Mascot Daemon マニュアル
Contents
1. Accession lt no result gt Result file URL Mascot Server 3 4 Status 3 Mascot Daemon File Edit Help Eyent Log Task Editor Farameter Editor Task Database Q 1 Simple test search running Parameter set tour1 par 1 Simple test search Helresh F 9 2 5575 DB 3 5 Status 93 Mascot Daemon Eile Edit Help Eee Eyent Log Task Editor Parameter Editor Task Database 1 Simple test search 01260005 pkl Search title Accession Search submitted Search completed C Program Files sBBIKMatiis ScienceskMascot Daeman dal Submitted from Simple test search by Mascot Daemon on ME CYC_ALLMI Cutochrome c OS Alligator mississippiensis PE2. Mascot Daemon 27 4 5 Event Log Event Log Mascot Daemon 4 21 Event Log warning error Mascot Daemon Dals fle FT 181003 2012 06 07 1 mple best seasc O2500CE pkl CO Everr 181025 20120607 1 Smple bes seasch 01250005 pkl Seach compieted OG Everr 181037 2012706 07 1 Simple bes seasc Evert 95353 2012 06708 OEvert 95427 2012 06708 i em Eve 35427 2012706708 Mascot Daemy CSV Pe JP Mascot Daemon Service Windows Event Log C Program Files x86 Matrix Science Mascot Daemon Mascot_ Daemon_Event Log csv
3. 1 Variable modifications 2 WMascot Server Show all modifications Decoy database Decoy FDR False Discovery Rate http www matrixscience com help decoy_help html Protein Mass
4. Select Modifications Select Modifications 4 8 4 8 Select Modifications PRRmSRakEiemates Fix Modifications Variable A a Modifications gt Ro Q lt Bain te Modification Fixed Variable 9 CH BR DES soot Server Fued GO modifications BO Variable modifications MGS EE Fixed modifications Carboxymethy C
5. B Status Task action polling interval 4 23 Mascnt Daemom Results seconds Edit Preferences Timer settings lt wlo PC F5 U CiinetpubMascotum skkm sm sSam ple 2 m gf Title Submitted from on saki by Mascot Daemon on SAKI 3 PC MR We RNA polymerase Bacteriophage K11 core 111 Mass 101064 c gt Database SwissProt_55 n fasta Mascot Daemon ka a 9 Returned 2008 04 25 14 20 54 a a URL http sakitmascoti cgilmnaster_results pl file datal20080425 F O05439 dat Mascot Daemon CulnetpubiMa
6. lt mascot_user_name gt lt mascot_user_ful name gt lt mascot_user_email gt Search title Search title lt mascot_user gt 1d name ful1l name email Mascot Mascot lt taskname gt lt parameters gt lt localhost gt PC lt localuser gt Windows lt datafilename gt l
7. Event Log Task Halt on error External processes Mascot Daemon Service Mascot Daemon Service External processes lt resultur1l gt lt taskname gt lt parameters gt 1ocalhost gt localuser gt lt datafi ename gt lt datafilepath gt lt cachedpeaklist gt Data import filter
8. Database Ct1 Enzyme None sub sequence Trypsin HMC None Trypsin None semiTrypsin semiTrypsin Trypsin N
9. Mascot Options OKI 4 10 Mascot Distiller Mascot Daemon Data import filter options Mascot Distiller Mascot Daemon PC Mascot Distiller Mascot Distiller Options 4 10 Processing Options opt lcq_da exe Micromass sal Sciex Anast Data Explorer
10. Windows 7 Daemon msi Rk a ee 5 Mascot Mascot Daemon Mascot Daemon Mascot SeTVeT MascotserverURL up to and including cg directory e g httD our_seryer mmascol cai Preferences Internet lt HTTP timeout seconds i Mascot Server URL Mascot Server HTTP access type Registry default URL Save HTTP proxy server HTTF protocol CO HTTPA 0 HTTP 1 I
11. IM PC 5B 3 Windows Mascot Daemon Service 5 1 Mascot Daemon Service a F A V H 9 PD me 3
12. Task Simple test search Parameter set tour1 par Data file list Add Files 01260005 pkl Runm 3 4 Status Status running 3 4 3 4 Status 3 5 PO 01260005 pkl 01260005 pkl l
13. Mascot Daemon 32 5 Microsoft SQL Server Mascot Daemon Microsoft SQL Server Access Upsizing Wizard Mascot Daemon Jet Access Access Upsizing Wizard SQL Server Access Upsizing Wizard Access 2000 Access 97 SQL Enterprise Manager Mascot Daemon MS SQLS qrt Microsoft Query Mascot Daemon MS_SQUIS qrk C Program Files x86 Matrix Science
14. 0 05 No enzyme follower LCO_Digest03 0921 0924 2 dta 0 05 No enzyme follower LCQ_Digest03 0921 0924 2 dta Tryptic peptide 9 0 CN CO DE Status LCQ_Digest03 0921 0924 2 dta No Enzyme follower No Enzyme follower Mascot Daemon
15. 1 Owner Mascot 2 Task Status Event Log Search title Status CGlone Copy of New Run 3 Parameter set Parameter Editor par 4 Data import filter
