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: PILEDRIVER (2015.04.01)
This release adds a new output format (mzIdentML) and several variants of the mzML input format (MSNumPress compression). It also corrects an undesired behavior when searching for protein N-terminal and C-terminal modifications when using a protein modification specification XML file.
  1. New files (MSNumPress.cpp, MSNumPress.hpp) were added to the project (Johan Teleman) to implement the compression modes that have been added to the mzML specification.
  2. New files (mzid_report.cpp, mzid_report.hpp) were added to the project to implement the output of an mzIdentML file, in addition to the existing BIOML output. To generate an mzIdentML output, set the new parameter:
    • "output, mzid": if "yes" the file will be created with the extention .mzid.
  3. The "score_terminus_single" method has been removed from mprocess and replaced by an altered version of "score_terminus", which corrects the bad behavior associated with searching for protein N- and C-terminal modifications when using a protein modification specification file. It also improves the display progress reporting for this type of search.
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Use of all documentation for X! Tandem, X! P3 and X! Hunter is governed by the Artistic License.