OpenMS: IDFileConverter

Converts identification engine file formats.

potential predecessor tools	$\longrightarrow$ IDFileConverter $\longrightarrow$	potential successor tools
TPP tools: PeptideProphet, ProteinProphet		TPP tools: ProteinProphet (for conversion from idXML to pepXML)
Sequest protein identification engine

Conversion from the TPP file formats pepXML and protXML to OpenMS' idXML is quite comprehensive, to the extent that the original data can be represented in the simpler idXML format.

In contrast, support for converting from idXML to pepXML is limited. The purpose here is simply to create pepXML files containing the relevant information for the use of ProteinProphet.

Details on using 'mz_file': Some search engine output file (like Sequest .out files) do not contain retention times, only scan numbers, thus the raw file is used to reconstruct actual RT values. For pepXML and mascotXML this file can additionally be used to define what parts to extract (some pepXMLs contain results from multiple experiments).

Some information about the supported input types: mzIdentML pepXML protXML idXML mascotXML omssaXML .out directory

The command line parameters of this tool are:

IDFileConverter -- Converts identification engine file formats.
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  IDFileConverter <options>

Options (mandatory options marked with '*'):
  -in <path/file>*      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.
                        (valid formats: 'pepXML', 'protXML', 'mascotXML', 'omssaXML', 'idXML')
  -out <file>*          Output file (valid formats: 'idXML', 'mzid', 'pepXML', 'FASTA')
  -out_type <type>      Output file type -- default: determined from file extension or content
                        (valid: 'idXML', 'mzid', 'pepXML', 'FASTA')
                        
  -mz_file <file>       [Sequest, pepXML, mascotXML only] Retention times will be looked up in this file
                        
                        
  -mz_name <file>       [pepXML, mascotXML only] Experiment filename/path to match in the pepXML file ('base_
                        name' attribute). Only necessary if different from 'mz_file'.
  -use_precursor_data   [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.
                        
Common TOPP options:
  -ini <file>           Use the given TOPP INI file
  -threads <n>          Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>     Writes the default configuration file
  --help                Shows options
  --helphelp            Shows all options (including advanced)

INI file documentation of this tool:

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