16. D Data Proteins QStar 20031102 Trypsin234 wiff D Data Proteins QTof Default pro Data rypsin234 raw Specify path to root folder D Data Proteins QTof pro Data Optional wild card file or name raw Specify path to root folder D Data Proteins QTof pro Data Optional wild card file or name D Data Proteins QTof pro Data Include sub folders Specify path to root folder Mascot Daemon 24 4 18 Follow up Data file list Sc
17. Exit Mascot Daemon GUI Mascot Daemon Service MRU MRU Most Recently Used 2 Edit 4 Parameter Editor Task Editor Cut Copy Paste Clear Preferences Preferences ODBC Information ODBC connection Refresh Status 3 Help Mascot Daemon Help
18. 10 000 Da 10 000 Da 1 1 1 Peptide Charge Monoisotopic Averagej C Monoisotopic Average Peptide tol CD mmu milli mass units 0 001Da ppm Da 13C CO 0 C 1 2
19. lt samplenumber gt lt mascot_user_id gt Mascot ID lt mascot_user_name gt Mascot Aascot Daemon 25 lt mascot_user_ful1 name gt Mascot lt mascot_user_email gt Mascot lt resulturl gt URL lt resultfilename gt lt resultfilepath gt External processes 4 19 net PC usami is starting C Mascot usami has finished N6 We6
20. 7 Actions Auto print results PC External processes Mascot Daemon External processes Before starting task Before each search After each search After completing task Wait for completion hung
21. NCBInr NCBInr 3 10 File Edt Help Eyent Log Task Ei Pasameter EdMor Taik Dalabasa 1 Smple test search Value C Program Files xb6Mah ScenceVdascol D semon dataL CO_Digeat13 032 Mo ercyme folicwer Seach Me Submwiled hom No rme kolkomet by Mssco Daemon cn MBA11W7 1LCU_DoesiUB 0S21 03242 Accesscn HBA_HUMAN 3 Tepsm rt pass each Pole MW 15248 LCU_Digestn3 0495 0432 2 da 5 EE st03 0321 0324 2 LCADppeO3 09Z1 0924 2 Desciphon Hemoglobin su ur aiphs 0S Homo sapers GN HBA1 PE 1 SV lt 2 Dalabass SwmsiProl_ 2012_05 sta Riesuk fic URL http 7 localhost mascot cgi master_results pl file data 72012060 Search subemited 2012 06 08 10 41 41 Search compleled 2U12 O5 06 10 41 54 Retresh F5 3 11 Ne Mascot Search Results 0 Mascot Kensak Enail m
22. Authentication l Web Server nip77ocaosmasco cg Authentication HTTP tmeout seconds Em 0 6 tt Mascot Server Mascot Daemon 4 HTTP HTTP access lype Registry default lt HTTP access HTTP poxy server type Proxy server HTTP UCS RE URL HTTP timeout seconds Mascot Daemon Service canoal timeout Mascot Daemon GUI HTTP timeout setting 60 2 Data import filters 4 3 Data import filter
23. 2 NCBInr dbEST Discard results Status Event Log Search results discarded Score is less than 61 specified threshold Repeat at interval of Pass data to
24. PC Mascot Daemon Pause Resume Delete Clone UNC Universal Naming Conversion path to TaskDB mdb Mascot Daemon 33 5 3 Stop Masses PMF Stop Mass Stop Mass Mascot Daemon ei SE C Program Files x86 Matrix Science MWascot Daemon Stop_mass Mascot_Daemon_PMF_stop_masses txt Stop Mass m z m z
25. Mascot Daemon Service 4 19 Microsoft Windows Script net PC usami is starting has finished C temp links txt Mascot URL simple vbs lt simple vbs gt Option Explicit Result file name and result URL are passed as command ine arguments Dim objArgs ResultFileName ResultURL Set objArgs WScript Arguments ResultFileName objArgs 0 ResultURL objArgs 1 Format result URL as hyperlink and append to Iinks file Dim fso MyFile ForAppending ForAppending 8 S
26. Event Logl C Program Files x86 Matrix Science Mascot Daemon Mascot_Daemon_Event_Log csv Mascot Daemon Mascot Server Web 3 5 MS MS Human 0 05 None 2
27. Completed task Cancelled task OO Paused task Pause Resume C1one De1etey Clone Task Editor Copy of Delete Mascot Daemon Mascot Server
28. Mascot Daemon 28 4 6 Status Status Task Database 4 22 Status ee aeron File Edit Help EventLog Task Editor Parameter Editor S Task Database Parameter 9 9 O 2 1 Simple test search Dala file C inetpubmascotmskk sampledataterrorT ol5 ample ma Hf 2 No enzhme folower Search title Submitted from yeast phos 1 by Mascot Daemon on MEAT11w7 HH 3 Trypsin first pass search Accession ELM1_YEAST Test search 1 Prolein Mw 72903 5 Test search 2 Task Score dp 6 Test search 3 Descripi Serine threonine protein kinase ELM1 05 5acch isi 1 Database ya ped Databose SisPret 2012 Eat EN 9 Canis Fesul ile URL http localhos masco cqgi master_results_pl2file data 2012 _ Search submitted 2012 06408 14 35 55
