOW Se tette eed a pae ducks tue due eue dre e eee tee aua c ae Sabb d Re b ue 26 MONITOR POLLING STATUS WINDOW i e reses tr eoe teret dieto Ve eg see e He Ge Re Ea e e veo eese od ae Pe die ve be Ebo o cues 27 Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 4 of 28 1 Overview MSM uses the native data acquisition software dll s supplied by the vendor e g AB Thermo Waters whose use is defined the respective vendor software development kit SDK documentation At this moment AB is the only vendor supported Data is stored in a database The currently supported databases are Microsoft MS Access MS SQL Server and Oracle Data retrieved and stored by MSM is then viewed using a separate application from Gubbs Inc called MSM Viewer MSM Viewer is a MS Visual Studio Tools for Office VSTO Excel application MSM uses the dll s to open raw data files and extract at a minimum Acquisiti
24. e Cut off Date Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T RE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 15 of 28 5 12 Automated Polling Frequency hours When the Begin Polling button is clicked the user has a choice to perform a One time event or a Scheduled event If a Schedule event is performed a Polling Event will be performed at the frequency defined in the Automated Polling Frequency parameter PA Polling choice Do you wish to perform a one time polling event or activate a polling schedule that polls at a frequency defined in the Configuration window Please note that all Edit and Exit functions will be disabled while the schedule is active To enable Edit and Exit functions simply Quit the polling action Select a choice One time event Scheduled event Cancel Figure9 Polling Choice window 5 1 3 Use logic that allows for one injection wiff acquisition For AB data only AB Analyst allows users to acguire data in two different manners Acquire data from all injections defined in a sequence into a single wiff file Acquire data from each injection defined in a sequence into individual wiff files See Sections 2 2 1 2 1 and 2 2 1 2 2 for a description of the effect of this parameter Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T
25. ess has been completed then all information stored in memory is written to the database If a new mass spec instrument serial number is detected a new database table is created for it Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 10 of 28 3 MSM Procedure The following is general outline of events for executing MSM though the user is not restricted to this order of events 3 1 Configure Polling Locations The user must configure at least one polling location see Section 5 3 3 2 Begin Polling A polling event is executed by clicking the Begin Polling button The user will be prompted to choose a polling event type d Polling choice Do you wish to perform a one time polling event or activate a polling schedule that polls at a frequency defined in the Configuration window Please note that all Edit and Exit functions will be disabled while the schedule is active To enable Edit and Exit functions simply Quit the polling action Select a choice One time event C Scheduled event Cancel Figure2 Polling Choice window Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 11 of 28 3 2 1 First time polling 3 2 1 1 AB data The MSM polling
26. ing Responding MemSize 24 646 LastPolling Date March 23 2010 04 59 52 AM Log Item Polling_20100323_045952_000001 Next Polling Date Kill AnalystService Events 1 Memory Usage AnalystService killed 3 23 2010 5 01 17 4M Figure 22 Monitor Polling Status Window This window is used to monitor the status of an active polling session It sometimes happens that the polling action will stop responding because of a communication error between the MSM and the raw data file When this happens the memory usage of the polling action becomes static MSM monitors this memory usage If the polling action memory usage hasn t changed within 35 seconds 7 items in the Memory Usage listbox then MSM will kill a service called AnalystService exe and log the event in the Kill AnalystService Events listbox Killing AnalystService frees the communication error between MSM and the raw data file After AnalystService is killed MSM starts it again and continues the polling action 12 1 Check Status Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 28 of 28 Though this window reports the status of the polling event every 5 seconds the user may manually check the status by clicking the Check Status button 12 2 Kill MSM Polling If the user wishes to stop the polling event for some reason he she may click the Kill M
27. ion M401402 B4T0301 M3L1415 B3T0300 Component Name Triple Quadrupole LC MS MS Mass Spectrometer Component ID API 3000 Manufacturer AB Sciex Instruments Model 10096654 Serial Number D1265031 1 The following is an example of additional sample specific information retrieved from AB data Start Sample Start Periods NumberofPeriods 1 Start Period 1 Start Experiments NumberofExperiments 1 Start Experiment 1 Scan Type 4 MRM Polarity 0 Positive Scan Mode 1 Zero Width Scan Resolution O1 1 UnitResolution Q3 0 Low MCA 0 No Step Size 0 0 0000 amu End Experiment 1 End Period 1 End Sample Start Sample Start Periods NumberofPeriods 1 Start Period 1 Start Experiments NumberofExperiments 1 Start Experiment 1 Scan Type 4 MRM Polarity 0 Positive Scan Mode 1 Zero Width Scan Resolution Q1 1 Unit Resolution Q3 0 Low MCA 0 No Step Size 0 0 0000 amu End Experiment 1 End Period 1 End Sample Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 5 of 28 The MSM Viewer as published by Gubbs displays only mass spec instrument usage Customers may contract with Gubbs Inc to write custom applications to mine the additional information retrieved and stored by MSM 2 MSM Usage Notes 2 1 2 2 Edit Save Modes If users wish to make any changes to parameters within MSM he she must first place MSM in Edit mode by clicking
28. ling 20100321 021808 Q00001 Polling 20100321 021804 O00001 Polling 20100321 015408 Q00001 Polling 20100321 015404 D00001 Polling 20100321 013008 Q00001 Polling 20100321 013004 000001 Polling 20100321 010608 000001 Polling 20100321 010604 D00001 Polling 20100321 004216 Q00001 Polling 20100321 004211 000001 Polling 20100321 004208 000001 Polling 20100321 001804 D00001 Polling 20100320 235408 000001 Polling 20100320 235404 000001 Polling 20100320 233008 000001 Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc Iver Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 26 of 28 11 Requirements Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Menu Gubbs Mass Spec Metrics Polling Application Edit Save Cancel Exit eed About Configuration Configuration Location Mass Spec Instruments Data Files Mass Spec Entries View Logs Requirements Monitor Polling Status Requirements SYSTEM REQUIREMENTS Listed below are the components that must be installed on this workstation in order for MSM to operate properly For ABI Analyst data AB Analyst AB Analyst must be installed on this workstation server Note Analyst backwards and forward compatability rules apply For example if the latest Analyst version used to acquire wiff files in a data location is Analyst 1 5 then Analyst 1 5 MUST be installed on this MSM workstation
29. o completely inventory all files in the slk polling directory Polling 20100323 055646 000001 Polling 20100323 055642 000001 nnaniri erceria ERNEUT Figure3 Polling has not finished o If the 6 item reads Polling action completely inventoried then the Polling Location has been completely polled and the Scheduled Polling Event may be canceled by clicking the Quit Polling button Configuration View Logs Configuration Location Copy to Include logs after Saturday March 13 2010 Mass Spec Instruments Clipboard Select Log yyyymmdd hhmmss Polling event began 3 23 2010 10 08 28 AM Polling 20100323 100828 000001 Polling event ended 3 23 2010 10 08 29 AM Polling 20100323 100825 D00001 Number of new data files inventoried scroll down to Inventoried Data Files section 0 Polling 20100323 100333 000001 Data Files Mass Spec Entries Requirements Number of new mass spec instruments found 0 Poling 20100323 100330 000001 Monitor Polling Status Number of problems experienced 0 in 0 data extraction events i 3 051440 OD0001 Polling action completely inventoried all non polled files in the polling directory Polling 20100323 061435 000001 Polling 20100323 055646 000001 PROBLEM SECTION problems observed 0 in this polling event Polling 20100323 055642 000001 Figure4 Polling has finished Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration
30. on date Mass spec instrument serial number The intent of the MSM MSM Viewer suite is to allow managers to plot actual mass spec usage in order to make such decisions as instrument usage instrument allocation instrument decommissioning and new instrument purchase Additional acquisition event specific and sample specific information may be extracted from the raw data and is somewhat vendor specific The additional data is stored as a large string within the database For example the following is an example of additional acquisition event specific information retrieved from AB data Pump Agilent 1100 G1312A 0 binary pump Firmware Version A 04 11 Serial Number DE23912037 Mass Spectrometer QTrap 0 Qtrap Config Table Ver 03 Firmware Ver M401400 B4T0301 M3L1408 B3T0300 Component Name QTrap Linear lon Trap LC MS MS Mass Spectrometer Component ID QTrap Manufacturer AB Sciex Instruments Model 027170 A S N M0630208 Valve Valco 2 Position 0 ver S N I PD APX88RD Integrated System Shimadzu Controller CBM20A Serial L20234350424 ROM Version 1 06 Pressure Units psi Pump Shimadzu LC20AD Serial L20104450801 ROM Version 1 07 Pump Shimadzu LC20AD Serial L20104450798 ROM Version 1 07 AutoSampler Shimadzu SIL20AC Serial L20174450168 ROM Version 1 04 Column Oven Shimadzu CTO20A Serial L20204450179 ROM Version 1 06 Injection Volume used 10 00 ul Mass Spectrometer API 3000 0 Config Table Version 00 Firmware Vers
31. ple Star July 23 2004 03 18 41 PM 1 Z MSMTesting Human microsom 10 Start Sample Star fi d Figure 19 Mass Spec Entries Window Users may view the individual injection entries and data in this window Users may filter for each individual instrument In addition users may copy the information to the clipboard by clicking the Copy button Version 1 0 March 23 2010 CAGubbsIncAppsWSciexMetricsTool Administration Manuals MSM AdminUserManual 01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 25 of 28 10 View Logs 2A Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Menu Gubbs Mass Spec Metrics Polling Application Begin About Polling View Logs Copy to Configuration Configuration Location Include logs after Friday March 12 2010 Mass Spec Instruments Data Files Mass Spec Entries Clipboard Polling event began 3 21 2010 3 54 08 AM Polling event ended 3 21 2010 4 09 00 AM Number of new data files inventoried scroll down to Inventoried Data Files section 100 Number of new mass spec instruments found 0 Number of problems experienced 40 in 6 260 data extraction events Polling limit of 100 files was reached Polling action must be repeated to completely inventory all files in the polling directory PROBLEM SECTION problems observed 40 in this polling event 000001 Problem with thewWFa GetDAB
32. ser Manual Page 13 of 28 4 MSM Service MSM may be run as a service in which MSM is minimized to an icon in the system tray by choosing from the menu Menu Minimize to System Tray PA Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Menu Polling Application Figure 6 MSM Minimize to System Tray menu item Figure 7 MSM minimized to system tray Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 14 of 28 5 MSM Features Configuration 5 1 Configuration Global The Global Configuration window is used to configure the following parameters PA Gubbs Mass Spec Metrics MSM Polling Application v1 0 9 0 Menu Gubbs Mass Spec Metrics Polling Application Edit BN E ER Per About Configuration Confiquration Configuration Location Configuration Type Global Md Mass Spec Instruments Data Files Mass Spec Entries View Logs b Automated Polling Frequency hours Requirements Monitor Polling Status Parameter Setting Cut off Date 1 1 2000 Use logic that allows for one injectionZ wif acquisition Polling Locations Add Row Delete Row Browse Allow manual path entry Label Directory EET Figure 8 Configuration Window Global Window 5 1 1 Cut off Date MSM will ignore and not record any file that is older than th
