OpenMS
|
Merges several idXML files into one idXML file.
potential predecessor tools | → IDMerger → | potential successor tools |
---|---|---|
MascotAdapter (or other ID engines) | ConsensusID | |
IDFileConverter | IDMapper |
The peptide hits and protein hits of the input files will be written into the single output file. In general, the number of idXML files that can be merged into one file is not limited.
If an additional file is given through the add_to
parameter, identifications from the main inputs (in
) are added to that file, but only for those peptide sequences that were not already present. Only the best peptide hit per identification (MS2 spectrum) is taken into account; peptide identifications and their corresponding protein identifications are transferred.
Alternatively, with the pepxml_protxml
option, results from corresponding PeptideProphet and ProteinProphet runs can be combined. In this case, exactly two idXML files are expected as input: one containing data from a pepXML file, and the other containing data from a protXML file that was created based on the pepXML (meaningful results can only be obtained for matching files!). pepXML or protXML can be converted to idXML with the IDFileConverter tool.
The command line parameters of this tool are:
IDMerger -- Merges several protein/peptide identification files into one file. Full documentation: http://www.openms.de/doxygen/release/3.3.0/html/TOPP_IDMerger.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 To cite OpenMS: + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7. Usage: IDMerger <options> Options (mandatory options marked with '*'): -in <files>* Input files separated by blanks (all must have the same type) (valid form ats: 'idXML', 'oms') -out <file>* Output file (must have the same type as the input files) (valid formats: 'idXML', 'oms') -out_type <type> Output file type (default: determined from file extension) (valid: 'idXML ', 'oms') -add_to <file> Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum). (valid formats: 'idXML') -annotate_file_origin <annotate> Store the original filename in each protein/peptide identification (meta value: 'file_origin') - idXML input/output only (default: 'true') (valid: 'true', 'false') -pepxml_protxml Merge idXML files derived from a pepXML and corresponding protXML file. Exactly two input files are expected in this case. Not compatible with 'add_to'. -merge_proteins_add_PSMs Merge all identified proteins by accession into one protein identificatio n run but keep all the PSMs with updated links to potential new protein ID#s. Not compatible with 'add_to'. 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: