<?xml version="1.0" encoding="UTF-8"?>
<!-- Modified 2005-01-14 by Shao-En Ong -->
<!-- Modified 2005-01-14 by Peter Mortensen -->
<!-- Created 2004-08-13 by Peter Mortensen
Installation of DocBook on Windows
according to
<http://supportweb.cs.bham.ac.uk/documentation/tutorials/docsystem/build/tutorials/docbooksys/docbooksys.pdf>.
Orig DOCTYPE/SYSTEM ID: "-//OASIS//DTD DocBook V4.2//EN",
changed to use the same as file 'catalog',
"-//OASIS//DTD DocBook XML V4.2//EN"
Version 1:
<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd">
Note: direct reference works, but how do we get the
catalog method to work?
DocBook quick reference:
lists, <itemizedlist>/<listitem>/<para>, <orderedlist>/<listitem>/<para>.
HTML link, <ulink url="http://xyz">abc</ulink>
figure, <figure>
<title>
<mediaobject>
<imageobject>
<imagedata>
<textobject>
<caption>
<para>
Literals:
< : <
> : >
& : &
HHHHHHHHHH
GIF map:
Ref GIF
=======================================================
MSQmain-fig MSQ_main2.gif
MSQoptions1-fig MSQ_ToolsOptions.gif
MSQmain-fig MSQ_main2.gif
MSQmainAssoc-fig MSQ_main_assoc1.gif
MSQmainReadyToParse-fig MSQ_main_readyToParse.gif
-->
<!--
Markers for quick navigation:
-->
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SDUP: "file:///z:/zNEW/TRANSPORT/ToTARU/2004-08-16/to%20burn,2004-08-15/Installing%20and%20using/Windows/DTDs/docbook-xml-4.2/docbookx.dtd"
-->
<!DOCTYPE book SYSTEM
"file:///C:/DocBook/Installing%20and%20using/Windows/DTDs/docbook-xml-4.2/docbookx.dtd">
<book>
<bookinfo>
<title>MSQuant: The Definitive Guide HELLO WORLD</title>
<author>
<firstname>Peter</firstname>
<surname>Mortensen</surname>
<affiliation>
<address><email>NUKESPAMMERSdrmortensen@get2netZZZZZZ.dk</email></address>
</affiliation>
</author>
<copyright>
<year>2004</year>
<holder role="mailto:pmortensen@bmb.sdu.dk">Peter Mortensen</holder>
</copyright>
<pubdate role="rcs">$Date: 2005/01/14 18:15:55 $</pubdate>
<releaseinfo>$Id: MSQuant.xml,v 1.3 2005/01/14 18:15:55 shaoenong Exp $</releaseinfo>
<abstract>
<para>
MSQuant is a tool for quantitative
proteomics.
</para>
<para>
The primary purpose of this manual is as a user
guide, including installation instructions. It
also documents the tools surrounding MSQuant and
the associated data formats.
</para>
<para>
There is also a section for MSQuant developers on how
to contribute to the MSQuant source code, documentation
and helper tools.
</para>
<para>
Note: this manual is a work in progress and a first finished version is not
ready yet.
</para>
<para>
<To add somewhere:>
<itemizedlist>
<listitem><para>
Red/black in quant window, upper
right explain the colour
</para></listitem>
<listitem><para>
co-elution: trends, tails in one LC profile, e.g. heavy.
Deuterium problems.
</para></listitem>
</itemizedlist>
</para>
</abstract>
</bookinfo>
<part><title>User guide</title>
<chapter><title>Introduction</title>
<sect1><title>What is it?</title>
<para>
MSQuant is a tool for quantitative
proteomics/mass spectrometry and processes
spectra and LC runs to find quantitative
information about proteins and peptides. Though
automated it also allows manual inspection and
change.
</para>
<para>MSQuant's main purpose is to make quantitation of
proteins and peptides possible in the area of
mass spectrometry/proteomics (science/analytical
chemistry/molecular biology). E.g. an experiment
where one heavy isotope-labelled sample from
treated cells is compared to unlabelled,
untreated cells to give quantitative answers
about cellular processees. The input to MSQuant
is a search result file (HTML) from the Mascot
search engine (from
<ulink url="http://www.matrixscience.com/">
Matrix Science</ulink>
)
and one or more raw spectrum files.
