1 research outputs found
X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification
X!TandemPipeline
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!TandemPipeline allows
the users to launch X!tandem identification, to inspect spectra and
to manually validate their assignment to peptides, to launch the grouping
program, and to visualize elementary data as well as grouping and
redundancy information. Identification results obtained from other
search engines can also be processed. X!TandemPipeline 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!TandemPipeline runs fast, is easy to use, and can process
hundreds of samples simultaneously. It is freely available under the
GNU General Public License v3.0 at http://pappso.inra.fr/bioinfo/xtandempipeline/