Commit c014b9bc authored by Olivier Langella's avatar Olivier Langella
Browse files

documentation : example file

parent 363a2a00
......@@ -32,18 +32,25 @@
<peptide_list>
<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1"
seq="TCVADESHAGCEK">
<modifications><!-- this tag is optional but gives an exact mass computation -->
<psimod at="2" acc="MOD:00397"></psimod>
<psimod at="11" acc="MOD:00397"></psimod>
</modifications>
<observed_in data="samp0" scan="655" z="2" />
<observed_in data="samp1" scan="798" z="2" />
</peptide>
<peptide id="pep1" mh="1103.461" mods="57.04" prot_ids="P1.1"
seq="ADESHAGCEK">
<modifications><!-- this tag is optional but gives an exact mass computation -->
<psimod at="8" acc="MOD:00397"></psimod>
</modifications>
<observed_in data="samp3" scan="663" z="2" />
</peptide>
</peptide_list>
<isotope_label_list>
<isotope_label id="iso1">
<mod at="Nter" value="28.0" />
<mod at="K" value="28.0" />
<mod at="Nter" value="28.0" acc="MOD:00429"/>
<mod at="K" value="28.0" acc="MOD:00429"/>
</isotope_label>
<isotope_label id="iso2">
<mod at="Nter" value="32.0" />
......
......@@ -22,17 +22,24 @@
</protein_list>
<peptide_list>
<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1" seq="TCVADESHAGCEK">
<modifications><!-- this tag is optional but gives an exact mass computation -->
<psimod at="2" acc="MOD:00397"></psimod>
<psimod at="11" acc="MOD:00397"></psimod>
</modifications>
<observed_in data="samp0" scan="655" z="2"/>
<observed_in data="samp1" scan="798" z="2"/>
</peptide>
<peptide id="pep1" mh="1103.461" mods="57.04" prot_ids="P1.1" seq="ADESHAGCEK">
<modifications><!-- this tag is optional but gives an exact mass computation -->
<psimod at="8" acc="MOD:00397"></psimod>
</modifications>
<observed_in data="samp3" scan="663" z="2"/>
</peptide>
</peptide_list>
<isotope_label_list>
<isotope_label id="iso1">
<mod at="Nter" value="28.0"/>
<mod at="K" value="28.0"/>
<mod at="Nter" value="28.0" acc="MOD:00429"/>
<mod at="K" value="28.0" acc="MOD:00429"/>
</isotope_label>
<isotope_label id="iso2">
<mod at="Nter" value="32.0"/>
......
......@@ -1517,7 +1517,7 @@ masschroqML file.
\section{Identified peptides and proteins }
Once it has parsed the given peptide identification files, {\mcq}
automatically puts the results in the following form :
\mylst{19}{31}
\mylst{19}{38}
It creates two blocks :
\bi
\item the \ttt{protein\_list} block containing the description of
......@@ -1562,7 +1562,7 @@ The peptide and protein list blocks are not mandatory in a masschroqML file.
\section{Isotope labels}\label{iso-labels}
The \ttt{isotope\_label\_list} block contains the list of the
isotopic labels performed on the data being analyzed if any.
\mylst{32}{41}
\mylst{39}{48}
\bi
\item The \ttt{id} attribute uniquely identifies an isotope label
(mandatory).
......@@ -1597,7 +1597,7 @@ file.
\newpage
\section{Alignments} \label{alignment_files}
\mylst{42}{61}
\mylst{50}{69}
In the \ttt{alignments} block we define the different alignment methods
that we will use to align our different groups of data. In this
example we have defined two alignment methods:
......@@ -1638,7 +1638,7 @@ file.
In the \ttt{quantification\_methods} block we define the different
quantification methods we will use in this analysis.
\mylst{62}{81}
\mylst{70}{89}
As we can see in the lines above, a quantification method consists in a
XIC extraction method, XIC filters and a peak detection method.
......@@ -1666,7 +1666,7 @@ background noise removal filter and a smoothing moving-window filter;
In the next lines of our example file :
\mylst{82}{97}
\mylst{90}{105}
we define the \ttt{my\_qmoulon}
quantification method which extracts XICs based on
the max intensity, using a ppm (parts per million) range of $10 -
......@@ -1685,7 +1685,7 @@ rt)$ values) and the quantification methods to be used.
\subsection{Quantifying peptides}
\mylst{116}{118}
\mylst{124}{126}
As we can see in the lines above, we have chosen to:
\bi
......@@ -1722,7 +1722,7 @@ other unmatched peaks. For details on this method see section
\newpage
\subsection{Quantifying isotopes}
\mylst{119}{120}
\mylst{127}{128}
As you can see above, to quantify isotopes it suffices to add the
attribute \ttt{isotope\_label\_refs} containing the references to the
......@@ -1734,14 +1734,14 @@ quantification.
The list of the desired m/z values to be quantified can be given as
follows:
\mylst{119}{121}
\mylst{127}{129}
\subsection{Quantifying \texorpdfstring{$(m/z, rt)$}{(m/z, rt)} values}
The list of the desired $(m/z, rt)$ values to be quantified can be given as
follows:
\mylst{119}{126}
\mylst{127}{134}
......@@ -1751,7 +1751,7 @@ follows:
\subsection*{Quantification result files}
\mylst{98}{104}
\mylst{106}{112}
In the \ttt{quantification\_results} block we define the
format and name of the files that will contain the final
quantification results. The format can be :
......@@ -1818,7 +1818,7 @@ its results via \ttt{.time} files in masschroq's analysis.
You can tell {\mcq} to produce detailed quantification traces in the
following way :
\mylst{105}{115}
\mylst{113}{123}
Three types of traces can be produced :
\bi
\item \ttt{peptide\_traces} : traces for a given list of space separated
......
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