I can do "SpectraST Library Import" with .pepxml in tandem or spectrast formats.
But it always failed if I imported .pepxml in Mascot results format. Below are error messages: How can I fix it? The different of .pepxml file between mascot format and non-mascot formats is mascot's pepxml produce "date format" for filename of mzXML but not the filename of original mzXML. # Commands for session 7PJCJPOR1 on Fri Apr 16 17:52:14 2010 # BEGIN COMMAND BLOCK ###### BEGIN Command Execution ###### [Fri Apr 16 17:52:14 2010] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ data/test; c:\Inetpub\tpp-bin\spectrast -c_ANN -c_PLT! -cnAlpha - cP0.9 c:/Inetpub/wwwroot/ISB/data/test/ interactms1_nnit_fasp_0302_2d-1.pep.xml OUTPUT: SpectraST started at Fri Apr 16 17:52:15 2010. Importing all spectra with probability >= 0.9... Processing "c:\Inetpub\wwwroot\ISB\data\test \interactms1_nnit_fasp_0302_2d-1.pep.xml"...500...1000...1500...DONE! Importing spectra...10%...20%...30%...40%...50%...60%...70%...80%... 90%...DONE! Library file (BINARY) "c:\Inetpub\wwwroot\ISB\data\test \interactms1_nnit_fasp_0302_2d-1.splib" created. Library file (TEXT) "c:\Inetpub\wwwroot\ISB\data\test \interactms1_nnit_fasp_0302_2d-1.sptxt" created. M/Z Index file "c:\Inetpub\wwwroot\ISB\data\test \interactms1_nnit_fasp_0302_2d-1.spidx" created. Peptide Index file "c:\Inetpub\wwwroot\ISB\data\test \interactms1_nnit_fasp_0302_2d-1.pepidx" created. Total number of spectra in library: 0 Total number of distinct peptide ions in library: 0 Total number of distinct stripped peptides in library: 0 CHARGE +1: 0 ; +2: 0 ; +3: 0 TERMINI Tryptic: 0 ; Semi-tryptic: 0 ; Non-tryptic: 0 METHIONINE MOD Oxidized: 0 CYSTEINE MOD CAM: 0 ; Cleavable-ICAT: 0 ; Uncleavable-ICAT: 0 PROBABILITY >0.9999: 0 ; 0.999-0.9999: 0 ; 0.99-0.999: 0 ; 0.9-0.99: 0 <0.9: 0 NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 0 Total Run Time = 13 seconds. SpectraST finished at Fri Apr 16 17:52:28 2010 with 1567 error(s): PEPXML IMPORT: Peptide ID has unknown modification: "DC[278]DTGVK". Skipped query "Wed_Mar_24_15-45-38_2010.spectrum1156.3103.3103.2". PEPXML IMPORT: Peptide ID has unknown modification: "SQ[129]PSSGSSPC[119]R". Skipped query "Wed_Mar_24_15-45-38_2010.spectrum1779.3087.3087.3". PEPXML IMPORT: Cannot open file "c:/Inetpub/wwwroot/ISB/data/test/ Wed_Mar_24_15-45-38_2010.spectrum1002.mzXML|c:/Inetpub/wwwroot/ISB/ data/test/Wed_Mar_24_15-45-38_2010.spectrum1002.mzML|c:/Inetpub/ wwwroot/ISB/data/Leo/mouse/Wed_Mar_24_15-45-38_2010.spectrum1002.mzXML| c:/Inetpub/wwwroot/ISB/data/Leo/mouse/ Wed_Mar_24_15-45-38_2010.spectrum1002.mzML". No scan from this file will be imported. PEPXML IMPORT: Cannot open file "c:/Inetpub/wwwroot/ISB/data/test/ Wed_Mar_24_15-45-38_2010 -- 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.
