Mascot Daemon マニュアル
Contents
1.2. Ex ne Pause Resume Running task Follow up task Trying to pause a running task Completed task Cancelled task Paused task C1one Del1ete Aascot Daemon vV2 2 27 C1one
3. File PP Status Task Database v 1 Simple test search Data file C Program Fileshdatrix ScienceNkMascnt DaemondataLC No enzyme follower Search title Submitted from Trypsin first pass search by Mascot Daemal 3 Trpsin first pass sean Accession HBB_HUMAN LCO Prolein Mw 15989 LEH_Digestn3 0321 4C fT a Score 7D 4 Me of Trypsin first pt Description Hemoglobin subunit beta Homo sapiens Human 9 12 pmf Database SwissProt_54 0 fasta 7 0 mie Hesult file URL http ZIlocalhos mascol cqi master_results pl fil 4 15 on smle at smile Search suhmitted 20H7 3 14 03 38 nf 17 fle on smle MD on s Search completed 2007 410 403 14 10 02 Hf 19 on smile at smile 20 real ime monitor 21 real time monitor 22 real ime manitar 23 real me monitor 2 24 14132 falder1 25 14192 falder1 1 Hf 26 Copy of 14192 faldei Hf 27 14192 folder1 2nd Refresh Fl
4. Options LOK 1 Mascot Distiller Mascot Daemon PC TWO Mascot Distiller wwwel Dua Egot Wavea De es Wax SoenceMascot egNaToep Em saeas Dala Fie Foma Options Mascot Disti11er Maex Mossl ye SON 6 eee ee ll Processing Options opt Output PMF Masses as Oupu MS4S Fragmerts as Distmer Peoiect Fie myz MHz Me myz MHe CM Save Data File Format
5. Aascot Daemon v2 2 31 0K Mascot Daemon Preferences Save PC Mascot Daemon RAR Eg Np oe gt Pause Resume elete Clone I UNC Universal Naming Conversion path to TaskDB mdb 5 3 Stop Masses PMF i i Stop Mass Oe Stop Mass Mascot Daemon C Program Files Matrix Science
6. 2 Parameter Editor 3 7 Enzyme Trypsin Data format Sequest DTA Save As tour2 par 3 7 EL Fhascot Daemon File Edit Help ag Farameter set Tryps h Filename C Program FilestMalris Scien Mtour3 par New Dpen Save Save as none tour2 Dar Ser name IM tk k ser emmal lk ku Gmalriwsci i ascot kensaku ensaku Qmalrissciehce ID toUr3 par Search te Submited from lt taskname gt by Mascot Daemon on lt localhosb SESE Fieport top amp UTO rl hits 9 DTA Taxonomy Database SwissProt Enzyme Trypsin ER 5 Fised amp cetyl K Acetyl K ariahle Decoy database
7. About Mascot Daemon 4 2 Preferences Preferences Windows Preferences Mascot Daemon Internet Mascot Server URL scnt DaErmnrii PrETErEnCES Me Mascot Server Ms me lpas Import filters ADO connection Timer settings Mascot logn warning Mascot seryer URL up to ad including cgi directory e g http dAyour_ server mascot cgir Mascot Server URL http Alocahost mascot cgiy U1B liqiqu u Web
8. Event Log Search results discarded score is less than 61 specified threshold Repeat at interval of Pass data to Aascot Daemon v2 2 26 4 5 Event Log Event Log Mascot Daemon warning error Mascot Daemon
9. External processesl Mascot Daemon External processes 1 Before starting task 2 Before each search 3 After each search 4 After completing task Wait for completion hung Event Log Task Halt on error
10. NCBInr 6 AAascot Daemon v2 2 11 4 4 1 File 4 Parameter Editor Parameter Editor EE E iti ET rrTelal File Edit Help Task Edior Parameter Editor Parameter set Filename C Program Fileshd atriw Scie default par i i Save Gave As New Open Save Save As 1 Print Status
11. http www matrixscience com distiller html 2 Applied Biosystems MDS Sciex Analyst Analyst PC Mascot Daenon Analyst mascot d11 WIFF 3 Applied Biosystems Data Explorer Data Explorer PC Mascot Daenon Data Explorer DAT Mascot Daemon vV2 2 1 4 Thermo Fisher Scientific Xcalibur BioWorks 1cq_dta exe extract_msn exe PC Mascot Daemon RAW 5 Waters MassLynx MassLynx sample list sample list PKL 6 Applied Biosystems 4000 TS2Mascot GPS Explorer
12. Nw Fe Schedule Start now Start at ASCII ia Add Files CS YY Windows Data file list amp o w Delete Add Files 4 4 a W1indows 0 Merge MS MS fles to single search 32 000 Windows Aascot Daemon v2 2 22 Data file 1ist De1ete
13. TIf probabi1ity that match is random gt 1 in 0 051 20 20 Pass data to No enzyme fo11ower 3 9 Fi hascot Daemon File Edit Help Task Editor Task Trypsin first pass search New Run Parameter set Data import filter liix SciehcekMascat Daeman taur2 par Nane 1 Data file list Schedule Draa and drop data files into the area Start now below or click on amp dd Start at a UIIZU monNdataNLC_DigestD3 048E 0432 2 dta FeaHime monitor mondataLCO_ Digest03 0921 0924 2 dta Follow up Search priority In actions Auto print results Esternal processes Pass da ta to Follow up p if probability that match is random gt 1 in gt 20 2 Discard results S 2 No enzZyme follower lt Delete IF Add Files Hepeatatintervasof lt Merqe MS M5S files into single search lv
14. 0 Modifications Shift Ctrl1 PC Fixed modifications Variable modifications 9 Mascot Fixed modifications Variable modificat
15. 3 Mascot Daemon Service 4 5 Mascot Daemon Failed to start Mascot Daemon Service OK Choose Ignore to run the Mascot Daemon service component on the desktop ETErrlmll Lnahle to start the Mascnt Daemon Seryice hoose Abort to to exit Mascot Daeman 6 Chaose Retry to yerify Task datahase caonnectinn string and try again Choose hnore to run the Mascot Daemon seryice component on the desktap mwe mewo 2 Mascot Daemon OLEDB SQL Server MySQL Oracle C Program Files Matrix Science Mascot Daemon
16. 2 1 a lk a a 2 2 External Processes Prafile 1 Pe 6 DPI PC 2
17. Save defau1t par Save As AII Searches PMF MIS User name User email Mascot lt mascot_user_name gt lt mascot_user_full_name gt lt mascot_user_email gt Search title Search title lt mascot_user_ gt id name full name email Mascot
18. 2 Mascot Daemon Service 5 FE 5 H Mascnt Daemon Service Rs Matrix Science Mascot S 5 Messenger MS Saftwiare Shadaw Cop EL a Net Logon IN a NetMeeting Remote Desk E Rs Network Connections KO Network DDE a Netwaork DDE DSDM Dynamic F y Network Location Awaren R mW Mascot Daemorrs 3 4
19. Tryptic peptide 3 10 PE Mascot Daemaon I File Edit Help Eyent Ln Farameter Editor Parameter Task Editor Status Task Database Hf 1 Simple test search Dala file C Program Files Malix Sciencetklascot Daemon dala L 1 lt No enzyme follower Search title Suhmitted from Trypsin first pass search by Mascot Daemoi LCH_DigesU3 0321 08 Accession SIABF_HUMAN vr Trypsin first pass search Protein Mw n LCH_DigestU3 048E H4 EE no a LL Digest03 0921 09 en Database SwissProt 54 0 fasta Result ils URL http 7localhost mascot cgifmaster_results pl fil Search submitted 2007 7 10 403 1410 14 FAFA NI Wh Peptide Summary Report Submitted from No enzyme follomer by Mascot Daer FE E A iQ Oro D http localhost mascot ceifmaster_results plfile 2Fdata 2F20071 003 CFF002648dat amp REPTYPE peptide8_sigttresho 4 Search completed inn snkD NicrosoftilterrnetiExplorer on Number of Hits a 30 40 5 Probability Based Mowse Score 20 Riefresh Fl Peptide S
20. 0 Mascot Daemon v2 2 3 5 Mascot Mascot Daemon Mascot Daemon Mascot Server Preferences Internet ascot ae mnrii PrETETEhCES 3 was ba import fiters AD connection Timer settings Mascot login URL P http mascot cgi EE HTTF timeout seconds 360d 2 HTTF access type Registry default HTTF proxy serwer HTTF pratacal HTTP A 0D HTTPA1 1 Mascot Server URL http mascot cgi Save Mascot Server Mascot Daemon Task Edior Status Task Parameter set R
21. Mascot lt taskname gt lt parameters gt 1ocalhost gt PC lt 1ocaluser gt Windows lt datafilename gt lt datafilepath gt lt cachedpeaklist gt lt samplenumber gt lt mascot_user_id gt ID NK Mascot Daemon v2 2 16 lt mascot_user_name gt lt mascot_user_full_name gt lt mascot_user_email gt Taxon
22. D Data Proteins QTof Default pro Data TTypsin234 raw Specify path to root folder D Data Proteins QTof pro Data Optiona wild card file or name raw Specify path to root folder D Data Proteins QTof pro Data Optional wild card file or name D DataYProteins QTofY proYData Y Y Aascot Daemon v2 2 23 Include sub folders Specify path to root folder Schedule Follow up lascotDaemon File Edit Help DZ a lumited Parameter set Data import fiter ENProgram Files Maliis Scie
