OpenMS
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Computes a protein identification score based on an aggregation of scores of identified peptides.
pot. predecessor tools | → ProteinInterference → | pot. successor tools |
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CometAdapter (or other ID engines) | PeptideIndexer | |
FalseDiscoveryRate | ||
IDFilter |
This tool counts and aggregates the scores of peptide sequences that match a protein accession. Only the top PSM for a peptide is used. By default it also annotates the number of peptides used for the calculation (metavalue "nr_found_peptides") and can be used for further filtering. 0 probability peptides are counted but ignored in aggregation method "multiplication".
The command line parameters of this tool are:
ProteinInference -- Protein inference based on an aggregation of the scores of the identified peptides. Full documentation: http://www.openms.de/doxygen/release/3.3.0/html/TOPP_ProteinInference.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: ProteinInference <options> Options (mandatory options marked with '*'): -in <file>* Input file(s) (valid formats: 'idXML', 'consens usXML') -out <file>* Output file (valid formats: 'idXML', 'consensus XML') -out_type <file> Output file type (valid: 'idXML', 'consensusXML ') -merge_runs <choice> If your idXML contains multiple runs, merge them beforehand? Otherwise performs inference separately per run. (default: 'all') (valid: 'no', 'all') -protein_fdr <option> Additionally calculate the target-decoy FDR on protein-level after inference (default: 'false' ) (valid: 'true', 'false') Merging: -Merging:annotate_origin <choice> If true, adds a map_index MetaValue to the Pept ideIDs to annotate the IDRun they came from. (default: 'true') (valid: 'true', 'false') -Merging:allow_disagreeing_settings Force merging of disagreeing runs. Use at your own risk. Algorithm: -Algorithm:min_peptides_per_protein <number> Minimal number of peptides needed for a protein identification. If set to zero, unmatched prot eins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are remov ed but the spectrum info is kept. (default: '1') (min: '0') -Algorithm:score_aggregation_method <choice> How to aggregate scores of peptides matching to the same protein? (default: 'best') (valid: 'best', 'product', 'sum', 'maximum') -Algorithm:treat_charge_variants_separately <choice> If this is true, different charge variants of the same peptide sequence count as individual evidences. (default: 'true') (valid: 'true', 'false') -Algorithm:treat_modification_variants_separately <choice> If this is true, different modification variant s of the same peptide sequence count as individ ual evidences. (default: 'true') (valid: 'true' , 'false') -Algorithm:use_shared_peptides <choice> If this is true, shared peptides are used as evidences. Note: shared_peptides are not delete d and potentially resolved in postprocessing as well. (default: 'true') (valid: 'true', 'fal se') -Algorithm:skip_count_annotation If this is set, peptide counts won't be annotat ed at the proteins. -Algorithm:annotate_indistinguishable_groups <choice> If this is true, calculates and annotates indis tinguishable protein groups. (default: 'true') (valid: 'true', 'false') -Algorithm:greedy_group_resolution If this is true, shared peptides will be associ ated to best proteins only (i.e. become potenti ally quantifiable razor peptides). 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: