Bug#693800: ITP: tandem-mass -- mass spectrometry software for protein identification
Package: wnpp
Severity: wishlist
Owner: Olivier Langella <Olivier.Langella@laposte.net>
* Package name : tandem-mass
Version : 20121001
Upstream Author : The Global Proteome Machine Organization
* URL : http://www.thegpm.org/TANDEM/
* License : Artistic License 1.0
Programming Lang: C++
Description : mass spectrometry software for protein identification
X! Tandem can match tandem mass spectra with peptide sequences, in a
process that is commonly used to perform 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
\fI`http://www.thegpm.org/docs/X_series_output_form.pdf'\fR.
.
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.
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