23. Jet 4 0 Microsoft Access 20000 AD Connection string Provider Microsoft Jet DLEDE 4 0 Data Source C Program Fileshd atris TaskDB mdb lt Sciencehlascot Daemon TaskDE mdb Mode Headlwyritel5hare Deny Nane Persist Securit Info Fal TaskDB a nne Persist Security Info False Restore defaultl TaskDB mdb Restore defaut Change ADO connection string ADO Change se coe Timer settings Mascot Daemon 0 PC Intranet Data mport fiters ADO connectio Timer tick interval between 1 and 60 se
24. Exit Mascot Daemon GUI Mascot Daemon Service MRU Most Recently Used Edit 4 Parameter Editor Task Editor Cut LCopy Paste Cl1ear Preferences Preferences ODBC Information Aascot Daemon v2 2 12 ODBC connection Refresh Status Help Mascot Daemon Help Register Mascot Distiller Mascot Distiller Mascot Daemon
25. Minimum delay between monitor searches 60 10 Minimum delay between follower searches 60 60 Take action polling interva Mascot Daemon Service TaskDB mdb 15 10 Mascot login Mascot Server
26. 2 SQL Enterprise Manager Mascot Daemon 3 MS SQLS qrt Microsoft Query Mascot Daemon MS SQLS qrt Mascot Server CD Microsoft Query Office SQL Server MySQL Mascot Server CD mySQL txt Mascot Daemon 52 C mysql b1in gt mysql exe lt D SQL mySQL txt Mascot Daemon Oracle Oracle Masc
27. Repeat at intervals of Pass data to 1 2 NCBInr dbBST Discard results Status
28. MS MS tol 1 mmu mil1i mass units 0 001Da 2 Da Instrument http mascot help search_field_help html INSTRUMENT CV 4 4 Task Editor TD scot Daemon File Edit Help Task Untitled 4 ce Nane Status Event Log Js C sma Fm a ID 3 A ei Data file 1ist No folow up required
29. Mascot Mascot Daemon 4 3 Mascot Daemon 3 2 Parameter Editor 3 1 par Mascot Daemon default par Mascot Server Parameter Editor Mascot Server 3 1 Save As tourl par 3 1 Parameter Editor
30. Task Status Event Log Search title Status Clone Copy of New Run l Parameter set Parameter Editor Mascot Daemon Data import filter Mascot
31. 2 1 Mascot Daemon Windows 2000 Windows XP Professiona1 Windows Server 2003 Windows Vista Business U1timate Mascot Daemon HTTP Mascot Server Mascot Server http www matrixscience com cg1 C Microsoft Internet Explorer Mascot Daemon 2 2 Mascot Daemon Mascot Server Mascot Server Mascot Daemon 1 Mascot Daemon PC Mascot Mascot Server Mascot Server Mascot Daenon 2 Mascot Server
32. No enzyme fo11ower 3 8 Ea Fi hascot Daemon File Edit Help Task Editar No enzyme follower Task 0 ehnzurme ollower N ll tour3 par Follow up Parameler set Data import filter lt lix SciencetkMlascant Daemontour3 par v i Run Dala file list amp fallow up ask does not haye a Start now pre defined list of data files It runs Start at 55 11 III2I continuously waiting to receive data from other tasks Realtime monitor Follow up Search priority In actions Auto print results External processes Follow up No follow up required Task Editor 3 9 Trypsin first pass search tour2 par LCQ_Digest03 0486 0492 2 dta LCQ_Digest03 0921 0924 2 dta C Program Files Matrix Science Mascot Daemon data
33. None Trypsin None semilrypsin SemiTrypsin Trypsin None K R C K R P N C N None CNBr Variable modifications Met gt Hs1 Homoserine lactone Met gt Hse Homoserin Max Missed Cleavages 1 2
34. Specify path to root folder IStatus Pause Delete 1 Specify path to root folder D Data P Q 200311 D Data Proteins QStar 20031102 D Data Peptides QTrap 20031103 Optional wild card file or name wiff D Data Proteins QStar 20031102 TTypsin234 wiff
35. Externa1 processes Mascot Daemon Service MMseet Daemon Service External processes Aascot Daemon v2 2 24 lt taskname gt lt parameters gt lt localhost gt loealltleet2 9 lt datafilename gt lt datafilepath gt NK cachedpeaklist gt data import filter lt samplenumber gt lt mascot_user_id gt Mascot ID lt mascot_user_name gt Mascot lt mascot_user full name gt Mascot lt mascot_user_email gt Mascot lt resultur gt URL lt resultfilename gt lt resultfilepa
