Mascot Server チュートリアル
Contents
1. Significant match OR Random match N HERIZ 10 x log 1 N 0 05 5 000 500 000 2 50 70 60 5 000 Protein score is 10 Log P where F is the probability ZICH LU TRR LE Gr ABA 50 na cesta poe ne sgn nn2. Data file Mascot generic MGF Data format Instrument Start Search MIS mis
3. http mascot help msms_summaries_help html FORMAT2 http www matrixscience com help msms_summaries_help htm FORMAT2 Mascot Server 26 5 3 MIS SQ 27 Same set Sub set Intersection 27 A 3 p1 p2 p3 B EAD Same set
4. 2 31 Protein Family Summary URL http mascot cgi master_results_2 pl2file F981139 dat http www matrixscience com cgi master_results_2 pl file F981139 dat LT OR Z VAN Protein Family LTZ E Protein Family 1 2 1 Homology 3 2
5. Mascot Server 36 10 Peptide View 3565 1 TVIIEQSWGSPK 64 4 2 VVDLOESSQPSR 23 0 41 10000 1 2 MS MS Mascot Delta score MD score
6. Mascot Mascot Server Mascot Server O ama Instrument Specific Tips http mascot help_index html http www matrixscience com help_index html Mascot Distiller Mascot Server Mascot Server http www matrixscience com distiller
7. 2 30 30KDa 9 Da mmu ppm 1 0 Da 1 0 Da 1 0 Da 3C MS MS Peptide tol 1 2Da
8. Mascot Mascot Daemon Mascot Daemon Mascot Daemon Mascot Server URL Preferences Mascot Server URL http mascot cgi Save Mascot Server Mascot Daemon Windows 7 Mascot Daemon Mascot Server URL C ProgramFiles x86 Matrix Science Mascot Daemon Daemon exe l2 http www matrixscience jp pdf jap_mdaemon_ manual 2 4 pdf Help Mascot Daemon Help
9. 10 Show pop ups Suppress pop ups 8 Sort unassigned 9 Require bold red 1 Mascot Server 25 10 Dendrograms cut at 11 Preferred taxonomy NCBInr
10. Format As Filter l 26 NY Mascot Search Results a Peptide Summary Report Format As Peptide Summary Help Significance threshold p lt 0 05 Max number of hits AUTO Standard scoring MudPIT scoring lons score or expect cut off 0 Show sub sets 0 Show pop ups Suppress pop ups Sort unassigned Decreasing Score lt Require bold red E Protein Family Summary Significance threshold p lt 0 05 Max number of families AUTO 4 help Ions score or expect cut off 0 Dendrograms cut at 0 Preferred taxonomy All entries 1 Format As Summary Report HED Summary Report 26 Peptide Summary Report Protein Family Report 2 Siginificance threshold p lt 0 99 gt 1E 18
11. Identity BH AAT k Homology 2 23 MS MS FECT Homology B A TIdentity i ae CW 23 MS MS 10 Homology Identity Identity 0 05 Mascot Server 20 23 Homology Identity His 250 ote 200 ae Identity Rafa e r 0 05 Homology Bafa 20 Outliner 25 594 47
12. WMascot Server 13 3 13 Mascot Server Mascot Server Mascot MAKAAIGIDLAGTTYSCVGVNRTTPSYVAFTDTE i f WNL It Moa J MM 1 Mascot 2 3 DAKRLDGTTYLASCVGNRTTAAIGIDLGTTYSTY TD 2 2 Mascot Server Web Mascot Server PC Web IIS Apache Web Mascot IE Web
13. 10 Security Mascot security Mascot Server 46 5 ea a Mascot Server Mascot Server Mascot http mascot pdf manual pdf http www matrixscience D pdf jap_security pdf 8 6 N Wh BE i BRE H o SS V EPR Nee TO 43 Set Mascot search form defaults Welcome PRES SCIENCES HOME i MASCOT iHELP Mascot Y Search Form Defaults URL
14. Mascot search overview A History of Mascot and Mowse ASMS 2001 2012 User Meeting presentations Mascot FAQ s Using Mascot Mascot Server Search parameter reference Data file format Scoring algorithm Result Report Overview Summary Reports for PMF Summary Reports for MS MS MS MS Results Interpretation Sharing result reports Error tolerant search Exporting result reports Decoy Databases Top down Searches Percolator Quantitation Mascot System Administration Seduence database setup PC Hardware for Mascot Server Instrument Specific Tips Mascot Server AB SCIEX Analyst AB SCIEX Data Explorer AB SCIEX 4000 5000 Series TOF TOF Micromass Masslynx Thermo Finnigan Xcalibur Mascot Server 11 Protein Identification Peptide Mass Fingerprint Sequence Query MS MS Ion Search Protein chemistry
15. 30 Protein View Mascot Search Results OPSD_HUMAN Windows Internet Explorer ae OW http localhost mascot cgi protein_view pl file v 4 microsoft word 64E w h F REE V A T H x Variable modifications Oxida qro i5b amp maa EAZ We 88 concise Masc x A My SG my P gt S lt O r 2 MASCOT Search Results Protein View OPSD_HUMAN m Rhodopsin OS Homo sapiens GN RHO PE 1 SV 1 Database SwissProt Score 102 Expect 3 4e 005 Nominal mass M 39437 Calculated pI 6 21 Taxonomy Homo sapiens Sequence similarity is available as an NCBI BLAST search of OPSD HUMAN against nr Search parameters MS data file C inetpub mascot mskk sampledata pmfSample mgf Enzyme Trypsin cuts C term side of KR unless next residue is P Fixed modifications Carbamidomethyl C Variable modifications Oxidation M Mass values searched 19 Mass values matched 11 Protein sequence coverage 25 Matched peptides shown in bold red 1 MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL 51 GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVLGG
16. Post translational modifications Enzymes Autolysis Sequence databases Nucleic acid translation Amino acid reference Contaminants BLAST amp FastA JFE Mass spectrometry MS MS fragmentation Accuracy amp resolution Miscellaneous Mascot brochure PDF 2 7 Mb PC Hardware for Mascot Privacy FAQ Web Browser Compatibility 2 7 Mascot http www matrixscience com 1 WHAT S NEW 2 SUPPORT Mascot Server 12 gt 3 Mascot 3 1 Mascot Mascot Server 3
17. Mascot Distiller Mascot Distiller Average mass 1086 26 1085 1086 1087 1088 1089 1090 504 5808 512 5816 http www matrixscience com distil ler html 3 2 Mascot Server 13 1 Mascot Server ZAIN at Ei NE g http mascot help search_field_help html http www matrixscience com help search_field_help html 1 Your name Email Search title Database s Enzyme Allow up to missed cleavages Quantitation Taxonomy Fixed modifications Variable modifications Protein mass Peptide tol 19 AaAeATIL CK FAV Email
18. gt o s T gt F p3 p4 p5 F gt G oe p2 OBMBAAT HBN o O y a c F p4 F GC Score Mass Matches Sequences emPAI A 113 1 2 PRDX4_MOUSE 126 33667 4 4 3 3 0 36 Peroxiredoxin 4 OS Mus musculus GN Prdx4 PE 1 SV 1 4s 7 7 113 2 2 PRDX1_MOUSE 76 25228 3 3 2 2 0 31 Peroxiredoxin 1 OS Mus musculus GN Prdx1 PE 1 SV 1 ff y PF p2 Redisplay All None Score gt 31 indicates identity 34 31 3 gt 2 PRDX4_MOUSE El 5 peptide matches 4 non duplicate 1 di Pe Homology E E Identity BE v Auto fit to window S 3 Query Dupes Observed Mr expt Mr calc Delta M Score Expect Rank U 1 2 Peptide 22694 488 2970 974 5794 974 5518 0 0276 0 0 03 bi U SVDEIIR L 24806 527 3665 1579 0778 1579 8926 0 81480 34 0 0043 D1 UW R VSVADHSLHLSK A 31 9533 605 0467 1208 0787 1207 7056 0 3731
19. HTTP Mascot 14 2 Mascot Server 14 Mascot Server Fal af Ethernet Ethernet PC z2 Bs i Ta E PC MASCOT Server SleS NOR CVeEry I D PC Mascot Server PC Ethernet 1
20. 23 2 Mascot Server 21 4 3 FDR False Discovery Rate Mascot 24 24 BE GKE DHR 0 05 6 24 Mascot 24
21. Mascot Server PC http mascot Mascot Server 1 Welcome Mascot 2 Mascot Search 1 1 2 MS Mascot PMF Peptide Mass Fingerprint MS Mascot Search 22 Peptide Mass Fingerprint l 3 PMF MASCOT Peptide Mass Fingerprint 1 1 3 MASCOT Peptide Mass Fingerprint 3 Ce Database s Enzyme Allow up to D Fixed modifications Variable modifications
22. Mascot Server Ric Ce inlA OC ee Ca eT 2 MassLynx Mascot Server 41 MassLynx Mascot pk1 MassLynx sample list Mascot Daemon Data import filter WMascot Daemon Mascot http mascot help instruments_masslynx html http www matrixscience com help instruments_masslynx html 6 6 Mascot MGF 6 7 Mascot MGF
23. 6 8 BioTools Mascot Server Mascot Server Mascot Server 42 gt 7 Mascot Mascot Daemon Web Mascot 100 Mascot PC 100 Mascot Daemon Mascot 100 Mascot Mascot
24. 2 2 ete OIC Aye ie OS 8 Vice Ai 2 SU ae Ctrl1 2 2 1 0 MD Mascot Distiller NCBInr Fix
25. MASCOT search status page Version 2 4 0 Matrix lt 2 logical 1 physical Intel pro Search log imonitor log error bg Error message descriptions Do not auto refresh this page cRAP Fas _ fasta cRAP_20100519 fasta Pathname C inetpub mascot sequence cRAP current cRAP_20100519 fasta Statisti ESI hwa EST _husan 2012052 In us e ine Wea mapped Nunber of threads e ine Ven mapped YES Nuaber of threads 2 n use e Mon Jun 04 09 59 45 s ped YES Nuaber of thread 76ZE 4EVA 64HG FMVY UCU3 Licence Info ors No hyper threading in cpu dual core CPUs 0 J available using 0 7 Science K K LO searches runn ngl Cess ily inetpub mascot sequence cRAP current cRAP_ utSUISUICS 0 Request u earches YES YES Request to mew map Current YES C inet pub nascot sequence EST_husan current EST_human_ fasta ci net pub sascot sequence EST_human current EST_ human 20120523 fasta fied t nony Fawily 3 fasta use on Jun 04 09 59 46 YES Request to m a i In use on Jun 04 09 59 46 se S Request to new map Current YES CP Ce Searches log error log
