SYNOPSIStandem <input.xml> <output.xml>
DESCRIPTIONThis manual page documents briefly the tandem-mass package that brings a mass spectrometric software software for peptide sequencing and protein identification.
This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at `http://www.thegpm.org/docs/X_series_output_form.pdf'.
Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used.
BIBLIOGRAPHICAL REFERENCE TO BE CITEDRobertson Craig and Ronald C. Beavis. (2004) TANDEM: matching proteins with mass spectra. Bioinformatics, 20, 1466-1467.
See more references pertaining to this software at `http://www.thegpm.org/GPM/references.html'.
AUTHORThis manual page was written by Filippo Rusconi <[email protected]>. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation.
On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.