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IDFileConverter

Converts identification engine file formats.

potential predecessor tools $ \longrightarrow $ IDFileConverter $ \longrightarrow $ potential successor tools
TPP tools: PeptideProphet, ProteinProphet TPP tools: ProteinProphet
(for conversion from idXML to pepXML)
Sequest protein identification engine

Conversion from the TPP file formats pepXML and protXML to OpenMS' idXML is quite comprehensive, to the extent that the original data can be represented in the simpler idXML format.

In contrast, support for converting from idXML to pepXML is limited. The purpose here is simply to create pepXML files containing the relevant information for the use of ProteinProphet.

Details on additional parameters:

mz_file:
Some search engine output files (like pepXML, mascotXML, Sequest .out files) may not contain retention times, only scan numbers. To be able to look up the actual RT values, the raw file has to be provided using the parameter mz_file. (If the identification results should be used later to annotate feature maps or consensus maps, it is critical that they contain RT values. See also IDMapper.)

mz_name:
PepXML files can contain results from multiple experiments. However, the idXML format does not support this. The mz_name parameter (or mz_file, if given) thus serves to define what parts to extract from the pepXML.

scan_regex:
For Mascot results exported to XML, the scan numbers (used to look up retention times using mz_file) should be given in the "pep_scan_title" XML elements, but the format can vary. If the defaults fail to extract the scan numbers, a Perl-style regular expression can be given through the advanced parameter scan_regex, and will be used instead. The regular expression should contain a named group "SCAN" matching the scan number or "RT" matching the actual retention time. For example, if the format of the "pep_scan_title" elements is "scan=123", where 123 is the scan number, the expression "scan=(?<SCAN>\\d+)" can be used to extract the number. (However, the format in this example is actually covered by the defaults.)

Some information about the supported input types: mzIdentML pepXML protXML idXML mascotXML omssaXML Sequest .out directory

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 1.11.1 Documentation generated on Mon Aug 18 2014 14:41:09 using doxygen 1.8.7