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OpenMS
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Refreshes the protein references for all peptide hits from an idXML file and adds target/decoy information.
pot. predecessor tools | → PeptideIndexer → | pot. successor tools |
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IDFilter or any protein/peptide processing tool | FalseDiscoveryRate |
PeptideIndexer refreshes target/decoy information and mapping of peptides to proteins. The target/decoy information is crucial for the FalseDiscoveryRate tool. (For FDR calculations, peptides hitting both target and decoy proteins are counted as target hits.)
PeptideIndexer allows for ambiguous amino acids (B|J|Z|X) in the protein database and peptide sequence.
Enzyme cutting rules and partial specificity are derived from input idXML automatically by default or can be specified explicitly by the user.
All peptide and protein hits are annotated with target/decoy information, using the meta value 'target_decoy'. For proteins the possible values are "target" and "decoy", depending on whether the protein accession contains the decoy pattern (parameter decoy_string
) as a suffix or prefix, respectively (see parameter prefix
). Resulting protein hits appear in the order of the FASTA file, except for orphaned proteins, which will appear first with an empty 'target_decoy' metavalue. Duplicate protein accessions & sequences will not raise a warning, but create multiple hits (PeptideIndexer reads the FASTA file piecewise for efficiency reasons, and thus might not see all accessions & sequences at once).
Peptide hits are annotated with metavalue 'protein_references', and if matched to at least one protein also with metavalue 'target_decoy'. The possible values for 'target_decoy' in peptides are "target", "decoy" and "target+decoy", depending on whether the peptide sequence is found only in target proteins, only in decoy proteins, or in both. If the peptide is unmatched the metavalue is missing.
Runtime: PeptideIndexer is usually very fast (loading and storing the data takes the most time) and search speed can be further improved (linearly) by using more threads. Avoid allowing too many (>=4) ambiguous amino acids if your database contains long stretches of 'X' (exponential search space).
PeptideIndexer supports relative database filenames, which (when not found in the current working directory) are looked up in the directories specified by OpenMS.ini:id_db_dir
(see TOPP_advanced). The database is by default derived from the input idXML's metainformation ('auto' setting), but can be specified explicitly.
Further details can be found in the underlying OpenMS::PeptideIndexing implementation.
The command line parameters of this tool are:
INI file documentation of this tool: