Update documentation

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@322 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/doc/xtandem_pipeline.tex

@@ -20,7 +20,7 @@ PAPPSO - \url{http://pappso.inra.fr/}\\
 \includegraphics[width=1cm]{images/pappso.pdf}
 }
 \title{$\X$\\Automated analyses, filtering and export of X!Tandem MS/MS results}
-\date{06 June 2012}
+\date{22 June 2012}
 
 %Modification des entetes et pied de page + marges
 \geometry{top=3cm, bottom=3cm, left=2cm, right=2cm}
@@ -168,7 +168,7 @@ X!Tandem software uses only protein databases in fasta format. It doesn't work w
 
 \section{Processing the results}
 \paragraph*{Warning:}
-To process results, $\X$ needs to have X!Tandem result files (.xml). The names of the files are used as \textbf{sample names}.
+To process results, $\X$ needs to have X!Tandem result files (.xml) or Mascot result files (.dta). The names of the files are used as \textbf{sample names}.
 
 \subsection{Three modes of analysis}
 \label{mode}
@@ -189,7 +189,7 @@ In all modes, you have to defined the filter parameters.
 The filter window (Fig~\ref{filter}) defines the automated filtering process parameters :
 \small
 \begin{description}
-\item[Add files] \hfill \\At this stage, you can add other MS/MS result files to the analysis. If two files have the same name, they are combined in one result file. Interesting if one wants to combine X!Tandem results of the same LC-MS/MS run using different modification parameters or protein databases.
+\item[Add files] \hfill \\At this stage, you can add other MS/MS result files to the analysis. If two files have the same name, they are combined in one result file. Interesting if one wants to combine X!Tandem and/or Mascot results of the same LC-MS/MS run using different modification parameters or protein databases.
 \item[Peptide E-value] \hfill \\Defines the E-value above which a peptide is considered as valid.
 \item[Peptide number] \hfill \\Defines the number of valid unique\footnote{Unique peptides are defined as peptides with different sequences. This excludes peptides with different modifications.} peptides necessary to validate a protein.
 \item[Protein E-value] \hfill \\Defines the E-value above which a protein is considered as valid.