X! Tandem open source is software that can match tandem mass spectra with
peptide sequences, in a process that has come to be known as protein
This software has a very simple, sophisticated 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 format is described here (PDF).
This format is used for all of the X! series search engines, as well as the GPM and GPMDB.
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