29. PC 10 Delay after opening empty dataset 10 10 Delay after failing to open read locked file Mascot Daemon 14 4 4 ADO connection Mascot Daemon Preferences i ADO connection DTimer settings Authentication Intranet Data import filte aDO Connection string Provider Microsoft Jet OLEDE 4 0 Data Source C Program Files lsBBjKMatis SciencekMascot Daemon TaskDE mdb Mode Read ritel5hare Den None Persist 5ecurit Info False Hestare default Change Save Cancel 4 5 Timer settings Mascot Daemon Preferences Qi Timer settings A thentication Intranet Data import fiters AaDO connectid Timer tick interyal between 1 and 60 seconds 10 Delay after opening empty dataset seconds In Delay after Failing to open read locked file seconds ln Minimum delay between monitor searches seconds ln Minimum delau between follower searches seconds ln Task action polling
30. or pecusor 50 mpwecusr gt 10000 lessthan 01 ofhghe _ _ Piecusce moss toletance foe goupm9 1 Mv et ono OK Ma numbe cycles boween gops 0 Percentage height 5n so od clo 1 Merge stance 2 aw Mascot Daemon Help Reference Data Import Filter Options Dialog AB Sciex Analyst http www matrixsclience com help instruments_analyst html Data Explorer Voyager MS Data 4 12 Data Explorer Mascot Daemon PC Applied Mascot Daemon Data import filter options Icq_daexe Micromass spl Sciex Anas Biosystems Data Explorer 3 5 Peocessing sethmos Voyager DAT Take selings om delau SET Rie Take setings hom data fle VBA macio Baselne RunVBA macro asssgred to button hh FZ Conectbssegne Data Explorer Voyager MS Data Options ll 4 12 Peak fiters Un monotsotopwc Deaks Hr singb charged peaks
31. ES EV Dala file list Parameter set C Program Files x56 atrix Sciencet Data import filter Mascot Distiller Start now skrtat 5429 eal time monitor Drag and drop data files into the area below or click on add 8 Bll 2012 CFollow up Search priority 4 Actions Auto print results External processes Follow up No follow up required In Delete dd Folder dd Files 1 days Merqe MS MS files into single search Data file list Aascot Daemon 23 Delete l Merge MS MS files into single searchl Data file list Mascot Bruker XML mzData Data import filter l mascot_daemon_merg
32. Log Bluetooth Servic al 3e Ee 5 E Ma SOerre SScSt Service Managesl Local Sy Media Center Extender Service Media Cen Local Se 5 2 Mascot Daemon Service Mascnt Daemon eryicE RT WW O77 Profile 1 Docked Profile 5 3 Mascot Daemon Service Mascot Daemon Beryice mascot Px L Da Profile 1 Dacked Prafile
33. ho an N 8 hp Mascot Wizard 1941MB PO A Message Center 205MB Microsoft NET Framewark 1 1 6 C Program Files x86 Matrix Science Mascot Daemon Aascot Daemon 7 Mascot Daemon Mascot Web Mascot 1 2 Mascot 3 Mascot 4 C Program Files x86 Matrix Science Mascot Daemon data MS MS Mascot Daemon 3 1 Mascot Daemon Mascot 3 1 Mascot Daemon Mascot Daemon Le te M
34. OK PSD Inemwy es Alpeaks Select 10 most riense peaks per 100 Da MS MS Mascot Intensity filter All peaks Mascot Daemon Help Reference IData Import Filter Options Dialog Applied Biosystems Data Explorer http www matrixscience com help instruments_data_explorer html Thermo Fisher Scientific LCQ DECA RAW file 4 13 lcq dta exe Se De vV PC 1cq_dta ee el Daemon Data import filter options icromass snl Sciex Anaysll Data Explorer Mascot Distier extract_msn exe First cn Last cn Edit Preferences Data es Import filters Directory for storing peak list files Groupng toletance 1 4 lvemedee scans 1 Mn scans7group Piecusce chsoe AUTO lt created by data import filters 6 Verson 2 or calbur Xcalibur RAW
35. gt 2 3 MS MS MIS MS MS Ions Search MIS Data format Mascot generic MGE Mascot Daemon 19 Finnigan ASC Micromass PKL Sequest DTA PerSeptive PKS 6 Sciex API III Bruker XML mzData XML mzML mzML Quantitation Error tolerant search Error Tolerant Variable modification 2 mascot dat Decoy Quantitation MS MS
