Legend:

required parameter

advanced parameter

+IDFileConverterConverts identification engine file formats.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IDFileConverter'

in Input file or directory containing the output of the search engine.
Sequest: Directory containing the .out files
pepXML: Single pepXML file.
protXML: Single protXML file.
mascotXML: Single Mascot xml file.
omssaXML: Single OMSSA xml file.
idXML: Single idXML file.
input file*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.idXML

out Output fileoutput file*.idXML,*.mzid,*.pepXML,*.FASTA

out_type output file type -- default: determined from file extension or content
idXML,mzid,pepXML,FASTA

mz_file [Sequest, pepXML, mascotXML only] Retention times will be looked up in this file

ignore_proteins_per_peptidefalse [Sequest only] Workaround to deal with .out files that contain e.g. "+1" in references column,
but do not list extra references in subsequent lines (try -debug 3 or 4)true,false

mz_name [pepXML, mascotXML only] Experiment filename/path to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'.

use_precursor_datafalse [pepXML, mascotXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra.true,false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false