[spctools-discuss] SCRIPT: OMSSA search with PeptideProphet/ProteinProphet validation

[Robert]

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

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