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. 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 be used.

1. A stacking system is used to track redundant protein sequences to eliminate multiple processing of identifical sequences. The redundant information is re-inserted into the results following processing, so that the resulting output is the same as would have been generated by older versions.
2. The letter "X" in protein sequences is now interpreted the same as an asterisk "*", i.e., it is processed as a stop in translation.
3. A new input parameter, spectrum, skyline path, was introduced to make the output easier to parse for the Skyline MRM utility suite.