This wrapper application serves for getting peptide identifications for MS/MS spectra. The wrapper can be executed in three different modes:
./nph-mascot.exe 1 -commandline -f outputfilename < inputfilename
Consult your Mascot reference manual for further details.
This mode is selected by the -mascot_in option in the command line.
This mode is selected by the -mascot_out option in the command line.
If your Mascot server is installed on the same computer as the TOPP applications the MascotAdapter can be executed in mode 1. Otherwise the Mascot engine has to be executed manually assisted by mode 2 and mode 3. The ProteinIdentification steps then look like:
./MascotAdapter -in mzDataFile -out mascotGenericFormatFile -mascot_in
./nph-mascot.exe 1 -commandline -f mascotOutFile < mascotGenericFormatFile
./export_dat.pl do_export=1 export_format=XML file=mascotOutFile _sigthreshold=0 _showsubset=1 show_same_sets=1 show_unassigned=0 prot_score=0 pep_exp_z=0 pep_score=0 pep_homol=0 pep_ident=0 pep_seq=1 show_header=1 show_queries=1 pep_rank=0 > mascotXMLFile
./MascotAdapter -in mascotXMLFile -out IdXMLFile -mascot_out
For mode 1 you have to specify the directory in which the Mascot server is installed. This is done by setting the option mascot_dir in the ini file. Furthermore you have to specify a folder in which the user has write permissions. This is done by setting the option temp_data_directory in the ini file. Two temporary files will be created in this directory during execution but deleted at the end of execution.
You can specify the Mascot parameters precursor_mass_tolerance (the peptide mass tolerance), peak_mass_tolerance (the MS/MS tolerance), taxonomy (restriction to a certain subset of the database), modifications, variable_modifications, charges (the possible charge variants), db (database where the peptides are searched in), hits (number of hits), cleavage (the cleavage enzyme), missed_cleavages (number of missed cleavages) and mass_type (Monoisotopic or Average) via the ini file.
Known problems with Mascot server execution:
Generated Tue Apr 1 15:36:39 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |