Hi, Following a DOS batch file, which converts all *.mzXML data in a directory to *.mgf, executes an OMSSA search with a decoy data base and subsequently carries out the PeptideProphet/ProteinProphet validation steps.
My raw data are generated on an Agilent XCTultra, which has the same hardware and data format as the Bruker HCTultra. For conversion of *.yep to *.mzXML I’m using the Bruker tool # compassxport -multi d: \data\directory. Note: I´m running a standard OMSSA search (binary *.oms output), for comparison; usually the automated workflow with OMSSA/TPP delivers more hits. Of course, one might wish to change some parameters. This file is copy & paste now. Unfortunately, I cannot upload the *.bat. --- omssavalidation.bat --- @ECHO OFF ECHO *** Converting mzXML files to mgf *** FOR %%I IN (*.mzXML) DO MzXML2Search -mgf -ACID -M2-2 -P5 -I0.01 -B10 - T5000.0 %%I ECHO *** OMSSA search: Decoy data base, trypsin, pep.xml output *** REM decoy entries in data base stdecoy start with decoy_; reverse decoy data base generated with FastaTools 0.9 and merged with original data base using mergeFasta.pl FOR %%I IN (*.mgf) DO omssacl -d c:\blastdb\stdecoy -fm %%I -v 2 -mf 3 -mv 4 -he 1e6 -w -op %%I_OMSSA_TPP.pep.xml FOR %%I IN (*.mgf) DO omssacl -d c:\blastdb\stdecoy -fm %%I -v 2 -mf 3 -mv 4 -w -ob %%I_OMSSA_DECOY.oms ECHO *** Validation of OMSSA results with PeptideProphet/ ProteinProphet *** FOR %%I IN (*OMSSA_TPP.pep.xml) DO interactparser ppval_%%I %%I -L5 - Etrypsin -C -P FOR %%I IN (ppval*.pep.xml) DO peptideprophetparser %%I DECOY=decoy MINPROB=0 NONPARAM FOR %%I IN (ppval*.pep.xml) DO refreshparser %%I c:\blastdb\stdecoy FOR %%I IN (ppval*.pep.xml) DO proteinprophet %%I %%I.prot.xml --- I´m using TPP v4.3r1, and OMSSA 2.1.7. Currently I am testing this *.bat with several data files. It looks promising, the *prot.shtml looks the same as with the built-in Tandem workflow. However, I cannot access directly the peptide mass spectra. Any ideas? Comments and suggestions are welcome. Hope, it might be useful. Best regards, 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.
