diff --git a/xtandempipeline/CMakeLists.txt b/xtandempipeline/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfdd1f82060e54f269d227efad24eb1a5a1ba90f
--- /dev/null
+++ b/xtandempipeline/CMakeLists.txt
@@ -0,0 +1,157 @@
+# The name of our project is "xtandempipeline". CMakeLists files in this project can
+# refer to the root source directory of the project as ${xtandemparser_SOURCE_DIR} and
+# to the root binary directory of the project as ${xtandemparser_BINARY_DIR}.
+PROJECT(xtandempipeline Java)
+
+SET (CMAKE_Java_COMPILER "/usr/lib/jvm/java-6-openjdk/bin/java")
+SET (Java_JAR_EXECUTABLE "/usr/lib/jvm/java-6-openjdk/bin/jar")
+SET (Java_JAVAC_EXECUTABLE "/usr/lib/jvm/java-6-openjdk/bin/javac")
+SET (ANT_EXECUTABLE "/usr/bin/ant")
+
+
+FIND_PACKAGE( Java REQUIRED )
+
+MESSAGE("CMAKE_Java_COMPILER : ${CMAKE_Java_COMPILER} ")
+MESSAGE("Java_JAR_EXECUTABLE : ${Java_JAR_EXECUTABLE} ")
+MESSAGE("Java_JAVAC_EXECUTABLE : ${Java_JAVAC_EXECUTABLE} ")
+
+#message ("compiler : ${CMAKE_CXX_COMPILER} ")
+
+
+cmake_minimum_required(VERSION 2.6)
+
+SET (XTANDEMPIPELINE_VERSION "3.0.1")
+
+SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
+SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
+#SET(CPACK_INSTALL_CMAKE_PROJECTS "/tmp;beads;src;/src")
+#SET(CPACK_NSIS_DISPLAY_NAME "CMake 2.5")
+SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
+#SET(CPACK_PACKAGE_DESCRIPTION_FILE ${xtandempipeline_SOURCE_DIR}/COPYING)
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "loads and parses the xml results product by X!Tandem")
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "xtandempipeline-${XTANDEMPIPELINE_VERSION}")
+SET(CPACK_PACKAGE_FILE_NAME "beads-${XTANDEMPIPELINE_VERSION}-Linux-i686")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "xtandempipeline ${XTANDEMPIPELINE_VERSION}")
+SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "xtandempipeline ${XTANDEMPIPELINE_VERSION}")
+SET(CPACK_PACKAGE_NAME "xtandempipeline")
+SET(CPACK_PACKAGE_VENDOR "INRA")
+
+SET(CPACK_PACKAGE_VERSION ${XTANDEMPIPELINE_VERSION})
+SET(CPACK_PACKAGE_VERSION_MAJOR "3")
+SET(CPACK_PACKAGE_VERSION_MINOR "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
+#SET(CPACK_RESOURCE_FILE_LICENSE ${xtandemparser_SOURCE_DIR}/COPYING)
+#SET(CPACK_RESOURCE_FILE_README ${xtandemparser_SOURCE_DIR}/README)
+#SET(CPACK_RESOURCE_FILE_WELCOME ${xtandemparser_SOURCE_DIR}/INSTALL)
+SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
+SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
+SET(CPACK_SOURCE_STRIP_FILES "")
+
+SET(CPACK_SOURCE_IGNORE_FILES
+ "/build/"
+ "/dist/"
+ "/lib/"
+ "/jnlp/"
+ "build_langella.xml"
+ "Makefile"
+ "cmake_install.cmake"
+ "cmake_install.cmake"
+ "CMakeCache.txt"
+ "CPackConfig.cmake"
+ "CPackSourceConfig.cmake"
+ "install_manifest.txt"
+ "/CMakeFiles/"
+ "/_CPack_Packages/"
+ "/Debug/"
+ "/Release/"
+ "/\\\\.externalToolBuilders/"
+ "/\\\\.svn/"
+ "/\\\\.settings/"
+ "Makefile"
+ "\\\\.cdtbuild"
+ "\\\\.cdtproject"
+ "\\\\.project"
+ "\\\\.cproject"
+ "beads$"
+ ".*\\\\.tar\\\\.gz"
+ "XTandem_Pipeline.jar"
+)
+# cpack -G TGZ --config CPackSourceConfig.cmake
+# dpkg-buildpackage -rfakeroot
+
+#.dput.cf
+#[olivier-langella]
+#fqdn = ppa.launchpad.net
+#method = ftp
+#incoming = ~olivier-langella/ubuntu/
+#login = olivier-langella
+#allow_unsigned_uploads = 0
+#
+# debuild -S -sa
+# dput -f olivier-langella *changes
+
+SET(CPACK_PACKAGE_EXECUTABLES "xtandempipeline" "xtandempipeline")
+
+
+INCLUDE(CPack)
+
+
+#INCLUDE(CPack)
+
+
+# Recurse into the "src" subdirectories. This does not actually
+# cause another cmake executable to run. The same process will walk through
+# the project's entire directory structure.
+#SUBDIRS (src)
+
+#http://www.airport1.de/blog/archives/456-cMake-and-Java-it-works!-How-to-build-Java-Projects-with-cMake.html
+#SET (JAR_FILE MyXtandemParser.jar)
+#SET (JAVA_FILES My_Xtandem_Parser)
+
+# compile all .java files with javac to .class
+#ADD_CUSTOM_COMMAND(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${JAVA_FILES}.class COMMAND ${CMAKE_Java_COMPILER} ARGS -d ${CMAKE_CURRENT_SOURCE_DIR}/${CLASS_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/*.java)
+
+# build .jar file from .class files
+#ADD_CUSTOM_COMMAND(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${JAR_FILE} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/${JAVA_FILES}.class COMMAND ${CMAKE_COMMAND} ARGS -E chdir ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_Java_ARCHIVE} -cfCv ${JAR_DIR}/${JAR_FILE} ${CLASS_DIR} org/java2cpp)
+
+# the target
+#ADD_CUSTOM_TARGET(${JAR_FILE} ALL DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/${JAR_FILE})
+
+
+#ADD_CUSTOM_TARGET( ant_build ALL )
+
+#ADD_CUSTOM_COMMAND(
+# TARGET ant_build
+# COMMAND ant
+#)
+
+if (NOT CMAKE_INSTALL_PREFIX)
+ SET (CMAKE_INSTALL_PREFIX /usr/local)
+endif (NOT CMAKE_INSTALL_PREFIX)
+
+configure_file (${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline.desktop.cmake ${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline.desktop)
+configure_file (${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline_online.desktop.cmake ${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline_online.desktop)
+configure_file (${xtandempipeline_SOURCE_DIR}/share/xtandempipeline/xtandempipeline.sh.cmake ${xtandempipeline_SOURCE_DIR}/share/xtandempipeline/xtandempipeline.sh)
+
+SET(work_dir ${xtandempipeline_SOURCE_DIR})
+ADD_CUSTOM_TARGET(ant_build ALL
+ COMMAND ${ANT_EXECUTABLE} -Dworking.dir=${work_dir} -f build_ubuntu.xml
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ COMMENT "Running Ant ...")
