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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 IDPosteriorErrorProbability tools.

Note
Make sure that your protein names in the database contain a correctly formatted decoy string. This can be ensured by using DecoyDatabase. If the decoy identifier is not recognized successfully all proteins will be assumed to stem from the target-part of the query.
E.g., "sw|P33354_REV|YEHR_ECOLI Uncharacterized lipop..." is invalid, since the tool has no knowledge of how SwissProt entries are build up. A correct identifier could be "rev_sw|P33354|YEHR_ECOLI Uncharacterized li ..." or "sw|P33354|YEHR_ECOLI_rev Uncharacterized li", depending on if you are using prefix annotation or not.
This tool will also give you some target/decoy statistics when its done. Look carefully!

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'.

Some search engines (such as Mascot) will replace ambiguous AA's ('B', 'Z', and 'X') in the protein database with unambiguous AA' in the reported peptides, e.g., exchange 'X' with 'H'. This will cause this peptide not to be found by exactly matching its sequence to the database. However, we can recover these cases by using tolerant search (done automatically).

Two search modes are available:

No matter if exact or tolerant search is used, we require ambiguous AA's in peptide sequence to match exactly in the protein DB (i.e., 'X' in peptide only matches 'X' in database). The exact mode is much faster (about x10) and consumes less memory (about x2.5), but might fail to report a few protein hits with ambiguous AAs for some peptides. Usually these proteins are putative, however. The exact mode also supports usage of multiple threads (use @ -threads option) to speed up computation even further, at the cost of some memory. This is only for the exact search though (Aho Corasick). If tolerant searching needs to be done for unassigned peptides, the latter will consume the major time portion.

Once a peptide sequence is found in a protein sequence, this does not imply that the hit is valid! This is where enzyme specificity comes into play. By default, we demand that the peptide is fully tryptic (since the enzyme parameter is set to "trypsin" and specificity is "full"). So unless the peptide coincides with C- and/or N-terminus of the protein, the peptide's cleavage pattern should fulfill the trypsin cleavage rule [KR][^P]. We make one exception for peptides which start at the second AA of the protein where the first AA of the protein is methionin (M), which is usually cleaved off in vivo, e.g., the two peptides AAAR and MAAAR would both match a protein starting with MAAAR.

You can relax the requirements further by chosing semi-tryptic (only one of two "internal" termini must match requirements) or none (essentially allowing all hits, no matter their context).

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 1.11.1 Documentation generated on Sun Sep 7 2014 06:42:38 using doxygen 1.8.8