Commit e274ab80 authored by Filippo Rusconi's avatar Filippo Rusconi
Browse files

Started the actual writing of the user manual.

parent 534a96f4
......@@ -17,9 +17,9 @@ xml:lang="en">
<dedication>
<para>To all the admirable people acting in the <emphasis><quote>Free
Software Movement</quote></emphasis> for a better and more ethical
computing world</para>
<para>To all the admirable people acting in the <emphasis><quote>Free
Software Movement</quote></emphasis> for a better and more ethical
computing world</para>
<para>To all the readers who helped with this manual.</para>
......
<?xml version='1.0' encoding='utf-8' ?>
<!DOCTYPE authorgroup [
<!ENTITY % entities SYSTEM "pappso-user-manuals.ent">
%entities;
]>
<authorgroup xmlns="http://docbook.org/ns/docbook" version="5.0">
......@@ -16,6 +20,8 @@
<orgdiv>Institut national de chimie (INC)</orgdiv>
</affiliation>
<personblurb><para>Main author of the &xtpjava; software</para></personblurb>
</author>
<author>
......@@ -30,6 +36,8 @@
<orgdiv>Institut national de chimie (INC)</orgdiv>
</affiliation>
<personblurb><para>Main author of the &xtpcpp; software</para></personblurb>
</author>
<author>
......@@ -39,6 +47,8 @@
<surname>Renne</surname>
</personname>
<personblurb><para>Intern in bioinformatics</para></personblurb>
</author>
<author>
......@@ -53,6 +63,8 @@
<orgdiv>Institut national de chimie (INC)</orgdiv>
</affiliation>
<personblurb><para>Main author of the user manual</para></personblurb>
</author>
<author>
......@@ -67,6 +79,9 @@
<orgdiv>Institut national de chimie (INC)</orgdiv>
</affiliation>
<personblurb><para>Directory of the PAPPSO facility where the &xtpcpp;
software is being developed</para></personblurb>
</author>
</authorgroup>
This diff is collapsed.
......@@ -34,13 +34,88 @@ xml:id="chap_graphical-user-interface" version="5.0">
<para>
Data exploration, in mass spectrometry, entails, for a large part, the
relentless scrutiny of the mass spectra by an expert eye. Without a powerful
mass spectrum viewer, capable of numerous data display modes, the expert eye
remains powerless. In this chapter, the graphical user interface is described
in detail, starting from the opening of a mass spectrometry data file, to the
navigation through all the data depth within a large set of graphical
representations of the data.
Proteomics data exploration, with &xtpcpp;, entails, for a large part, the
following steps:
<itemizedlist>
<listitem>
<para>
Configuration of the &xtandem; external software that runs the database
searches (producing peptide vs mass spectrum matches, leading to the
peptide identifications);
</para>
</listitem>
<listitem>
<para>
Loading of the database files (both the organism-specific databases and
optional contaminants databases);
</para>
</listitem>
<listitem>
<para>
Loading of the mass spectrometry data acquisition files;
</para>
</listitem>
<listitem>
<para>
Running of &xtandem; from inside of &xtpcpp;, with production of a set of
peptide vs mass spectrum matches (peptide identification results);
</para>
</listitem>
<listitem>
<para>
Relentless scrutiny of the peptide identification results. Optional
modification of the results;
</para>
</listitem>
<listitem>
<para>
Protein inference, that is, protein identification on the basis of the
peptide identifications. &xtpcpp; has a powerful interface to ease the
scrutiny of the protein groups (<quote>grouping</quote>) that leads
ultimately to protein identification. The default protein groups
calculated by &xtpcpp; can be modified by the user.
</para>
</listitem>
</itemizedlist>
</para>
<para>
In this chapter, the graphical user interface is described in detail, going
from the first step above to the last one.
</para>
......@@ -92,18 +167,18 @@ xml:id="chap_graphical-user-interface" version="5.0">
</para>
</sect1>
</sect1>
<sect1>
<sect1>
<title>The Window Layout</title>
<title>The Window Layout</title>
<para>The graphical interface of comprises a number of windows where data
and informations are displayed. When first started, the program shows the
main program window. Upon loading of a MS run data set from file, new
windows do show up as described below (see <xref
linkend="fig_minexpert-whole-window-set"/>):</para>
<para>The graphical interface of comprises a number of windows where data
and informations are displayed. When first started, the program shows the
main program window. Upon loading of a MS run data set from file, new
windows do show up as described below (see <xref
linkend="fig_minexpert-whole-window-set"/>):</para>
<itemizedlist>
......@@ -419,7 +494,7 @@ xml:id="chap_graphical-user-interface" version="5.0">
</sect1>
</chapter>
</chapter>
<!ENTITY xtpcpp "<application>X!TandemPipeline</application>">
<!ENTITY xtpjava "<application>X!TandemPipeline-Java</application>">
<!ENTITY xtandem "<application>X!Tandem</application>">
<!ENTITY msxps "<application>msxpertsuite</application>">
<!ENTITY msXps "<application>msXpertSuite</application>">
<!ENTITY minexp "<application>minexpert</application>">
......@@ -12,6 +14,8 @@
<!ENTITY xpc "<application>XpertCalc</application>">
<!ENTITY xpm "<application>XpertMiner</application>">
<!ENTITY emdash "—">
<!-- nbnsp is non breaking *no* space, that is a non breaking no-width space-->
<!ENTITY nbnsp "&#xFEFF;">
......
......@@ -30,41 +30,59 @@
<itemizedlist>
<listitem>
<para> Load mass spectometry data files in the mzML format, thanks
to the excellent <application>libpwiz</application> library of
ProteoWizard<footnote><para><link xlink:href="http://proteowizard.sourceforge.net/"/>.</para></footnote>
fame; Mass data file loading can be performed in
<emphasis>full-memory</emphasis> mode (all the data read from file
are stored in memory) for faster operations or in
<emphasis>streamed</emphasis> mode when loading files largers than
the available memory. </para>
</listitem>
<listitem>
<para> Display the data in powerful ways in a unified
graphical user interface. The interface was designed to
integrate all the most useful characteristics of the various
proprietary environments known by the author, thanks to the
excellent
<application>libqcustomplot</application><footnote><para><link xlink:href="http://qcustomplot.com/"/>.</para></footnote>
library;</para>
<listitem> <para> Load mass spectometry data files in the mzXML or mzML
format, thanks to the excellent <application>libpwiz</application> library
of ProteoWizard<footnote><para><link
xlink:href="http://proteowizard.sourceforge.net/"/>.</para></footnote>
fame. </para> </listitem>
<listitem>
<para>
Configure the way the peptide spectrum matches (PSM) are to be performed;
</para>
</listitem>
<listitem>
<para> Configure the way mass spectrometry data integrations are
performed from a combination standpoint and optionally apply a
Savitzky-Golay smoothing; </para>
</listitem>
<listitem>
<para> Configure the level of MS data
(MS<superscript>n</superscript>) for which the integrations are
performed. Optionally filter data by precursor ion m/z values or
precursor spectrum indices; </para>
</listitem>
<para>
</itemizedlist>
Configure the database files to be used (target organism databases and
contaminant databases);
</para>
</listitem>
<listitem>
<para>
Use the MS/MS data in the file to feed the &xtandem; program that produces
peptide identification results by matching the measured ion masses with
peptide fragments calculated <emphasis>in silico</emphasis> on the basis
of the databases contents;
</para>
</listitem>
<listitem>
<para>
Display the data in powerful ways in a unified graphical user interface to
allow the user to inspect the peptide identifications and also control the
way these identifications are used to infer the protein identications.
</para>
</listitem>
</itemizedlist>
</sect1>
......@@ -73,20 +91,13 @@
<title>Feedback from the users</title>
<para>We are always grateful to any constructive feedback from the users.</para>
<para>The msXpertSuite software team might be contacted
<foreignphrase>via</foreignphrase> the following addresses</para>
<figure xml:id="fig_feedback-addresses">
<title>Addresses to report feedback to</title>
<mediaobject>
<imageobject role="fo">
<imagedata fileref="print-feedback-addresses.png" format="PNG" scale="100"/>
</imageobject>
<imageobject role="html">
<imagedata fileref="web-feedback-addresses.png" format="PNG" scale="100"/>
</imageobject>
</mediaobject>
</figure>
<para>The PAPPSO software team might be contacted
<foreignphrase>via</foreignphrase> the following contact page:</para>
<para><link
xlink:href="http://pappso.inrae.fr/en/travailler_avec_nous/contact/"/> (search
for team members having the <quote>Bioinformatics</quote> specialty
mentioned, like Olivier Langella or Filippo Rusconi).</para>
</sect1>
......@@ -98,21 +109,30 @@
&xtpcpp; software suite are available at <link
xlink:href="http://pappso.inrae.fr/en/bioinfo/xtandempipeline/"/>. Most of the
time, a new version is published as source, and as binary install packages for
<productname>MS-Windows</productname> (64-bit systems only). No
<productname>GNU/Linux</productname> binary packages are created outside of
the autobuilder of the various distributions. As a Debian Developer, the
author creates <productname>Debian</productname><footnote><para><link
xlink:href="http://www.debian.org/"/></para></footnote> packages that are
uploaded on the distribution servers. These packages are available using the
system's software management infrastructure (like using the
<productname>Debian</productname>'s <command>apt</command> command, for
example, or the graphical application).</para>
<productname>MS-Windows</productname> (64-bit systems only).
</para>
<para>
For <productname>GNU/Linux</productname>, binary packages are created
locally (see <link
xlink:href="http://pappso.inrae.fr/en/bioinfo/xtandempipeline/download/"/>)
but are also built in the
<productname>Debian</productname><footnote><para><link
xlink:href="http://www.debian.org/"/></para></footnote> autobuilders and are
uploaded to the distribution servers. These packages are available using the
system's software management infrastructure (like using the
<productname>Debian</productname>'s <command>apt</command> command, for
example, or the graphical application).
</para>
<para>The software and all the documentation are all provided under the Free
Software license <emphasis>GNU General Public License, Version&nbsp;3, or
later, at your option</emphasis>. For an in-depth study of the
<emphasis>Free Software</emphasis> philosphy, I kindly urge the reader to
visit <link xlink:href="http://www.gnu.org/philosophy"/>.</para>
Software license <emphasis>GNU General Public License, Version&nbsp;3, or later,
at your option</emphasis>. For an in-depth study of the <emphasis>Free
Software</emphasis> philosphy, the reader is kindly urged to visit <link
xlink:href="http://www.gnu.org/philosophy"/>.</para>
</sect1>
......
......@@ -13,22 +13,51 @@
<revhistory xmlns="http://docbook.org/ns/docbook" version="5.0">
<revision>
<revnumber>0.7.24</revnumber>
<date>28 May 2021</date>
<authorinitials>Filippo Rusconi</authorinitials>
<revdescription>
<itemizedlist>
<listitem>
<para>
Start actually documenting the software with the Preface.
</para>
</listitem>
</itemizedlist>
</revdescription>
</revision>
<revision>
<revnumber>0.7.24</revnumber>
<date>21 April 2021</date>
<authorinitials>fr</authorinitials>
<authorinitials>Filippo Rusconi</authorinitials>
<revdescription>
<itemizedlist>
<listitem><para>
<listitem>
<para>
Very first setting up of the user manual using the mineXpert2
project as a template.
</para></listitem>
</para>
</listitem>
</itemizedlist>
......
......@@ -3,7 +3,6 @@
<!ENTITY BOOKID "xtpcpp_user_manual">
<!ENTITY HOLDER "The PAPPSO team">
<!ENTITY push-pin-button-green-unpressed " <inlinemediaobject> <imageobject> <imagedata
fileref='push-pin-button-green-unpressed.svg' valign='middle' width='1.3em'/>
</imageobject> <textobject> <phrase>push-pin-button-green-unpressed</phrase>
......
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