+
+
+#INSTALL(PROGRAMS src/beads DESTINATION bin)
+#INSTALL(PROGRAMS src/qtbeads/qtbeads DESTINATION bin)
+#INSTALL(DIRECTORY doc/man1 DESTINATION share/man/man1)
+#INSTALL(FILES doc/man1/beads.1 DESTINATION share/man/man1)
+INSTALL(FILES share/applications/xtandempipeline_online.desktop DESTINATION share/applications)
+INSTALL(FILES share/applications/xtandempipeline.desktop DESTINATION share/applications)
+#INSTALL(FILES share/beads/beads_blue.conf DESTINATION share/beads)
+#INSTALL(FILES share/beads/beads_silver.conf DESTINATION share/beads)
+#INSTALL(FILES share/beads/beads_silver_small.conf DESTINATION share/beads)
+INSTALL(PROGRAMS share/xtandempipeline/xtandempipeline.sh DESTINATION bin)
+INSTALL(FILES share/xtandempipeline/xtandempipeline.jnlp DESTINATION share/xtandempipeline)
+INSTALL(FILES share/xtandempipeline/XTandem_Pipeline.jar DESTINATION share/xtandempipeline)
+INSTALL(FILES share/xtandempipeline/proticws_svgutils.jar DESTINATION share/xtandempipeline)
+INSTALL(FILES share/xtandempipeline/xtandempipeline_icon.svg DESTINATION share/xtandempipeline)
+
diff --git a/xtandempipeline/build_ubuntu.xml b/xtandempipeline/build_ubuntu.xml
new file mode 100644
index 0000000000000000000000000000000000000000..69a63b5f7d32e7df6c8acb9828cb7a696ecefb4e
--- /dev/null
+++ b/xtandempipeline/build_ubuntu.xml
@@ -0,0 +1,81 @@
+<project name="MyXtandemParser" default="jarWithClasspath" basedir=".">
+ <description>
+ MyXtandemParser ant build file
+ </description>
+
+ <!-- set global properties for this build -->
+
+ <property name="lib" location="/usr/share/java" />
+ <property name="share" location="share" />
+ <property name="conf" location="conf" />
+ <property name="resources" location="src/resources" />
+ <property name="src" location="src" />
+ <property name="build" location="build" />
+ <property name="dist" location="dist" />
+ <property name="confDir" location="conf" />
+ <property name="docDir" location="doc" />
+
+ <target name="reset">
+ <!-- reset the build and dist directory -->
+ <delete dir="build" />
+ <delete dir="dist" />
+ <mkdir dir="build" />
+ <mkdir dir="dist" />
+ <mkdir dir="conf" />
+ </target>
+
+
+ <target name="init" depends="reset">
+ <!-- Create the time stamp -->
+ <tstamp />
+ </target>
+
+ <path id="classpath">
+ <!--xml-apis-ext.jar xml-apis.jar xercesImpl.jar xalan2.jar swt.jar batik.jar-->
+ <fileset dir="${lib}" includes="xml-apis-ext.jar xml-apis.jar xercesImpl.jar xalan2.jar swt.jar batik.jar" />
+ <fileset dir="${share}/xtandempipeline" includes="proticws_svgutils.jar" />
+ </path>
+
+
+ <target name="compile" depends="init" description="compile the source and put in build directory">
+ <!-- Compile the java code from ${src} into ${build} -->
+ <javac srcdir="${src}" destdir="${build}" target="1.6" source="1.6" classpathref="classpath" includeantruntime="false">
+ <compilerarg line="-encoding utf-8"/>
+ <classpath>
+ <pathelement location="${build}/My_XTandem_Pipeline.class" />
+ </classpath>
+ </javac>
+ </target>
+
+
+ <target name="jarWithClasspath" depends="compile" description="generates the jar file for Ubuntu">
+
+
+ <mkdir dir="${build}/conf" />
+ <copy todir="${build}/conf" overwrite="true">
+ <fileset dir="${conf}" includes="*" />
+ </copy>
+ <mkdir dir="${build}/resources" />
+ <copy todir="${build}/resources" overwrite="true">
+ <fileset dir="${resources}" includes="**" />
+ </copy>
+
+ <jar jarfile="./share/xtandempipeline/XTandem_Pipeline.jar" basedir="${build}">
+ <fileset dir="${confDir}" />
+ <!--<fileset file=".classpath" />-->
+ <manifest>
+ <attribute name="Main-Class" value="My_XTandem_Pipeline" />
+ <attribute name="Class-Path" value="/usr/share/java/xml-apis-ext.jar /usr/share/java/xml-apis.jar /usr/share/java/xercesImpl.jar /usr/share/java/xalan2.jar /usr/share/java/swt.jar /usr/share/java/batik.jar /usr/share/xtandempipeline/proticws_svgutils.jar /usr/local/share/xtandempipeline/proticws_svgutils.jar" />
+ </manifest>
+ </jar>
+
+ <!-- cd bin; jar -cf client.jar; -->
+ <!-- <jar jarfile="client.jar" basedir="bin"/> -->
+ </target>
+
+ <target name="clean" depends="jarWithClasspath">
+ <delete dir="jnlp" />
+ <delete dir="build" />
+ <delete dir="dist" />
+ </target>
+</project>
\ No newline at end of file
diff --git a/xtandempipeline/debian/changelog b/xtandempipeline/debian/changelog
new file mode 100644
index 0000000000000000000000000000000000000000..e18f8a3aff5453ab983d5f581e5578fc003cffbd
--- /dev/null
+++ b/xtandempipeline/debian/changelog
@@ -0,0 +1,141 @@
+xtandempipeline (3.0.1-9) maverick; urgency=low
+
+ * not related to a particular ubuntu serie
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Sat, 12 mar 2011 12:18:51 +0200
+
+xtandempipeline (3.0.1-8~maverick1) maverick; urgency=low
+
+ * <compilerarg line="-encoding utf-8"/> added to javac in ant build
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Sat, 12 mar 2011 12:18:51 +0200
+
+xtandempipeline (3.0.1-7~maverick1) maverick; urgency=low
+
+ * sources ubuntu package was not depending on JDK, only JRE. fixed
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Sat, 12 mar 2011 11:18:51 +0200
+
+xtandempipeline (3.0.1-6~maverick1) maverick; urgency=low
+
+ * ubuntu source package should really compile and build jar now
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Sat, 12 mar 2011 10:18:51 +0200
+
+xtandempipeline (3.0.1-5~maverick1) maverick; urgency=low
+
+ * with jar it is better
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 11 mar 2011 20:18:51 +0200
+
+xtandempipeline (3.0.1-4~maverick1) maverick; urgency=low
+
+ * Java_JAR_EXECUTABLE & Java_JAVAC_EXECUTABLE added
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 11 mar 2011 18:18:51 +0200
+
+xtandempipeline (3.0.1-3~maverick1) maverick; urgency=low
+
+ * fixed an other cmake java compiler variable problem
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 11 mar 2011 17:18:51 +0200
+