26. G p2 p4 A Intersection Mascot Server 27 5 4 Concise Protein Summary PMF PMF 28 Concise Protein Summary 28 Concise Protein Summary SS a E 6x 9 cose summary feel TE S MATRIX cwcz Mascot Search Results usami Email usami matrixscience com Search title Quick start for a PMF search MS data file C inetpub mascot mskk sampledata pmfSample mgf Database SwissProt 2011 02 525207 sequences 185522689 residues Timestamp 22 Feb 2011 at 05 07 34 GMT 102 for OPSD HUMAN Rhodopsin OS Homo sapiens GN RHO PE 1 SV 1 Top Score Mascot Score Histogram Protein score is 10 Log P where P is the probability that the observed match is a random event Protein scores greater than 70 are significant p lt 0 05 EE i 1 75 100 Protein Score Concise Protein Summary Rep
27. Mascot Mascot Server 14 Da mu MS MS tol F I J J EUW Chae lb 72a Peptide Charge i wr PARTE di ia aD eae E T E i Mono sotopic Monoisotopic Average Average Data file Data file uery 1 DL TS recursor ee f TY BY AVY OMBRABETAP AUT nstrumen Error tolerant D Ge NY 000
28. 221 2851 x 100 7 75 25 above identity threshold Adjust to RA VA CHE LZEFDR 5 FATED FDR 4 96 0 06710 Decoy http mascot help decoy_help html http www matrixscience com help decoy_help html Mascot Server 23 Po 5 1 2 3 Summary Report Protein View Peptide View Summary Report 5 Ae gy
29. Peptide tol Fixed modifications Variable modifications S gt Your name Email Searchtitle Mascot Data file 3 Database s SwissProt Enzyme Trypsin 1 Welcome Matrix Science Home Windows Internet Explorer _ ye Matrix Science Home fi MATRIX SCIENCE Welcome This site features Mascot a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases To assist you the help text for Mascot forms a substant
30. 0PSD_HUMAN 11 Loved Max number of hits Format As 50 Significance threshold p lt Format As 1 1 Concise Protein Summary http mascot help pmf_summaries_help html CONCISE http www matrixscience com help pmf_summar ies_help html CONCI SE Mascot Server 28 5 5 Protein Summary
31. Web Report top AUTO hits Save defaults as cookie 8 7 Mascot Server C inetub macot logs errorlog txt Welcome Database Status error log l Error M00422 Job 16 X00308 compress Wed Aug 17 15 08 09 2011 Accession gi 323714265 is a duplicate database file name nr_human_20110817x fasta MO0422 Welcome Database Status Error message descriptions Mascot Server 47 8 8 Mascot Server C inetpub mascot
32. 0 05 BREL LTES P N E 22 Mascot Score Histogram Significant match FF LO i Humber of Hits on a 79 Lon Protein Score Mascot Server 19 E P x N Mascot E P x N Mascot Server 0 05 0 05 P
33. RAW extract_msn Mascot Server PC Mascot Server 1cq_dta_sha11 extract_msn Mascot Daemon Data import filter Mascot Daemon Mascot http mascot help instruments_xcalibur htm LCQ_DTA http www matrixscience com help instruments_xcal ibur html LCQ DTA http www matrixscience jp pdf jap _settingsOfMs MdForXcal iburRawFi le pdf 4 RAW http mascot help instruments_xcalibur html EXTRACT http www matrixscience com help instruments_xcal ibur html EXTRACT 6 5 1 ProteinLynx Global Server PLGS PLGD Mascot Server
34. Sort filterl Your name Email Search title User Name Email Title 40 MASCOT search log Log File logs searches log Start at 1 end 1 start 1 Job PID dbase User Name Em Title 9 i W Pd A M usami example 30000 3044 SwissPro usami us SiteLocalizationAnalysisExample 1 from T 20597 272 SwissPro usami us auto ETsearch for MS MS Example 20596 20595 lt 20594 7392 SwissPro usami us MS MS Example 20593 6172 IPI huma usami us MS MS Example 20592 8788 cRAP usami us MS MS Example 20482 8784 SwissProltaru Usami us MS MS Example 20470 9756 SwissPro usami us Peptide Mass Fingerprint Example 20468 4932 SwissPro usami us Error tolerant search example Manual O 20467 3580 SwissPro usami us Error tolerant search example Manual O 20305 11032 SwissPro usami us MS MS Example how many 50 GETs E Pr Typ EnzymeIP User ID 7434 in log 51 after filters Data dir Dur In start time Status Fri Jun 0 Fri Apr 201537595 201214 User read res 0 Fri Apr 20 14 16 19 2012 11 User read res MIS Yes 0 Fri Apr 20 14 1550 2012 8 User read res MIS Yes 0 Thu Apr 19 18 17 32 2012 10 User read res MIS Yes 0 Thu Apr 19 17 59 39 2012 5 User read r
35. 60 5 000 5000X10 0 005 E 0 05 0 5 500 000 500000X10 0 5 0 05 50 SQ MIS 4 2 Identity amp Homology Ea es SQ MIS 2
36. 1 2 CH60_DROME 1 CH60_HUMAN 27 1 CH60_HUMAN K VGGTSDVEVNEK K 1 2 CH60_DROME 2 R VGGSSEVEVNEKJK 1 Require bold red lFormat As Peptide matches not assigned to protein hits no details means no match
37. CH60_HUMAN CH60_DROME Peptide Summary http mascot help msms_summaries_help html PEPSUM http www matrixscience com help msms_summar ies_help html PEPSUM 5 9 Select Summary MIS SQ Mascot Server 34 33 Select Summary Protein hits Format As 34 Select Summary Report Select Summary Report Peptide Summary Report 34 Select Summary Report SMATRIX SCIENCE Mascot Search Results User Email Search title MS data file MS MS Example C Auto MSMS output Sample 1 pkl Protein hits CH60 HUMAN 60 kDa heat shock protein CH60 DROME 60 kDa heat shock protein Select Summary Report Select Summary protein hits Significance threshold p lt 0 05 Standard scoring Mu
38. 1 PMF Peptide Mass Fingerprint MS 2 SQ Sequence Query 3 MIS MS MS Ions Search MS MS MS MS 17 m z 1085 5803 m z NE ee 1085 5803 1 17 1 MH
39. 16 Mascot Server PC C inetpub mascot config data logs robocopy Windows http www matrixscienc
40. 43 Set Mascot Search Go Logged in as admin Logout Mascot gt Set Search Defaults Set Mascot search form defaults search form defaults Database EST human SwissProt http mascot cgi form_defaults pl RE an craves Enzyme Trypsin X ee o Li Allow upto 1 missed cleavages aa l Save defaults as cookie amidated Eterm n Your search form defaults have been saved as cookie modifications Aceb N term S S EERE an midated C term x Tin sented ee C term Show all mods 3 Web Cookie Quantitation None X Peptide tol 1 2 Da gt 13C 0 Mascot Server XT MS MS tol 0 6 Da Web Cookie SSR instrument a eousoeo Web
41. Modifications Mascot Configuration Modification Add new modification Mascot Configuration Editor 1 Elements 2 Amino Acids 3 Modifications 4 Symbols 5 Enzymes 6 Instruments MIS 7 Quantitation 8 Configuration Option mascot dat Options 9 Database Manager
42. SM 5 Protein View Mascot Search Results OPSD_HUMAN Windows Internet Explorer bobo JQ fe ntp oos tein_view prfe gt 3 x Google pe A ERTAN we e m 5 Mascot Search Results OPSD_HUMAN A S we P 5 Q SOAS MASCOT Search Results Protein View OPSD_HUMAN Rhodopsin OS Homo sapiens GN RHO PE 1 SV 1 Database SwissProt Score 102 Expect 3 4 005 Nominal mass M 39437 Calculated pi 6 21 Taxonomy Homo sapiens Sequence similarity is available as an NCBI BLAST search of OPSD HUMAN against nr Search parameters MS data file C inetpub mascot mskk sempledata prfSample mgt Enzyme Trypsin cuts C term sade of KR unless next residue is P Fixed modifications Carbamedomethy C Variable modifications Oxidation M Mass values searched 19 Mass values matched 11 Protein sequence coverage 25 Matched peptides shown in bold red 1 MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWOFSML AAYMFLLIVL 51 GFPINFLTLY VIVQHKKLRT PLNYILLNLA VADLFMVLGG FISTLYTSLH 101 GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRIGE 151 NHAIMGVAFT WVMALACAAP PLAGWSRYIP EGLQCSCGID YYTLKPEVNN 201 ESFVIYMFVV HFTIPMIIIF FCYGQLVFTY KEAAAQQQES ATTQKAEREV 251 TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFARKSAAT 301 YNPVIYIMG KQFPRNCMLTT ICCOK
43. 3 Max number of hits AUTO 0 MIS ce 4 Standard scoring MudPIT scoring 5 Ions score or expect cut off 0 1 1 6 Show sub sets 0 1 0 5 Sub set 7
44. http www matrixscience com pdf asms_tutorial_2005 pdf http www matrixscience com help scoring_help html Mascot Server MIS random event MIS P a priori P 10 x OZ 49 P 4 4 P P 0 000001 1x10 60
45. 0 05 3 3E 005 2 40 18 903 3420 1373 6810 1403 7220 1727 9160 1743 9510 1759 9660 1788 7210 1804 7100 1818 9630 2159 1430 2256 8710 11 Protein Summary http mascot help pmf_summaries_help html PROTSUM http www matrixscience com help pmf_summaries_help html PROTSUM Mascot Server 29 5 6 Protein View PMF MIS SQ Summary Report 30 Protein View
46. http mascot help results_help html http www matrixscience com help results_help html 2 1 Summary Report Concise Protein Summary Protein Summary Protein Family Summary MS MS 300 MIS SQ Peptide Summary MS MS 300 Select Summary Peptide Summary 2 Protein View 3 Peptide View Mascot Server 24 5 2 26 Summary Report Summary Report
47. 7 PMF 4 Clk BYE A AT 0 4 Mascot Search Results OOE GT F E V A T H gt Cond x A A A mm P gt S KONG Mascot Search Results User usami Email usami matrixscience com Search title Quick start for a PMP search MS data file C inetpub mascot mskk sampledata pmfSample mgf Database SwissProt 2011 02 525207 sequences 185522689 residues Timestamp 22 Feb 2011 at 05 07 34 GMT Top Score 102 for OPSD HUMAN Rhodopsin OS Homo sapiens GN RHO PE 1 SV 1 Mascot Score Histogram Protein score is 10 Log P where P is the probability that the observed match is a random event Protein scores greater than 70 are significant p lt 0 05 100 Protein Score Concise Protein Summary Report FormatAs Concise Protein Summary Help Significance threshold p lt 0 05 Max number of hits AUTO Re Search All Search Unmatched 1 OPSD HUMAN Mass 39437 Score 102 Rhodopsin OS Homo sapiens GN RHO PE 1 Sv 1 OPSD MACFA Mass 39606 Expect 3 3e 005 Matches 1 Score 65 Expect 0 15 Matches amp
