The X! search engine project

X! Search Engine Development

  X! TANDEM Spectrum Modeler
Note: For versions of X! Tandem that have been modified to run on cluster computer systems, please see Parallel Tandem or X!!Tandem.

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.

Latest release: SLEDGEHAMMER (2013.09.01)
This release updates the E-value estimation algorithm and corrects several issues associated with using very high accuracy fragment ion mass tolerances.
  1. The E-value estimation algorithm has been totally rewritten to simplify the code.
  2. The new E-value algorithm deals more effectively with malformed protein sequence lists, particularly sequence lists that deliberately have very large numbers of protein sequences that have very similar sequences.
  3. The method for determining high accuracy fragment ion tolerances has been corrected.
Copyright © 2004-2013, The Global Proteome Machine Organization
Use of all documentation for X! Tandem, X! P3 and X! Hunter is governed by the Artistic License.