</para>
<para>MSQuant is written in Microsoft's .NET and thus
can only run on Windows computers that have the
.NET runtime runtime installed. The runtime is installed
by default in later versions of Windows.
</para>
</sect1>
<sect1><title>Overview</title>
<para>
<Data flow diagram: helper tools, MSQuant, Mascot.>
</para>
</sect1>
<sect1><title>References</title>
<para>
< -refs from home page >
</para>
</sect1>
</chapter>
<chapter><title>Quick start</title>
<!-- Note: quantation is not set to triple encoding, even though
the data is triple labelled. Reason: triple encoding is not
in the default set of quantitation modes. -->
<sect1><title>Introduction</title>
<para>
This chapter shows how to get to work with MSQuant
as fast as possible.
A specific example for a particular instrument
(QSTAR) is presented.
</para>
</sect1>
<sect1><title>Installation</title>
<para>
If Analyst is not already installed:
<orderedlist>
<listitem><para>
Install it from the CD labelled "Analyst QS".
</para></listitem>
<listitem><para>
Apply SP5 or SP7 (Service Packs) for Analyst QS.
This is a one-step process for SP5 and a
two-step process for SP7 (install SP5 first).
</para></listitem>
</orderedlist>
</para>
<para>
Add the path to Analyst bin folder to the system path
(see appendix xyz for the full details):
<orderedlist>
<listitem><para>
Right-click "My Computer" to get the "System Properties" dialog.
</para></listitem>
<listitem><para>
go to the "Advanced" tab and click "Environment Variables"
</para></listitem>
<listitem><para>
for "System variables" click on the "Path" entry then click "Edit"
</para></listitem>
<listitem><para>
add ";C:\Program Files\Analyst\bin"
(or wherever you've installed Analyst to the end of the string)
</para></listitem>
<listitem><para>
Restart the computer.
</para></listitem>
</orderedlist>
These instructions are for Windows 2000. For other versions of Windows,
see appendix xyz.
</para>
<para>
Download an MSQuant installer,
<ulink url="http://www.pil.sdu.dk/1/MSQuant/MSQuantInstallerQuick.zip">
http://www.pil.sdu.dk/1/MSQuant/MSQuantInstallerQuick.zip</ulink>.
</para>
<para>
Extract the file to a suitable location using WinZip. Run the installer -
open Setup.Exe.
</para>
<para>
Note that full installation instructions are in appendix xyz.
</para>
</sect1>
<sect1><title>Sample data set</title>
<para>
In this section a sample data set is used that was
generated at the famous CEBI centre at University
of Southern Denmark.
</para>
<para>
Download the dataset from
<ulink url="http://www.pil.sdu.dk/1/MSQuant/QSTARsampleDataSet1,2004-02-19.zip">
http://www.pil.sdu.dk/1/MSQuant/QSTARsampleDataSet1,2004-02-19.zip</ulink>.
Size: 21 MB.
</para>
<para>
Extract the zip file to a suitable location using WinZip.
</para>
</sect1>
<sect1><title>Preparing for parsing the Mascot result file</title>
<para>
Start MSQuant - open MSQuant.exe.
The main MSQuant window as in figure
<xref linkend="MSQmain-fig"/>
should open.
</para>
<figure id="MSQmain-fig" float="0">
<title>main MSQuant window</title>
<!-- Old: <GRAPHIC fileref="linus.&magic;" scale="60"></GRAPHIC> -->
<mediaobject>
<imageobject>
<imagedata fileref="MSQuantMisc/MSQ_main2.gif" format="GIF"/>
</imageobject>
<textobject><phrase>xyz</phrase></textobject>
<caption><para>
<caption>
Main MSQuant window
</para>
</caption>
</mediaobject>
</figure>
<para>
Set quantitation mode to "Arg13C6": open menu Tools/Options.
The dialog shown in figure
<xref linkend="MSQoptions1-fig"/>
should open.
Locate pop-up dialog "Quantitation mode" and select "Arg13C6".
