Refreshes the protein references for all peptide hits from an idXML file and adds target/decoy information.
pot. predecessor tools | ![]() ![]() | pot. successor tools |
IDFilter or any protein/peptide processing tool | FalseDiscoveryRate |
A detailed description of the parameters and functionality is given in PeptideIndexing.
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
). For peptides, the possible values 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. The target/decoy information is crucial for the FalseDiscoveryRate tool. (For FDR calculations, "target+decoy" peptide hits count as target hits.)
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 for Advanced Users).
The command line parameters of this tool are:
INI file documentation of this tool:
OpenMS / TOPP release 2.1.0 | Documentation generated on Tue Jul 11 2017 14:38:45 using doxygen 1.8.13 |