Hi, This is my recent and functional version of OMSSAVALIDATION.BAT.
The DOS skript converts the Agilent MSD/XCTultra Trap (=BrukerHCTultra) trap data to mzXML, executes an OMSSA search against a decoy database, and performs a PeptideProphet/ProteinProphet validation. The ProteinProphet *prot.shtml files can be examined in the TPP; the *pep.shtml peptide files are linked correctly to the spectra. Output PeptideProphet/ProteinProphet files can be converted by PRIDEconverter and deposited in the PRIDE DB. The additional OMSSA search generates the binary OMSSA *.oms output (For analyses with the OMSSA browser). **************** START @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\customdb -fm %%I -v 2 -mf 3 -mv 4 -he 1e6 -w -op %%I_OMSSA_TPP.pep.xml ECHO *** Fix linking of MS/MS spectra *** sed -i "s/\.mgf_OMSSA_TPP\.pep\.xml//ig" *OMSSA_TPP.pep.xml ECHO *** Validation of OMSSA results with PeptideProphet/ ProteinProphet; NOOCAM NOGROUPS *** 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\customdb FOR %%I IN (ppval*.pep.xml) DO proteinprophet %%I %%I.prot.xml NOOCCAM NOGROUPS DEL ppval_ppval* DEL sed* ECHO *** Standard OMSSA Search *** FOR %%I IN (*.mgf) DO omssacl -d c:\blastdb\customdb -fm %%I -v 2 -mf 3 -mv 4 -w -ob %%I_OMSSA_DECOY.oms **************** END 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.