+xtandempipeline (3.0.1-2~maverick1) maverick; urgency=low
+
+ * fixed cmake java compiler variable problem
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 11 mar 2011 16:18:51 +0200
+
+xtandempipeline (3.0.1-1~maverick1) maverick; urgency=low
+
+ * fixed encoding problem concerning project files
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 11 mar 2011 10:18:51 +0200
+
+xtandempipeline (3.0.0-1~maverick1) maverick; urgency=low
+
+ * use swt instead of swing
+ * use jar ubuntu package for libswt and batik
+ * new SVG icon
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Wed, 9 mar 2011 16:18:51 +0200
+
+xtandempipeline (2.9.8-5~maverick1) maverick; urgency=low
+
+ * package fix
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Sat, 18 dec 2010 16:18:51 +0200
+
+xtandempipeline (2.9.8-4~maverick1) maverick; urgency=low
+
+ * package fix
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Sat, 18 dec 2010 16:18:51 +0200
+
+xtandempipeline (2.9.8-3~maverick1) maverick; urgency=low
+
+ * package fix
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 17 dec 2010 16:18:51 +0200
+
+xtandempipeline (2.9.8-2~maverick1) maverick; urgency=low
+
+ * depends on the new Xtandem cyclone package or old Xtandem tornado
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 17 dec 2010 16:18:51 +0200
+
+xtandempipeline (2.9.8-1~maverick1) maverick; urgency=low
+
+ * new version from Benoit Valot
+ * package renamed from xtandemparser to xtandempipeline
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 17 dec 2010 15:18:51 +0200
+
+xtandemparser (2.9.5-1~maverick1) maverick; urgency=low
+
+ * new version from Benoit Valot
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Wed, 27 Oct 2010 16:18:51 +0200
+
+xtandemparser (2.9.3-6~maverick1) maverick; urgency=low
+
+ * embedded help html pages
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Mon, 25 Oct 2010 16:18:51 +0200
+
+xtandemparser (2.9.3-5~maverick1) maverick; urgency=low
+
+ * debian/rules modified
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Mon, 25 Oct 2010 15:18:51 +0200
+
+xtandemparser (2.9.3-4~maverick1) maverick; urgency=low
+
+ * debian/rules modified
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Mon, 25 Oct 2010 14:18:51 +0200
+
+xtandemparser (2.9.3-3~maverick1) maverick; urgency=low
+
+ * problem with xtandem-tornado dependency fixed
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Mon, 25 Oct 2010 11:18:51 +0200
+
+xtandemparser (2.9.3-2~maverick1) maverick; urgency=low
+
+ * added dependency to default-jdk
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Mon, 25 Oct 2010 10:18:51 +0200
+
+xtandemparser (2.9.3-1~maverick1) maverick; urgency=low
+
+ * fixed dependencie mistake
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Mon, 25 Oct 2010 10:18:51 +0200
+
+xtandemparser (2.2.6-1~maverick1) maverick; urgency=low
+
+ * maverick package
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Thu, 9 Sep 2010 10:18:51 +0200
+
diff --git a/xtandempipeline/debian/compat b/xtandempipeline/debian/compat
new file mode 100644
index 0000000000000000000000000000000000000000..b8626c4cff2849624fb67f87cd0ad72b163671ad
--- /dev/null
+++ b/xtandempipeline/debian/compat
@@ -0,0 +1 @@
+4
diff --git a/xtandempipeline/debian/control b/xtandempipeline/debian/control
new file mode 100644
index 0000000000000000000000000000000000000000..a5cf73117ee35cf64c540d6b8bdbc3002dd5b8b0
--- /dev/null
+++ b/xtandempipeline/debian/control
@@ -0,0 +1,19 @@
+Source: xtandempipeline
+Section: science
+Priority: optional
+Maintainer: Olivier Langella <olivier.langella@moulon.inra.fr>
+Homepage: http://pappso.inra.fr/
+DM-Upload-Allowed: yes
+Uploaders: Olivier Langella <olivier.langella@moulon.inra.fr>
+Standards-Version: 1.0
+Build-Depends: debhelper (>= 5), cmake (>= 2.6), ant (>=1.8), openjdk-6-jdk (>=1.6), libswt-gtk-3.5-java (>=3.5.1), libbatik-java (>=1.7)
+
+Package: xtandempipeline
+Architecture: all
+Replaces: xtandemparser (<< 2.9.8-2~)
+Conflicts: xtandemparser (<< 2.9.8-2~)
+Depends: ${shlibs:Depends}, openjdk-6-jre (>=1.6), libswt-gtk-3.5-java (>=3.5.1), libbatik-java (>=1.7), xtandem-cyclone | xtandem-tornado
+Description: loads and parses the xml results product by X!Tandem
+ This Java application loads and parses the xml results product by X!Tandem, applies filters on
+ E-value at peptide and protein levels, filters proteins on the basis of a minimun number of
+ unique peptides, removes proteins specified in a contaminant database...
diff --git a/xtandempipeline/debian/copyright b/xtandempipeline/debian/copyright
new file mode 100644
index 0000000000000000000000000000000000000000..afd820b36ad5fd6af9fa1d5e82d3ace82fe96217
--- /dev/null
+++ b/xtandempipeline/debian/copyright
@@ -0,0 +1,9 @@
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Olivier Langella <olivier.langella@moulon.inra.fr>
+X-Debianized-Date: Wed, 25 Jun 2008 11:18:51 +0200
+X-Source-Downloaded-From:
+X-Upstream-Author:
+
+Files: *
+Copyright: © 2010 Benoit Valot <benoit.valot@moulon.inra.fr>, Michel Zivy <zivy@moulon.inra.fr>, Olivier Langella <olivier.langella@moulon.inra.fr>
+License: GPL v3
diff --git a/xtandempipeline/debian/rules b/xtandempipeline/debian/rules
new file mode 100755
index 0000000000000000000000000000000000000000..53ec7337e790a238998e4f6333741fada0d704f3
--- /dev/null
+++ b/xtandempipeline/debian/rules
@@ -0,0 +1,91 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+
+configure: configure-stamp
+configure-stamp:
+ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_Java_COMPILER=/usr/lib/jvm/java-6-openjdk/bin/java .
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ #docbook-to-man debian/beads.sgml > beads.1
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp CMakeCache.txt
+
+ # Add here commands to clean up after the build process.
+ -$(MAKE) clean
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/xtandempipeline.
+ $(MAKE) DESTDIR=$(CURDIR)/debian/xtandempipeline install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+# dh_installchangelogs ChangeLog
+ dh_installdocs
+ dh_installexamples
+# dh_install
+# dh_installmenu
+# dh_installdebconf
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_python
+# dh_installinit
+# dh_installcron
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
diff --git a/xtandempipeline/doc/Xtandem_batch.pdf b/xtandempipeline/doc/Xtandem_batch.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..9aab71a4962b348c33e08888c0849145c503e0f9
Binary files /dev/null and b/xtandempipeline/doc/Xtandem_batch.pdf differ
diff --git a/xtandempipeline/doc/Xtandem_batch.tex b/xtandempipeline/doc/Xtandem_batch.tex
new file mode 100644
index 0000000000000000000000000000000000000000..2a51906ce19b84f9267f3517982cb57f8a9b0a2e
--- /dev/null
+++ b/xtandempipeline/doc/Xtandem_batch.tex
@@ -0,0 +1,153 @@
+\documentclass[10pt,a4paper]{article}
+\usepackage[utf8x]{inputenc}
+\usepackage{ucs}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+\usepackage{amssymb}
+\usepackage[colorlinks=true,urlcolor=blue,linkcolor=black]{hyperref}
+\usepackage{graphicx}
+\usepackage{fancyhdr}
+\usepackage{geometry}
+
+%\usepackage{enumitem}
+%\setdescription{labelsep=\textwidth}
+
+\author{Benoit Valot\\
+\texttt{valot@moulon.inra.fr}\\
+PAPPSO - \url{http://pappso.inra.fr/}\\
+\includegraphics[width=1cm]{images/pappso.pdf}
+}
+\title{X!Tandem Batch Analysis\\ Automated performed database searching using X!Tandem\\ in local version}
+\date{14 Avril 2010}
+
+%Modification des entetes et pied de page + marges
+\geometry{top=3cm, bottom=3cm, left=2cm, right=2cm}
+%\pagestyle{headings}
+\pagestyle{fancy}
+%\fancyhead{}
+\fancyfoot{}
+\rfoot{\thepage}
+\lfoot{\includegraphics[width=1cm]{images/pappso.pdf}}
+
+
+\begin{document}
+\maketitle
+
+\begin{abstract}
+\href{http://www.thegpm.org/tandem/index.html}{X!Tandem} software is an open-source software to performed peptides/proteins identifications from MS/MS mass spectra. To easily performed automated search using predefined parameters in a local version, we developed this perl script. This system is an alternative to install an local server of the Global Proteome Machine (\href{http://www.thegpm.org/}{GPM})
+\paragraph*{}
+\textbf{X!Tandem Batch Analysis} script applied database searching with defined parameters in a list of MS/MS analysis with a list of protein databases.
+\end{abstract}
+
+\tableofcontents
+
+\pagebreak
+
+\section{Installation}
+\subsection{Windows}
+\begin{enumerate}
+\item If not installed, download and installed Active-perl (Version 5.8.XXX) using this \href{http://www.activestate.com/activeperl/downloads/}{link}.\\
+\textbf{Warning :} The script need version 5.8, and does not work on 5.10 or 5.12!!!!
+\item Download the \href{http://pappso.inra.fr/documents/bioinformatique/xtandem_batch_win.zip}{archive} and unzip it.
+\item Move the complete ''Benperl/'' folder directly at the C:/
+\item Inside, go to the folder Benperl/installation/
+\item Install perl library using \textit{Perl-library-installation.pl} script\footnote{Simply double-clic it}
+\end{enumerate}
+
+\subsection{Linux}
+\subsubsection*{Requirements}
+\begin{itemize}
+\item Installed \textit{libwx-perl} package
+\end{itemize}
+\subsubsection*{Ubuntu}
+\begin{itemize}
+\item Add this software \href{https://launchpad.net/~olivier-langella/+archive/ppa}{repository}
+\item Installed the \textit{xtandem-tornado} package
+\end{itemize}
+\subsubsection*{Other distribution}
+\begin{itemize}
+\item Download \href{ftp://ftp.thegpm.org/projects/tandem/source/}{source} of the X!Tandem and followed the instruction of compilation.
+\end{itemize}
+\subsubsection*{Script adaptation}
+\begin{enumerate}
+\item Download the \href{http://pappso.inra.fr/documents/bioinformatique/xtandem_batch_linux.zip}{archive} and unzip it.
+\item Move the complete ''benperl/'' folder in your /home/user/ folder
+\item Inside, go to the folder Benperl/
+\item Open on a text editor the perl script \textit{xtandem-batch-analysis.pl} and modified the path to the X!Tandem executable and to the folder containing the model (xml files).
+\end{enumerate}
+
+\subsection{License}
+Copyright (C) 2010 Valot Benoit\\
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\\
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the \href{http://www.gnu.org/licenses/gpl.html}{GNU General Public License} for more details.
+
+\pagebreak
+
+\section{Utilization}
+
+It permits to analysis a list of peak list files on a list of protein database using the X!Tandem software.
+Three successive box permit to select mzXML file or other peaklist, to select protein databases and finally the folder were results are stored. The databases must be proteins, X!Tandem doesn't work on DNA database.
+
+\subsection{Running Script}
+To performed analysis, start the perl script \textit{xtandem-batch-analysis.pl}\footnote{Simply double clic it.}
+\begin{enumerate}
+\item Select peak lists files to be analyzed. (See~\ref{peak})
+\item Select databases files to be searched. (See~\ref{database})
+\item Select the folder to save the results files.
+\item Select in the model containing searching parameters. (See~\ref{model} and Fig~\ref{terminal1})
+\end{enumerate}
+
+\begin{figure}[!h]
+\center \includegraphics[scale=0.7]{images/batch_terminal.png}
+\caption{Model selection}
+\label{terminal1}
+\end{figure}
+
+\subsection{Peak lists}
+\label{peak}
+X!Tandem works with open peak list files like mzXML, mgf, mzData, mzML or pkl files.
+
+\subsection{Databases}
+\label{database}
+X!Tandem software uses only protein database in fasta format. It does'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 for direct \href{http://pappso.inra.fr/documents/bioinformatique/database_manager.jnlp}{running}.\\
+
+\subsection{Models}
+\label{model}
+To performed database searching, you must created or edited a model xml file. Some example are presents in the ''/benperl/Xtandem'' folder. Each xml file in this folder could be select in the terminal during analysis (Fig~\ref{terminal1}).\\
+To modified the parameter xml file, open it in a text editor (Fig~\ref{xml}) and then follow the \href{http://www.thegpm.org/TANDEM/api/index.html}{documentation} at the X!Tandem web site.
+
+\begin{figure}[!h]
+\center \includegraphics[scale=0.7]{images/batch_xml_search.png}
+\caption{Model edition}
+\label{xml}
+\end{figure}
+
+To used complete performance of our computer, specify the number of cpu in the model at the line : type="input" label="spectrum, threads''.
+
+\pagebreak
+
+\section{Results}
+\subsection{Database searching}
+
+Each peak list files are analyzed in series. You can follow advance of the processing in the terminal (Fig~\ref{terminal2}). To stop processing, simply close the terminal windows.
+
+\begin{figure}[!h]
+\center \includegraphics[scale=0.7]{images/batch_process.png}
+\caption{Database searching progress}
+\label{terminal2}
+\end{figure}
+
+\subsection{Viewing result}
+The result are in xml format, you can view results on the \href{http://h003.thegpm.org/tandem/thegpm_upview.html}{GPM web site} (Fig ~\ref{acceuil}).
+
+\begin{figure}[!h]
+\center \includegraphics[scale=0.7]{images/batch_acceuil.png}
+\caption{Viewing results on GPM site}
+\label{acceuil}
+\end{figure}
+
+\subsection{Automated export result}
+To automated processing the result files in excel view, you can used our application \textit{My Xtandem parser} available \href{http://pappso.inra.fr/documents/bioinformatique/Xtandem_parser.pdf}{here}.
