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'.