Commit cae44263 authored by Edlira Nano's avatar Edlira Nano
Browse files

preparing post_matching release

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2261 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 75d8614d
...@@ -158,7 +158,7 @@ ...@@ -158,7 +158,7 @@
\vskip 4cm \vskip 4cm
\textbf{\Huge MassChroQ manual}\\[0.5cm] \textbf{\Huge MassChroQ manual}\\[0.5cm]
\Large First edition for MassChroQ version 1.2 \emph{Hungry Crocklet}\\[1cm] \Large First edition for MassChroQ version 1.2 \emph{Longteeth Crocklet}\\[1cm]
\small \small
Author: Edlira \textsc{Nano}\\ Author: Edlira \textsc{Nano}\\
Contributors: Olivier \textsc{Langella}, Beno\^it \textsc{Valot}, Contributors: Olivier \textsc{Langella}, Beno\^it \textsc{Valot},
...@@ -205,7 +205,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>. ...@@ -205,7 +205,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
\chapter{Preface} \chapter{Preface}
{\M} is an open-source software released under the {\M} is an open-source software released under the
\href{http://www.gnu.org/licenses/gpl.html}{Gnu General Public Licence \href{http://www.gnu.org/licenses/gpl.html}{Gnu General Public License
version 3}. It is developed at the version 3}. It is developed at the
\href{\sitepappso}{PAPPSO} team (Plateforme d'Analyse Prot\'eomique de \href{\sitepappso}{PAPPSO} team (Plateforme d'Analyse Prot\'eomique de
Paris Sud-Ouest) by: Paris Sud-Ouest) by:
...@@ -217,7 +217,7 @@ Paris Sud-Ouest) by: ...@@ -217,7 +217,7 @@ Paris Sud-Ouest) by:
\end{description} \end{description}
This manual contains detailed information about the concepts and This manual contains detailed information about the concepts and
features of {\Mv}. It is intended to provide all the features of {\Mv}, called \emph{Longteeth Crocklet}. It is intended to provide all the
technical information needed for an advanced comprehension and use. technical information needed for an advanced comprehension and use.
In chapter \ref{intro} you will be introduced to the main features of In chapter \ref{intro} you will be introduced to the main features of
...@@ -277,7 +277,7 @@ format data. ...@@ -277,7 +277,7 @@ format data.
framework. Version $1.2$ is its latest public release. framework. Version $1.2$ is its latest public release.
{\M} comes as a stand-alone command-line program and {\M} comes as a stand-alone command-line program and
also with a library for integration in other softwares or proteomic also with a library for integration in other software or proteomic
pipelines. pipelines.
On the {\M} homepage (\href{\sitemasschroq}{\sitemasschroq}) On the {\M} homepage (\href{\sitemasschroq}{\sitemasschroq})
...@@ -310,6 +310,12 @@ peptide, and allows matching of previously missed peaks in some cases. ...@@ -310,6 +310,12 @@ peptide, and allows matching of previously missed peaks in some cases.
For more details on the post-matching mode and when to use it, see section For more details on the post-matching mode and when to use it, see section
\ref{peak_matching}. \ref{peak_matching}.
\textdbend The masschroqML schema has changed in {\Mv}: the current
schema version being $1.2$ (the same version number as
MassChroQ). Older masschroqML files stay functional with the new
schema, but new masschroqML files (containing the post matching
feature for example) will not work with older schema versions.
\section{{\M} features overview}\label{groups-sec} \section{{\M} features overview}\label{groups-sec}
{\M} has been designed to perform quantification on a wide range of {\M} has been designed to perform quantification on a wide range of
...@@ -328,7 +334,7 @@ To achieve this {\M} can combine and perform the following features : ...@@ -328,7 +334,7 @@ To achieve this {\M} can combine and perform the following features :
\item Alignment of samples within each group (two different alignment methods \item Alignment of samples within each group (two different alignment methods
are proposed). are proposed).
