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PeptideIndexer

Refreshes the protein references for all peptide hits from a idXML file.

pot. predecessor tools $ \longrightarrow $ PeptideIndexer $ \longrightarrow $ pot. successor tools
IDFilter or
any protein/peptide processing tool
FalseDiscoveryRate

Each peptide hit is annotated by a target_decoy string, indicating if the peptide sequence is found in a 'target', a 'decoy' or in both 'target+decoy' protein. This information is crucial for the FalseDiscoveryRate tool.

This tool supports relative database filenames, which (when not found in the current working directory) is looked up in the directories specified by 'OpenMS.ini:id_db_dir' (see TOPP for Advanced Users).

By default the tool will fail, if an unmatched peptide occurs, i.e. the database does not contain the corresponding protein. You can force the tool to return successfully in this case by using the flag 'allow_unmatched'.

Todo:
: speed increase of 200% possible when loading the SA from disk instead of building it.

The command line parameters of this tool are:

 

OpenMS / TOPP release 1.9.0 Documentation generated on Sun Oct 27 2013 01:11:36 using doxygen 1.8.4