48. Job Welcome Search Log URL 40 MASCOT search log http mascot x cgi ms review exe Job 1 1 Sort filter Sort filter l Mascot Server 44
49. 4 D True Positive Negative Decoy True Positive False Positive 1 False Positive 3 NY 2 False Positive 1 CH False Positive True Positive FDR FDR False Positive False Positive True Positive Decoy DB Target DB Mascot Server Target O ecoy Target Decoy FDR
50. Protein Sumary http mascot help results_help html PROT http www matrixscience com help results_help htmI PROT Mascot Server 30 5 Protein Family Summary MIS SQ Mascot MS MS 300 31 Protein Family Summary 31 Protein Family Summary MASCOT Search Results User E mail Search title iPRG2008 SwissProt Mouse MS data file D WPRG2008 mgf merged mgf Databases 1 CRAP 20090731 111 sequences 37 180 residues 2 SwissProt 57 14 514 789 sequences 181 163 771 residues Taxonomy 1 none 2 Mus 16 273 sequences Timestamp 5 Mar 2010 at 14 04 48 GMT Warning No taxonomy indexes for CRAP taxonomy Mus ignored Searching ali entries in CRAP Re search All Non significant Unassigned help Expor As XML Not what you expected Try ofthe select summary gt Search parameters gt Score distribution PLegend Protein Family Summary Filter Significance threshold p lt 0 05 Max number of families AUTO help lons score or expect cut off 0 Dendrograms cutat 0 Show Percolato
51. 1Da nm z 17 Mascot Server Mascot Mascot Distiller ee Mascot SQ MIS 1 2 b bt y y 3 MS MS deconvolve 1
52. 500 000 70 Random match 22 Mascot Score Histogram Significant match Random match 70 HERIT Expect value
53. Mascot Search 1 2 2 MS MS Mascot MIS MS MS Ion Search MS MS Principle of Parsimony Mascot Search 77 MS MS Ion Search MIS IMASCOT MS MS Tons Search 8 MASCOT MS MS Ions Search 8 Database s Enzyme Allow up to D Fixed modifications Variable modifications Peptide tol MS MS tol d2 Instrument Fixed modifications Vari
54. http www ncbi nim nih gov BLAST fasta shtml http help seq_db_setup html httbp www matrixscience com help seq_db_setup html http www matrixscience jpD pdf jap_database_setup pdf Mascot Server 10 2 6 e____________EsEsFE____________ XI Welcome 1 Welcome URL http www matrixscience jp jap_manual_ index html 2 Welcome Setup amp Installation Manuall 3 Welcome HELPI URL http help_index html http www matrixscience com help_index html Help Topic Index MASCOT General ASMS
55. N X 7 AS Mascot Daemon is a application which automates the submission of data files to a Mascot server It runs under Micrds T shoot Install Upgrade Trouble AY P4 O ie a D Kkt We come Mascot Documentation Help on using Mascot and understanding the results is contained in these HTML pages Click on Help at the top of the page to browse the help topics or Oo Oo ye gt 4 use the keyword search facility The following documents are mainly of interest to system administrators URL hea elease otes http www matr ixscience com Mascot Server Setup amp Installation Manual Program Reference http mascot pdf manual pdf 8 2 Search Log Mascot Server Mascot
56. Site Analysis MD score 10 91 35 2 S4 84 N9 100 Peptide View http mascot help msms_summaries_help html PEPSUM http www matrixscience com help msms_summaries_help html PEPSUM Site Analysis http mascot help pt_mods_help html SITE http www matrixscience com help pt_mods_help htmI SITE Mascot Server 3 5 11 PMF MIS S0 Export Search Results Format As 36 Export search result
57. Mr calc Delta Miss Score Expect Rank 4 2 Identity ie amp HomologyBHB z lt w Unique Uniqaue U Peptide 1 PR to 1 2 2 3 4 11 1 ICH60_HUMAN K APGFGDNRIK 11
58. 10 MS MS Bs MOC 2 30 tk Peptide View 11 3 Peptide View 9 MIS 3 HLM1_YEAST ELM1_YEAST 11 3 MS MS Q17 PSSPLMDRTVGK N 3
59. DS 1 Web IE Safari Firefox Chrome 2 Mascot Daemon Mascot Distiller 3 Analyst QS BioTools Launchpad Bioworks Mascot Server DTACA s noi HTML eo Proteome Discoverer MassLynx need AROMAT Mascot Mascot 4 ER e l Client Mascot Server Server EURON eA I OCRE T k aT EON YD a Mascot Server 2 4 Mascot Server C inetpub mascot 16 Mascot Server 16 cgi x cgi html
60. PMF missed cleavages Variable modifications Peptide tol MS http www matrixscience com cgi master_results pl file data F981138 dat 3 4 MIS MS MS Ions Search MIS 2 Mascot Server 16 1 Ei
61. Summary Report MTS 20 Decoy L Start Search Mascot Database s Target Decoy 2 2 2 25 FDR URL ProteinFamily Summary yr Decoy search summary random protein sequences Mascot Server 22 http mascot cgi master_results_2 pI2file F981139 dat http www matrixscience com cgi master_results_2 pl fi le F981139 dat 25 False Discovery Rate FDR Protein Family Summary Significance threshold p lt
62. 05 fe Sy a O ecoy B Po Te Report top AUTO Start Search Mascot Error tolerant Mascot Server 15 3 3 PMF Peptide Mass Fingerprint PMF MS 6 A 18 PME AAT MS MASCOT Peptide Mass Fingerprint Web PMF 18 Welcome ene Kne aaa Y Mascot Y 7 Peptide M
63. 2 1 KU MS MS 19 Web MIS 20 Welcome Mascot MS MS Ion Search 1 MIS
64. 2 Mascot Score Histogram BE IT 4 70 3 Concise Protein Snmmary Report PMF 2 Concise Protein Summary Report Protein Summary Report 4 Concise Protein Summary Report 4 Bia 4 11 4 4 OPSD_HUMAN Mass BORE 4 139437 Score 4 1102 Expect 4 3 3e 005 Matches 4 11 4 Rhodopsin 0S Homo 4 OPSD_MACFA 5 Search Parameters ae 4 TOPSD_HUMAN ze tk Protein View 0 5
65. p1 p2 p3 C E A Sub set F G A p4 p5 A Intersection 27 F http mascot help interpretation_help html http www matrixscience com help interpretation_help html 27 5 p1 p5 A pl p2 p3 B pl p2 p3 A gt A Same set C pl p2 D p2 p3 A A Sub set E pl F p3 p4 p5 A
66. http mascot help msms_summaries_help html BUILDER http www matrixscience com he lp msms_summaries_help html BUILDER 37 Protein Family Summary Report Builder szvce MASCOT Search Results User Mel Anogaster E mail mel bioc cam ac uk Search title Time flies like an arrow MS data file U Docs Quantitation iTRAQ cantab denisef28QSTARcor mgf Database SwissProt 51 6 257 964 sequences 93 947 433 residues Timestamp 19 Feb 2007 at 14 31 55 GMT Re search Al Not what you expected Try athe peptide summary Non significant Unassigned help Export As XML gt Search parameters gt Score distribution gt Legend Protein Family Summary Filter Significance threshold p lt 0 05 Ions score or expect cut off 0 Max number of families AUTO Dendrograms cutat 0 4 help None bd Automatic Preferred taxonomy All entries Quantitate Protein ratio type Weighted v Min precursor charge 1 Min peptides Unique peptides only Display Report peptide ratios ess ener Buco Protein hits 13 proteins Normalisation Outlier removal help 4 YColumns custom 13 out of 27 Saved arrangement _ Standard default Custom Enabled Available Family Protein hits Database Member Accession emPAl Score 115 114 Mass Number of peptides 115 114 Num of matches Sign
67. Mascot Server 45 8 4 Configuration Editor Mascot Server 42 Mascot Configuration Mascot Configuration Administrator legeuts Elements Element masses Vy i Amino Acids Amino Acid Data C netpub mascot cont 8 7 10g Modifications Modification definitions Symbols Symbols used in chemical formulae a S Mascot Enzymes Enzyme definitions Instruments Fragmentation Rules 1 Be a gt Quantitation Quantitation Methods Conf 1 gurat lon Edi tor L ue bal wh Configuration Options Global Options in mascot dat 5 8 NS Database Manager Sequence databases Parse Rules and automated downloads X o We come 7 Security Security Administration Pages Configuration Editor URL 42 Mascot Configuration http mascot x cgi ms config exe
68. 1 2 4 117 2 102 4 30 20 lar 37ER S3 S2 T9 Site Analysis S3 1 85 5 PITT AVP Hav Mascot Server 10 Protein View ree x Search Results ELNI YEAST Wiadows Ieternet Biore e f w Mu P A we 5 BPeptige Summary Repo A Mascot Sameh Mand Mencet Search Resets 0 mh Aee 5 yA Oe i222 MASCOT Search Results Protein View ELM1_YEAST Serine threonine protein kinase ELM1 OS Saccharomyces cerevisiae strain ATCC 204508 S288c GN ELM1 PE 1 SV 2 Database SwaaProt Score 259 Nominal mass M 72990 Calculated pt Taxonomy Saccharomyces cogitat 5238c atte as an NORI BLAST search of ALMI YEAST against nr Search parameters MS dasta Me rorTolSample ryme CJP cuts tmmm side ixed Cakandomnsttni lt aiaie modificat
69. Format As MS MS http mascot cgi master_results pIl2file data F981123 dat http www matrixscience com cgi master_results pI2file data F981123 dat 33 Peptide Summary SEE Mascot Search Results User Email Search title MS MS Example MS data file C Anto MSMS output Sample 1 pkl Database SwissProt 51 6 257964 sequences 93947433 residues Timestamp 19 Feb 2007 at 14 09 47 OMT Protein hits HED MUMAN 60 kDa heat shock protein mitochondriel precursor UHsp 0 60 kDa chaperonin CPNGO Heat shock wm EO kDa heat shock protein mitochondrial precursor Hap kDa chaperonin CPN Heat shock Mascot Score Histogram Ions score is 10 Log P where P is the probability that the observed match is a random event Individual ions scores gt 38 mxdicate identity or extensive homology p lt 0 05 Protein scores are derived from ions scores as a non probabilistic basis for ranking protein hits Member of Hits r T T 7 0 5or 100 Protein Score Peptide Summary Report Format As Peptide Summary Significance threshold p lt 0 05 Max number of tats 2 Standard scoring