36. 3 MH m z 1 Distiller Project File Save Mascot Distiller roy AB Sciex Analyst WIFF file 4 11 Sciex Analyst Mascot Daemon PC Analyst 0 Mascot Daemon Data import filter options Icq_eaeye Micromass sp CA Mascot Distier Analyst Script mascot d11 RS Analyst WIFF 5 Meige al samples rto sole eaich Sepaate seech fo each sample Delau precursot Charge state IDA survey scan centroid parameters i 2 3 4 Re detemine Percentage heigh 50 Discard 5 or higher tt Merge distance fo1 ww AB MDS Sciex Analyst WIFF file Options MS MS averaging MS MS data cermoed threshold 5 9 Reiect spectra if less han 0 peaks Remove pooks wiih tone 4 11
37. 5 5 5 5 Mascot Daemon Service a aggEnt HaErinh PF Etn magsEgtst EE H Tingerbrint samarches submitted rom Mascot Daemon alues listed here are the promirnent trypsin autnlysis ffragments listed in Parker FE C et al 1998 Identification of weast proteins Tram two dimernsiornal ggls working out spot crass cantaminatign Elect rophoresis 18 1 183 Format is strictly pairs of monoisotopic and ayerage mz yalues separated by a comma For example 19 33 919 54 2012 6 2 CopyrIight 2012 Matrix Science Ltd Aascot Daemon 34 MATRIX SCIENCE 03 5807 7895 support jp matrixscience com 03 5807 7896 101 0021
38. 03 Da Fised Modifications Aascot Daemon 18 161 Da 103 1 59 Variable modifications 2 Oxidation 0 3 0 1 2 3 Variable modifications
39. 6 10 12 KN 3
40. Mascot Server R 1 Batch Mascot 2 Real time monitor Mascot Mascot Daemon Mascot Server 3 Follow up 1 1 Mascot Daemon 6
41. Drag and dran data files into he area belaw or click on amp dd Startat 54 29 8 Bl 2012 CC Realtime manitor Follow up Search priority In 59 Actions Auto print results External processes SN RNN Fallow up batch 1 Delete Add Files F da Merqe MS MS files into single search None Mascot Mascot Real time monitor Mascot Mascot Server Follow up Mascot Daemon
42. ak Search completed 2012 406 08 14 36 08 2 b peptide 01 URL SR 1 13 b peptide 02 14 bpeptide 03 15 ecoli s 01 Running task Follow up task Trying to pause a running task
43. Mascot Mascot Daemon 5 2 2 1 Mascot Daemon Windows 2000 XP Professiona1 32 64bit Server 2003 32 64bit Windows Vista Business U1timate 32 64bit Seryver 2008 32 64bit 7 Professiona1 U1timate 32 64bit Mascot Daemon HTTP Mascot Server Mascot Server http www matrixscience com cgi C Microsoft Internet Explorer Mascot Daemon BN 2 2 Mascot Daemon Mascot Server Mascot Server Mascot Daenon 1 Mascot Daemo
44. Take action polling interval Mascot Daemon Service TaskDB mdb 15 10 5 Authentication Mascot Server Mascot Security lTask Editor Owner l Web Web Server Authentication Proxy Server Authentication
45. Parameter Editor 3 7 Enzyme Trypsin Data format Sequest DTA Save As tour2 par 9 7 Enzyme Trypsin None Save As tour3 par Task Editor 3 8 Task No enzyme follower Parameter set tour3 par Schedule Follow up Run l No enzyme 3 7 tour2 par Mascot Daemon Ex File Edit Help Status Eyent Log Task Editor Farameter set Filename CAPragram Files x86 Matix Mour2 par New Dpen save saveas D All Searches User name IMascotKensskh User emall mkensaku Gmarixscience Com
46. MassLynx MassLynx sample list sample list PKL 6 Xcalibur 1cq_dta exe extract_msn exe PC Mascot Daemon RAW MGF C Program Files x86 Matrix Science Mascot Daemon MGF 1 3 Mascot Server Mascot Daemon PC Mascot Daenon PC Mascot Daemon 1 4 External processes
47. Mascot Dagemon 31 Mascot Daemon Help 3 Mascot Daemon Mascot Daemon Service Mascot Daemon Service Mascot Daemon 5 4 Failed to start Mascot Daemon Service OK Choose Ignore to run the Mascot Daemon service component on the desktop 5 4 BE ITinIr Lnable to start the Mascot Daemon Seryice Chaose Abort to to exit Mascot Daeman Choose Retry to ver
48. Status Pause Resume Clone Cancel Delete 3 6 Follow up Clone Copy of Task Editor Status Delete Mascot Server C inetpub mascot data yyyymmdd Fxxxxxx dat Mascot Daenon C Program Files x86 Matrix Science Mascot Daemon TaskDB mdb Mascot Server Mascot search 1og
49. 1 2 par 3 4 5 Follow up 6 External processes 4 Running Paused Completed Canceled Paused Resume Paused Completed 1 2 Mascot Daemon Mascot Server Mascot Server
50. Oracle sql SQL gt start oracle sdl SQL Mascot Daemon Mascot Daemon Mascot Daemon Oracle Mascot Daemon Edit Preferences Mascot Daemon Preferencesl ADO Database Change Microsoft OLE DB Provider for Oracle ND gt gt T 0K Mascot Daemon Preferences Save 8
