X!TandemPipe
line is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal
list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!TandemPipe
line allows the users to launch X!tandem identification, to inspect spectra and to manually va
lidate their assignment to peptides, to launch the grouping program, and to visua
lize elementary data as well as grouping and redundancy information. Identification results obtained from other search engines can also be processed. X!TandemPipe
line results can be exported as ready-to-use tabulated files or as XML files that can be directly used by the PROTICdb database or by the MassChroQ quantification software. X!TandemPipe
line runs fast, is easy to use, and can process hundreds of samples simultaneously. It is freely available under the GNU General Pub
lic License v3.0 at
line/" class="extLink">http://pappso.inra.fr/bioinfo/xtandempipeline/.