phosphopeptide tab added

doc/xtandem_pipeline.tex

@@ -370,9 +370,8 @@ If the expert output is enabled, the ODS output contains extra tabs :
 \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, only peptides containing one or more phosphorylation site are taken into account. These peptides are called phosphopeptides. Phosphopeptides sharing the same peptide sequence (possible overlaps) are represented by subgroups. A phospisland is a set of phophopeptides sharing the same peptide sequence, specific to a protein. Thus PhosphoIslands in the same subgroups share the same set of phosphopeptides.
+Subgroups are grouped together if they share at least one protein.
 In this mode, the ODS report contains three tabs :
 \begin{itemize}
 \item ``phosphoislands'' (see~\ref{ods_phosphoisland_tab})
@@ -584,7 +583,7 @@ This tab displays the phosphoisland list.
 \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)
+\item [number of proteins sharing these phosphosites] Number of proteins in this subgroup (sharing the same phosphopeptides)
 \end{description} 
 \normalsize
 
@@ -598,12 +597,21 @@ This tab displays the phosphoisland list.
 
 \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.
+This tab displays details about each identified phosphopeptides. A phosphopeptide is a merge of identified peptides including phosphorylations and sharing the same unique sequence + \mhplus mass modification.
 \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
+\item[Group ID] Group ID of this phosphopeptide
+\item[Sub-Group ID] Sub-Group of this phosphopeptide (it regroups overlapping peptide sequences)
+\item[Phosphopeptide ID] Phosphopeptide identifier
+\item[Sequence] Phosphopeptide sequence
+\item[Modifs] Modification mass
+\item[Number of phosphorylations (phosphosites)] number of phosphorylation sites in this peptide sequence (observed by the identification engine)
+\item[Best Position in sequence] The phosphosites position that gives the best peptide E-value
+\item[All positions] List of all possible phosphosite positions (observed by the identification engine)
+\item[Charges] List of all possible peptides charges (observed by the identification engine)
+\item[MH+ theo] Theoretical \mhplus of this phosphopeptide.
+\item[Number of proteins] Number of protein identified with this phosphopeptide.
+\item[Number of spectra] Number of spectra identifying this phosphopeptide.
 \end{description}
 \normalsize