51. Monoisotopic Enzume Trwpsin F en ame Be MP Max missed cleawaqes 1 r Select Modifications Vaiable Dxidation MM Peptide charge 2 and 3 vr Peptide tol 8 Da 13C 0 MS S MS MS lons search Dataformat Mascot generic Quantitation None New Error tolerant search MS MStol 8 Da gt Instrument Default 0pen Save default par Save As 2 All Searches PMF MIS User name User email Mascot
52. Cacuaechage Mnpeakslo ExactMSn gel 20 AA sequence Uphons Theeshold Thermo Fisher Scientific LCQ DECA RAW file IN OK SW Mascot Daemon 22 Mascot Daemon Help Reference Data Import Filter Options Dialog Lcq_dta exe Extract_msn exe http www matrixsclience com help instruments_xcalibur html Masslynx sample list Mass1ynx sample list PKL Masslynx sample list Options Micromass spl 4 14 Path to PKL file folder PKL Browse OK PKL sample 1ist PKL Ma
53. Mascot Daemon Service ko Network DDE DSDM Dynamic Moo Locatian Awaren R D Mascot Daemorr 3 Windows 7 4 Mascot Daemon D Lernout amp Hauspie TruVaice American English TTS Engine Windows 7 J Ce 0 2007 5 Mascot Daemon
54. 2 par 3 4 5 Follow up 6 3 2 tour1 par AAascot Daemon 8 3 3 93 Mascot Daemon File Edit Help Farameler set is SciencetMascat Daemonstour1 par Data file list Drag and drop data files into the area below or click on dd ncehascot Daemondata 012E60005 pkl Delete Merge MSAkMS files into single search Status Eyent Log Parameter Editor Task Simple test search Data import filter lg Nane Schedule lt Shart now Y Startat 9 54 29 8 Bll 2012 Healtime manitor CC Follow up Search priority 0 4 Actions Auto print results External processes Follow up No follow up required a hp days MOTTE C Program Files x86 Matrix Science Mascot Daemon data 01260005 pkl Simple test search 2 Task Editor 3 3
55. MGF 1 Mascot Distiller RAW WIFF mzML http wWww matrixscience com distiller html 2 Analyst Analyst PC Mascot Daemon Analyst mascot d11 WIFF 3 Data Explorer Data Explorer PC Mascot Daenon Data Explorer Aascot Daemon 4 DAT 4 4000 5000 TS2Mascot GPS Explorer 5
56. MGF mE Browse mim CEaaiweotmes Doocorosrl fime setwgel aenicsi Directar for starin peak list files created by dala import filters O C Program Files xBb hd atriw Sciencekklascat D aemornmagf C Program Files x86 Matrix Science Mascot Daemon MGF 0 extract_msn exe rom Browse extract_msn exe se cm http www matrixscience com help instruments_xcalibur html http www matrixscience D pdf jap_settingsOfMs MdForXcaliburRawFile pdf 3 ADO connection ADO ActiveX Data Object connection Mascot Daemo
57. Mascot Daemon 12 Register Mascot Distiller Mascot Distiller Mascot Daemon About Mascot Daemon Mascot Daemon 13 4 2 Preferences Preferences Windows 09 Mascot Daemon 1 Internet Mascot Server URL Mascot Server 4 2 Internet warning CHDaemonipreferences Mascot Server URL me DD ata import fiters ADO connection Timer settings Authenticatian Mascot serwer URL up to and including cgi directory Web eg hp Vour_seryer mascoMcai
58. Mascot Daemon 15 4 6 Authentication ntranet Data Import filers aDD connection Timer settinAs Authentication 1 ee lt web Server A amp uthentication Proxy Server A amp uthentication User name Password User name Password Mascot Security User name Save Cancel Passwunrd Mascot Daemon 16 4 3 Parameter Editor par 4 7 Parameter Editor Task Editor pogo i Parameter set Mascot Daemon a Parameter set de fau t pa Filename C Program Files xs86 AM atrix default par New Hpen Save Save As All Searches User name lt mascot_user_fulLnamey User emall lt mascot_user_emall gt Search title Submitted from lt taskname gt by Mascot Daemon on lt localhost gt Taxonomy A amp ll entried Reporttop jAUTD vr hits 1 Pa amet e S et Database oe Decoy database Protein mass kDa SvcsPoo
59. Search title Submitted from lt taskname gt by Mascot Daemon on lt localhost gt Taxonomy i Homo sapiens human Reporttop jaAUTD vr hits Database a Decoy database Protein mass kDa Monoisotopic lt Enzume Trwpsin verage Max missed cleavages 1 Fised modifications Select Modifications 0 Marea Peptide charge 2 and 3 modifications Peptide tol 1 5 Da 13CID MS S MS5 MS lons search JIY Datafomat Sequest DTA Quantitation None Eror tolerant search MSMStgl na ba sument ESLTRAP lt 3 8 8 Mascot Daemon Eee Eile Edit Help Status Event Log Task Editor Farameter Editor Task No enzume follower New Parameter set Data import filter is Science kascat Daemonstour3 par None Data file list Schedule Start now follow up task does not have a pre defined list of data files It runs Startat 9 54 29 8 Bll 2H12 continuously waiting to recely data from other tasks Real tme monitor iFollow upt Search priority lo gt ctions uto print results External processes Fallow up No follow up required 0 1 days None follower Sta