Press the OK button use the chosen quantitation mode.
</para>
<figure id="MSQoptions1-fig" float="0">
<title>MSQuant options dialog - TITLE</title>
<!-- Old: <GRAPHIC fileref="linus.&magic;" scale="60"></GRAPHIC> -->
<mediaobject>
<imageobject>
<imagedata fileref="MSQuantMisc/MSQ_ToolsOptions.gif" format="GIF"/>
</imageobject>
<textobject><phrase>xyz</phrase></textobject>
<caption><para>
<caption>
MSQuant options dialog.
'Quantitation mode' should match the type of datafiles
from which the search input to Mascot was generated.</para>
</caption>
</mediaobject>
</figure>
<para>
Right click in the left pane of the main window.
Select 'Add single Mascot file' in the pop-menu
(see <xref linkend="MSQmainFileAdd-fig"/>).
Find and select the file "Mascot Search
Results_band65_1.htm". It was placed on your hard
disk when you extracted the files from example
data set. Press the Open button. This file has now
been added to the left pane.
</para>
<para>
Right click in the right pane of the main window.
Select 'Add single raw data file' in the pop-menu
(see <xref linkend="MSQmainFileAdd-fig"/>).
Find and select the file "Q1LCMS190203_01DoubleArg.wiff".
It was placed on your hard disk when you extracted
the files from example data set. Press the Open
button. This file has now been added to the right
pane.
</para>
<figure id="MSQmainFileAdd-fig" float="0">
<title>
Adding Mascot result files and raw files to the main MSQuant window.
</title>
<!-- Old: <GRAPHIC fileref="linus.&magic;" scale="60"></GRAPHIC> -->
<mediaobject>
<imageobject>
<imagedata fileref="MSQuantMisc/MSQ_main2a.gif" format="GIF"/>
</imageobject>
<textobject><phrase>xyz</phrase></textobject>
<caption><para>
<caption>
Added files to the association window.
</para>
</caption>
</mediaobject>
</figure>
<para>
Select the two newly added files.
Right click and select 'Associate with highlighted raw data file'.
See <xref linkend="MSQmainAssoc-fig"/>.
This tells MSQuant which raw file generated the peak lists that
were used as input to the Mascot search.
The end result should look like <xref linkend="MSQmainReadyToParse-fig"/>.
</para>
<!-- introduce save assoc option here? -->
<figure id="MSQmainAssoc-fig" float="0">
<title>Associate result file with raw data file - TITLE</title>
<mediaobject>
<imageobject>
<imagedata fileref="MSQuantMisc/MSQ_main_assoc1.gif" format="GIF"/>
</imageobject>
<textobject><phrase>xyz</phrase></textobject>
<caption><para>
<caption>
xyz, MSQ_main_assoc1.gif</para>
</caption>
</mediaobject>
</figure>
<figure id="MSQmainReadyToParse-fig" float="0">
<title>Ready to parse result file... - TITLE</title>
<mediaobject>
<imageobject>
<imagedata fileref="MSQuantMisc/MSQ_main_readyToParse.gif" format="GIF"/>
</imageobject>
<textobject><phrase>xyz</phrase></textobject>
<caption><para>
<caption>
xyz, MSQ_main_readyToParse.gif</para>
</caption>
</mediaobject>
</figure>
</sect1>
<sect1><title>The rest</title>
<para>
<
Tour through major features with stated numbers
for a quantitation result.
>
</para>
</sect1>
</chapter>
<chapter><title>How do I xyz?</title>
<sect1><title>How do I abc?</title>
<para>
Hi there!
</para>
</sect1>
<sect1><title>How do I def?</title>
<para>
Hi there!
</para>
</sect1>
<sect1><title>How do I ghi?</title>
<para>
Hi there!
</para>
</sect1>
</chapter>
<chapter><title>MSQuant stories</title>
<sect1><title>Introduction</title>
<para>
<Particular stories of using MSQuant - usage by
way of example.
Correlation profiling.
Parsing only.
Memory trouble.
Mascot Result Launcher.
