NAME

       tandem - X!Tandem mass spectrometry software for peptide sequencing

SYNOPSIS

       tandem <input.xml> <output.xml>

DESCRIPTION

       This   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 CITED

       Robertson  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'.

AUTHOR

       This  manual  page  was  written  by  Filippo  Rusconi <lopippo@debian.org>. 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'.

                                          November 2012                                 TANDEM(1)