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SequestAdapter

Identifies peptides in MS/MS spectra via Sequest.

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 Sequest is executed. Inputfile is one (or more) mz file containing the MS/MS spectra (Supported spectrum file formats are .mzXML, .mzData) for which the identifications are to be found and one database in FASTA format containing the possible proteins. The results are written as an IdXML output file. This mode is selected by default. Note: You need a user with network access on the computer hosting sequest.

  2. Only the first part of the ProteinIdentification process is performed. This means that a Sequest input file is generated and dta files are created from the mz file. Calling a Sequest process should look like the following:

    sequest -P\<inputfilename\> \<path to dta files\>*.dta
      Consult your Sequest reference manual for further details.
    
      This mode is selected by the <b>-sequest_in</b> option in the command line.
      </li>
    
      <li>
      Only the second part of the ProteinIdentification process is performed.
      This means that the output of sequest is translated into IdXML.
    
      This mode is selected by the <b>-sequest_out</b> option in the command line.
      </li>
    
Todo:
Check for missing precursors (Andreas)

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