>
</para>
</sect1>
</chapter>
<chapter><title>MSQuant reference</title>
<sect1><title>Introduction</title>
<para>
In great detail, much more than xyz.
Correlation options:
</para>
</sect1>
<sect1><title>Options</title>
<para>
Main options.
Correlation options.
</para>
</sect1>
<sect1><title>Parsing</title>
<para>
Formats, Internet Explorer, Mascot Server
</para>
</sect1>
<sect1><title>Working with proteins</title>
<para>
MS3 scoring, batch features, export,
</para>
</sect1>
<sect1><title>Peptide validation</title>
<para>
Fragment spectra, MS3 scoring, export,
</para>
</sect1>
<sect1><title>Quantitation</title>
<para>
LC peaks, quantitation mode export, external quantitation.
Correlation profiling: options, inserting of (pseudo) peptides, .
</para>
</sect1>
</chapter>
</part>
<part><title>Tools surrounding MSQuant</title>
<chapter><title>Introduction</title>
<sect1><title>Tools for Finnigan</title>
<para>
DTA SuperCharge: .
DTA2Mascot: what is does, how to use/setup, pre.
Stripper.
IDA processor.
Mascot Daemon
Internet Explorer vers 6.
</para>
</sect1>
<sect1><title>Some more tools</title>
<para>
More good tools there!
</para>
</sect1>
<sect1><title>Who are those tools anyway?</title>
<para>
Even more good tools there!
</para>
</sect1>
</chapter>
</part>
<part><title>Software development</title>
<chapter><title>Introduction</title>
<sect1><title>Overview</title>
<para>
Open Source, how do I contribute (code, documentation, money, ),
.NET, .
Quantitation
CVS. SourceForge. File releases. How to actually use SourceForge;
navigate SourceForge pages, SourceForge file release system is
not straightforward.
Wanted:
1. Stand-alone tool for defining modifications and
quantitation modes. Completely independent.
XML specification/interface/file.
</para>
</sect1>
</chapter>
</part>
<part><title>Appendixes</title>
<chapter><title>Installation</title>
<sect1><title>MSQuant</title>
<para>
Post installation: QSTAR, Finnigan.
</para>
</sect1>
<sect1><title>Post installation</title>
<para>
Analyst path; Howto, explanation, error messages if not set.
Different places and names for setting environment variables
in Windows 2000, NT, XP, 98.
Virtual memory settings.
</para>
</sect1>
<sect1><title>Perl</title>
<para>
We recommend: ActiveState on Windows.
URL - general and specific, version, .
</para>
</sect1>
</chapter>
<chapter><title>Supported instruments</title>
<sect1><title>Introduction</title>
<para>
This appendix describes the various instruments
with associated software and data formats that is
supported by MSQuant.
</para>
</sect1>
<sect1><title>QSTAR</title>
<para>
.wiff Sciex Analyst MDS
</para>
</sect1>
<sect1><title>LTQ-FT</title>
<para>
.raw Finnigan XCalibur Thermo Electron
</para>
</sect1>
<sect1><title>Qtof</title>
<para>
.dat Micromass MassLynx? Waters
</para>
</sect1>
</chapter>
<chapter><title>Data formats</title>
<sect1><title>Supported Mascot formats</title>
<para>
Different Mascot format, 1.x, 2.0 ver1, 2.0 ver.
Internet Explorer reformatting.
</para>
</sect1>
<sect1><title>Quantitation modes and modifications</title>
<para>
File xyz.xml. Description of the different elements.
How Hys tag is modelled.
Table with overview of the values Hys tag and other quantitation modes.
How to define a new quantitation mode, with an example.
</para>
</sect1>
</chapter>
<chapter>
<title>Web resources</title>
<sect1><title>SourceForge</title>
<para>
MSQuant's official home page is located at
<ulink url="http://msquant.sourceforge.net/">
http://msquant.sourceforge.net/</ulink>
</para>
</sect1>
</chapter>
<chapter>
<title>Possible errors during and after installation</title>
<sect1>
<title>xyz</title>
<para>
The decimal point problem.
The FMWIFFCompDocNTDriver.dll problem.
The empty period field problem.
</para>
</sect1>
</chapter>
</part>
</book>
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