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OpenMS
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Converts peptide/protein identification engine file formats.
| potential predecessor tools | → IDFileConverter → | potential successor tools |
|---|---|---|
| TPP tools: PeptideProphet, ProteinProphet | TPP tools: ProteinProphet (for conversion from idXML to pepXML) | |
| Sequest protein identification engine |
IDFileConverter can be used to convert identification results from external tools/pipelines (like TPP, Sequest, Mascot, OMSSA, X! Tandem) into other (OpenMS-specific) formats. For search engine results, it might be advisable to use the respective TOPP Adapters (e.g. CometAdapter) to avoid the extra conversion step.
The most simple format accepted is '.tsv': A tab separated text file, which contains one or more peptide sequences per line. Each line represents one spectrum, i.e. is stored as a PeptideIdentification with one or more PeptideHits. Lines starting with "#" are ignored by the parser.
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. We use the following heuristic: if peptideprophet_analyzed is set, we take the scores from the idXML as is and assume the PeptideHits contain all necessary information. If peptideprophet is not set, we only provide ProteinProphet-compatible results with probability-based scores (i.e. Percolator with PEP score or scores from IDPosteriorErrorProbability). All secondary or non-probability main scores will be written as "search_scores" only.
Support for conversion to/from mzIdentML (.mzid) is still experimental and may lose information.
The xquest.xml format is very specific to Protein-Protein Cross-Linking MS (XL-MS) applications and is only considered useful for compatibility of OpenPepXL / OpenPepXLLF with the xQuest / xProphet / xTract pipeline. It will only have useful output when converting from idXML or mzid containg XL-MS data.
Also supports generation of .mzML files with theoretical spectra from a .FASTA input.
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 or spectrum IDs. 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:
This advanced parameter defines a spectrum reference format via a Perl-style regular expression. The reference format connects search hits to the MS2 spectra that were searched, and may be needed to look up e.g. retention times in the raw data (mz_file). See the documentation of class SpectrumLookup for details on how to specify spectrum reference formats. Note that it is not necessary to look up any information in the raw data if that information can be extracted directly from the spectrum reference, in which case mz_file is not needed.
For Mascot results exported to (Mascot) XML, scan numbers that can be used to look up retention times (via mz_file) should be given in the "pep_scan_title" XML elements, but the format can vary. Some default formats are defined in the Mascot XML reader, but if those fail to extract the scan numbers, scan_regex can be used to overwrite the defaults.
For pepXML, supplying scan_regex may be necessary for files exported from Mascot, but only if the default reference formats (same as for Mascot XML) do not match. The spectrum references to which scan_regex is applied are read from the "spectrum" attribute of the "spectrum_query" elements.
For Percolator tab-delimited output, information is extracted from the "PSMId" column. By default, extraction of scan numbers and charge states is supported for MS-GF+ Percolator results (retention times and precursor m/z values can then be looked up in the raw data via mz_file).
Some information about the supported input types:
The command line parameters of this tool are:
IDFileConverter -- Converts identification engine file formats.
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/TOPP_IDFileConverter.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
To cite OpenMS:
+ Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for
mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.
Usage:
IDFileConverter <options>
This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option
Options (mandatory options marked with '*'):
-in <path/file>* Input file or directory containing the data to convert. This may be:
- a single file in OpenMS database format (.oms),
- a single file in a multi-purpose XML format (.idXML, .mzid, .pepXML, .protXML)
,
- a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA:
.omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),
- a single file in fasta format (can only be used to generate a theoretical mzML
),
...
(valid formats: 'oms', 'idXML', 'mzid', 'fasta', 'pepXML', 'protXML', 'mascotXM
L', 'omssaXML', 'xml', 'psms', 'tsv', 'xquest.xml')
-out <file>* Output file (valid formats: 'oms', 'idXML', 'mzid', 'pepXML', 'fasta', 'xquest.x
ml', 'mzML')
-out_type <type> Output file type (default: determined from file extension) (valid: 'oms', 'idXML
', 'mzid', 'pepXML', 'fasta', 'xquest.xml', 'mzML')
-mz_file <file> [pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and
native spectrum ids (spectrum_references) 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'.
-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.
-score_type <choice> [Percolator only] Which of the Percolator scores to report as 'the' score for a
peptide hit (default: 'qvalue') (valid: 'qvalue', 'PEP', 'score')
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)
The following configuration subsections are valid:
- fasta_to_mzml [FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical
spectra.
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
- http://www.openms.de/doxygen/release/3.0.0/html/TOPP_IDFileConverter.html
INI file documentation of this tool:
1.9.1