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doc/xtandem_pipeline.tex

@@ -17,7 +17,7 @@
 \author{Benoit Valot and Olivier Langella\\
 \texttt{valot@moulon.inra.fr; langella@moulon.inra.fr}\\
 PAPPSO - \url{http://pappso.inra.fr/}\\
-\includegraphics[width=1cm]{images/pappso.pdf}
+\includegraphics[width=1cm]{images/pappso}
 }
 \title{$\X$\\Automated analyses, filtering and export of X!Tandem MS/MS results}
 \date{22 June 2012}
@@ -29,7 +29,7 @@ PAPPSO - \url{http://pappso.inra.fr/}\\
 %\fancyhead{}
 \fancyfoot{}
 \rfoot{\thepage}
-\lfoot{\includegraphics[width=1cm]{images/pappso.pdf}}
+\lfoot{\includegraphics[width=1cm]{images/pappso}}
 
 
 \begin{document}
@@ -106,7 +106,7 @@ At the firt start, the application open the configuration path window:
 \end{itemize}
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_configuration.png}
+\center \includegraphics[scale=0.5]{images/tandem_configuration}
 \caption{Configuration window}
 \label{configuration}
 \end{figure}
@@ -124,7 +124,7 @@ Three successive graphical boxes help you select first the mzXML files or other
 To perform database searching, you must create or edit a model XML file (stored in the xtandem models folder). Open the menu \textit{Option $\rightarrow$ X!Tandem preset} (Fig~\ref{xtandem_parameter}).
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.4]{images/tandem_parameter.png}
+\center \includegraphics[scale=0.4]{images/tandem_parameter}
 \caption{X!Tandem preset window}
 \label{xtandem_parameter}
 \end{figure}
@@ -153,7 +153,7 @@ X!Tandem works with open peak-list files like mzXML, mgf, mzData, mzML or pkl fi
 X!Tandem software uses only protein databases in fasta format. It doesn't work with EST\footnote{Expressed Sequenced tag} sequences. You can transform your database using our application \textit{Protein database manager}, available \href{http://pappso.inra.fr/bioinformatique.html}{here}, or you can directly run it \href{http://pappso.inra.fr/documents/bioinformatique/database_manager.jnlp}{here}.
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.4]{images/tandem_analysis.png}
+\center \includegraphics[scale=0.4]{images/tandem_analysis}
 \caption{X!Tandem parameter window}
 \label{xtandem_analysis}
 \end{figure}
@@ -204,7 +204,7 @@ Interesting because it allows you to always include the same contaminant protein
 \end{description}
 \normalsize
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_filter.png}
+\center \includegraphics[scale=0.5]{images/tandem_filter}
 \caption{Filter window}
 \label{filter}
 \end{figure}
@@ -229,7 +229,7 @@ After loading the results, you can select the result to view in the main window
 
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_principal.png}
+\center \includegraphics[scale=0.5]{images/tandem_principal}
 \caption{Main window}
 \label{principal}
 \end{figure}
@@ -245,7 +245,7 @@ View the list of protein identified on the result. For more details on column se
 \end{itemize}
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_protein.png}
+\center \includegraphics[scale=0.5]{images/window_protein}
 \caption{Proteins List}
 \end{figure}
 
@@ -254,7 +254,7 @@ View the list of protein identified on the result. For more details on column se
 View the protein sequence and coverage on a identified protein. To view this window, you must open it in the menu \textit{Windows $\rightarrow$ Protein details}.
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.7]{images/window_protein_detail.png}
+\center \includegraphics[scale=0.7]{images/window_protein_detail}
 \caption{Protein details}
 \end{figure}
 
@@ -269,7 +269,7 @@ View the peptides identified a protein. For more details on column see Fig~\ref{
 \end{itemize}
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_peptide.png}
+\center \includegraphics[scale=0.5]{images/window_peptide}
 \caption{Peptides List}
 \end{figure}
 
@@ -283,7 +283,7 @@ View the MS/MS spectra of an identified peptide.
 \end{itemize}
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_peptide_detail.png}
+\center \includegraphics[scale=0.5]{images/window_peptide_detail}
 \caption{Peptides Details}
 \end{figure}
 
@@ -310,7 +310,7 @@ The export window (Fig~\ref{export}) shows the different types of available expo
 \end{description}
 \normalsize
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_export.png}
+\center \includegraphics[scale=0.5]{images/tandem_export}
 \caption{Export window}
 \label{export}
 \end{figure}
@@ -344,7 +344,7 @@ The identified proteins are represented by sample (individual mode) or for all s
 \normalsize
 
 \begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_prot.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_prot}
 \caption{Protein results}
 \label{prot}
 \end{figure}
@@ -381,7 +381,7 @@ Identified peptides are grouped by group (Fig~\ref{pep}). One line corresponds t
 \normalsize
 
 \begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide}
 \caption{Peptide results}
 \label{pep}
 \end{figure}
@@ -412,7 +412,7 @@ The list of proteins is repeated 4 times, corresponding to the 4 parameters that
 \normalsize
 
 \begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison}
 \caption{Comparison results}
 \label{compar}
 \end{figure}
@@ -427,7 +427,7 @@ In this case, the column corresponding to the normal and reverse search are indi
 \end{itemize}
 
 \begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_fdr.png}
+\center \includegraphics[scale=0.5]{images/tandem_fdr}
 \caption{FDR results}
 \label{fdr2}
 \end{figure}