+
+
+\end{document}
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+\documentclass[10pt,a4paper]{article}
+\usepackage[utf8x]{inputenc}
+\usepackage{ucs}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+\usepackage{amssymb}
+\usepackage[colorlinks=true,urlcolor=blue,linkcolor=black]{hyperref}
+\usepackage{graphicx}
+\usepackage{fancyhdr}
+\usepackage{geometry}
+
+%\usepackage{enumitem}
+%\setdescription{labelsep=\textwidth}
+
+\author{Benoit Valot\\
+\texttt{valot@moulon.inra.fr}\\
+PAPPSO - \url{http://pappso.inra.fr/}\\
+\includegraphics[width=1cm]{images/pappso.pdf}
+}
+\title{My XTandem parser\\Automated filtering and export of X!Tandem MS/MS results}
+\date{14 Avril 2010}
+
+%Modification des entetes et pied de page + marges
+\geometry{top=3cm, bottom=3cm, left=2cm, right=2cm}
+%\pagestyle{headings}
+\pagestyle{fancy}
+%\fancyhead{}
+\fancyfoot{}
+\rfoot{\thepage}
+\lfoot{\includegraphics[width=1cm]{images/pappso.pdf}}
+
+
+\begin{document}
+\maketitle
+
+\begin{abstract}
+\href{http://www.thegpm.org/tandem/index.html}{X!Tandem} is an open-source software allowing peptide/protein identification from MS/MS mass spectra. X!Tandem is fast and accurate, but the Global Proteome Machine (\href{http://www.thegpm.org/}{GPM}) is relatively limited regarding the processing of identification results.
+\paragraph*{}
+\textbf{My XTandem parser} permit to filtered data according to statistical value at peptide and protein levels. The results are accessible to tabulated files (excel). Moreover, redundancy of protein database are fully filtered as :
+\begin{itemize}
+\item Proteins identified without specifics peptides compared to others are eliminated.
+\item Proteins identified with the same pool of peptides are assembled.
+\item Proteins are grouped by function (identified with at least one common peptide), and the specific peptides for each of the sub-group of proteins are indicated.
+\end{itemize}
+\end{abstract}
+
+\tableofcontents
+
+\pagebreak
+
+\section{Installation}
+\subsection{Requirements}
+My XTandem parser works on all plateforms (linux, windows). Java 1.6 must be installed :
+\href{https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u14-oth-JPR@CDS-CDS_Developer}{link}
+
+\subsection{Start My XTandem parser}
+To run My XTandem parser, simply :
+\begin{itemize}
+\item Open My XTandem parser by using this \href{http://pappso.inra.fr/documents/bioinformatique/xtandem_parser.jnlp}{link}
+\item Allow the program to be executed
+\item The principal window will appear (Fig~\ref{principal})
+\end{itemize}
+
+\begin{figure}[!h]
+\label{principal}
+\center \includegraphics[scale=0.5]{images/tandem_principal.png}
+\caption{Principal window}
+\end{figure}
+
+\subsection{License}
+Copyright (C) 2010 Valot Benoit\\
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\\
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the \href{http://www.gnu.org/licenses/gpl.html}{GNU General Public License} for more details.
+
+\pagebreak
+
+\section{Utilisation}
+\paragraph*{Warning}
+To perform analysis, My X!Tandem parser needs the have X!Tandem result files (.xml). The names of the files are used as \textbf{sample names}.
+To perform local X!Tandem identification in automated process, you can use our xtandem batch processing script available \href{http://pappso.inra.fr/documents/bioinformatique/Xtandem_batch.pdf}{here}.
+\subsection{Two modes}
+\paragraph*{}
+You can filter the MS/MS identifications and export the results in two different modes :
+\begin{description}
+\item[Individual mode] \hfill \\ Each MS/MS result file is processed individually.\\
+You cannot perform comparison by using this process.
+\item[Combined mode] \hfill \\ The MS/MS result files are combined in one result file, and this file is filtered / exported.\\
+This mode is usefull to compare different results.
+\end{description}
+\paragraph*{}
+In both modes, you have to :
+\begin{enumerate}
+\item Select the xml result files
+\item Define the filter parameters (~\ref{filtering})
+\item Define the name of the result file to export
+\item Define the export parameters (~\ref{exporting})
+\end{enumerate}
+
+\subsection{Filter parameters}
+\label{filtering}
+The filter window (Fig~\ref{filter}) defines the automated filter process :
+\small
+\begin{description}
+\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 \\Defined the E-value above which a protein is considered as valid
+\begin{itemize}
+\item The protein E-values are re-calculated by the product of the valid unique peptides E-values, and are different from the protein E-values determined by X!Tandem.
+\item The values are expressed in log(E-value)
+\end{itemize}
+\item[Sum to all] \hfill \\Defines how protein filter is performed when MS/MS results are combined :
+\begin{description}
+\item[No] To validate a protein, the 2 parameters (peptide number and protein E-value) must be valid in at least one result.
+Interesting to compare 2DLC-MS/MS results, where peptides from a protein are in the same LC-MS/MS run
+\item[Yes] To validate a protein, the 2 parameters (peptide number and protein E-value) must be valid in the sum of all results.
+Interesting to compare SDS-PAGE-LC-MS/MS results, where peptides from a protein are split in different LC-MS/MS runs
+\end{description}
+\item[Phosphopeptide] \hfill \\Conserves only peptides containing phosphorylated residue modifications.
+All other peptides are invalided.
+\item[Contaminants] \hfill \\When you perform an analysis using different fasta databases, you can remove the result from one database by selecting this database.
+Interesting because it allows to always include the same contaminant proteins during the database search, and because it removes the contaminant proteins from the results.
+\item[Add results] \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 to combine X!Tandem results of the same LC-MS/MS run using different modification parameters or protein databases.
+\end{description}
+\normalsize
+\begin{figure}[!h]
+\center \includegraphics[scale=0.5]{images/tandem_filter.png}
+\caption{Filter window}
+\label{filter}
+\end{figure}
+
+\pagebreak
+
+\subsection{Export parameters}
+\label{exporting}
+The export window (Fig~\ref{export}) shows the different types of available exports:
+\small
+\begin{description}
+\item[Default] \hfill \\Creates tabulated files containing identification results for proteins (*protein.txt) and peptides (*peptide.txt). When you perform a combined analysis, a *compar.txt file is created that contains the results of comparison between samples.
+\item[Fasta] \hfill \\Creates a fasta file for valid proteins.
+\item[PepNovo] \hfill \\Creates an xml file containing the peptide results to be removed for an automated \textit{De Novo} interpretation in sequence using our \href{http://pappso.inra.fr/documents/bioinformatique/Denovo_pipeline.pdf}{pipeline}.
+\item[FDR] \hfill \\Creates a tabulated file containing the number of valid peptides for the different peptide E-values in each database. Interesting to determine the E-value above which FDR value is acceptable.\\
+\label{fdr}\textbf{Warning} : Use very low parameters in peptide (0.1) and protein (-1) evalues, and set the number of unique peptides to validate a protein to 1.
+\item[Protic] \hfill \\Internal export in xml, defined to store results in a proteomic database called \href{http://pappso.inra.fr/bioinformatique.html}{PROTICdb}.
+\item[Quantimscpp] \hfill \\Internal export in xml, used as input to perform quantitative analysis using a home-made software 'Quantimscpp' currently in development.
+\end{description}
+\normalsize
+\begin{figure}[!h]
+\center \includegraphics[scale=0.5]{images/tandem_export.png}
+\caption{Export window}
+\label{export}
+\end{figure}
+
+\pagebreak
+
+\section{Export results}
+\subsection{*protein.txt}
+All proteins identified are presented by sample (MS/MS file, Fig~\ref{prot}). Proteins are grouped by function.
+\small
+\begin{description}
+\item[Group] Group to which the protein belongs. All the proteins in a group have at least one peptide in common.
+\item[Sub-group] Sub-group to which the protein belongs. All the proteins in a sub-group are identified with the same valid peptides.
+\item[Description] Protein description as it is in the header of the fasta file.
+\item[log(E value)] Protein E-value expressed in log.
+\begin{itemize}
+\item Statistical value representing the number of times this protein would be identified just by random.
+\item Calculated as the product of unique peptide E-values in the sample.
+\end{itemize}
+\item[Coverage] \% of protein coverage.
+\item[MW] Molecular weight of the protein expressed in KDa.
+\item[Spectra] Total number of MS/MS spectra identified for the protein
+\item[Specifics] Number of MS/MS spectra that are specific to the protein, compared to the other proteins of the same group.
+\item[Uniques] Number of unique peptide sequences identified for the protein.
+\item[PAI] Protein Abundance Index\label{pai}
+\begin{itemize}
+\item PAI estimates the relative abundance of the protein.
+\item PAI is calculated as the number of identified spectra divided by the number of theoretical peptides\footnote{Theoretical peptides correspond to the peptides resulting from the theoretical digestion of the protein sequence by trypsin and that are visible in mass spectrometry ($800<MH<2500$)} of the protein.
+\end{itemize}
+\item[Redundancy] Number of proteins identified with the same pool of spectra. When there is redundancy, the above described parameters are shown only for the first protein of the subgroup (arbitrary chosen).Only the description of the other members of the subgroup is shown.
+\end{description}
+\normalsize
+
+\begin{figure}[!h]
+\center \includegraphics[width=1.0\textwidth]{images/tandem_prot.png}
+\caption{Protein results}
+\label{prot}
+\end{figure}
+
+\subsection{*peptide.txt}
+Identified peptides are grouped by group (Fig~\ref{pep}). One line corresponds to 1 MS/MS spectrum identifying one peptide, that can be present in one or more proteins.
+\small
+\begin{description}
+\item[FDR] False discovery rate at peptide level, calculated by the peptide E-value of the complete analysis.
+\item[Group] Group of the proteins containing this peptide.
+\item[Description] Protein description if the peptide is specific to this protein.
+\item[Sample] Name of MS/MS run file.
+\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[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.\\
+\textit{Rq :} If the peptide is specific, there is only $'-'$.
+\item[Sub-groups] Protein sub-groups where the peptide is present.
+\item[E-value] Peptide E-value.
+\begin{itemize}
+\item Statistical value representing the number of times this peptide would be identified at random.
+\item Calculated by the X!Tandem with an empiric model.
+\end{itemize}
+\item[Charge] Charge level of the precursor.
+\item[MH+ Obs] Monoisotopic observed mass for the peptide + one proton (MH$^{+}$)
+\item[MH+ Theo]Monoisotopic calculated mass for the peptide + one proton (MH$^{+}$)
+\item[DeltaMH+] Error in the precursor mass between observed and theoretical data (Da)
+\item[Delta-ppm] Error in the precursor mass between observed and theoretical data (ppm)
+\end{description}
+\normalsize
+
+\begin{figure}[!h]
+\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide.png}
+\caption{Peptide results}
+\label{pep}
+\end{figure}
+
+\subsection{*compar.txt}
+All identified proteins are presented in a list: one protein per protein, and one column per sample, i.e. per MS/MS run file (Fig~\ref{compar}).
+The list of proteins is repeated 4 times, corresponding to the 4 parameters that are used to compare samples (see Type for details).
+\small
+\begin{description}
+\item[Group] Protein group. Groups roughly correspond to the different functions.
+\item[Sub-group] Protein sub-group. All the proteins of a sub-group are identified with the same valid peptides.
+\item[Description] Protein description extracted from the fasta file.
+\item[MW] Molecular weight of the protein (KDa).
+\item[log(E value)] log of protein's E-value.
+\begin{itemize}
+\item Statistical value representing the number of times this protein would be identified just by random.
+\item Calculated by the product of unique peptide E-value in all sample.
+\end{itemize}
+\item[Type] Defines the item that is compared between samples
+\begin{description}
+\item[Spectra] Number of MS/MS spectra identified for the protein
+\item[Specifics] Number of specific MS/MS spectra identified for the protein compared to the other proteins belonging to the same group.
+\item[Uniques] Number of unique peptide sequences identified for this protein.
+\item[PAI] Protein Abundance Index (~\ref{pai})
+\end{description}
+\end{description}
+\normalsize
+
+\begin{figure}[!h]
+\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison.png}
+\caption{Comparison results}
+\label{compar}
+\end{figure}
+
+\subsection{*fdr.txt}
+The result file indicates the number of peptides with an E-value less than the E-value indicated in the fist column (Fig~\ref{fdr2}). You just have to divide the number of peptides in the reverse or decoy database by the number of peptides in the normal database to obtain the false discovery rate at each E-value level.\\
+This methods has 2 limitations :
+\begin{itemize}
+\item Normal and reverse databases must be saved in different fasta files.
+\item The filter parameters must be low (~\ref{fdr})
+\end{itemize}
+
+\begin{figure}[!h]
+\center \includegraphics[scale=0.5]{images/tandem_fdr.png}
+\caption{FDR results}
+\label{fdr2}
+\end{figure}
+
+\end{document}
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diff --git a/xtandempipeline/doc/xtandem_pipeline.pdf b/xtandempipeline/doc/xtandem_pipeline.pdf
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+\documentclass[10pt,a4paper]{article}
+\usepackage[utf8x]{inputenc}
+\usepackage{ucs}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+\usepackage{amssymb}
+\usepackage[colorlinks=true,urlcolor=blue,linkcolor=black]{hyperref}
+\usepackage{graphicx}
+\usepackage{fancyhdr}
+\usepackage{geometry}
+
+\newcommand{\X}{\textbf{X!Tandem pipeline}}
+
+%\usepackage{enumitem}
+%\setdescription{labelsep=\textwidth}
+
+\author{Benoit Valot\\
+\texttt{valot@moulon.inra.fr}\\
+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{29 October 2010}
+
+%Modification des entetes et pied de page + marges
+\geometry{top=3cm, bottom=3cm, left=2cm, right=2cm}
+%\pagestyle{headings}
+\pagestyle{fancy}
+%\fancyhead{}
+\fancyfoot{}
+\rfoot{\thepage}
+\lfoot{\includegraphics[width=1cm]{images/pappso.pdf}}
+
+
+\begin{document}
+\maketitle
+
+
+\begin{abstract}
+\href{http://www.thegpm.org/tandem/index.html}{X!Tandem} is an open-source software performing peptide/protein identification from MS/MS mass spectra. X!Tandem is fast and accurate, but the Global Proteome Machine (\href{http://www.thegpm.org/}{GPM}) is relatively limited regarding the processing of identification results.
+$\X$ is an alternative to the installation of the GPM on local servers.
+
+\paragraph*{}
+$\X$ performs database searching and matching on a list of MS/MS runs in one shot, using a list of easily user selected paramaters and databases.
+
+\paragraph*{}
+$\X$ also performs filtering of data according to statistical values at peptide and protein levels. The results are stored into TSV (Tab Separated Values) files. Moreover, redundancy of protein databases are fully filtered as follows :
+\begin{itemize}
+\item proteins identified without specific peptides compared to others are eliminated;
+\item proteins identified with the same pool of peptides are assembled;
+\item proteins are grouped by function (identified with at least one common peptide), and the specific peptides for each sub-group of proteins are indicated.