70. Mascot Server 17 3 5 SQ Sequence Query FS o Pt oo EE gt SQ JJ JJ 21 SQ MATRIX sae MASCOT Sequence Query Your name usami Email usami matnxscence com a Search title SQt FiH 1489 430 tag 650 213 GWSV 1079 335 7 Database s EST human Enzyme Trypsin PME MIS lees yg SQ gals Allow upto 1 missed deavages SwissProt Quantitation None J L ae ss a All entries X i Carbamidomethyl C A 00 osm pray oA 4 Cte a M seq comp ions tag etag Dooy af mosSScations Anonas loss tem Oh E oa ren none selected 8 a tin ON term lt arbamyl N term O 5 Bele Carboxymethyl C Mi USTA seq comp SR Peptide tol 0 6 Da sC 0 MS MStol 0 6 Da
71. gt Your name Email Search title Mascot Data file Start Search 8 Database s SwissProt Enzyme Lys C P Allow up to 1 missed cleavages Mascot Server 6 D Fixed modifications Carbamidomethyl C Variable modifications Phospho ST Peptide tol 50 ppm Data file Mascot Server PC C inetpub mascot mskk sampledata errorTolSample mf 1 2 4 3 Start Search Mascot IMascot Search Results E e Swis 11 02 5
72. 2 Data Explorer Data Explorer Visual Basic Mascot Server Data Explorer Mascot Daemon Data import filter Mascot Daemon Mascot http mascot help instruments_data_explorer html http www matrixscience com he lp instruments_data_explorer html Mascot Server 40 3 AB SCIEX 4000 5000 TOF TOE GPS Explorer TS2Mascot Mascot Server 0Oracle Mascot Server MS Data Converter Oracle WMascot MF V
73. 33 2 CH60_HUMAN CH60_DROME CH60_HUMAN 1 CH60_HUMAN Mass 61016 Score 1176 WMS MS MS MS Matches 27 27 Sequences 17 17 60 kDa heat shock protein mitochondrial precursor Hsp60 60 kDa chaperonin CPN60 Heat shock Query MS MS Peptide View Observed Mr expt
74. 5 3 5 4 Concise Protein Summary PMF 5 5 Protein Summary PMF 5 6 Protein View PMF MIS SQ 5 7 Protein Family Summary MIS SQ 5 8 Peptide Summary MIS SQ 5 9 Select Summary MIS SQ 5 10 Peptide View MIS SQ 5 11 PMF MIS SQ 5 12 Report Builder MIS SQ 6 38 6 1 62 63 6 4 65 66 6 7 6 8 1 Mascot Mascot Daemon Af 7 1 7 2 8 Mascot Server 42 8 1 Welcome 8 2 Search Log 8 3 Database Status 8 4 Configuration Editor 8 5 8 6 8 7 8 8 Mascot Server 3 gt 1 Mascot 1 1 PMF Peptide Mass Fingerprint 1 1 1 Mascot Server eb
75. 3 3 Sequences 9 13 3 9 Ser ine threonine protein Query MS MS F Observed Mr expt Mr Mr calc Mr ppom ppm Miss Score Expect Rank Unique U Peptide 5 Search Parameters 9 ELM1_YEAST Protein View
76. TRY1_BOVIN Mass 26453 Score 64 Matches 1 1 Sequences 1 1 Cationic trypsin OS Bos taurus PE 1 SV 3 Query Observed Mr expt Mr calc Delta Miss Score Expect Rank Unique Peptide 1 1489 4300 1489 4300 1489 7348 0 3048 0 64 4e 007 1 U K LOGI VSWGSGCAQK N IK LQGIVSWGSGCAQK N 64 4E10 007 SwissProt TRY1_BOVIN TRY1_BOVIN http mascot help sq_help html http www matrixscience com help sq_help html Mascot Server 18 gt 4 4 1 Mascot Server 2 Mascot Server
77. http mascot help instruments_4000 Hhtml http www matrixscience com help instruments_4000 html 6 3 LAUNCHPAD Mascot Server Mascot Server 6 4 1 Bioworks Mascot Server Mascot Server http mascot help instruments_xcalibur htm BIOWORKS http www matrixscience com he lp instruments_xcalibur html BIOWORKS 2 Proteome Discoverer Mascot Server Mascot Server http mascot help instruments_xcalibur htm PROTD http www matrixscience com help instruments_xcalibur html PROTD 3 leq _dta_shell
78. A gt gt Peptide charge Mr X Monoisotopic Average 10nNS 7 A X tag S etag Error Tolerant 1489 430 tag 650 213 GWSV 1079 335 gt 0 x s gt Semi 0 tag 1 Error OC TE Start Search Reset Form Tolerant etag Error tolerant etag ions tag etag seqa comp seqC Blast 21 Query 1489 430 tag 650 213 GWSV 1079 335 Start Search Mascot
79. Mascot Daemon Mascot Server Web Mascot Server PC Mascot Server PC PC 1 Mascot Daemon Mascot Server Mascot Server Welcome 38 Welcome Mascot Daemon Mascot Daemon Mascot Daemon is a client application which automates the submission of data files te a Mascot server It runs under Microsoft Windows 2000 and later C install pgrade Troubleshoot http mascot Installl 38 Installing Mascot Daemon 5 Install Mascot Daemon by clicking on this link Daemon msi l
80. 24 BYR Ho CO OO 4 True Positive False Positive True Negative False Negative False Positive FDR False Discovery Rate D False Positive True Negative 1 True Positive False Positive
81. S3 y 10 y 11 98Da y 10 98 yQ 1 98 3 MS MS Peptide View 10 12 Score 1 2 Sequence Peptide View 12
82. URL cgi http mascot cgi l C inetpub mascot x cgi gt http mascot x cgi html http mascot Web Help Mascot Server config data DB Taxonomy logs sequence C inetpub mascot config data logs 2 5 FASTA Mascot FASTA
83. 0 0000 Ions Score 117 Expect 1 6e 009 Matches 11 83 fragment ions using 10 most intense peaks help b b b Seq y y y 1 98 0600 P 12 2 185 0921 167 0815 S 1172 6092 1155 5827 1154 5987 11 3 254 1135 236 1030 S 1085 5772 1068 5506 1067 3666 10 4 351 1663 333 1557 P 1016 5557 999 5292 998 5452 9 5 464 2504 446 2398 L 919 5030 902 4764 901 4924 8 6 595 2908 577 2803 M 806 4189 789 3924 788 4083 7 7 710 3178 692 3072 D 675 3784 658 3519 657 3679 6 8 866 4189 849 3923 848 4083 R 560 3515 543 3249 542 3409 5 9 967 4666 950 4400 949 4560 T 404 2504 387 2238 386 2398 4 12 10 Sequence Site Analysis 102 4 1366 63 16 0 0089 PSSPLMDRIVGK phospho 52 15 41 30 2 1366 6316 0 0089 PSSPLMDRTVGK Phospho T9 0 00 23 2 1366 6616 0 0389 SDVDYIDSGLVGK 20 4 1365 6639 0 9589 FAEETPMLPGFR 20 1 1366 6605 0 0378 ILASRLEEERGK 19 4 1365 5925 1 0302 PALDTNDAARDK 19 3 11366 558810 0639 PSHCEGVSISSK Mascot Server 8 gt 2 21 Mascot Server
84. MudPIT scoring lons score or expect cut off 0 05 Show sub sets 0 Show pop ups Suppress pop ups Sort unassigned Decreasing Score Require bold red Select All Select None Search Selected Error tolerant Archive Report 1 MOO NUMAN Mase 61016 Score 1170 Matches 27 27 Sequences 17 0 kDa heat shock protein matochondrisl precursor iMsp 60 kDs chaperonin CPN60 Meat shock heck to include this hit in error tolerant search or archive report Query Observed Mr expt Mr calc Delts Miss Score Expect Rank Unique Peptide 417 1822 832 3496 3 0 0325 a 45 0 016 2 R APOFGONR K 7433 043 4720 0 0346 0 46 0 017 1 y KW VGEVTVTE D 2499 900 4853 0 0428 52 0 0039 R LSDGVAVLE V y 456 7806 911 5467 0 0337 59 0 00056 3 u K VOLOVVAVKE A v 400 959 4740 0 0200 45 017 R VTDALNATH A J 24 3 u EICHIISDAMEK X 7 i K EIGNIISDAHK K Oxidation 7 j j K WAGVRGSLIVER 1 7 27 2 u K VOOTSDVEVNEK K v v R TVIIBOSWOSPR V y u R GVMLAVDAVIABLE K 7 2 J R GVMLAVDAVIAELE K 7 u R GVMLAVDAVIABLE K Oxidation M y U R GVMLAVDAVIAELE K Oxidation M Top scoring peptide matches to query ii 7 U K TLNDELEIIEGMK P Score greater than 27 indicates homology A a esc asane A Score greater than 40 indicates identity 7 3 6 u K ISSIQSTVPALELANAHR E J i P Sc Expect Delta Hit Protein Peptide 7 Rg i u R ALHL LLADAVAVTIGGE G i SN y U RALOGVDLLADAVAVTMGRPE G Oxidation M 0 016 0 0
85. 1 QFRNCMLTTICCGK N 1804 7100 1803 7027 1803 7889 0 0861 312 325 1 QFRNCMLTTICCGK N Oxidation M 1818 9630 1817 9557 1817 8755 0 0802 232 248 1 EAAAQQQESATTQKAER E 2159 1430 2158 1357 2158 1067 0 0290 297 314 1 SAAIYNPVIYIMMNKQFR N 2256 8710 2255 8637 2256 0634 0 1996 E 2A 0 MNGTEGPNFYVPFSNATGVVR S No match to 832 6620 1186 4390 1515 4440 1617 8570 2174 8120 2190 1120 ama h e OPSD MACFA Mass 39606 Score 65 Expect 0 15 Matches 8 Rhodopsin OS Macaca fascicularis GN RHO PE 2 SV 1 Observed Mr expt Mr calc Delta Start End Miss Peptide 903 3420 902 3347 902 4345 0 0998 340 348 0 K TETSQVAPA 1373 6810 1372 6737 1372 5608 0 1130 315 325 0 R NCMLTTICCGK N Oxidation M 1403 7220 1402 7147 1402 6576 0 0571 326 339 0 K NPLGDDEASATVSK T 1743 9510 1742 9437 1742 8735 0 0702 297 3ii 0 K SASIYNPVIYIMMNK Q 1759 9660 1758 9587 1758 8684 0 0903 297 311 0 K SASIYNPVIYIMMNK Q Oxidation M 1788 7210 1787 7137 1787 7939 0 0802 312 325 1 K QFRNCMLTTICCGK N 1804 7100 1803 7027 1803 7889 0 0861 312 325 1 K QFRNCMLTTICCGK N Oxidation M 2256 8710 2255 8637 2256 0634 0 1996 22 0 MNGTEGPNFYVPFSNATGVVR S a No match to 832 6620 1186 4390 1515 4440 1617 8570 i 2174 8120 2190 1120 2273 2660 2288 4890 J N 9160 1818 9630 2159 1430 Search Parameters Type of search Peptide Mass Fingerprint Enzyme Trypsin E Fixed modificat
86. 102 Chorion peroxidase precursor 16 SwissProt GBLP_DROME 38892 4 5 4 1 117 2 172 2 501 Guanine nucleotide binding prd 17 SwissProt TOP2_DROME 188379 4 10 4 1 096 4 004 6 741 DNA topoisomerase 2 EC 5 99 19 SwissProt H2B_ACRFO 16544 2 3 2 1 442 4 721 9 121 Histone H2B Acropora formo4 25 SwissProt FAS1_DROME 78934 2 3 2 1 492 1 413 1 066 Fasciclin 1 precursor Fasciclil 27 Swis Dro ZRLO DROM aca 3 3 1 256 1 958 2 789 60S ribosomal protein L9 Drg 28 Swis 8 4 1 422 1 906 1 087 Heat shock 70 kDa protein coq Not what you expected Try athe peptide summary Mascot Server 39 gt 6 RAW LC Mascot