36. 1 3 Mascot Server Mascot Daemon PC Mascot Daemon PC Mascot Daenon 1 4 MGF MGF Mascot Distiller Mascot Raw External processes Mascot Mascot Daemon v2 2 2 2
37. Intranet Data import fiters AD connection Timer seting Mascot login Save Mascotusername sam vo 60 Task Editor 0wner Rd Web Internet Mascot Server URL Save Cancel My hebp 90 mascot cgi Aascot Daemon v2 2 15 4 3 Parameter Editor File Edit Hab Task Editor Parameter 1 ema Takesa Euaneter Eo Parameter set Se t 2 Ma scot Da emon Filename C Program Fileshdatrix Scie default par New Save Save As
38. Status Completed AAascot Daemon vV2 2 8 Paused 3 6 Completed Task File Edit Help Paused Task Statung Mascot Server Mascot Daemon TaskDB mdb Mascot Server 22 5 PD EE Mascot search 1og ce IPgUS61 Rs ICOWel 0 Cancel Delete Mascot Daemon
39. net PC usami is starting has finished C temp links txt URL simple vbs 2 NN MA Mascot Daemons Externalprocesses Before starting task net send usami lt taskname gt is starting Wait for completian Before each search No external nrocess vr Wait for completian After each search C Program FilesMnternet EsplarerEXPLHHE EXE lt resulturl gt ait for caompletian After completing task net send usami lt taskname gt has Finished wait for completion Cancel Befare starting task net send usami lt taskname gt is starting Wait for completion Befare each search No external process wait for completion After each search wscript c temp simple wbs lt resultfilename lt resulturls Wait for completion mfter completing
40. Data import filters Directory for storing peak list files created by data import filters Xcalibur BioWorks RAW Options lcq_dta exe Mascot Daemon Data import filter options lcq_da ete Meows SeiexAnayat oh a Eyplorer Mascot Distier Muih sample thes Merge al samples rito sngle seaich Sepaate seach for each sample Default precursos charge state i Ra Tt 4 Discard 5 or higher IDA survey scan centioid parameters Mesge distarce 0 1 Su MS MS data cerMowd Ihreshod Remove peak with witensiy less than ot of highest Centoid al MS MS data Smooth belowe cerMowdimo Percertage height 5n Merge starcer 2 amy MS MS averagng Rieject spectra if less than 10 peaks orpecuisor lt 50 opecusce gt 10000 _ Piecusce mass tolesance lot gcupm9 1 Max number cycles between goups fio Min rumber cycles per group h Mascot Daemon Data import filter options lcq_daexe Micromass snl soy Ows Eswier ecoosml Processing settings Take selhmos io delauk SET fie Take settings from dsla fie VBA macio FunVBA macio assigred to button Baselne Conect baselne Noise fiers Appy noee flter Noise Fiter Corelsion fsclor 7 Feak
41. Variable modifications 1 Variable modifications 2 Mascot Server Show al1 mods Decoy database Decoy
42. Data fo rmat modifications Acetyl N term Acetyl N term madificatians acetyl Protein N term Aacetyl Protein N term Pt ass kDa Sequ est DTA Amidated C term amidated C term 2 amidated Protein C term Amidated Protein terml 2 and 3 gt mmaonia loss N term C mmonia loss N term C Fep6de charge 2 and 3 Biotin K Biotin K 8 Biotin NN terml Biotin N term Monoisotapic Average Show all mads Peptide tol 1 5 Da 13C I Task Editor MS MS MS MS lons search Data format Sequest DTAl Quantitation INane Error tolerant search MS MS tol Ing Da Instrument ESI TRAP Enzyme None Save As tour3 par Mascot Daemon v2 2 9 Task Editor 3 8 Schedule Fo11ow up Run Status
43. Multi Sample Files AB MDS Sciex Analyst WIFF Aascot Daemon v2 2 20 Select Range multi scan files LC Output MS MS Fragment as Mascot 1 2 3 MH 1 2 3 4 Mascot Distiller AB MDS Sciex Analyst WIFF file Mascot Daemon PC Analyst Analyst Script mascot d11
44. URL HTTP access type eaistru defau http typ Registry defaul HTTF proxy serwer a HTTP protocol Re RN HTTP timeout seconds 3600 mascot cgi Mascot Server Mascot Daemon 3 HTTP HTTP Ea access typel Proxy server HTTP URL HTTP timeout seconds Mascot Daemon Service 3600 1 timeout Mascot Daemon GUI HTTP timeout setting 60 Aasco