33. u ee EE GR Re ee GE ee ee ee E Re be ee ee De Re Ee ee ge eb ee ie 9 MASS SPEC ENTRIES sissies 10 VIEW ELOGS oes EE A gede seed EE di se re ek se de Gee soog ede de de dee Ee oe se ee de eek do deed P 11 RE QUEREMEN ME EG c Rd 12 MONITOR POLLING STATUS see ee see se ee Ge Ge ee Ge Ge ses e Ge Ge Ge Ge ee ee Ge Ge ee ee ee 12 1 CHECK STATUS EE ENE EE EE EE eise iens niii ses 12 2 KALE MSMPOLLING EE EE ER oe ESE GE GE ER GE EG E E ee sies 12 3 KIEL ANALYSTSERVICE 2 2 EER De oed e Ee te GE e Se EE Ge Eo ee 13 MSM VIEWER sisie seed sees e dee vee ed es sog se bede ed esse ees de ode eeue Wee doe dee boeie Ge de Fe en Page Number Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 3 of 28 Table of Contents Section Page Number Figure FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU FIGU RE 1 RE2 RE3 RE4 RE5 RE6 RE7 RES REO RE 10 RE 11 RE 12 RE 13 RE 14 RE 15 RE 16 RE 17 RE 18 RE 19 RE 20 RE 21 RE 22 Table of Figures Page Number EXAMPLE OF RAW FILE DATA RETRIEVAL ERROR MESSAGE BOX ees ese ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee 6 POLLING CHOICE AI EA ER N EE KO OE ON ER OR EG 10 POLLING HAS NOT EINISHED 5 3 e
34. x of the sample within the sequence The path of the raw data file The filename of the raw data file Actual duration time of the sample Sample specific Additional Information as described in Section 1 Actual duration time is determined in such a way that autosampler preparation times between sample injections are accounted for so that total mass spec instrument time is recorded The logic for determining actual duration is dependent on the Configuration Global parameter Use logic that allows for one injection wiff acquisition herein referred to as Parameter A The default setting for this parameter is No The following is a description of how the logic is defined for this parameter Version 1 0 March 23 2010 C GubbsIncApps SciexMetricsTool Administration Manuals MSM_AdminUserManual_01 doc T VRE Gubbs Mass Spec Metrics 1 x x Admin User Manual Page 8 of 28 2 2 1 2 1 Parameter A No In this logic each wiff file is considered a separate sequence that can include one or more injections samples intR number of samples in sequence cAD acquisition date time of current sample AD 1 acquisition date time AD 2 acquisition date time nDur duration of current sample as defined in data acquisition method DAM file in minutes nADur duration of current sample as defined by AD pAD in minutes Alnfo Sample specific additional information For Count 1 to intR If Count
35. y or corrupt Z MSM Testing Folder01 Projects O0006 Andreas_LTHep Data 1 7 A455 BLd SDF pos wift Sample 2 000010 Problem with thew Fa GetDABSInfo Sample is probably empty or corrupt Z MSM Testing Folder01 Projects O0006 Andreas_LTHep Data 19 455 BLd SDF pos wiff Sample 12 ANNAN Problem with the wFa RetN amp RSInfn amp amnle is nrohahliiemnhi ar earrint Requirements Monitor Polling Status Figure 20 View Logs Window A log entry is entered for each of the following events Start a polling event Finish a polling event Kill a polling event Users may shorten the Select Log list by choosing a date from the Include logs after date dropdownbox Select Log yyyymmdd hhmmss Polling_20100321_072707_000001 Polling_20100321_070608_000001 Polling_20100321_070604_000001 Polling_20100321_064208_000001 Polling_20100321_064204_000001 Polling_20100321_061808_000001 Polling_20100321_061804_000001 Polling_20100321_055408_000001 Polling_20100321_055404_000001 Polling_20100321_053008_000001 Polling_20100321_053004_000001 Polling 20100321 Polling 20100321 050604 D00001 Polling 20100321 044208 Q00001 Polling 20100321 044204 000001 Polling 20100321 041808 00001 ing 20100321 041804 000001 ing 20100321 035408 000001 Polling 20100321 035404 000001 Polling 20100321 033008 00001 Polling 20100321 033004 D00001 Polling 20100321 030609 Q00001 Polling 20100321 Polling 20100321 E Polling 20100321 024204 D00001 Pol
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