87. 1186 4390 1515 4440 1617 8570 2174 8120 2190 1120 2273 2660 2288 4890 100 1000 1500 2000 1000 1500 2000 RMS error 59 ppa Mass Da RMS error 59 ppa Mass Da ID OPSD_HUMAN Reviewed 348 AA AC P08100 Q16414 Q2M249 DT 01 AUG 1988 integrated into UniProtKB Swiss Prot DT 01 AUG 1988 sequence version 1 DT 16 MAY 2012 entry version 144 DE RecName Full Rhodopsin DE AltName Full Opsin 2 CN Name RHO Synonyms 0PN2 os Homo sapiens Human oc Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi sl Protein View NCBI1 False Positive
88. FISTLYISLH 101 GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE 151 NHAIMGVAFT WVMALACAAP PLAGWSRYIP EGLQCSCGID YYTLKPEVNN 201 ESFVIYMFVV HFTIPMIIIF FCYGQLVFIV KEAAAOOOES ATTOKAEKEV 251 TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI 301 YNPVIYIMMN KOFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA Unformatted sequence string 348 residues for pasting into other applications Sort peptides by Residue Number Increasing Mass Decreasing Mass Show predicted peptides also Start End Observed Mr expt Mr calc Delta M Peptide L 21 2256 8710 2255 8637 2256 0634 0 1996 0 MNGTEGPNFYVPFSNATGVVR S 232 248 1818 9630 1817 9557 1817 8755 0 0802 1 K EAAAQOQOQESATTQKAEK E oor SIL 1727 9160 1726 9087 1726 8786 0 0301 0 K SAAIYNPVIYIMNK Q 297 311 1743 9510 1742 9437 1742 8735 0 0702 0 K SAAIYNPVIYIMMNK Q Oxidation M 297 311 1759 9660 1758 9587 1758 8684 0 0903 0 K SAAIYNPVIYIMMNK Q 2 Oxidation M 297 314 2159 1430 2158 1357 2158 1067 0 0290 1 K SAAIYNPVIYIMMNKDER N 312 325 1788 7210 1787 7137 1787 7939 0 0802 1 K QFRNCMLTTICCGK N 312 325 1804 7100 1803 7027 1803 7889 0 0861 1 K QFRNCMLTTICCGK N Oxidation M 315 325 1373 6810 1372 6737 1372 5608 0 1130 0 R NCMLTTICCGK N Oxidation M 326 339 1403 7220 1402 7147 1402 6576 0 0571 0 K NPLGDDEASATVSK T 340 348 903 3420 902 3347 902 4345 0 0998 0 K TETSQVAPA Error ppm Error Oa No match to 832 6620
89. H Data file Query NB Contents of this field are ignored if a data file is specified X Decoy ADi Start Search Monoisotopic Average Report top AUTO hits Copyright 2008 Matrix Science Ltd All Rights Reserved Start Search Allow up to 1 missed cleavages D Fixed modifications Carbamidomethy C Variable modifications Oxidation M Peptide tol 0 2 Da Mascot Server 4 Data file Mascot Server PC C inetpub mascot mskk samp edata pmfSample mgf 1 1 4 Start Search Mascot Mascot Search Results 4 Mascot Search Results 1 MS
90. Mascot Server PC PC PC Mascot Server PC Ethernet 2 Mascot Server Mascot Server 9 PC Mascot Server Mascot Server eal Mascot Server 15 Mascot Server
91. Mascot Server 43 gt 8 Mascot Server Mascot Server Mascot Server 8 1 Welcome 39 Welcome Mascot Mascot Eom E et Scenes nome i Database Status Wercome ERE Search Log Mascot Esie your trat iot rere Got Crone ee 39 Welcome the 1999 abstr Security Su YS o gt y S erver D EX JE pes LS Mascot incorporates a role based security model which the system administrator to c
92. PMF Prote in Summary Format Asl 29 Protein Summary 29 Protein Summary EE ae E http localhost mascot cgi master_results plrfiie 2Fdt O BOX F WSE V A T H Protein Summary Repor x jill Index Accession Mass Score Description 1 OPSD HUMAN 39437 102 Rhodopsin OS Homo sapiens GN RHO PE 1 SV 1 2 OPSD MACFA 39606 65 Rhodopsin OS Macaca fascicularis GN RHO PE 2 SV 1 Results List 3 OPSD HUMAN Mass 39437 Score 102 Expect 3 3 005 Matches 11 i Rhodopsin OS Homo sapiens GN RHO PE 1 SV 1 Observed Mr expt Mr calc Delta Start End Miss Peptide TETSQVAPA NCMLTTICCGR N O NPLGDDEASATVSK T SAAIYNPVIYIMMNK O s 903 3420 902 3347 902 4345 0 0998 340 348 0 1373 6810 1372 6737 1372 5608 0 1130 315 325 0 1403 7220 1402 7147 1402 6576 0 0571 326 339 0 1727 9160 1726 9087 1726 8786 0 0301 297 311 0 K R K K K K SAAIYNPVIYIMMNEK Q K K K K 1743 9510 1742 9437 1742 8735 0 0702 297 311 0 SAAIYNPVIYIMMNE Q 1759 9660 1758 9587 1758 8684 0 0903 297 311 0 1788 7210 1787 7137 1787 7939 0 0802 312 325
93. 0 05 Max number of families AUTO Ions score or expect cut off 0 Dendrograms cut at 0 Show Percolator scores E aT YDecoy search summary random protein sequences Peptide matches in target inDecoy FDR above identity threshold 2343 96 4 10 Adjustto 1 above identity or homology threshold 2851 221 7 75 Adjust to 1 Decoy results are available in the decoy report Protein Family Summary Filter Significance threshold p lt 0 06710 Max number of families AUTO help Ions score or expect cut off 0 _ Dendrograms cutat 0 Show Percolator scores E YDecoy search summary random protein sequences Peptide matches in target inDecoy FDR above identity threshold 2479 123 4 96 Adjustto 5 above identity or homology threshold 3104 359 11 57 1 Decoy results are available in the decoy report K25D EOP Cla FRE LEA AVY AAT OBMBAE SHE TASS PHL FDReEKMCWEDT Target DB 0 05 Identity above identity threshold 2343 Decoy DB 96 FDR 96 2343 x 100 4 10 ARIZ Identity Paid SV IX Homology REO Eb OAY AWHO Re BEA L L above identity or homology threshold FDR
94. 0 57 0 0002 bi U MM R GLFIIDDK G 49531 605 0112 1208 0078 1207 7056 0 30220 50 0 0011 b U WW R GLFIIDDK G v 224446 590 4919 1768 4540 1767 8550 0 59900 71 1 6e 006 gt UW K DYGVYLEDSGHTLR G p2 F G 34 31 3 Protein Family Summary http help msms_summaries_help html FAMILY http www matrixscience com help msms_summaries help html FAMILY Mascot Server 32 5 8 Peptide Summary MIS SQ Mascot MS MS 300 Peptide Summary 33 URL Ions score or expect cut off 0 05 Max number of hits 2
95. 0 803 P 244 1656 122 5864 227 1390 114 0731 2 12 K 147 1128 74 0600 130 0863 65 5468 1 100 09 x oC 1 024 9 4 T T T ad T T T T 1 T T T T rr T T T 1 200 4 Bo 1 200 2 4i 800 1 12 RMS error 32 ppa Ma error 32 ppa NCBI BLAST search of TVIEQSWGSPK Parameters blastp nr protein database expect 20000 no filter PAM30 Other BLAST web gateways All matches to this query Score Mricale Delta 644 1343 7085 23 0 1343 6681 22 8 1343 8176 15 7 1343 6681 15 4 1343 7409 15 2 1343 749 14 0 1343 6932 13 5 1343 7296 1343 7409 1343 7045 Sequence 0 0480 TVIIEOSWGSPK 0 0076 VVDLQESSQPSR 0 1571 SIIIKOALPYAK 0 0076 KALNENDGDLOK 0 0804 TIVLOEGNSOKK 0 0844 TVLWKVDDAVAK 0 0327 VDVIOKAEEADK 0 0691 VTDGETLOGLALK 0 0804 TLVLESGDGGIRK 0 0440 VATGVQOQSIENAK 13 0 12 1 Mascot http www matrixscience com Score Mr calc Delta Sequence Site Analysis 83 4 1846 717910 1889 IDIGSESTEDQAMEDIK Phospho S4 84 56 75 8 1846 717910 1889 DIGSESTEDQAMEDIK Phospho S6 14 73 6
96. 1 Protein Family 1 4 3 Homology 1 Protein Family 1 5 6 Protein Family Homo1ogy 7 Protein Family 8 7 Same set Sub set TIntersection 9 Homology Tdentity 32 E ee 32
97. 2 7 1846 717910 1889 DIGSESTEDQAMEDIK Phospho T7 0 72 26 9 1846 7808 0 1261 KLNSNPENYCESELK 22 8 1846 772910 1339 KMEDSVGCLETAEEVK 15 5 1846 9230 0 0161 1GAYTIEOHPVLGLEIK 4A _ iaaa PIV AH 499 Zh4a Score Mr calc Delta Sequence Site Analysis 84 5 3541 790010 0191 KRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIK Deamidated N9 99 79 57 2 3541 7900 0 0191 KRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIK Deamidated N19 0 19 47 9 3541 790010 0191 KRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIK Deamidated Q21 0 02 14 3 3541 773510 0355 INKRLNYIKRQPHQSDDEPAQIMGYKNK 14 3 3541 773510 0355 INKRLNYIKRQPHQSDDEPAOQIMGYKNK 12 S 25A1 747n 0 1690 ENEVDERKNYEDEMOWVTKI DVYNONTI KAI Mascot Server 10
98. 25207 sequences 18552268 dues Timestamp 15 Feb 2011 at 05 10 41 Gur threonine 9 Mascot Search Resu ts ng 2 If Protein hits ELMI YEAST Serine protein kinase ELH1 OS Ssccharomyces cerevisiae GN ELM1 PE 1 5 Mascot Score Histogram o lons score is 10 LogP where P is the probability that the observed match is a random event 7 indicate Individual ions scores gt 3 identity or extensive homology p lt 0 05 1 9 Peptide Summary Report MATRIX Cuvee Mascot Search Results Protein scores are derived from ions scores as a non probabilistic basis for ranking protein hits l aie E E EY A H T a 7 ee Peptide S R 7 MS At 7 A NMA eptide Summary Report Format As Peptide Summary Help o For Mz E J Significance threshold p lt 0 05 Max mmber of hits AUTO Standard scoring MudPIT scoring Ions score or expect cut off 0 Show sub sets 0 a Show pop ups Suppress pop ups Sort unassigned Decreasing Score Require bold red gt o FF Select Al Select None Search Selected Error tolerant Archive Report i ELMi YEAST Mass 7230
99. 3 Score 266 Matches 3 3 Sequences 3 3 Serine threonine protein kinase ELM1 OS Sacchsromyces cerevisiae GN ELM PE 1 SV 2 2 Mascot Score Hi sto ram Check to include this hit in error tolerant search or archive report 8 Query Observed Mr expt Mr calc ppm Miss Soore Expect Rank Unique Peptide e Es TI if 1 748 4300 747 4227 747 3932 39 5 9 5 0 0011 1 uv K IPTPIK A Phospho ST Zz 9 Bl 37 2 1084 5600 1083 5527 1083 5349 16 4 9 96 6 6e 008 1 u RK RDFVTDOFK L 1367 6300 1366 6227 1366 6316 6 49 9 118 5e 010 1 y K PSSPLADRTVGE R Phospho ST 3 MIS 3 Protein Family Summary Report Peptide Summary Report Select Summary Report 9 Peptide Summary Report 4 9 1 9 ELM1_YEAST Mass 9 72903 Score MICK 266 Matches 9