\item Extraction of the XIC-s (Extracted Ion Chromatogram) of the \item Extraction of the XICs (Extracted Ion Chromatogram) of the
predetermined items of interest. predetermined items of interest.
\item XIC filtering (several filters are provided for signal noise \item XIC filtering (several filters are provided for signal noise
removal, spike removal, signal smoothing, etc.). removal, spike removal, signal smoothing, etc.).
...@@ -362,7 +368,7 @@ the MS2 alignment method which uses MS level 2 retention times. ...@@ -362,7 +368,7 @@ the MS2 alignment method which uses MS level 2 retention times.
The quantification results in {\M} are The quantification results in {\M} are
summarized in a single file, sorted by group and sample, allowing summarized in a single file, sorted by group and sample, allowing
comparisons to be performed easily. Several results file formats are comparisons to be performed easily. Several results file formats are
available: gnumeric, TSV, xhtml and XML (masschroqML XML format). available: gnumeric, tsv, xhtml and xml (masschroqML xml format).
\section{Help} \section{Help}
...@@ -441,7 +447,7 @@ console. You will also have access to masschroq's manpage by typing ...@@ -441,7 +447,7 @@ console. You will also have access to masschroq's manpage by typing
\subsection{Windows platforms} \subsection{Windows platforms}
A win32 setup installer named \ttt{masschroq\_setup.exe} is available A win32 setup installer named \ttt{masschroq\_setup.exe} is available
for download. This setup installs {\M} in the chosen directory of for download. This setup installs {\M} in the chosen directory of
your system together with a set of example files that you can immediatly your system together with a set of example files that you can immediately
try by double-clicking on the masschroqML (MassChroQ input files) they try by double-clicking on the masschroqML (MassChroQ input files) they
contain. contain.
...@@ -612,7 +618,7 @@ temporary files in \ttt{DIRECTORY} instead of its current working directory. ...@@ -612,7 +618,7 @@ temporary files in \ttt{DIRECTORY} instead of its current working directory.
\textdbend The total size of temporary files produced during an \textdbend The total size of temporary files produced during an
analysis, is very close to the total size of the data analysis, is very close to the total size of the data
files (mzXML/mzML files) being analysed . Be careful when specifying files (mzXML/mzML files) being analyzed . Be careful when specifying
another working directory not to choose one that has size limitations. another working directory not to choose one that has size limitations.
\chapter{How {\M} works}\label{works-sec} \chapter{How {\M} works}\label{works-sec}
...@@ -654,16 +660,16 @@ these files and puts the information they contain in its input masschroqML ...@@ -654,16 +660,16 @@ these files and puts the information they contain in its input masschroqML
file. file.
Most of the identification tools (Mascot, X!Tandem, Phenyx) offer the Most of the identification tools (Mascot, X!Tandem, Phenyx) offer the
possibility to export identification results in TSV files. Our {\Xp} offers the possibility to export identification results in \ttt{tsv} files. Our {\Xp} offers the
possibility to directly export X!Tandem identification results in a possibility to directly export X!Tandem identification results in a
masschroqML input file (no parsing is necessary). masschroqML input file (no parsing is necessary).
\subsection{Identified isotopes} \subsection{Identified isotopes}
If isotopic labelling has been performed and the user needs to If isotopic labeling has been performed and the user needs to
quantify all the identified isotopes, he simply describes the quantify all the identified isotopes, he simply describes the
different isotopic labelings performed on the different data different isotopic labelings performed on the different data
being analysed in the masschroqML file. During analysis {\M} being analyzed in the masschroqML file. During analysis {\M}
automatically computes isotopic masses (using these descriptions) automatically computes isotopic masses (using these descriptions)
and quantifies the desired isotopes. and quantifies the desired isotopes.