45. Mascot Server HTTP Mascot Daemon Event Logl Status A Task Database Hf 1 Simple test search 3 No enzume follower LEI_DigestH3 0321 9 LCO Digest03 0486 0492 Submitted fron LC Digest03 0921 0924 Submitted fron D485 04 921 09 Clone 0 5 MS MS human 0 05
46. Merge MS MS files into single searchl Data file 1ist Data import fi1lter mascot_daemon_merge mgf Mascot Distiller Mascot Disti11er Project 2 Schedule Real time monitor ET New files only i a res Include sub folders Sa New files only Include sub folders
47. ODBC Mascot Daemon O0DBC ODBC Mascot Daemon v2 2 30 DSN Data Source Name MDAC MS Query MS Query Office Version 4 0 Excel Version 5 0 Office Excel Microsoft SQL Server Mascot Daemon Microsoft SQL Server 1 Access Upsizing Wizard Mascot Daemon Jet Access Access Upsizing Wizard SQL Server Access Upsizing Wizard Access 2000 Access 97
48. http mascot 3 Mascot Daemon TInstall lasCnt Daemon ascot iagrm nh 15 a cient ahhlicatinn which utnrmatas the submission of data files tn a scnt seryer It Funs gaF_Micr snf WhH nw NT 4 SSPE HHH PP or HH Inetall lpgrade Trnuhlashnnt 4 Mascot Daemon Installation TInstal1ing Mascot Daemon 5 Daemon msi 5 Install scnt haarnnh hy chckin on this Iink Daeman msi and choosing Ren oF nen eS Daemon msi EIR Windows 671 MB saki
49. Mascot Daemon D Sy Lernout amp Hauspie TruVoice American English TTS Engine amp Logicool SetPaint 42 43MB i Mascot Daemon EE E 200712 06 2 L 3 Ma Iler 26 24MB Mascot Server 1 288nnMB Mascot Wizard 1941MB Message Center 2n5MB Microsoft NET Framework 1 1 Mascot Daemon v2 2 5 3 Mascot Daemon Mascot Mascot 1 2 3 4 3 1 Mascot Daemon
50. Mascot Daemon Pause Resume Delete C1one Task Database IFile l Print File l Print asrntaE orests Foam 1 Miascot Daemon Results Chetpubhascotim skkm sms Sample 2 m gf Title uhrnitted from on saki by Mascnt Daemon on Sa IT PL_BPK11 Description tete R oy merase acterinhhage R11 ET IL 111 Mass 1 1IE4 Databhase SsProt 5S D fasta Subrmittech anH8 4 1 23E Retulrier anH8 5 1 5 URL FtB TasctE HHTiastEF_ FESus IFPTlE HHBHH25 da Crnlihetpubhascotim SKKIHm sms sample 1 m gf Title Subhimitted from on saki by hascot Daeiminri on Sel
51. Task Editor Delete Mascot Daemon Task Database Mascot Server EO TPA RIT 1 OT ET Status Task action polling interval seconds Edit Preferences Timer settings PC Refresh 5 PC
52. 1 2 3 4 5 Fol1ow up 6 External processes 4 Running Paused Completed Canceled Paused Resume Paused Completed 1 2 Mascot Daemon Mascot Server Mascot Server 1 Mascot Distiller
53. 1 PC 2 0 2 Mascot Daemon Servicel Mascat Daemon Sery Oa Matrix Science Masc Manages local Masc Messenger MS Software Shadow Mascot Daemon Servicel I A ascnt Daermpn BeryicE
54. Mascot Daemon Stop_mass Mascot_Daemon_PMF_stop_masses txt Mascot Daemon Stop Mass m z m z a ggEnt aera hhFstnp magsEgtst EE This file cantains a list ot mz walues that will be automatically excluded from any peptide mass Tingerbrint searches submitted from scot Daemon Walues listed here are the UN trwpsin autolsis rasmernts listed in Farker Eb et a 1 dernt itication of weast proteins trom tmo dimensional gsls working out spot crass caontaminatign Elect rophoresis 18 182 183 Format is strictly pairs of monoisotopic and ayerage mz yalues separated by a comma For example ff 919 33 919 B4 Aascot Daemon v2 2 32 PASS OS a SCITENCE support jp matrixscience com 03 5807 7895 03 5807 7896 101 0021 6 10 12 KN 3 2008 4 1 Copyright 2008 Matrix Science Ltd
55. On D ME LN 4 Windows 9 3 mascot so Py OOK Frafile 1 Mascot Daemon Service a Mascot Daemon v2 2 29 UL 10 ITI Mascot Daemon Help 1 Mascot Daemon 2 Mascot Daemon Service
56. RPOL BPK11 Description irecte hnlyimErasE acterinhhagE 11 Pages 1 Mascot Daemon v2 2 28 5 5 1 Mascot Daemon Service Mascot Daemon 2 GUI Graphical User Interface Mascot Daemon GUI Mascot Daemon Mascot Daemon Service Mascot Daemon GUI Mascot Daemon Windows Mascot Daemon Service security permission
57. FDR False Discovery Rate Protein Mass 10 000 Da 10 000 Da 1 1 1 Peptide Charge Monoisotopic Average JI Monoisotopic Average MC Peptide tol 1 2 mmu milli mass units 0 001Da 3 ppm 4 Da 13C CC MC
58. CC 1 2 gt 1 2 MS MS MIS Aascot Daemon v2 2 18 MS MS Ions Search MIS Data format Mascot generic MGF Finnigan ASC Micromass PKL Sequest DTA PerSeptive PKS Sc1ex AP III Bruker XML mzData XML Quantitation Error tolerant search Error Tolerant 1 2 Variable modification 2 mascot dat 3 Decoy 4 Quantitation
59. amp 4 Run l Sample test search Run 3 3 Status 3 3 Status SE Mascnt Dae man IIE3 File Edit Help Status Eventtog TaskEdio Er i asK SGD3S6 slalus lask Farameter e T Simple test search Jrunnin 1 Simple test search tour1 par status running AAascot Daemon vV2 2 7 3 4 3 3 3 4 01260005 pk1 012
60. Mascot 1 Batch Mascot 2 Real time monitor Mascot Mascot Daemon Mascot Server 3 Follow up 1 1 Mascot Daemon 6
61. All Searches gt NN defau 1 par HJL User name lt mascot user_full name gt User emal lt mascot_user_email gt Search tle Submitted om lt taskname gt by Mascot Daemon on lt locahosb em ne WD ts m Database SwissProt Enzyme Trypsin kMax missed cleayaaes 1 gt Fised A amp cetul KK MeL gt Hse C M Wariable Pa amet e S et modifications A Nam MTS modifications MR cehul Protein N term Hethyl terml n Amadated Cam 1 etl DE Da idated Protein C term Methylthio C IF 1 lename Ammonis_oss N teim C NIPCAM Peptide charge 2 and 3 gt itin KJ Dxidation Hw Biotin IN term idalion M Monoistopic Average Show almods Peptide tol 8 Da i13c 0 MS MS MS MS lons search IF Dalaformat Mascot generic YY Huantitation Nane Error tolerant search MS MStol pe ba lt Instrument Defaut gt New Open
62. Analyst WIFF Sciex Analyst OK http mascot help instruments_analyst html Options Data Explorer Voyager MS Data Mascot Daemon PC Applied Biosystems Data Explorer 3 5 Voyager DAT Data Explorer LOK http mascot help instruments_data_explorer html Options Thermo Fisher Scientific LCQ DECA RAW file Mascot Daemon PC lcq_dta exe extract_msn exe Edit Preferences
63. Delete Add Files Merge MS MS fles into single search 1 batch Aascot Daemon v2 2 19 2 Rea1 time monitor Mascot Mascot Daemon Mascot Server 3 Fo11ow up 0wner Mascot
64. 3 2 File Edit Help Eyent Log Farameter Editor Task Editor Parameter set Data import fiter Task S mp le test search li Sciehceklascat Pamonozrrt Nane gt Data file list 2 Schedule Add Files 20 Shart now D d drop dala fi h EE a Rt ty Stlarl at ll lt a Realime monit Run Simple ience Mascot Daemon dala n12Ennn5 pkl Ao ie Follow up Search priority In test search Actions Auto print results External processes Follow up No follow up required hp ro Fis 1 Taskl Simple test search 2 tour1 par 3 Add Files 01260005 pk1 Windows Data file jstl
65. File Edit Help Status Eyewlos Task Editor Parameter Editor Parameter set Filename C Program Files Matrix Scien Mtourl par New nen Sawe saveas all Searches A User name IMascotKensaku Useremall kensakuGmalrisscience jp Save As Search title Submitted from lt taskname gt by Mascot Daemon on lt localhosb tourl par Taxonomy alenties Fieport top IauTn lt hits 3 Database swissProt Enayme rwpsin Max missed cleavages 1 Methyl term arable Decay dalabase madificatinns Pratein mass kDa Feptide charge 2 and3 Deamidated NO Phospho Y Manoisatopic f Average Show all mads Peptide tol pa gt 13C In r MS MS MS5 M5 lons search Iv Dataformat Micromass PKL Quantitation INane Error tolerant search MS MS tol In3 pa Instrument ESI QUAD TOF Mascot Daemon v2 2 6 3 3 Task Editor 3 2 tourl par C Program Files Matrix Science YMascot Daemon data 01260005 pk1 Simple test search
66. Pass data to 2 Na enzyme follower Mascot Daemon v2 2 10 Trypsin first pass search tour2 par 0 05 No enzyme fol1ower tour3 par Status 3 10 LCQ_Digest03 0486 0492 2 dta 0 05 No enzyme fol1ower LCQ_Digest03 0921 0924 2 dta 0 05 No enzyme fol1ower LCQ_Digest03 0921 0924 2 dta