100. 329 CH60 HUMAN APGFGDNR y 3 1 2 J R ALMLQOVDLLADAVAVTMOPE O 2 Oxidation MW i 3 42 0 0001 K APMNNDR R SRR oe nie EEE 0 4 52 0 0001 K ANAPSCDR L 2 u R EPLVITAEDVDGEALSTLVLAR L 55 0 0727 x APGSSRMK T y 1 uU R EPLVIIAEDVDGEALSTLVLNR L os d 4 R TALLDAAGVASLLTTARVVVTEIPR E 8 8 74 0 0801 K APVLMMR M 7 64 654 0568 2559 1545 25593 2413 0 0868 a 715 5 i1e 006 R LVQDVANNTNEEAGDOTTTATVLAR S 8 8 74 0 0801 K APVMIMR D 7 4 1e 002 0 0540 K SASNIADR R ee te ate a R TTSPGTCGR Check to include this hit in error tolerant search or archive report 7 2 1e 002 0 0541 R TTSPGTGGR L 6 9 1 2e 002 0 0727 K ATVAVCGGR L Query Observed Mr expt Mr calc Delta Mies Soa Expect Rank Unique Peptide i 23 232 3498 252 3026 2 5 APGFGDUR 27 637 265 31232 5560 1232 5885 0 0536 42 032 2 R V k Peptide matches not assigned to protein hits inc details means no match Query Observed Mr expt Mr calc Delta Miss Soore Expect Rank Unique Peptide J 430 7328 4510 859 4837 6327 0 36 0 25 1 IPAMTIAK Oxidat mM y 714 3649 7153 1426 0143 0 0990 1 31 0 32 1 EASPLSSKELILR 828 1238 2 3495 3942 0 0447 0 26 0 42 1 TALLDAADVASLLTTAEVVVTEIPR 7 1272 0 0172 0 26 0 63 1 ALMLQUVDLLADAVAVTHGPK Oxidation MI y 5536 0 1118 25 3 2 1 IAQTPLE J 3671 0 0218 t 15 24 1 ECETRAR J 3 3501 0 0898 3 x 1 KNAMAK 7 55 5023 015 D 13 6 7 1 DMALATGGAVPGEEGLTLNLEDVQVEDLGE Oxidation M J 2 6012 0 0132 0 12 31 1 QLLMVAOVDR y 3217 0 0002 12 51 1 AL
101. 668 0 60 0 00048 1 U K EIGNIISDAMK K 26 608 3099 1214 6052 1214 6507 0 0455 0 73 2 2e 005 1 U K NAGVEGSLIVEK I 27 617 2857 1232 5569 1232 5885 0 0316 0 81 4e 006 1 U K VGGTSDVEVNEK K 31 672 8375 1343 6605 1343 7085 0 0480 0 64 0 00016 1 U R TVIIEQSWGSPK V 35 714 8938 1427 7730 1427 8058 0 0327 0 73 2 1e 005 1 U R GVMLAVDAVIAELK K 34 36 722 8849 1443 7552 1443 8007 0 0455 0 75 1 2e 005 1 U R GVMLAVDAVIAELK K 37 39 752 8643 1503 7141 1503 7490 0 0349 0 90 4 3e 007 3 U K TLNDELEIIEGMK F 40 760 8461 1519 6777 1519 7439 0 0662 0 89 4 7e 007 1 U K TLNDELEIIEGMK F 45 640 3281 1917 9625 1918 0636 0 1010 0 102 2 1e 008 gt U K ISSIQSIVPALEIANAHR K 46 960 0327 1918 0509 1918 0636 0 0127 0 87 5 1e 007 U K ISSIQSIVPALEIANAER K 48 1019 5106 2037 0067 2037 0153 0 0087 0 52 0 0015 3 U R IQEIIEQLDVTTSEYEK E 51 1057 0537 2112 0929 2112 1323 0 0394 0 116 6 8e 010 1 U R ALMLQGVDLLADAVAVTMGPK G 52 1065 0399 2128 0653 2128 1272 0 0619 0 72 1 7e 005 1 U R ALMLQGVDLLADAVAVTMGPK G 54 1073 0477 2144 0809 2144 1221 0 0412 0 93 1 3e 007 1 U R ALMLOGVDLLADAVAVTMGPK G 59 1183 1570 2364 2994 2364 3264 0 0270 0 65 5 3e 005 1 U R KPLVIIAEDVDGEALSTLVLNR L 60 789 1094 2364 3063 2364 3264 0 0201 0 95 6 3e 008 1 U R KPLVIIAEDVDGEALSTLVLNR L 58 62 828 1322 2481 3748 2481 3942 0 0194 0 48 0 003 1 U R TALLDAAGVAS LLTTAEVVVTEIPK E 64 854 0588 2559 1545 2559 2413 0 0868 0 75 5 1e 006 1 K LVQDVANNTNEEAGDGTTTATVLAR S 2 CH60 DROME Mass 60771 Score 162 Ma
102. 86 17800 4140 1779 9375 0 4765 52 69 2 98 005 1 E MY TL IP LAM ay 599 0568 1795 3466 1794 9489 0 3997 Oo E 72 1 de 005 i R TKPHVAVGT IG Top scoring peptide matches to query 52 t GITINTSHVEY Efa a I OL nk guec t AIDEPFLLEIE Score greater than 32 indicates homology Score greater than 36 indicates identity Expect Delta Hit Protein Peptide 2 3e 005 O 4765 1 EFTU ECOLT K AVVTLIHPIARDDGLE F 7 4 0 4699 R TI THPLGHVEDDIVTE I 0 4145 R ILTVLIGENHFPFSALR Q 0 4774 R GLOVTINGEP IOVPVGTE T 0 5209 F DITVYAIDIAEFDAPE A 0 4257 R DTLDVHLVPVSIFICGE T 0 4965 R IDVEPVFTAHPTEAVE R 0 4046 R SGAIDVLVVDSVAALVPR A 0 5215 E DSAGAAALAGAVGYFVLTE A 0 4671 R DGRDTLIISSGLATAR A Opi AAT CH ADIT Homology Out1iner Homology gt Identity 1dentity Homo1ogy 23 Homology lt Identity BAIT Homology
103. ACER 7 4072 0 0419 13 43 1 LAPAQSK 7 3539 0 0133 0 13 71 1 AVNDVR F 2 5349 3 0056 9 B 1 ENVI PADSER J 5 1862 0 0113 t a 35 1 LNAEAVRTLLSANOQEPSEAK 7 0431 u 67 1 VVGVAGQGASALVR i 2 0 0277 g 78 3 DTVSVSQCPOPR 7 0 7 Te 1 TPLLVOVARUESR y 0 6 re 1 ALDET LEYONYPVVCARE J 0773 0 2 5 7 1 VMOSAPTALLDANEDAQKAIG y 45 70 1 9 1 2e 002 1 IORLSOLMOTALPROOR Oxtdatton M a 4658 0 3 4 2e 002 1 TGMTANPE 7 2 3006 o 0 4 1 2e 002 1 LAVPT J 1 6e 002 1 I ADMD J Oxeidatian H J 2 4498 0 t 3 2 76002 1 SROPQNR Oxidation M y 4 ssm 0 1 2 2e 002 1 ALNQEVMAPEATEC y 3633 2 8 3m 002 1 TP Oxidation H 7 5294 9 2 2 2e 002 t LOSOIKAER y 3711 0 0 1 2 3e 002 1 I K j 5545 0 t i 3 4e 002 1 KTIOAETYE 7 44 0 0 2 3e 002 1 LLSWDSVPFIRWITSK 7 J 7 y 4 v 4 665 0096 1992 0069 F 56 1119 0452 2236 0758 7 832 7986 2495 3739 y 1113 8947 3338 6621 J 67 126 1775 3345 5106 Search Parameters Type of search MS MS Ion Search Enzyne Trypsin Variable modifications Oxidation M Mase values Monoiasotepic Protein Mass Unrestricted Peptide Mass Tolerance 0 2 Da Pragment Masa Tolerance 0 2 Da Max Missed Cleavages 1 Instrument type ESI QUAD TOF Number of queries 67 Mascot Server 33 Peptide Summary
104. Mascot Server 2 4 MATRIX SCIENCE gt LT Number of Matches 1et d LLL wy gt dt Bi Hn 100 120 Peptide Score Fa gt Peptide score distribution Ions score is 10log P where P is the probability that the observed match is a random event Individu ions scores gt 32 indicate identity or extensive homology p lt 0 05 gt gt gt gt gt gt gt 1 Mascot Server 2 lt P gt Mascot 3 1 1 PMF Peptide Mass Fingerprint 1 2 MIS MS MS Ions Search 2 8 2 1 2 2 23 2 4 2 5 2 6 2 7 Mascot 3 Mascot 12 3 1 Mascot 3 2 3 3 PMF Peptide Mass Fingerprint 3 4 MIS MS MS Ions Search 3 5 SQ Sequence Query 4 18 4 1 4 2 Identity Homology 4 3 FDR False Discovery Rate 22 5 1 5 2
105. NPLGD DEASATVSKT ETSQVAPA Unformatted sequence string 248 residues for pasting into other applications Sort peptides by Residue Number Increasing Mass Decreasing Mass Show predicted peptides aiso Start End Observed Mr expt Mr calc Delta M Peptide 1 21 2256 8710 2255 8637 2256 0634 0 1996 0 NNGTEGPNFYVPFSNATOVVR S 232 248 1818 9630 1817 9557 1817 8755 0 0802 1 K EZAAAQQQESATTQKAEK E 297 311 1727 9160 1726 9087 1726 8786 0 0301 0 K SAAITYNPVIYIM IE O Q SM ay 100 0OPSD_HUMAN Rodopsin 102 5 1 2 MIS MS MS Ions Search 1 2 1 Mascot Server Web Mascot Server PC http mascot Mascot Server 6 Welcome Mascot 7
106. U D a w N a co Ss oc oo TYIIGELHPDDR S FPLEEHPGCEEVLR E FLEEHPGOEEVLR E EQAGGDATENFEDVGHSTDAR E BQAGGDATENPEDVGHSTDAR E Observed Mr expt Mr calc Delta M Score Expect Rank U Peptide 513 9603 1025 7060 1025 6001 0 1059 0 36 0 018 pi U K VYDLTK F 520 0 2972 0 3 2 4 Pa U Oxidation M 704 1407 8230 0 8994 0 11 1 5 Ps T E 470 4068 1408 1987 1407 8230 0 3756 0 39 0 0073 Py U amp STWVILHER V Lecua 8 448 3 Score gt 32 indicates identity 718020 b7 738 0084 1474 0022 1473 7959 0 2064 0 74 3 5e 606 Wy U K YYTLEBIQK 0 3683 1 22 0 54 2 Bc HMKXEELQK 0 8213 0 18 1 4 3 AQQLTELEQK 0 2729 0 12 8 3 4 GSEPSTEHSQK 0 6213 0 9 13 5 LLDGGNTEIQK 0 8698 1 e 146 PRKATEEQLE 0 7437 0 8 15 7 DPSEEIEILMR 0 2178 1 7 16 8 PAGITAMRSGLPR Oxidation M 0 1465 1 7 169 YSKIFEQER 39 1 20 19 14 0 6 2 bg U R 509 21 3 3 bo U 787 0462 1572 0778 2 76 5 96 007 pi U TYIIGELHPDDR S v U 552 6631 1654 9676 1654 826 5314 1655 0463 1654 8437 0 2047 1175 6897 2349 3647 2349 0227 0 3420 PPAR AA 184 1341 2343 3805 2349 0227 0 3578 gt 1 subset or Intersection 1 subset protein in total PS 2 PDIA1_MOUSE 1116 Protein disulfide isomerase OS Mus musculus GN P4hb PE 1 SV 1 s A i 2 2 TXND5_MOUSE 46 Thioredoxin domain containing protein 3 OS Mus musculus GN TxndcS PE 1 SV 2 6 2 CP1A2 MOUSE 1048 Cytochrome P450 142 OS lt Mus musculus GN Cypis2 PE 1 3V 1 b 1 2 RDH7_MOUSE 1023 Retinol dehydrogenase 7 OS Mus m
107. able modifications Mascot Server 5 6 Welcome Matrix Science Home Windows Internet Explorer Google pr F E V A T H w Matrix Science Home A Gy GS my P S rf MATRIX SCIENCE Search Gal HOME MASCOT HELP Welcome This site features Mascot a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases To assist you the help text for Mascot forms a substantial knowledge base concerning protein identification by MS 7 Mascot Search i MATRIX SCIENCE HOME i MASCOT iHELP Mascot Mascot Search e Peptide Mass Fingerprint The experimental data are a list of peptide mass values from an enzymatic digest of a protein o Example of results report o More information Mascot Help Mascot Overview Search parameter ce referen Data file format Results Report Overview MS MS Results Interpretation Error tolerant search Decoy database search Quantitation e Sequence Query One or more peptide mass values associated with information
108. ass Fingerprint n a EE 1 PMF o La ae ea Slo CREE LIT HOMBRE CT DIME LIMBTERRTE AL L O weewe ee On Ome mente see O am e Query esata ee Lee Data file PME SwissProt EST Start Search
