Robert, You need an mzXML file present in order for the spectrum viewer and Pep3D viewer to work. Both of those reads the spectrum data from that file. Additionally, the various files (pep.xml, base_name attribute in the pep.xml, mzXML, etc.) must follow a standard convention for it all to work correctly. Check out the following two previous spctools-discuss posts and see if they help any then report back further questions.
http://bit.ly/aOmifn http://bit.ly/bKxtyx (You'll probably want to keep things simple and end up with files like P1.mgf, P1.mzXML, P1.pep.xml, etc.) - Jimmy On Wed, Feb 17, 2010 at 3:31 PM, Robert <[email protected]> wrote: > Hi, > > The automated OMSSAVALIDATION.BAT (see previous posts) works quite > fine; However, the linking to the MS/MS spectra is a bit buggy. > > In the PepXML Viewer the entries look like following: > > prob spectrum pvalue expect ions peptide protein > calc_mass > 1.0000 P1.01341.01341.3SpectraST 0.000000000000026 > 0.000000014849023 36/54 > R.NSVDELNNNVEAVSQ129.04TSSSSFQYMYLLK.DPeptideAtlas FIBB|FIBB_ +7 > 3167.46 > > Clicking on the prob-score (1.0000) or on the protein identification > (FIBB) give the expected results (The nice Peptide Prophet person with > graphs, and the COMET representation respective). > > 1) However, clicking on the ions (36/54) in the PepXML Viewer does not > give the spectrum, but an error message: > > command "c:\Inetpub\wwwroot\..\tpp-bin\tar.exe -tzf c:/Inetpub/wwwroot/ > ISB/data/projects/FIBB_HUMAN/090724/ppval-OMSSA/ > P1.mgf_OMSSA_TPP.pep.xml.tgz "*P1.01341.01341.3.dta" > /dev/null" > failed: Operation not permitted Error - cannot read spectrum; tried > direct .dta, from mzXML/mzData and from .tgz > > The link from the PepXML Viewer looks as follows: > > http://localhost/tpp-bin/plot-msms.cgi?MassType=1&NumAxis=1&Mod15=129.04258&Pep=NSVDELNNNVEAVSQTSSSSFQYMYLLK&Dta=C:/Inetpub/wwwroot/ISB/data/projects/FIBB_HUMAN/090724/ppval-OMSSA/P1.mgf_OMSSA_TPP.pep.xml/P1.01341.01341.3.dta&Global_Mod=CS57.021000000000001&Global_Mod=NV0.98399999999999999&Global_Mod=QV0.98399999999999999 > > At least the path to the pep.xml is correct, but somehow the MS/MS > scan is not processed correctly (the original data are in P1.mgf for > the OMSSA search; mzXML works only for X!Tandem). > > 2) In the Protein Prophet, the links to weight and nsp work fine, > clicking on the individual peptides does not show the list of > identified peptides with the possibility to access the individual > spectra, but a page: > > 3_MGPTELLIEMEDWK > > Proteins: Ref all Show all > > C:/Inetpub/wwwroot/ISB/data/projects/FIBB_HUMAN/090724/ppval-OMSSA/ > ppval_p1.mgf_omssa_tpp.pep.xml > > Generate Pep3D.htm > > Which does not work; Error message: > > Error: Could not open input file c:/Inetpub/wwwroot/ISB/data/projects/ > FIBB_HUMAN/090724/ppval-OMSSA/P1.mgf_OMSSA_TPP.pep.xml.mzXML > > 3) The export of the PeptideProphet/ProteinProphet results to PRIDE > XML fails (PRIDEconverter) > OMSSA and X!Tandem/Prophets work (with some small deficiencies); I > contacted the developers with Error.logs; however, I guess, also here > the linking to the spectrum data is causing trouble. > > I really would appreciate your comments. I think the combination OMSSA/ > TPP really would be exciting, if everything works finally (viewing, > PRIDE etc.). > > Thanks and greetings, Robert > > -- > 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. > > -- 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.