...@@ -703,8 +709,8 @@ know and we will try to implement it sooner than scheduled. ...@@ -703,8 +709,8 @@ know and we will try to implement it sooner than scheduled.
technical similarities : for instance, in case of fractionation, samples of technical similarities : for instance, in case of fractionation, samples of
the same fraction will be grouped together in order to be aligned together, the same fraction will be grouped together in order to be aligned together,
or a group of samples obtained from an LTQ low resolution spectrometer or a group of samples obtained from an LTQ low resolution spectrometer
can be grouped together so that the appropriate xic extraction range can be grouped together so that the appropriate XIC extraction range
and xic filtering can be applied on them, etc. It is up to the user to and XIC filtering can be applied on them, etc. It is up to the user to
define the different groups of LC-MS runs in its analysis. define the different groups of LC-MS runs in its analysis.
Here are the main grouping possibilities that can be performed in Here are the main grouping possibilities that can be performed in
...@@ -771,7 +777,7 @@ But technically speaking, they also allow the following extra features in ...@@ -771,7 +777,7 @@ But technically speaking, they also allow the following extra features in
\begin{description} \begin{description}
\item[Efficient XIC extraction:] XICs for a given identified \item[Efficient XIC extraction:] XICs for a given identified
peptide will only be extracted in groups where the MS/MS allowed its peptide will only be extracted in groups where the MS/MS allowed its
identification, no unneccessary extractions will be performed. identification, no unnecessary extractions will be performed.
\item[Smart quantification:] peptides identified in at least one run of \item[Smart quantification:] peptides identified in at least one run of
the group, will be quantified in every run of this group, including the group, will be quantified in every run of this group, including
those where they have not been identified. See section those where they have not been identified. See section
...@@ -962,7 +968,7 @@ indeed a noisy pulsing spectrometer effect. ...@@ -962,7 +968,7 @@ indeed a noisy pulsing spectrometer effect.
\newpage \newpage
\begin{lstlisting}[style=algo, mathescape, caption = The Zivy peak \begin{lstlisting}[style=algo, mathescape, caption = The Zivy peak
detection] detection]
input: $X$ a Xic (i.e. a set of (retention time, intensity) values); input: $X$ a XIC (i.e. a set of (retention time, intensity) values);
$detection\_threshold\_on\_max$, $detection\_threshold\_on\_min$ : integers; $detection\_threshold\_on\_max$, $detection\_threshold\_on\_min$ : integers;
output: the set $\mathscr{P}$ of the detected peak positions on $X$ output: the set $\mathscr{P}$ of the detected peak positions on $X$
...@@ -973,7 +979,7 @@ compute $Max_{\mathscr{C}_X}$: the set of $(retention time, intensity)$ points ...@@ -973,7 +979,7 @@ compute $Max_{\mathscr{C}_X}$: the set of $(retention time, intensity)$ points
corresponding to the local maximum intensities on the close corresponding to the local maximum intensities on the close
$\mathscr{C}_X$ curve signal; $\mathscr{C}_X$ curve signal;
forall point $P$ in $Max_{\mathscr{C}_X}$ do forall point $P$ in $Max_{\mathscr{C}_X}$ do
let $P_{\mathscr{O}_X}$ be the point having the same coordiates that let $P_{\mathscr{O}_X}$ be the point having the same coordinates that
$P$ in the open curve signal $P$ in the open curve signal
if ( $intensity(P_{\mathscr{O}_X}) > detection\_threshold\_on\_min$ and if ( $intensity(P_{\mathscr{O}_X}) > detection\_threshold\_on\_min$ and
$intensity(P_{\mathscr{O}_X}) > detection\_threshold\_on\_max$ ) $intensity(P_{\mathscr{O}_X}) > detection\_threshold\_on\_max$ )
...@@ -1194,7 +1200,7 @@ generated by other external alignment tools. The user just puts the ...@@ -1194,7 +1200,7 @@ generated by other external alignment tools. The user just puts the
them and analyzes the runs with the aligned time values automatically. them and analyzes the runs with the aligned time values automatically.
