\href{http://www.thegpm.org/tandem/index.html}{X!Tandem} is an open-source software performing peptide/protein identification from MS/MS mass spectra. X!Tandem is fast and accurate, but the Global Proteome Machine (\href{http://www.thegpm.org/}{GPM}) is relatively limited regarding the processing of identification results.
$\xtp$ is an alternative to the installation of the GPM on local servers.
\href{http://www.thegpm.org/tandem}{\xt} is an open-source software performing peptide/protein identification from MS/MS mass spectra. \xt\ is fast and accurate,
but is not sufficient in itself to filter, validate and group identification results. Third party softwares are needed.
Some of these tools are available on the Global Proteome Machine web site (\href{http://www.thegpm.org/}{The GPM}).
\xtp\ is an alternative to the installation of the GPM tools. It is a standalone software, very easy to install, light and powerfull.
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$\xtp$ performs database searching and matching on a list of MS/MS runs in one shot, using a list of easily user selected paramaters and databases.
\xtp\performs database searching and matching on a list of MS/MS runs in one shot, using a list of easily user selected paramaters and databases.
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$\xtp$ also performs filtering of data according to statistical values at peptide and protein levels. Moreover, redundancy of protein databases are fully filtered as follows :
\xtp\also performs filtering of data according to statistical values at peptide and protein levels. Moreover, redundancy of protein databases are fully filtered as follows :
\begin{itemize}
\item proteins identified without specific peptides compared to others are eliminated;
\item proteins identified with the same pool of peptides are assembled;
