peptide_pos tab added

doc/xtandem_pipeline.tex

@@ -343,7 +343,7 @@ database.
 \paragraph*{Individual mode}
 If you are running \xtp\ in individual mode, the ODS report will contain two tabs  called ``proteins'' (see~\ref{ods_protein_tab}) and ``peptides'' (see~\ref{ods_peptide_tab}).
 Proteins are listed for each samples. In each samples, the proteins are grouped generally by functions.
-If the expert output is enabled, the ODS output will also contain ``spectra'' (see~\ref{ods_spectra_tab}) and ``peptide_pos'' tab.
+If the expert output is enabled, the ODS output will also contain ``spectra'' (see~\ref{ods_spectra_tab}) and ``peptide\_pos'' (see~\ref{ods_peptide_pos_tab}) tab.
 
 \subsection{Proteins tab (Fig~\ref{ods_individual_proteins})}
 \label{ods_protein_tab}
@@ -438,6 +438,24 @@ The spectra tab contains details on each spectrum match. It is only available th
 \label{ods_individual_spectra}
 \end{figure}
 
+\subsection{Peptides position tab (Fig~\ref{ods_individual_peptide_pos})}
+\label{ods_peptide_pos_tab}
+List of all peptides (unique sequence + \mhplus) per protein identified, containing the position of this peptide in a protein. It is only available the expert ODS output was chosen.
+\small
+\begin{description}
+\item[Peptide ID] The Peptide ID to which the spectrum belongs.
+\item[Protein ID] The protein ID in this grouping experiment (unique within a sample in individual mode).
+\item[accession] The protein accession (database reference).
+\item[description] The protein description.
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/ods_individual_peptide_pos_expert}
+\caption{peptides\_pos results}
+\label{ods_individual_peptide_pos}
+\end{figure}
+
 \subsection{Files *peptide.txt}
 Identified peptides are listed by group (Fig~\ref{pep}). One line corresponds to
 one MS/MS spectrum identifying one peptide that can be present in one or more proteins.
@@ -449,8 +467,8 @@ one MS/MS spectrum identifying one peptide that can be present in one or more pr
 \item[Scan] Scan number of the MS/MS run analysis.
 \item[Rt] Retention time of the peptide.
 \item[Sequence] Sequence of the peptide.
-\item[Modifs] Modifications on the peptide.
-\footnote{For example, M2:+15.99 means that the mass of the second amino acid, which is a methionine, is increased by 15.99. This mass increase indicates that the peptide is oxidized.}
+\item[Modifs] Modifications\footnote{For example, M2:+15.99 means that the mass of the second amino acid, which is a methionine, is increased by 15.99. This mass increase indicates that the peptide is oxidized.} on the peptide.
+
 \item[Valid] Indicates whether the peptide was validated by the filter parameters or not.
 \item[Used] Number of protein sub-groups in which the peptide is present.
 \item[on a total of] Total number of protein sub-groups in the group.\\