This is the command tandem that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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'.
Use tandem online using onworks.net services
