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
identification.

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. 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. Therefore, separate assembly and statistical analysis
software, e.g. PeptideProphet and ProteinProphet, do not need to be used.