67. fiters Un moncisotopsc peaks Onk singky charged peaks lntensity hers CC Alpeaks Select ho most raense peaks per hoo Da Mascot Daemon Data import filter options icromass spl Sciex Anayst Data Explorer Mascot Distiee Al veessons Fustscon Minimum mass 300 Groupnng toletance 14 Mn scans goup 2 Vesson 2 or calbu Lastscan Mavamum mass ao00 Intemedate scans Precursce chaige AUTO lt Calculate charge Min peaks 0 Chugetemglte AAsequence Ops Thehog ExAact MSn 1 OK AAascot Daemon vV2 2 21 http mascot help instruments_xcalibur html 5 Masslynx sample list Masslynx samplelist PKL ee Meemse eenba owsEwow opel J Options Micromass sp1 a HL Path to PKL file folder PKL OK pk
68. task net send usami lt taskname gt has Finished wait for completion Cancel Aascot Daemon v2 2 25 lt simple vbs gt Option Explicit Result file name and result URL are passed as command Iine arguments Dim objArgs ResultFileName ResultURL Set objArgs WScript Arguments ResultFileName objArgs 0 ResultURL objArgs 1 Format result URL as hyperlink and append to links file Dim fso MyFile ForAppending ForAppending 8 Set fso CreateObject Scripting FileSystemObject Set MyFile fso 0penTextFile c temp links txt ForAppending True MyFile WriteLine lt A HREF amp CHR 34 amp ResultURL amp CHR 34 amp gt amp ResultFileName amp lt A gt Follow up If score 1ess than actions If probability that match in random gt 1 Auopintresuls Eemal processes 0 05 20 i 20 0 Discard results Fies Repeat al interyals of op
69. 1 Event 14 09 25 2007 10 403 3 Trypsin first pas rch Starting new task i Event 14 093 36 2007 10 03 3 Trypsin first pas rch Connected to Mascot seryer at http localhost mascot cgid 1 Event 14 09 38 2007 10 03 3 Trypsin first pass search LCO_Digest03 0486 0492 2 dta Search submitted 1 Event 14 09 59 2007 10 403 3 Trypsin first pass search LCO_Digest03 0486 0492 2 dta Search completed 9 Event 14 10 14 2007 10 403 3 Trypsin first pass s LCO_Digest03 0921 0924 2 dta Search submitted 9 Event 14 10 25 2007 10 403 3 Trypsin first pass search LCOQ_Digest03 0921 0924 2 dta Search completed C Program Files Matrix Science Mascot Daemon Mascot_Daemon_Event_Log csv Mascot Daemon Service Windows Event Log 4 6 Status Status Task Database Task Database
70. 60005 pk1 3 4 Eo EEmm Eimin File Edit Help Status Eventlog TsskEdio Task Database Yalue wy 1 Simple test search Data file C MProgram Fileshdatriw Sciencehdascot Daemondata01 a DZEOODS pkl Search title Submitted from Simple test search by Mascot Daemon on ccession CYC ALLMI Protein MWy 11731 Score 84 Description Cutochrome c Alligator mississippiensis merican alligator Database SwissProt_ 54 0 fasta Result file URL http localhos mascol cq master results_ nlEI Search submited 2007 10402 13 32 47 Result file URL Search completed 2007 10A02 13 33 58 PS SE Pa Result file URL http localhost mascot cgi master_results pl file Mascot Server 3 5 3 5 Result file URL Peptide Summar
71. MASCOT Daemon Version 2 2 7 li EN 1 del he fm by oF 0 1 1 2 2 2 2 2 3 2 2 3 od 4 2 4 5 2 5 5 3 3 1 Wa amen 6 3 2 6 3 3 LL A 7 3 4 8 3 5 9 er 2 Pr 0 0 4 1 12 4 2 Preferences 13 4 3 Parameter Editor 16 4 4 Task Editor 19 4 5 Event Log 27 4 6 Status 27 5 5 1 Mascot Daemon Service 29 5 2 30 5 3 Stop Masses 32 MATRIX SCIENCE 1 Mascot Daemon Mascot Server
72. SQL WTaskDB_schema xls MicrosoTt Jet Mascot Daemon Jet 4 0 Microsoft Access 2000 TaskDB mdb TaskDB mdb Preferences ADO connection Restore default TaskDB mdb Change OLE DB Mascot OLE DB Object Linking and Embedding for Databeses OLD DB OLE DB ODBC Open Database Connectivity 0DBC Mascot Daemon MDAC 2 5 Microsoft Data Access Components OLE DB ODBC
73. conds ho Timer tick interyval Delay after opening empty dataset seconds In Delay ater failing to open read locked fle seconds En Minimum delay between monitor searches seconds En PC Minimum delay between follower searches secands En 8 LA Task action nallina interyal secands 5 10 Delay after opening empty dataset Save Cancel a 10 10 Delay after failing to open read locked filel Aascot Daemon vV2 2 14 5 60 10 60