\textdbend For this to work, the masschroqML input file should not \textdbend For this to work, the masschroqML input file should not
contain an alignment isntruction (the <align> tag in the masschroqML contain an alignment instruction (the <align> tag in the masschroqML
file) that concerns the runs whose .time file have file) that concerns the runs whose .time file have
been provided. Indeed, if an alignment instruction asks been provided. Indeed, if an alignment instruction asks
{\M} to align a sample whose \ttt{.time} file has been loaded before, he {\M} to align a sample whose \ttt{.time} file has been loaded before, he
...@@ -1207,7 +1213,7 @@ alignment files. ...@@ -1207,7 +1213,7 @@ alignment files.
The \ttt{.time} files mechanism can also be used to perform cascade The \ttt{.time} files mechanism can also be used to perform cascade
alignments. Let us take an example: suppose we have three LC-MS run alignments. Let us take an example: suppose we have three LC-MS run
files to analyse : files to analyze :
run1.mzXML, run2.mzXML and run3.mzXML. In a previous different {\M} analysis, we run1.mzXML, run2.mzXML and run3.mzXML. In a previous different {\M} analysis, we
have aligned run1.mzXML, we have a corresponding run1.time file have aligned run1.mzXML, we have a corresponding run1.time file
containing the aligned values of run1. In the current analysis we containing the aligned values of run1. In the current analysis we
...@@ -1322,7 +1328,7 @@ a new peak to this peptide, instead of trying to match the \emph{real\_or\_mean ...@@ -1322,7 +1328,7 @@ a new peak to this peptide, instead of trying to match the \emph{real\_or\_mean
this peptide, we could try to match the previously computed \emph{best this peptide, we could try to match the previously computed \emph{best
matched RT} of the peptide. But we could do even better! If we could matched RT} of the peptide. But we could do even better! If we could
have all the matched peaks of the peptide for a given group, we could have all the matched peaks of the peptide for a given group, we could
compute the mean of their \emph{best matched RTs} before tryig to compute the mean of their \emph{best matched RTs} before trying to
rematch the previously unmatched peaks. rematch the previously unmatched peaks.
That is what the post-matching mode does. The post-matching process is That is what the post-matching mode does. The post-matching process is
...@@ -1349,7 +1355,7 @@ performed as follows : ...@@ -1349,7 +1355,7 @@ performed as follows :
group, we try to rematch the unmatched peaks of this run to the group, we try to rematch the unmatched peaks of this run to the
\emph{best matched RT} of this peptide in the group. The \emph{best \emph{best matched RT} of this peptide in the group. The \emph{best
matched RT} of a peptide in a group is the mean value, over all the matched RT} of a peptide in a group is the mean value, over all the
msruns of the group, of the previously defined \emph{best matched RTs} of this peptide in runs of the group, of the previously defined \emph{best matched RTs} of this peptide in
each run of the group, if any. each run of the group, if any.
\end{itemize} \end{itemize}
...@@ -1374,7 +1380,7 @@ matching round. In the post-matching round, the peptide's retention ...@@ -1374,7 +1380,7 @@ matching round. In the post-matching round, the peptide's retention
time being computed by taking into account the retention time of the time being computed by taking into account the retention time of the
maximum intensity point of previously matched peaks, the chances to maximum intensity point of previously matched peaks, the chances to
match thin peaks are higher. But there is always a risk of peak match thin peaks are higher. But there is always a risk of peak
missassignments. misassignments.
According to numerous tests performed in our laboratory, the peak According to numerous tests performed in our laboratory, the peak
post-matching feature is interesting in cases of samples acquired in high post-matching feature is interesting in cases of samples acquired in high
resolution systems. Indeed, in these cases, the peaks are well defined resolution systems. Indeed, in these cases, the peaks are well defined
...@@ -1701,7 +1707,7 @@ quantification results. The format can be : ...@@ -1701,7 +1707,7 @@ quantification results. The format can be :
\item \ttt{gnumeric} : Gnome spreadsheet format to use with Gnumeric software; \item \ttt{gnumeric} : Gnome spreadsheet format to use with Gnumeric software;
\item \ttt{xhtmltable} : xhtml (eXtensible HyperText Markup Language) \item \ttt{xhtmltable} : xhtml (eXtensible HyperText Markup Language)
format; all the results are in an xhtml table and you can visualize format; all the results are in an xhtml table and you can visualize
them via an internet browser for example; them via an Internet browser for example;
\item \ttt{maschroqml} : masschroqML format, XML format, used as an \item \ttt{maschroqml} : masschroqML format, XML format, used as an
input but also output format to MassChroQ; it is intended for development use, input but also output format to MassChroQ; it is intended for development use,
for example to integrate masschroq results in databases. for example to integrate masschroq results in databases.
