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InspectAdapter

Identifies peptides in MS/MS spectra via Inspect.

pot. predecessor tools $ \longrightarrow $ InspectAdapter $ \longrightarrow $ pot. successor tools
any signal-/preprocessing tool
(in mzML format)
IDFilter or
any protein/peptide processing tool
Experimental classes:
This tool has not been tested thoroughly and might behave not as expected!

This wrapper application serves for getting peptide peptide_identifications for MS/MS spectra. The wrapper can be executed in three different modes:

  1. The whole process of ProteinIdentification via Inspect is executed. Inputfile is an mz file containing the MS/MS spectra (Supported spectrum file formats are .mzXML, .mzData) for which the identifications are to be found and one ore more databases in either trie, FASTA or Swissprot format containing the possible proteins. The given databases are converted and merged into one trie database. This is done because Inspect does the conversion anyway (though with a bug) and may actually not use more than two databases (one of them in trie format). Additionally you thus can reuse the database without having Inspect done the conversion every time. The drawback is, of course, that you need the same amount of space for the trie database as well, which can, in case of large and/or many databases, be a problem. The results are written as a idXML output file. This mode is selected by default.

  2. Only the first part of the ProteinIdentification process is performed. This means that an Inspect input file is generated and the given databases are converted and merged into one trie database. This file can be used directly with Inspect whereas the created database and the spectrum file(s) have to remain at the given positions. Calling an Inspect process should look like the following:

    ./inspect -i inputfilename -o outputfilename

    Consult your Inspect reference manual for further details.

    This mode is selected by the -inspect_in option in the command line.

  3. Only the second part of the ProteinIdentification process is performed. This means that the output of an Inspect run is analyzed and the result written to an idXML file.

    This mode is selected by the -inspect_out option in the command line.

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 command line parameters of this tool are:

INI file documentation of this tool:

Todo:
rewrite the Adapter! It uses old formats and coding style, e.g. mzData input allowed, no input restrictions, manual (unneccessary file checking of input files) etc... + the interface is not convenient, etc ...

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11