60. 1 SV 2 SwissProt_ 2012_05 fasta http localhos mascol cqg master_results_pl 2rile 2012406 08 10 20 47 2012 06 408 10 21 10 Refresh F5 Web oo lo Mascot Daemon 9 Data import filter Mascot Distiller LResult file URL Mascot Distiller Mascot Distiller Mascot Distiller Status 3 6
61. Mascot Daemon SQL Microsoft Query Office SQL Server 6 MySQL mySQL txt Mascot Daemon C Program Files x86 Matrix Science Mascot Daemon SQL cd CC Program Files MySQL MySQL Server 5 0 bin mysSdl exe C Program Files Matrix Science Mascot Daemon SQL mySQL txt Mascot Daemon 7 Oracle Oracle Mascot Daemon Oracle sql Mascot Daemon C Program Files x86 Matrix Science Mascot Daemon SQL SQL Plus
62. 6 2027 0 5100 0 58 23 t EK LLSHCLLVTLAAHLPAEFTPA V Search Parameters Type of search MS MS Ion Search Enzyne Hone Mass values Mono op Protein Mass Unr ed Peptide Mass Toler t 1 Pragament Mass Tolerance tt 0 6 Da Hissed Cleavage 1 Instrument type ESI TRAP T qaeries Mascot Dagemon 11 4 4 1 1 File 4 Parameter Editor Parameter Editor Ex Status Event Log Task Editor Parameter Editor Parameter set Filename C Program Files x86 AM atriw default par New Ipen Save SaveAs New 0pen Save Save As Print Status
63. 7 5 1 Mascot Daemon Service 2 Mascot Daemon Service 5 2 External Processes Web Externa1 Processes
64. Aascot Daemon 2 4 Wersion Z 4 Copyriont 2002 12 Matrix Science 0 MATRIX SCIENCE Mascot Daemon 2 3 RG 3 2 gt OZ 3 1 3 4 1 4 5 4 2 9 2 1 2 5 2 5 2 3 6 2 4 6 2 5 6 3 3 1 Mascot Daemon 0 7 3 2 0 7 3 3 8 3 4 8 J 9 4 0 11 4 1 as 11 4 2 Preferences 13 4 3 Parameter Editor 9 16 4 4 Task Editor 20 4 5 Event Log 27 4 6 Status 28 5 5 30 5 1 Mascot Daemon Service 30 5 2 31 5 3 Stop Masses 33 Mascot Daemon 3 Mascot Daemon Mascot
65. E Mascot Daemon is a client application which automates the submission of data Mascot Daemonj 7 9 sa Mascot server It runs under Microsoft Windows 2000 and later Cnstal D parade Troubleshoot Mascot Daenon 2 4 Mascot Daemon Mascot Server Mascot Server PC Mascot Daemon 2 0 1 E iQ A Windows 7 dl JE 3 oar Ps 2 J Shadow Cap 2 Net Logan _ pe Remote Desk RG E 0D 2
66. Wsooss Masco Distller Processing Uphons C Program FesWMa ScaenceVMascot DistlerMTof opt Ed Save s Dala Fe Foemat Walers Massl rox Muh Sample Fes Merge al samples into sngle seaich lt Separale search oe each sample Select Hange riki scan es Peak List Fodma Stat End Unis Seconds lt Me Output PMF Masses as Output MS 45S Fragments as Djshie Fiotect Fe myz MHz CC Mi myz CMHx Mi Ssye Mascot Dagemon 21 IData File Format l IMulti Sample Files AB MDS Sciex Analyst WIFF WIFF Select Range multi scanfiles LC Output MS MS Fragment as WMascot Server 1 2
67. aemon Service Mascot Daemon GUI Mascot Daemon Windows Mascot Daemon Service security permission 1 2 N OU 2 0 PC 7 2 1 Windows
68. ascot Daemon Le 3 1 Status Eyent Log Task Editor Farameter Editar Ne Task Database atus 33 arameter e Mascot Daemon 4 0 Status Taskk Paanelerset IParameter Editor Task Editor Event Log Status 3 File Edit Help Helresh FI 3 2 Parameter Editor 3 2 Parameter Editor 3 2 Web em CE Status Event Log Task Editor Parameter Editor Parameter set par lt Filename IE VProgram Files sBBjKMatris defaulLnar New Hpen all Searches User name Mascot Kensaku User emal mkensaku Gmalrixscience com 3 9 Search title Submitted from lt taskname gt by Mascot Daeman on lt localhost gt Tax
69. e mgf Mascot Distil1ler Status Mascot Distil1ler Project C Program Files x86 Matrix Science Mascot Daemon MGF 4 17 Real time monitor Data file list Schedule Real time monitor Ge EE LO ui ae Stalus Eyent Log ParameterEditor ss Ps ea New Run R ef kBBjKMaig Sciencet Dptions New files only i Se Specify path to root folder J 4d 29 8 BH 2012 WU Search priority In 4 Ee ctions i ude Sub fo de rs ptional wild card file or Folder name uto pri