...@@ -2016,7 +2022,7 @@ These parameters depend on your spectrometer. ...@@ -2016,7 +2022,7 @@ These parameters depend on your spectrometer.
\item \textbf{half\_mediane (natural integer)}: half size of the \item \textbf{half\_mediane (natural integer)}: half size of the
moving window used to apply a median on the XIC intensity moving window used to apply a median on the XIC intensity
values. Usually a value of $5$ is sufficient, but depending on your values. Usually a value of $5$ is sufficient, but depending on your
spectrometer and the level of background noise intenisty it generates, it can be greater. spectrometer and the level of background noise intensity it generates, it can be greater.
\item \textbf{half\_min\_max (natural integer)}: half size of the \item \textbf{half\_min\_max (natural integer)}: half size of the
moving window used to apply an open transform (a min then a max) on the XIC moving window used to apply an open transform (a min then a max) on the XIC
intensities. This filter is sometimes useful in some LR signals intensities. This filter is sometimes useful in some LR signals
...@@ -2090,7 +2096,7 @@ These parameters depend on your spectrometer. ...@@ -2090,7 +2096,7 @@ These parameters depend on your spectrometer.
\subsection*{ The \emph{mode} parameter} \subsection*{ The \emph{mode} parameter}
The \emph{mode} parameter in the \emph{quantify} element indicates the The \emph{mode} parameter in the \emph{quantify} element indicates the
peak mathing mode and the computation mode of the retention time of peak matching mode and the computation mode of the retention time of
peptides and isotopes used to match these peptides to the detected peptides and isotopes used to match these peptides to the detected
peaks. For more details on peak matching see section peaks. For more details on peak matching see section
\ref{peak_matching}. It can be: \ref{peak_matching}. It can be:
......
...@@ -948,11 +948,11 @@ MasschroqmlParser::startElement_quantification_result(const QXmlAttributes &attr ...@@ -948,11 +948,11 @@ MasschroqmlParser::startElement_quantification_result(const QXmlAttributes &attr
else if (format == "tsv") { else if (format == "tsv") {
return startTsvResult(output_file); return startTsvResult(output_file);
} }
else if (format == "xml") { else if (format == "masschroqml") {
return startXmlResult(output_file, with_traces); return startXmlResult(output_file, with_traces);
} }
else { else {
_errorStr = QObject::tr("value '%1' of attribute format in quantification_result tag is not supported.\n Supported values are : gnumeric, tsv and xhtmltable."); _errorStr = QObject::tr("value '%1' of attribute format in quantification_result tag is not supported.\n Supported values are : gnumeric, tsv, xhtmltable and masschroqml.");
return false; return false;
} }
} }
......
...@@ -22,13 +22,13 @@ ...@@ -22,13 +22,13 @@
\newcommand{\sitepappso}{http://pappso.inra.fr/} \newcommand{\sitepappso}{http://pappso.inra.fr/}
\begin{document} \begin{document}
\title{\color{blue}\parbox[t]{\textwidth}{\centering MassChroQ \title{\color{blue}\parbox[t]{\textwidth}{\centering Readme file for \\
version 1.2 Readme file}} MassChroQ version 1.2 - \emph{Longteeth Crocklet}}}
\date{} \date{}
\maketitle \maketitle
Congratulations! MassChroQ version 1.2 is now installed on your Windows Congratulations! MassChroQ version 1.2, called \emph{Longteeeth Crocklet},
system. is now installed on your Windows system.
Your MassChroQ installation directory contains: Your MassChroQ installation directory contains:
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment