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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 additional parameters:

mz_file:
Some search engine output files (like pepXML, mascotXML, Sequest .out files) may not contain retention times, only scan numbers. To be able to look up the actual RT values, the raw file has to be provided using the parameter mz_file. (If the identification results should be used later to annotate feature maps or consensus maps, it is critical that they contain RT values. See also IDMapper.)

mz_name:
PepXML files can contain results from multiple experiments. However, the idXML format does not support this. The mz_name parameter (or mz_file, if given) thus serves to define what parts to extract from the pepXML.

scan_regex:
For Mascot results exported to XML, the scan numbers (used to look up retention times using mz_file) should be given in the "pep_scan_title" XML elements, but the format can vary. If the defaults fail to extract the scan numbers, a Perl-style regular expression can be given through the advanced parameter scan_regex, and will be used instead. The regular expression should contain a named group "SCAN" matching the scan number or "RT" matching the actual retention time. For example, if the format of the "pep_scan_title" elements is "scan=123", where 123 is the scan number, the expression "scan=(?<SCAN>\\d+)" can be used to extract the number. (However, the format in this example is actually covered by the defaults.)

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

The command line parameters of this tool are:

IDFileConverter -- Converts identification engine file formats.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

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 (val
                        id formats: 'mzML', 'mzXML', 'mzData')
                        
  -mz_name <file>       [pepXML only] Experiment filename/path (extension will be removed) to match in the 
                        pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'.
  -use_precursor_data   [pepXML 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.
version1.11.1 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 fileinput file*.mzML,*.mzXML,*.mzData
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 only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'.
use_precursor_datafalse [pepXML 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
scan_regex [mascotXML only] Regular expression used to extract the scan number or retention time. See documentation for details.
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

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5