+\end{itemize}
+\end{abstract}
+
+\tableofcontents
+
+\pagebreak
+
+\section{Installation}
+
+\subsection{License}
+\paragraph*{}
+Copyright (C) 2010 Valot Benoit\\
+$\X$ program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\\
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the \href{http://www.gnu.org/licenses/gpl.html}{GNU General Public License} for more details.
+
+\subsection{Requirements}
+$\X$ works on all platforms (Linux, Windows and Mac). Java 1.6 must be installed (it can be found :
+\href{https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u14-oth-JPR@CDS-CDS_Developer}{here}).
+
+\subsection{Third party softwares for Windows}
+\begin{enumerate}
+\item Download the \href{http://pappso.inra.fr/downloads/xtandem_pipeline.zip}{$\X$ archive} and unzip it.
+\item Create a folder named "Benperl/" directly in the C:/ directory.
+\item Move the folders "Xtandem", from the archive to the new folder "C:/Benperl/".
+\end{enumerate}
+You could also download the executable in the \href{ftp://ftp.thegpm.org/projects/tandem/binaries/}{GPM site} (32 and 64 bits).
+
+\subsection{Third party softwares for Linux}
+\subsubsection*{Ubuntu}
+\begin{itemize}
+\item Add this \href{https://launchpad.net/~olivier-langella/+archive/ppa}{repository}.
+\item Install the \textit{xtandem-tornado} package.
+\end{itemize}
+\subsubsection*{Other distributions}
+\begin{itemize}
+\item Download the \href{ftp://ftp.thegpm.org/projects/tandem/source/}{sources} and follow the instruction of compilation.
+\end{itemize}
+
+\subsection{Third party softwares for Mac}
+Download the executable from the \href{ftp://ftp.thegpm.org/projects/tandem/binaries/}{GPM site}.
+
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.5]{images/tandem_principal.png}
+\caption{Principal window}
+\label{principal}
+\end{figure}
+
+\subsection{Start X!Tandem pipeline}
+\paragraph*{}
+To run \X, simply :
+\begin{itemize}
+\item Open X!Tandem pipeline by using this \href{http://pappso.inra.fr/documents/bioinformatique/xtandem_parser.jnlp}{link}
+\item Wait for the program to execute
+\item The principal window will appear (Fig~\ref{principal})
+\end{itemize}
+
+\subsection{Configuration}
+\begin{itemize}
+\item Open the menu X!Tandem $\rightarrow$ Configuration (Fig~\ref{configuration}).
+\item Define the path to the X!Tandem executable
+\item Choose the folder where to store the X!Tandem parameters
+\item Choose the folder where the MS/MS data, the protein databases and the X!tandem results are stored
+\end{itemize}
+
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.5]{images/tandem_configuration.png}
+\caption{Configuration window}
+\label{configuration}
+\end{figure}
+
+\pagebreak
+
+\section{X!Tandem analysis}
+\paragraph*{}
+$\X$ allows you to analyze peak-lists files by searching a list of protein databases using the X!Tandem software.
+Three successive graphical boxes help you select first the mzXML files or other peak-lists, then the protein databases and finally the folder where the results will be stored. The databases must be protein ones, X!Tandem does not work on DNA databases.
+
+\subsection{Parameters}
+\label{parameter}
+\paragraph*{}
+To perform database searching, you must create or edit a model XML file (stored in the xtandem models folder). Open the menu X!Tandem $\rightarrow$ Parameters (Fig~\ref{xtandem_parameter}).
+
+\begin{figure}[!h]
+\center \includegraphics[scale=0.4]{images/tandem_parameter.png}
+\caption{Parameter window}
+\label{xtandem_parameter}
+\end{figure}
+
+\paragraph*{}
+To use complete performance of your computer, specify the number of CPU in the model : spectrum $\rightarrow$ threads.
+
+\subsection{Running analysis}
+\paragraph*{}
+To perform analysis, start the menu X!Tandem $\rightarrow$ Analysis.
+\begin{enumerate}
+\item Select the peak-list files to be analyzed (See~\ref{peak})
+\item Select the database files to be searched (See~\ref{database})
+\item Select the folder where to store the result files
+\item Select the searching parameters model (See~\ref{parameter})
+\end{enumerate}
+
+\subsection{Peak-lists}
+\label{peak}
+\paragraph*{}
+X!Tandem works with open peak-list files like mzXML, mgf, mzData, mzML or pkl files.
+
+\subsection{Databases}
+\label{database}
+\paragraph*{}
+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}.
+
+\pagebreak
+
+\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}.
+
+\subsection{Three modes of analysis}
+\label{mode}
+\paragraph*{}
+You can filter the MS/MS identification results and export them in three different modes : (menu Processing)
+\begin{description}
+\item[Individual mode] \hfill \\ Each MS/MS result file is processed individually.\\
+You cannot perform comparison by using this process.
+\item[Combined mode] \hfill \\ The MS/MS result files are combined in one result file, and this file is filtered / exported.\\
+This mode is useful to compare different results.
+\item[Phosphopeptide mode] \hfill \\ Same as the combined mode analysis except that only phosphopeptides are conserved and the result is oriented in order to validate phosphosites.
+\end{description}
+
+\paragraph*{}
+In all modes, you have to :
+\begin{enumerate}
+\item Select the XML result files
+\item Define the filter parameters (~\ref{filtering})
+\item Define the name of the result file to export
+\item Define the export parameters (~\ref{exporting})
+\end{enumerate}
+
+\subsection{Filter parameters}
+\label{filtering}
+The filter window (Fig~\ref{filter}) defines the automated filtering process parameters :
+\small
+\begin{description}
+\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.
+\begin{itemize}
+\item The protein E-value is the product of its valid unique peptide E-values and it is different from the protein E-values determined by X!Tandem.
+\item The values are expressed in log(E-value).
+\end{itemize}
+\item[Sum to all] \hfill \\Defines how protein filter is performed when MS/MS results are combined :
+\begin{description}
+\item[No] To validate a protein, the 2 parameters (peptide number and protein E-value) must be valid in at least one result.
+Interesting if one wants to compare 2DLC-MS/MS results, where peptides from a protein are in the same LC-MS/MS run.
+\item[Yes] To validate a protein, the 2 parameters (peptide number and protein E-value) must be valid in the sum of all results.
+Interesting if one wants to compare SDS-PAGE-LC-MS/MS results, where peptides from a protein are split in different LC-MS/MS runs.
+\end{description}
+\item[Phosphopeptide] \hfill \\Keep only peptides containing phosphorylated residue modifications.
+All other peptides are invalided.
+\item[Contaminants] \hfill \\When you perform an analysis using different fasta databases, you can remove the result from one database by selecting this database.
+Interesting because it allows you to always include the same contaminant proteins during the database search, and because it removes the contaminant proteins from the results.
+\item[Add results] \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.
