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. Additional testing for adventitious cleavage at Asp-Pro residues. These tests are made for all enzyme cleavage types, except [X]|[X] (cleavage at all residues). Testing Asp-Pro cleavage does not affect the "missed cleavage" count in an analysis.
2. The load balancing method for starting multiple threads has been improved to take account of data sets that have been re-arranged from their original order in an LC/MS/MS file.
3. Several changes have been made to keep up with changes to "standard" data file formats.