phosphosislands tab added

doc/xtandem_pipeline.tex

@@ -369,6 +369,22 @@ If the expert output is enabled, the ODS output contains extra tabs :
 \item ``peptide\_pos'' (see~\ref{ods_peptide_pos_tab})
 \end{itemize}
 
+\paragraph*{Phosphopeptide mode}
+In this mode, only peptides containing one or more phosphorylation site are taken into account.
+It builds a phosphoisland list. A phosphoisland is a merge of phosphopeptides sharing the same peptide sequence (possible overlaps). A phosphoisland could be present in one or several proteins : these phosphoislands are represented as subgroups.
+The proteins sharing one or more subgroups of phosphoislands are represented by groups.
+In this mode, the ODS report contains three tabs :
+\begin{itemize}
+\item ``phosphoislands'' (see~\ref{ods_phosphoisland_tab})
+\item ``phosphopeptides'' (see~\ref{ods_phosphopeptide_tab})
+\item ``compar\_Spectra'' (see~\ref{ods_phospho_compar_spectra_tab})
+\end{itemize}
+
+If the expert output is enabled, the ODS output contains extra tabs :
+\begin{itemize}
+\item ``spectra'' (see~\ref{ods_phospho_spectra_tab})
+\end{itemize}
+
 \subsection{Proteins tab (Fig~\ref{ods_individual_proteins})}
 \label{ods_protein_tab}
 \small
@@ -555,6 +571,85 @@ This tab displays the protein abundance index (PAI) and the exponentially modifi
 \end{figure}
 
 
+\subsection{PhosphoIsland tab (Fig~\ref{ods_phospho_phosphoislands})}
+\label{ods_phosphoisland_tab}
+This tab displays the phosphoisland list.
+\small
+\begin{description}
+\item[Group ID] Group ID of this phosphoisland : a group contains all proteins sharing one or more phosphoisland
+\item[Sub-Group ID] Sub-Group of this phosphoisland : a subgroup contains all proteins sharing the same phosphopeptides
+\item[PhosphoIsland ID] PhosphoIsland identifier : a set of phosphopeptides covering the same peptide sequence (possible overlaps) in a protein
+\item [Description] The description of the phosphoisland's protein
+\item [MW] The molecular weight of the phosphoisland's protein
+\item [Phosphosites positions] the phopshorylation sites positions of the phosphoisland's phosphopeptides in this protein
+\item [Spectra] Number of spectra identifying the phosphopeptides of this phosphoisland
+\item [Uniques] Number of unique phosphopetide sequences
+\item [number of proteins sharing these phosphosites] Number of proteins in this subgroup (sharing the same phosphoislands)
+\end{description} 
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/ods_phospho_phosphoislands}
+\caption{phosphoislands results}
+\label{ods_phospho_phosphoislands}
+\end{figure}
+
+
+
+\subsection{PhosphoPeptides tab (Fig~\ref{ods_phospho_phosphopeptides})}
+\label{ods_phosphopeptide_tab}
+This tab displays the protein abundance index (PAI) and the exponentially modified PAI (emPAI) by sample, for each top protein of a subgroup. This is convenient to have an idea of the presence/absence of a subgroup of proteins in a sample, and an indication about relative abundance in each samples.
+\small
+\begin{description}
+\item[Group ID] Group ID of this protein
+\item[Sub-Group ID] Sub-Group of this protein
+\item[PhosphoIsland ID] Sub-Group of this protein
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/ods_phospho_phosphopeptides}
+\caption{phosphopeptides results}
+\label{ods_phospho_phosphopeptides}
+\end{figure}
+
+\subsection{Phosphopeptide mode compar Spectra tab (Fig~\ref{ods_phospho_compar_spectra})}
+\label{ods_phospho_compar_spectra_tab}
+This tab displays the protein abundance index (PAI) and the exponentially modified PAI (emPAI) by sample, for each top protein of a subgroup. This is convenient to have an idea of the presence/absence of a subgroup of proteins in a sample, and an indication about relative abundance in each samples.
+\small
+\begin{description}
+\item[Group ID] Group ID of this protein
+\item[Sub-Group ID] Sub-Group of this protein
+\item[PhosphoIsland ID] Sub-Group of this protein
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/ods_phospho_compar_spectra}
+\caption{compar\_Spectra results (mode phospho)}
+\label{ods_phospho_compar_spectra}
+\end{figure}
+
+\subsection{Phosphopeptide mode Spectra tab (Fig~\ref{ods_phospho_spectra_expert})}
+\label{ods_phospho_spectra_tab}
+This tab displays the protein abundance index (PAI) and the exponentially modified PAI (emPAI) by sample, for each top protein of a subgroup. This is convenient to have an idea of the presence/absence of a subgroup of proteins in a sample, and an indication about relative abundance in each samples.
+\small
+\begin{description}
+\item[Group ID] Group ID of this protein
+\item[Sub-Group ID] Sub-Group of this protein
+\item[PhosphoIsland ID] Sub-Group of this protein
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/ods_phospho_spectra_expert}
+\caption{Spectra results (mode phospho)}
+\label{ods_phospho_spectra_expert}
+\end{figure}
+
+
+
+