Dear All, Here are first few lines of the the Mascot Search ... ========================================================================== Mascot Search Results
*User : Nathan Edwards* *Email : [email protected]* *Search title : Conversion of C:\Users\Nathan\Downloads\sergei_digest_A_full_01.mzXML to mascot generic* *MS data file : sergei_digest_A_full_01.mgf* *Database : decoy_SwissProt uniprot_sprot_generic (1038696 sequences; 366546324 residues)* *Timestamp : 3 Feb 2011 at 01:44:00 GMT* *Enzyme : semiTrypsin* *Fixed modifications : Carbamidomethyl (C)* *Variable modifications : Gln->pyro-Glu (N-term Q),Glu->pyro-Glu (N-term E),Oxidation (M),Pyro-carbamidomethyl (N-term C)* *Mass values : Monoisotopic* *Protein Mass : Unrestricted* *Peptide Mass Tolerance : ± 2 Da* *Fragment Mass Tolerance: ± 0.6 Da* *Max Missed Cleavages : 1* *Instrument type : ESI-TRAP* *Number of queries : 2165* *Protein hits :** P02666 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit1>* sp|P02666|CASB_BOVIN Beta-casein OS=Bos taurus GN=CSN2 PE=1 SV=2 * P02755 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit2>* sp|P02755|LACB_BUBBU Beta-lactoglobulin OS=Bubalus bubalis GN=LGB PE=1 SV=2 * P02754 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit3>* sp|P02754|LACB_BOVIN Beta-lactoglobulin OS=Bos taurus GN=LGB PE=1 SV=3 * P00921 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit4>* sp|P00921|CAH2_BOVIN Carbonic anhydrase 2 OS=Bos taurus GN=CA2 PE=1 SV=3 * P00489 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit5>* sp|P00489|PYGM_RABIT Glycogen phosphorylase, muscle form OS=Oryctolagus cuniculus GN=PYGM PE=1 SV=3 * P02769 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit6>* sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus GN=ALB PE=1 SV=4 * Q29443 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit7>* sp|Q29443|TRFE_BOVIN Serotransferrin OS=Bos taurus GN=TF PE=2 SV=1 * P67975 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit8>* sp|P67975|LACB_OVIMU Beta-lactoglobulin OS=Ovis orientalis musimon GN=LGB PE=1 SV=1 * P79334 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit9>* sp|P79334|PYGM_BOVIN Glycogen phosphorylase, muscle form OS=Bos taurus GN=PYGM PE=1 SV=3 * P00922 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit10>* sp|P00922|CAH2_SHEEP Carbonic anhydrase 2 OS=Ovis aries GN=CA2 PE=1 SV=2 * P02662 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit11>* sp|P02662|CASA1_BOVIN Alpha-S1-casein OS=Bos taurus GN=CSN1S1 PE=1 SV=2 * P14639 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit12>* sp|P14639|ALBU_SHEEP Serum albumin OS=Ovis aries GN=ALB PE=2 SV=1 * Q3B7M9 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit13>* sp|Q3B7M9|PYGB_BOVIN Glycogen phosphorylase, brain form OS=Bos taurus GN=PYGB PE=2 SV=3 * Q28554 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit14>* sp|Q28554|G3P_SHEEP Glyceraldehyde-3-phosphate dehydrogenase (Fragment) OS=Ovis aries GN=GAPDH PE=2 SV=4 * P49064 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit15>* sp|P49064|ALBU_FELCA Serum albumin OS=Felis catus GN=ALB PE=1 SV=1 * P49822 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit16>* sp|P49822|ALBU_CANFA Serum albumin OS=Canis familiaris GN=ALB PE=1 SV=3 * P09571 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit17>* sp|P09571|TRFE_PIG Serotransferrin OS=Sus scrofa GN=TF PE=1 SV=2 * P00432 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit18>* sp|P00432|CATA_BOVIN Catalase OS=Bos taurus GN=CAT PE=1 SV=3 * P06278 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit19>* sp|P06278|AMY_BACLI Alpha-amylase OS=Bacillus licheniformis GN=amyS PE=1 SV=1 * A6YF56 <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit20>* sp|A6YF56|ALBU_MESAU Serum albumin OS=Mesocricetus auratus GN=ALB PE=1 SV=1 -------------------------------------------------------------------------------------------------------------------------------------------------------------- I am able to produce pepXML file and able to view results without any issues, here is the output from the pepXML viewer