74. efresh FI Mascot Daemon Mascot Server Mascot Daemon Mascot Server 1 Mascot Server http www matrixscience Jp pdf jap_2 2_mascot_upgrade pdf 2 Mascot Daemon http www matrixscience Jp pdf jap_2 2_daemon_upgrade pdf Mascot Daemon v2 2 4 hlascot seryer URL up to and includinn cgi directory 2 Mascot Server URL e g http dyour_ server mascot cgir Save x Mascot Daemon Mascot Sserver Mascot Dacmon 2 4 Mascot Daemon Mascot Server Mascot Server PC Mascot Daemon 2 5 1
75. ions Fixed modifications Aascot Daemon v2 2 17 Carboxymethy Cys 103 Da 161 Da 103 1 59 Fixed modifications Variable modifications 2 Oxidation M 3 0 1 2 3
76. l sample 1ist pkl Masslynx http mascot help instruments_masslynx html 6 AB 4000 Series TS2Mascot Mascot Daenon PC nn TS2Mascot rasaeel Meom sl swwwlowpesel woo Tsatwea Pesk ermg 2 Mass range 5n Da mascot pdf TS2Mascot pdf 2 FRR AB 4000 Series ODBC So Merosocpe peaks only Options TS2Mascot OK AB 4000 Series AB 4000 Series http mascot help instruments_4000 htm Data file list
77. nce Masctc YU Data file list A follow up task does not have a pre defined list of data files It runs ing to receive dai inuously waiting to r ta asks Schedule Start mowl IStart all Real time monitor Fo11ow up Search priority 0 20 Actions Auto print results PC
78. omy Report Top AUTO Protein Summary Report 2 Database Enzyme None sub sequence Trypsin HMC
79. ot Daemon Mascot Server CD Oracle sql Mascot Daemon SQL Plus Oracle sal SQL gt start oracle sql SQL Mascot Daemnon Mascot Daemon Mascot Daemon Oracle Mascot Daemon Editl Preferences Mascot Daemon Preferences ADO Database Change Microsoft OLE DB Provider for Oracle gt
80. t Daemon v2 2 13 Data import filter MMascnt Daemonahretferences me Datainpor ters oo connection Timer setings Mascat login MGF Browse Directory for storing peak lst fles created by data import fiters C Program Files Matrix Science Mascot Daemonmgf Thermo Fisher Scientific lcq_dta exe extract_msn exe Full path to LEH_DTA EE ET TE Browse Browse Gave Cancel ADO connection ADO ActiveX Data Object connection NT Mascot Daemon Intranet Dala import filters DI connection Timer settings Mascot logn Mascot Daemon
81. th gt lt resulturl gt External processes External processes net PC usami is starting PC usani has finished Mascot Daemon Service Microsoft Windows Script
82. ummary Report Peptide Summary Help Significance threshold p lt I0 05 lax number of hits 1 Standard scoring MudPIT scoring Tons score or expect cut off 0 Show sub sets Show pop ups Suppress pop ups Sort unassigned Decreasing Scnre Require boldred Hmpott results into MT Select All Select Nane Search Selected Fror tolerant Archive Report 1 HB HUMAN Mass 15248 Score 53 Queries matched 1 Hemoglobin subunit alpha Hormo sapiens Hunan Check to include this hit in error tolerant search or archive report Query Observed Mrt expt Mrt calc Delta Miss Score Expect Rank Peptide i 1109 36 2216 71 2216 20 0 51 0 55 0 038 K LLSHCLLVTLAAHLPAEFTPA V Status LCQ_Digest03 0921 0924 2 dta No Enzyme follower amp amp No Enzyme follower Mascot Daemon NCBInr
83. y Report Submitted fromi Simple test search by Mascot Daemarn nn SakD Nicrosoft Tt CE H ORE OO PF AD httpy localhost mascat cgi master results pl file data 20071002 FO02635 dat 5 474772ZY Mac 5 LICIENCES Mascot Search Results Mascot kensaku ET GR CEE ANNE SE SO Parameter Ed tor Search t t e Timest amp 2 Oot 2007 at 04 33 43 GT Protein hits CYC ALLMT Cytochrome c Alligator mississippiensis American alligatol lt taskname gt Pataniisy Based Movee sn I js 10 LoatP where PF js the probability that the ob d imatch js a rando t a WHEN homoloey p lt 00 9 S ID 6 test search O Protein scores are dermyed frorn ions scores as a non probabilistic basis for ranking protein tuts Number of Hits 50 i Probability Based Mowse Score
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