+\end{description}
+\normalsize
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.5]{images/tandem_filter.png}
+\caption{Filter window}
+\label{filter}
+\end{figure}
+
+\pagebreak
+
+\subsection{Export parameters}
+\label{exporting}
+The export window (Fig~\ref{export}) shows the different types of available exports :
+\small
+\begin{description}
+\item[Default] \hfill \\Creates TSV files containing identification results for proteins (*protein.txt) and peptides (*peptide.txt). When you perform a combined analysis, a *compar.txt file is created that contains the results of comparison between samples.
+\item[Fasta] \hfill \\Creates a fasta file for valid proteins.
+\item[PepNovo] \hfill \\Creates a XML file containing the peptide results to be removed for an automated \textit{De Novo} interpretation in sequence using our \href{http://pappso.inra.fr/documents/bioinformatique/DeNovo_pipeline.pdf}{DeNovo pipeline}.
+\item[FDR] \hfill \\Creates a tabulated file containing the number of valid peptides for the different peptide E-values in each database. Allows you to determine the E-value above which FDR value is acceptable.\\
+\label{fdr}\textbf{Warning} : Use very low parameters in peptide (0.1) and protein (-1) E-values, and set the number of unique peptides to validate a protein to 1.
+\item[Protic] \hfill \\Creates a PROTICdb compatible XML file, so you can store results in the \href{http://pappso.inra.fr/bioinformatique.html}{PROTICdb} proteomic database.
+\item[MassChroQ] \hfill \\Creates a MassChroQ compatible XML file, so you can perform quantitative analysis using our home-made software \textbf{MassChroQ} (to be released soon).
+\end{description}
+\normalsize
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.5]{images/tandem_export.png}
+\caption{Export window}
+\label{export}
+\end{figure}
+
+\pagebreak
+
+\section{Exporting the results}
+\subsection{Files *protein.txt}
+The identified proteins are represented by sample (individual mode) or for all samples (combine/phosphopeptide modes) (Fig~\ref{prot}). Proteins are grouped by function.
+\small
+\begin{description}
+\item[Group] Group to which the protein belongs. All the proteins in a group have at least one peptide in common.
+\item[Sub-group] Sub-group to which the protein belongs. All the proteins in a sub-group are identified with the same valid peptides.
+\item[Description] Protein description as it appears in the header of the fasta file.
+\item[log(E value)] Protein E-value expressed in log.
+\begin{itemize}
+\item Statistical value representing the number of times this protein would be identified randomly.
+\item Calculated as the product of unique peptide E-values in the sample.
+\end{itemize}
+\item[Coverage] \% of protein coverage.
+\item[MW] Molecular weight of the protein expressed in KDa.
+\item[Spectra] Total number of MS/MS spectra identified for the protein
+\item[Specifics] Number of MS/MS spectra that are specific to the protein, compared to the other proteins of the same group (individual and phosphopeptide mode, see~\ref{mode}).
+\item[Specific uniques] Number of unique peptide sequences specific to the protein, compared to other proteins of the same group (combined mode, see~\ref{mode}).
+\item[Uniques] Number of unique peptide sequences identified for the protein.
+\item[PAI] Protein Abundance Index\label{pai} :
+\begin{itemize}
+\item PAI estimates the relative abundance of the protein.
+\item PAI is calculated as the number of identified spectra divided by the number of theoretical peptides\footnote{Theoretical peptides correspond to the peptides resulting from the theoretical digestion of the protein sequence by trypsin and that are visible in mass spectrometry ($800<MH<2500$)} of the protein.
+\end{itemize}
+\item[Redundancy] Number of proteins identified with the same pool of spectra. When there is redundancy, the above described parameters are shown only for the first protein of the subgroup (arbitrary chosen).Only the description of the other members of the subgroup is shown.
+\item[Position] Position(s) of the phosphosite in the protein. This value is only reported in phosphosite mode (see~\ref{mode}).
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/tandem_prot.pdf}
+\caption{Protein results}
+\label{prot}
+\end{figure}
+
+\subsection{Files *peptide.txt}
+Identified peptides are grouped 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.
+\small
+\begin{description}
+\item[Group] Group of the proteins containing this peptide.
+\item[Description] Protein description if the peptide is specific to this protein.
+\item[Sample] Name of the MS/MS run file.
+\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[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.\\
+\textit{Rq :} If the peptide is specific, there is only $'-'$.
+\item[Sub-groups] Protein sub-groups where the peptide is present.
+\item[E-value] Peptide E-value.
+\begin{itemize}
+\item Statistical value representing the number of times this peptide would be identified randomly.
+\item Calculated by X!Tandem with an empiric model.
+\end{itemize}
+\item[Charge] Charge level of the precursor.
+\item[MH+ Obs] Monoisotopic observed mass for the peptide + one proton (MH$^{+}$)
+\item[MH+ Theo]Monoisotopic calculated mass for the peptide + one proton (MH$^{+}$)
+\item[DeltaMH+] Error in the precursor mass between observed and theoretical data (Da)
+\item[Delta-ppm] Error in the precursor mass between observed and theoretical data (ppm)
+\item[Position] Position(s) of the phosphosite in the protein. This value is only reported in phosphosite mode (see~\ref{mode}).
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide.pdf}
+\caption{Peptide results}
+\label{pep}
+\end{figure}
+
+\subsection{Files *compar.txt}
+All identified proteins are represented in a list: one protein per row, and one sample per column (Fig~\ref{compar}).
+The list of proteins is repeated 4 times, corresponding to the 4 parameters that are used to compare samples (see Type for details).
+\small
+\begin{description}
+\item[Group] Protein group. Groups roughly correspond to the different functions.
+\item[Sub-group] Protein sub-group. All the proteins of a sub-group are identified with the same valid peptides.
+\item[Description] Protein description extracted from the fasta file.
+\item[MW] Molecular weight of the protein (KDa).
+\item[log(E value)] The log of protein's E-value.
+\begin{itemize}
+\item Statistical value representing the number of times this protein would be identified randomly.
+\item Calculated as the product of unique peptide E-values in all sample.
+\end{itemize}
+\item[Type] The item that is compared between samples.
+\begin{description}
+\item[Spectra] Number of MS/MS spectra identified for the protein.
+\item[Specifics] Number of specific MS/MS spectra identified for the protein compared to the other proteins belonging to the same group.
+\item[Uniques] Number of unique peptide sequences identified for this protein.
+\item[PAI] Protein Abundance Index (~\ref{pai}).
+\end{description}
+\item[Position] Position(s) of the phosphosite in the protein. This value is only reported in phosphosite mode (see~\ref{mode}).
+\end{description}
+\normalsize
+
+\begin{figure}[!ht]
+\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison.pdf}
+\caption{Comparison results}
+\label{compar}
+\end{figure}
+
+\subsection{Files *fdr.txt}
+This result file indicates the number of peptides with an E-value less than the E-value indicated in the fist column (Fig~\ref{fdr2}). You just have to divide the number of peptides in the reverse or decoy database by the number of peptides in the normal database to obtain the false discovery rate at each E-value level.\\
+This method has 2 limitations :
+\begin{itemize}
+\item normal and reverse databases must be saved in different fasta files;
+\item the filter parameters must be low (~\ref{fdr})
+\end{itemize}
+
+\begin{figure}[!h]
+\center \includegraphics[scale=0.5]{images/tandem_fdr.png}
+\caption{FDR results}
+\label{fdr2}
+\end{figure}
+
+
+\end{document}
\ No newline at end of file
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