Identifies peptides in MS/MS spectra via Sequest.
This wrapper application serves for getting peptide peptide_identifications for MS/MS spectra. The wrapper can be executed in three different modes:
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.
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:
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>
The command line parameters of this tool are:
OpenMS / TOPP release 1.9.0 | Documentation generated on Tue May 28 2013 12:41:58 using doxygen 1.8.3.1 |