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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.

Support for conversion to/from mzIdentML (.mzid) is still experimental and may lose information.

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 XTandem.xml Sequest .out directory

The command line parameters of this tool are:

IDFileConverter -- Converts identification engine file formats.
Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND

Usage:
  IDFileConverter <options>

Options (mandatory options marked with '*'):
  -in <path/file>*           Input file or directory containing the data to convert. This may be:
                             - a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid),
                             - a single file in a search engine-specific XML format (Mascot: mascotXML, OMSS
                             A: omssaXML, X! Tandem: xml),
                             - for Sequest results, a directory containing .out files.
                             (valid formats: 'pepXML', 'protXML', 'mascotXML', 'omssaXML', 'xml', 'idXML',
                             'mzid')
  -out <file>*               Output file (valid formats: 'idXML', 'mzid', 'pepXML', 'FASTA')
  -out_type <type>           Output file type (default: determined from file extension) (valid: 'idXML', 'mzi
                             d', 'pepXML', 'FASTA')
                             
  -mz_file <file>            [Sequest, pepXML, mascotXML, XTandem only] Retention times will be looked up in 
                             this file (valid 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_fi
                             le'.
  -use_precursor_data        [pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generate
                             d peptide identifications, instead of the RTs of MS2 spectra.
  -peptideprophet_analyzed   [pepXML output only] Write output in the format of a PeptideProphet analysis 
                             result. By default a 'raw' pepXML is produced that contains only search engine
                             results.
                             
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.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'IDFileConverter'
in Input file or directory containing the data to convert. This may be:
- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid),
- a single file in a search engine-specific XML format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml),
- for Sequest results, a directory containing .out files.
input file*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.idXML,*.mzid
out Output fileoutput file*.idXML,*.mzid,*.pepXML,*.FASTA
out_type Output file type (default: determined from file extension)idXML,mzid,pepXML,FASTA
mz_file [Sequest, pepXML, mascotXML, XTandem 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
peptideprophet_analyzedfalse [pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results.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
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:42 using doxygen 1.8.9.1