70. et fso CreateObject Scripting FileSystemObject 4 19 External processes Mascot Daemon External processes mm Before starting task net send usami lt laskname gt is starting walt for completion Before each search No external process walt for completion L After each search C VProgram Filgslnternet Explarertiesnlare ewe lt resulturls wait for completion Fter completing task net send usaml lt taskname gt has Finished ai for completion Cancel gy Mascot Daemon External processes Before starting task net se usami taskname gt Is slartin ai for completion Befare each search No external process wait for completion After each search wscript C temp simole wbs lt resultfilename gt lt resulturls at for completion after completing task net send usami lt taskname has finished rr Wait for completion Cancel 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 8 Follow up If score less than If probability that match i
71. hedule l Follow up Pa Status EyentLog TaskEditor PaamelerEdtor mm ET Er oe wm a Mascot Data file NR _ list Where 1 F Fe 6 Schedule Start now Start at Real time monitor l Follow up l Search priority O0 20
72. ify Task database connection string and try again Choose nore to run the Mascnt Daemon seryice component on the desktop BR 5 2 Mascot Daemon OLE DB SQL Server MySQL Oracle C Program Files Matrix Science Mascot Daemon SQL TaskDB_schema xls 1 Microsoft Jet Mascot Daemon Jet 4 0 Microsoft Access 2000 TaskDB mdb TaskDB mdb Edit Preferences ADO connection l Restore default l TaskDB mdb Change 2 OLE DB Mascot Daemon OLE DB Object Linking and Embedding for Databe
73. interyal seconds 15 Save Cancel 60 10 Minimum delay between monitor searches 60 60 10 Minimum delay between follower searches 60 60
74. kensakugma xsoienoe oom Search titie Submitted from No cnzyne follower by Mascot Daemorn on MBA11WT HMS data file C Program Files x56 Matrix Science Mascot Daemon data LCOQ Digest03 0921 0924 2 dta Database SwissPFrot 2012 05 536029 sequences 130235160 residues Taxronomy Homo sapiens human 20245 sequences Tinestanp B Jun 2012 at D1 41 47 Gr Protein hits HEA HUMAN Hemoglobin subunirt aipha CSeHonmo sapiens GNeHBAlL FEel Sve2 Mascot Score Histogram lons score js 10 Log P where P js the probabdity that the obscrvcd match is a random event lndinydnal ions scores gt 29 indicate pcptdcs with sigrificant bomology ndirvidual jons scores gt 54 indhcate identity or extensrve homology p lt 0 05 Protcm scores are dermed from jons scores as a non probabilistic basis for ranking protem hits 3 Peptide Summary Report FormatAs Pegtide Summary lt Help Segnificance threshold p lt 005 Mar mamber of hits AUTO Standard sconng ModPIT scoring Jons score or expect cut off 0 Show sub sets 0 Show pop ups Supprcss pop ups Sort unassigned Decreasing Score Requre bokired Select All Select None Search Selected Error tolerant Achve Repow 1 BBa_HUNAN Maas 15245 Soore 56 Matchea 1 1 Seqoences 1 1 Henogliobin subunit alpha OSeHcomo sapiens GHe HBAL PEel SVe2 nclude this hit in error toierant search Query Cbaerved Mr expt Mr caic Delta Nisa Score Expect ak Unique Peptide 7 1 1109 3636 2216 7127 221
75. n Mascot Daemon Jet 4 0 Microsoft Access 20000 TaskDB mdb TaskDB mdb Restore default TaskDB mdb ADO connection string ADO Change 4 Timer settings Mascot Daemon PC Timer tick interval
76. n PC Web Mascot Mascot Server Mascot Server Mascot Daemon SD 2 Web Mascot Server Welcome http mascot 3 Welcome Mascot Daemon Install Mascot Daemon Installation Mascot Daemon Mascot Daemonis a chent application which automates the submission of data ml a Mascot server It runs under Microsoft Windows 2000 and later Instal Upgrade Troubleshoct 4 Daemon msi PP 7 3 _ 3 ls Windows 9 671 MB 7 saki LE FS
77. n Actions Auto print results External processes Follow up 4 mm lf probability that match is randam gt 1 in 20 Discard results Delete dd Files Hepeal at interyals of h days Merge MS MS files into single search Pass datato 2 No enzyme follower If probability that match is random gt 1 in 0 05 1 20 20 Pass data to INo enzyme follower Run ITrypsin first pass search tour2 par 0 05 No enzyme follower tour3 par Status 3 10 2 3 ILCQ Digest03 0486 0492 2 dta