screen. --------------------------------------------------------------------------------------------------------------------- *trypsin* digest, *MASCOT* search engine, quantitation: [none] displaying * 2165 * of 2165 total spectra, page 1 of 44 * 2135 unique peptides, * * 2132 unique stripped peptides, 2037 unique proteins, 2012 single hits * PepXML Viewer, 2006 SPC/ISB -------------------------------------------------------------------------------------------------------------------------------------------------------------- We are experincing difficulties in running PeptideProphet for the output generated by Mascot search algorithm, I am here with enclosing the STDOUT and STDERR messages generated by PeptideProphet run. ============================================== STDOUT .... ============================================== Stdout of TPP for NEdwards-J2 ================================================= /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development prerelease) rev 0, Build 201007011135 (linux)) running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'NEdwards-J2.pepprophet.xml' 'NEdwards-J2.pep.xml' -L'7' -E'trypsin'" file 1: NEdwards-J2.pep.xml processed altogether 2165 results results written to file /mnt/sanfs/APCF-PROD/results/tpp/2011-02-03/NEdwards-J2.pepprophet.shtml command completed in 1 sec running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser 'NEdwards-J2.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 PI RT" using pI using RT Using Decoy Label "sp|decoy". (MASCOT) results for charge 1: 37 id tot and 1 adj scores adding pI mixture distr adding Retention Time mixture distr results for charge 2: 1085 id tot and 38 adj scores results for charge 2: -7.19405 adj_ion_mean and 15.0557 adj_ion_hom mean 62.9988id mean0.906181 correlation (r) 2+ ion - id = 0.965428*(ion - hom) + -21.7292 with error = 5.12625 mean ion - id: -7.19405, mean ion - hom: 15.0557 results for charge 3: 1043 id tot and 16 adj scores results for charge 4: 0 id tot and 0 adj scores results for charge 5: 0 id tot and 0 adj scores results for charge 6: 0 id tot and 0 adj scores results for charge 7: 0 id tot and 0 adj scores init with MASCOT trypsin MS Instrument info: Manufacturer: , Model: , Ionization: , Analyzer: , Detector: Initialising statistical models ... Iterations: .........10.........20....Estimating Retention Time Model ... please wait ... command "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser 'NEdwards-J2.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 PI RT" exited with non-zero exit code: 6 QUIT - the job is incomplete ===================================================================================== STDERR ===================================================================================== Stderr of TPP for NEdwards-J2/bin/ln: creating symbolic link `NEdwards-J2.mzXML' to `/home/APCF/uploads/2011-02-03/NEdwards-J2.mzXML': File exists filepath: /mnt/sanfs/APCF-PROD/results/tpp/2011-02-03/, extn: NEdwards-J2 trypsin : cut(KR) nocuts(P) sense(C) prev_aa and next_aa have already been read from .dat file. Replacing 21537 protein id with full ids by parsing through the database... searching /mnt/sanfs/APCF/databases/SwissProt/decoy_uniprot_sprot_generic.fasta.....5%.....10%.....15%.....20%.....30%.....35%.....40%.....45%.....50%.....60%.....65%.....70%.....75%.....80%.....90%.....95%...done PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev 0, Build 201007011135 (linux)) AKeller@ISB read in 32 1+, 1081 2+, 1038 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Found 956 Decoys, and 1195 Non-Decoys PeptideProphetParser: Validation/InterProphet/InterProphetParser/KDModel.cxx:143: bool KDModel::replaceProb(int, double): Assertion `idx < posprobs_->size()' failed. ==================================================================== I wonder whether anyone has any idea about this error. with regards, -- Dr. Jagan Kommineni Systems Administrator and Duty Programmer Australian Proteomics Computational Facility Ludwig Institute for Cancer Research, 6th Floor, Royal Melbourne Hospital, Royal Parade, Parkville, Victoria Ph:03 9341-3177. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