109. dPIT scoring Max number of hits 2 Show pop ups Suppress pop ups Database SwissProt 51 6 257964 sequences 93947433 residues Timestamp 19 Feb 2007 at 14 09 47 GMT Enzyme Trypsin Variable modifications Oxidation M Mass values Monoisotopic Protein Mass Unrestricted Peptide Mass Tolerance 0 2 Da Fragment Mass Tolerance 0 2 Da Max Missed Cleavages 2 Instrument type ESI QUAD TOF Number of queries 67 mitochondrial precursor Hsp60 mitochondrial precursor Hsp60 Ions score or expect cut off 0 05 60 kDa chaperonin 60 kDa chaperonin CPN60 CEPN60 Heat shock Heat shock Help Show sub sets 0 Require bold red Allqueries Unassigned Below homology threshold Below identity threshold a3 CH60 HUMAN Mass 61016 Score 1176 Matches 27 27 Sequences 17 17 60 kDa heat shock protein mitochondrial precursor Hsp60 60 kDa chaperonin CPN60 Heat shock Query Observed Mr expt Mr calc Delta Miss Score Expect Rank Unique Peptide 11 417 1822 832 3498 832 3828 0 0329 0 45 0 016 1 K APGFGDNR K 12 422 7433 843 4720 843 5066 0 0346 0 46 0 017 1 U K VGEVIVTK D is 451 2499 900 4853 900 5280 0 0428 0 52 0 0039 1 U K LSDGVAVLK V 16 456 7806 911 5467 911 5804 0 0337 0 59 0 00056 i U K VGLOQVVAVK A 21 480 7447 959 4748 959 5036 0 0288 0 45 0 017 1 U R VTDALNATR A 24 595 7855 1189 5565 1189 6012 0 0447 0 57 0 0011 E U K EIGNIISDAMK K 25 603 7720 1205 5294 1205 5962 0 0
110. difications V Number of fragment ion matches Query title V Unassigned queries peptide matches not assigned to protein hits Query Level Information Query title seq comp tag etc Query level search parameters MS MS Peak lists Raw peptide match data Show command line arguments K Export search results Copyright 2008 Matrix Science Ltd All Rights Reserved Mascot Server 38 5 12 Report Builder MIS SQ Protein Family Summary Repoet Builderl 37 Report Builder Report Builderl Proteins 50 CSV Repoet Builder
111. e jp pdf jap_robocopy_settings pdf Mascot Server 48 2012 6 10 Copyright 2004 2012 Matrix Science Ltd SCIENCE ee support jp matrixscience com 03 5807 7895 _ 03 5807 7896 101 0021 6 10 12 KN 3
112. es MIS Yes 0 Thu Apr 19 17 59 23 2012 4 User read res MIS Yes 0 Wed Jan 11 17 35 41 2012 11 User read res MIS Yes 0 Meon Dec 19 14 30 48 2011 8 User read res PMF Yes 0 Mon Dec 19 11 01 57 2011 4 User read res MIS No 0 Mon Dec 19 10 59 18 2011 5 User read res MS Yes 0 Tue Jul 26 18 52 12 2011 10 User read res MS Yes 0 MASCOT search log C inetpub mascot logs searches log MASCOT search log C inetpub mascot config mascot dat Optionsl ReviewColWidths Configuration Editor 8 3 Welcome Database Status Y Database Status 41 MASCOT search status page URI 41 MASCOT search status page http mascot x cgi ms status exe Ven nap Mascot Server ena Sta
113. html http www matrixscience p pdf MascotDistiller_guickstart pdf 6 1 MussHunter d Mascot MGF 6 2 1 Analyst Analyst Script mascot d11 Mascot Server Mascot Server mascot dll Mascot Daemon Data import filter WMascot Daemon Mascot http mascot help instruments_analyst html http www matrixscience com help instruments_analyst html mascot dll http www matrixscience com help instruments_analyst html
114. ial knowledge base concerning protein identification by MS 2 Mascot Search i MATRIX SCIENCE search HOME MASCOT iHELP Mascot Mascot Search O Peptide Mass Fingerprint The experimental data are a list of peptide mass values from an enzymatic digest of a protein o Example of results report o More information Mascot Help bescot Overton Search parameter reference e Sequence Query One or more peptide mass values associated with information such as partial or ambiguous sequence strings amino acid composition information MS MS fragment ion masses etc A Data file format Results Report 3 TMASCOT Peptide Mass Fingerprints MATRIX SCIENCE HOME MASCOT iHELP Mascot gt Peptide Mass Fingerprint MASCOT Peptide Mass Fingerprint Your name usami Email usami matrixscience com 6 Enzyme Trypsin v Allow upto 1 v missed cleavages Search title Database s EST_human CRAP D gallus NCBInr Taxonomy All entries v Fixed none selected Acetyl K R modifications Acetyl N term Acetyl Protein N term Amidated C term Amidated Protein C term Ammonia loss N term C Biotin K Display all modifications Variable none selected Biotin N term modifications Carbamidomethyl C Carbamyl K Carbamyl N term Protein mass kDa Peptide tol 10 Da Mass values MH O M M
115. ificant 115 114 Num of significant matches Not normal 115 114 Num of sequences SD geo 115 114 Num of significant sequences 116 114 115 114 E Number of peptides 116 114 116 114 m Significant 116 114 117 114 Not normal 116 114 Description SD geo 116 114 117 114 Number of peptides 117 114 Significant 117 114 Not normal 117 114 SD geo 117 114 be wd VFilters 115 114 gt 1 AND 116 114 gt 1 AND 117 114 gt 1 Apply Show column string 115 114 gt 1 Remove AND s 116 114 gt 1 Remove M AND lt 117 114 gt e 1 Remove AND lt Family el lt el Update Export as CSV r P Pep seq Lai sig q sig p Family DB Accession Score Mass Matches si Sequences ci 115 114 116 114 117 114 Description 1 SwissProt VIT3_DROME 50436 12 13 11 1 761 2 245 3 698 Vitellogenin 3 precursor Vitell 2 SwissProt FPDI_DROME 63614 7 14 F4 1 891 3 221 1 717 Protein disulfide isomerase Drd 5 SwissProt VIT1_DROME 52618 6 4 3 1 174 1 160 1 554 Vitellogenin 1 precursor Vitell 6 SwissProt YL_DROME 235777 6 6 5 1 090 1 839 1 182 Putative vitellogenin receptor F SwissProt FRL13_DROME 29639 3 4 2 1 577 3 060 5 007 60S ribosomal protein L13 BB4 8 SwissProt VDAC_DROME 34278 5 6 3 1 042 2 008 3 426 Voltage dependent anion sele 13 SwissProt PERC_DROME 98282 2 2 2 1 265 1 494 1
116. ions Carbamidomethyl C Variable modifications Oxidation M Mass values Monoisotopic Protein Mass Unrestricted Peptide Mass Tolerance t 0 2 Da Peptide Charge State it f Max Missed Cleavages gt 2 Number of queries 45 Mascot http Avww matrixscience com Protein Summary Mass Score xpect Matches 0bserved Mr expt Mr calc Delta Start End Miss Peptide No match 1 OPSD_HUMAN 102
117. ions aho ST Protein sequence coverage 4 Matched peptides shown n bold red sarir 7 a emt Se 11 Peptide View Mascot Search Results Peptide View Windows Internet Explorer oe http mba11w7 mascot cgi pept x I Google P w E web BB 7 amp Pepti Masc M x D D o why P gt 5 lt O Or Linci Mascot Search Results Peptide View MS MS Fragmentation of PSSPLMDRTVGK Found in ELM1_YEAST in SwissProt Serine en protein kinase ELM1 OS Saccharomyces cerevisiae strain ATCC 204508 S288c GN ELM1 PE 1 SV Match to Query 3 1366 622724 from 1367 630000 1 index 2 Data file errorTolSample mgf Click mouse within plot area to zoom in by factor of two about that point Or Plot from 100 to 1200 Da Fullrange Label all possible matches Show Y axis Label matches used for scoring Monoisotopic mass of neutral peptide Mr calc 1366 6316 Pixed modifications Carbamidomethyl C apply to specified residues or termini only Variable modifications Score Mri calc Delta 117 3 1366 6316 0 0089 PSSPLMDRIVGEK Phospho 53 84 59 31 0 1366 5959 0 0268 PSSGGGGLFSFFR 22 6 1366 5959 0 0268 IPSSGGGGLESEFK S3 Phospho ST with neutral losses 97 9769 shown in table
118. ontrol which functionality is available to individual users If security has been enabled you may be prompted to log in if you attempt to access a page or perform a task that requires authorisation If security is not enabled which is the default the following links wil si asl confirm thes h z my Configuration Editor niest Log out 8 x e Change password gt RO a e Edit settings N Na L Current session information Whether or not sige seny is enabled in order to comply with he licensing conditions access to thes Mascot server ae authorised users We strongly recommend that your server is protected by a secure firewall For more information start fr Mascot Utilities LUV Your system administrator may have restricted access to these utilities Database Stat A N V WHAT S ae _ the s status of all the sequence databases Links to database statistics search status log files etc A tabular view of the search log Can be filtered to find specific search results Edito r NEW HELP SU PPORT i yY 7 Browser based configuration editors including security adminestrabon and sequence database management N N Mascot Daemon
119. ormat CSV v Significance threshold p lt 0 05 Ions score cut off 0 05 Threshold type Identity Homology Max number of hits 3 Protein scoring Standard MudPIT Include same set protein hits additional proteins that span the same set of peptides Include sub set protein hits additional proteins that span 0 a sub set of peptides Group protein families Require bold red Preferred Taxonomy All entries Occasionally requires information to be retrieved from external utilities which can be slow Search Information y Header v Modification deltas V Search parameters V Format parameters Residue masses Protein Hit Information y Score Mass Da Description V v 7 Number of queries matched Percent coverage Length in residues pI Taxonomy Taxonomy ID Protein sequence emPAI Occasionally requires information to be retrieved from extemal utilities which can be slow Always requires information to be retneved from extemal utilities which can be slow Peptide Match Information 7 Experimental Mr Da Calculated Mr Da El Experimental charge V v 7 Mass error Da Start End Number of missed cleavages V Score V Homology threshold Identity threshold Expectation value v Sequence Vv Frame number F lt Variable Mo
120. ort Format As_ Concise Protein Summary v Help Significance threshold p lt 0 05 Max number of hits AUTO Re SearchAll Search All Search Unmatched a OPSD HUMAN Mass 39437 Score 102 Expect 3 3e 005 Matches 11 Rhodopsin OS Homo sapiens GN RHO PE 1 SV 1 PSD MACFA Mass 39606 Score 65 Expect 0 15 Matches 8 sete OS Macaca fascicularis GN RHO PE 2 SV 1 oOPSD CRIGR Mass 39641 Score 64 Expect 0 2 Matches 7 Serch n OS Cricetulus griseus GN RHO PE 1 1 OPSD CHICK Mass 39928 Score 50 Pee 5 Matches 6 Rhodopsin OS Gallus gallus GN RHO PE 1 SV SD ALLMI Mass 40005 Score 50 iets 5 1 Matches 6 Rhodopsin OS Alligator mississippiensis GN RHO PE 2 SV 1 LOXAF Mass 39594 Score 50 Expect 5 4 Matches 7 RE n OS Loxodonta africana GN RHO PE 1 SV 1 PSD PIG Mass 39571 Score 50 Expect 5 4 Matches 7 nal SEE OS Sus scrofa GN RHO PE 1 SV 1 OPSD TRIMA Mass 39624 Score 50 Expect 5 4 Matches 7 Rhodopsin OS Trichechus manatus GN RHO PE 1 SV 1 Der ANTA Mase 39597 Senre AR Ewert 7 4 Matchoes 28 OPSD_HUMAN 39437 Da 102 MAMIE 3 3E 005 11 OPSD_MACFA OPSD_HUMAN Sub set
121. r scores Preferred taxonomy Ali entries gt Decoy search summary random protein sequences Proteins 482 Report Builder unassigned 26230 PY Protein families 1 10 out of 482 10 per page 1 2 3 4 5 G 42 Next Expand al Collapse all Accession contains Find bi 1 TRY1_BOVIN 1597 TRYi_BOVIN mm bo 1 2 CPB2CT_MOUSE 1307 Cytochrome musculus GN Cyp2c29 PE 1 SV i 4 2 CP239_MOUSE 293 Cytochrome musculus GN Cyp2c39 PE 2 SV t 5 2 CP238_MOUSE 202 Cytochrome musculus GN Cyp2c38 PE jat 2 2 CP254_MOUSE S35 Cytochrome musculus GNeCyp2c54 PEe2 SVei 6 2 CP270_MOUSE 69 Cytochrome musculus GN Cyp2c 0 PE 2 SV 2 3 2 CY250_MOUSE 382 Cytochrome P450 2C50 OS Mus musculus GN Cyp2cS0 PE 1 SV i 140 N ks 1 2 GRP78_MOUSE 1292 78 kDa glucose regulated protein OS Mus musculus GN HspaS PE 1 SV 3 2 HSP7C_MOUSE 353 Heat shock cognate 71 kDa protein OS Mus musculus GN Hspad PE 1 SV 1 3 2 HS71L_MOUSE 16S Heat shock 70 kDa protein 1 like OS Mus musculus GN Hspal PE 2 Sv 4 e 2 S 2 a um va 2 CYB5_MOUSE 1228 Cytochrome b3 OS Mus musculus GN CybSa PE 1 Sv 2 Score Mass Matches Sequences emPAL 4 1 42 CYBS_ MOUSE 1228 16817 63 48 8 6 5 00 Cytochrome b5 OS Mus musculus GN CybSe PE Sv 2 v63 peptide matches 13 non duplicate 50 duplicate Auto fit to window 525 0861 1572 2366 57 4 6e 006 Pi 46 0 00035 pi 62 4 6e 005 pi u 100 56 009 Di U 104 1 7e 009 a
122. s KML CSV pepXML mzldentML DTASelect Mascot DAT File MGF Peak List Export format CSV Export search results CSV Windows XP C temp Windows 7 download CSV Export search results a http mascot help export_help html http www matrixscience com help export_help html 36 TExport Search Results Peptide Summary Report Format As Peptide Summary gt Protein Summary deprecated Protein Family Summary 0 05 Peptide Summary Select Summary protein hits IT scoring Select Summa unassigned Export Search Results pop ups MATRIX SCIENCE HOME MASCOT iHELP Mascot gt Export search results Export search results Export f
123. sed cleavages 19 X Ys 4g 2 Y2 42 4 Y 4 RO RO RIEO RA ees ee es i 1 HN REI I a S I Ho SAGA GAAT ARRA eal ere Lek ak TL Lui rel cecal ell a by Cy az Do Co as bs C3 20 MIS SCIENCES HOME MASCOT iHELP Go MASCOT MS MS lons Search Peptide charge 2 Monoisotopic Average MATRIX Your name usami Email usami matrixscience com Search title MIS search 1 for testing Database s EsT_human Enzyme Lys C P CRAP Allow upto 1 missed deavages Quantitation None Taxonomy All entnes Fixed Carbarnidomethyl C Acetyl K modifications gt Acetyl N term C Display all modifications Ammonia loss N term C in Variable phospho ST n N term modifications gt Carbamyl K Peptide tol 50 ppm uc 0 MS MStol 0 3 Da gt Data file sampledata errorTotSample mgf S Data format Mascot generic X Precursor m z Instrument ESI QUAD TOF X Error tolerant Decoy Report top AUTO hits Start Search Reset Form Variable modifications Peptide tol MS MS
124. such as partial or ambiguous sequence strings amino acid composition information MS MS fragment ion masses etc A super set of a sequence tag query o Example of results report o More information e MS MS Ion Search Identification based on raw MS MS data from one or more peptides o Example of results report o More information 8 MASCOT MS MS Ions Search rf MATRIX SCIENCE Search HOME MASCOT iHELP Mascot gt MS MS Ions Search MASCOT MS MS lons Search Your name usami Email usami matrixscience com Search title Database s EST_human 6 Enzyme Trypsin CRAP qallus Allow upto 1 v missed cleavages NCBInr Quantitation None Taxonomy All entries v Fixed none selected Acetyl K a modifications Acetyl N term D Acetyl Protein N term a Amidated C term Amidated Protein C term Ammonia loss N term C Biotin K Display all modifications Variable none selected Biotin N term modifications Carbamidomethyl C Carbamyl K Carbamyl N term hi Peptide tol 10 Da v 13C 2 v MS MStol 0 6 Da X Peptide charge 1 X Monoisotopic Average Data file Data format Mascot generic X Precursor m z 2 Instrument ESI TRAP Error tolerant Decoy pI Start Search Copyright 2008 Matrix Science Ltd All Rights Reserved Report top AUTO hits
125. tches 3 3 Sequences 3 3 60 kDa heat shock protein mitochondrial precursor Hsp60 60 kDa chaperonin CPN60 Heat shock Query Observed Mr expt Mr calc Delta Miss Score Expect Rank Unique Peptide 11 417 1822 832 3498 832 3828 0 0329 0 45 0 016 1 K APGFGDNR K 27 617 2857 1232 5569 1232 5885 0 0316 0 42 0 032 2 U R VGGSSEVEVNEK K 64 854 0588 2559 1545 2559 2413 0 0868 0 75 5 1e 006 1 K LVQDVANNTNEEAGDGTTTATVLAR A Select Summary Report http mascot help msms_summaries_help html SELECT http www matrixscience com he lp msms_summaries_help html SELECT Mascot Server 35 5 10 Peptide View MIS SQ Summary Report Protein View 35 Peptide View MICU 35 Peptide View SMATRIX y 3 iscexci Mascot Search Results Peptide View MS MS Fragmentation of TVIIEQSWGSPK Found in CH60_HUMAN in SwissProt 60 kDa heat shock protein mitochondrial precursor Hsp60 60 kDa chaperonin CPN60 Heat shock Match to Query 31 1343 660496 from 672 837524 2 Data file CAuto MSMS output Sampk 1 pki Click mouse within plot area to zoom in by factor of
126. te T Status In use Nane Fi lenam Status State T oe a Nane WCBInr Family C inetpub mascot sequence NCB8Inr current NCBInr_ faste SO H HE a 4 Filename MCBInr_20120523 fssta Pathname C inetoub mascot sequence NCBl nr current NCBlnr_20120523 fasta at N FIn Status In use Statistics Compression warnings Unidentified taxonomy State Time Yon Jun 04 09 59 46 searches 0 Wen mapped YES Request to mew map YES Request umwap NO Mew locked NO YR PSE S j j Y FL Number of threads 1 Current YES Statistics a i 1 xie z ame SwissProt ss Family C Inatpuh mascot sequence SwlssPrat current SwlssProt_ fasts 1 ya Filenas SwissProt_2012_05 fasta Pathname C inetpub sascot sequence SwissProt current SwissProt_2012_05 fasta N LE N Taa tatu In use Statistics Inident ified taxnnomy State Time Mon Jun 04 09 59 46 searches 0 Mem mapped YES equest to mew map YES Request unwap WO Mew locked NO unber of threads 2 Current YES
127. two about that point Or Plot from 0 to 2000 Da Full range Label all possible matches Label matches used for scoring Show Y axis ag 3 3 Ei in 3 3 Monoisotopic mass of neutral peptide Mr calc 1343 7085 Ions Score 64 Expect 0 00016 Matches 25 118 fragment ions using 52 most intense peaks help b ES b pa b b Seq y ahi yt y y 1 102 0550 51 5311 84 0444 42 5258 T 12 2 201 1234 101 0653 183 1128 92 0600 V 1243 6681 1622 3377 1226 6416 613 8244 1225 6575 613 3324 11 3 314 2074 157 6074 296 1969 14S 6021 I 144 5997 572 8035 1127 5732 564 2902 1126 5891 563 7982 10 4 427 2915 214 1494 409 2809 205 1441 I 1031 5156 516 2615 1014 4891 507 7482 1013 5051 507 2562 9 556 3341 278 6707 538 3235 269 6654 E 918 4316 459 7194 901 4050 451 2061 9004210 450 7141 8 6 684 3927 342 7000 667 3661 334 1867 666 3321 333 6947 Q 789 3890 395 1981 772 3624 386 6849 771 3784 386 1928 7 7 771 4247 386 2160 754 3981 377 7027 753 4141 377 2107 S 662 3304 331 1688 644 3039 322 6556 643 3198 322 1636 6 8 957 5040 479 2556 940 4775 470 7424 939 4934 470 2304 W 574 2984 287 6528 557 2718 279 1396 556 2878 278 6475 5 9 1014 5255 507 7664 997 4989 499 2531 996 5149 498 7611 G 388 2191 194 6132 371 1925 186 0999 370 2083 183 6079 4 10 1101 5575 551 2824 1084 5310 542 7691 1083 5469 542 2771 S 331 1976 166 1024 314 1710 157 5892 313 1870 157 0972 3 11 1198 6103 599 8088 1181 5837 591 2955 1180 5997 39
128. usculus GN Rdh7 PE 2 SV i eT 2 2 H17B6_MOUSE 612 Hydroxysteroid 17 beta dehydrogenase 6 OS Mus musculus GN Hsdi7b6 PE 2 SV i so o 1 ba 2 ENPL_MOUSE 1015 Endoplasmin OS Mus musculus GN Hsp90b1 PE 1 SV 2 bo 2 MGST1_MOUSE 833 Microsomal glutathione S trensfe b10 2 RL7A_MOUSE 771 605 ribosomal protein L7a OS M 10 per page 1 2 la l4 5 6 29 Next Expand ai Collapse all Not what you expected Try the select summary Mascot http www matrixsce Protein Family Sumary Protein Family 1 2 KE Mascot Server 31
Download Pdf Manuals
Related Search