78. n random gt 1 0 05 20 Repeat at intervals of 4 20 Fol low up auto print results probability that match is random gt 1 in 20 Discard results Repeat al Intervals of 1 Haus iv Pass datato 2Nn genzume follower a Aascot Daemon 26 Pass data to 1
79. nanet Do ata import filters amp ADO connection Timer settings Mascot login http mascot cgi Windows 7 Mascot Mascot Daemon Mascot Server URL Mascot Server URL Mascot Daemon 6 Mascot Server Mascot Daemon Jr Te Tas Deaa Riefresh F5 2 3 Mascot Daemon Mascot Server Mascot Daemon Mascot Server Mascot Server Mascot Server Welcome Upgrade Upgrading E
80. nt results External processes Specify path to root folder ms Falowup No folow up required 0 Include sub falders h duas 2 New files only Nane Status Pause Delete 1 Specify path to root folder D Data P Q 20031122 D Data Proteins QStar 20031102 D Data Peptides QTrap 20031103 Optional wild card file or name wiff
81. one K R C K R P N C N None CNBr Variable modifications Met gt Hs Homoserine lactone Met gt Hse Homoserin Max Missed Cleavages 1 2 0
82. onomy al entries Reporttop A amp AUTO hits Save As tour 1 Dar Database Ni Decoydatabase Protein mass kDa modifications Max missed cleavages 1 Database SwissProt Ei _Select Modiioatons aga zeas i modifications Enzyme Tryps Peptide tol In1 pa 13C 10 M5 M5 Pept de to 10 Da M54M5S lons search Dataformat Micromass PKL Duantitation None Data format M DS PKL Errar talerant search MS MS tol In3 pa Inslrument EslQUAD TOF ES MS MS tol 0 3 Da Instrument ESI QUAD TOF Mascot Daemon default par Mascot Server 3 3 Mascot Daemon 6 Q 4 5 6 1
83. scotiim skKum sm sSample 1 m gf N Pause N Resume ttle Submitted from on saki by Mascot Daemon on SAKI ion RPOL_BPK11 Delete Clone ls MI NT i RNA polymerase Bacteriophage K11 Aascot Daemon 29 Task Database File l Print File Print 5 Mascot Daemon 30 5 1 Mascot Daemon Service Mascot Daemon 2 GUI Graphical User Interfacep Mascot Daemon GUI Mascot Daemon Mascot D
84. ses gt OLD DB OLE DB ODBC Open Database Connectivity 3 0DBC Mascot Daemon MDAC 2 5 Microsoft Data Access Components OLE DB ODBC ODBC Mascot Daenon ODBC Windows 7 ODBC DSN Data Source Name MDAC 4 MS Query MS Query Office Version 4 0 Excel Version 5 0 Office Excel
85. sslynx http www matrixscience com help instruments_masslynx html AB 4000 Series TS2Mascot Mascot Daemon PC TS2Mascot AB 4000 Series ODBC TS2Mascot http www matrixscienc com pdf TS2Mascot pdf AB 4000 Series TS2Mascot Options 4 15 OK AB 4000 Series AB 4000 Series 0D 7 4 14 Micromass spl Hascot Daemon Data import lter options Paih to PKL ie older 4 15 TS2Mascot Mascot Daemon Data import filter options lcq_daexe Micromass sa Sciex Anast Data Explorer Mascot Dis
86. t datafilepath gt lt cachedpeaklist gt lt samplenumber gt lt mascot_user_id gt ID lt mascot_user_name gt Aascot Daemon 17 lt mascot_user_fu1l1 name gt lt mascot_user_email gt Taxonomy Report Topj AUTO Protein Summary Report
87. tid Peak Fikeng Massrange 50 Da lo 20 Ds below peecursor Mnmum S N 10 Monotsotopec peaks orky http www matrixscienc com mascot help instruments_4000 html 5 Data file list 4 16 Start now at Data file list 53 Mascot Daemon Schedule Start now Start at Ex Status EventLog Takewer Parameter Editor Ci Mascot Add Files Windows Data file list amp Windows 32 000 Windows
88. tol DD mmu milli mass units 0 001Da Da Instrument http www matrixscience com help search_field_help htmlI INSTRUMENT 4 4 Task Editor Mascot Daemon 20 Mascot Task 4 9 Task Editor Untitled em le EE EE ID Status Ce J Event Log ID rm ge 3 Datafile list RE SS 4 9
89. tus No enzyme follower Task Editor 3 9 Trypsinfirst pass search tour2 par C Program Files Matrix Science Mascot Daemon data 2 DTA LCQ_Digest03 0486 0492 2 dta LCQ Digest03 0921 0924 2 dta Mascot Daemon 10 3 9 SS File Edit Help Status Eyent Log Ce Parameter Editor Task Trypsin first nass searcH New Farameter set Dala impart filter ti ScienceNMascat Daemonstour2 par Naone sd Dala file list Schedule Drag and drop dala files into he area CStatnoW _ below nr click on dd Startat 9 54 29 8 Bll 2012 ontdalaNLC _Digest03 0486 0492 2 dta Realtime monitor onsdatasLCO_Digest03 0921 0924 2 dta Fallaw up Search priority I
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