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PeptideIndexer

Refreshes the protein references for all peptide hits from an idXML file and adds target/decoy information.

pot. predecessor tools $ \longrightarrow $ PeptideIndexer $ \longrightarrow $ 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).

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.
The tool and its parameters are described in detail in the PeptideIndexing documentation. Please make sure you read and understand it before using the tool to avoid suboptimal results or long runtimes!

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.3.0 Documentation generated on Thu Mar 8 2018 04:35:37 using doxygen 1.8.14