Commit 2d057c3d authored by Rusconi Filippo's avatar Rusconi Filippo
Browse files

New upstream version 0.4.43

parent f7940424
message("UNIX non APPLE environment")
message("Please run the configuration like this:")
message("cmake -G \"Unix Makefiles\" -DCMAKE_BUILD_TYPE=Debug ../development")
message("Please run the configuration like this (remove unwanted features):")
message("cmake -G \"Unix Makefiles\" -DCMAKE_BUILD_TYPE=Debug -DBUILD_USER_MANUAL=1 ../development")
set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES /usr/include)
set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES /usr/include)
......
......@@ -39,5 +39,5 @@ STYLEROOT="xslt"
#PROFOS=""
#PROFVENDOR=""
FOP_CMD_OPTIONS="-c /home/langella/developpement/git/xtandempipeline/doc/user-manual/fop.xconf"
FOP_CMD_OPTIONS="-c /home/rusconi/devel/xtpcpp/development/doc/user-manual/fop.xconf"
......@@ -1300,106 +1300,104 @@ xml:id="chap_exploring_identification_data" version="5.0">
</para>
<sect2 xml:id="sect_presets-for-phospho-proteomics">
<!--<sect2 xml:id="sect_presets-for-phospho-proteomics">-->
<title>Configuring &xtandem; for phospho-proteomics</title>
<!--<title>Configuring &xtandem; for phospho-proteomics</title>-->
<para>
<!--<para>-->
The configuration of &xtandem; needs to be performed by using the presets
method, described in <xref linkend="sec_xtandem-parameter-presets"/> and
following sections.
<!--The configuration of &xtandem; needs to be performed by using the presets-->
<!--method, described in <xref linkend="sec_xtandem-parameter-presets"/> and-->
<!--following sections.-->
</para>
<!--</para>-->
<figure xml:id="fig_xtpcpp-x-tandem-presets-phosphoproteomics-residue-tab">
<!--<figure xml:id="fig_xtpcpp-x-tandem-presets-phosphoproteomics-residue-tab">-->
<title>Setting the &xtandem; parameters in phosphoproteomics projects</title>
<!--<title>Setting the &xtandem; parameters in phosphoproteomics projects</title>-->
<mediaobject>
<!--<mediaobject>-->
<imageobject role="fo">
<!--<imageobject role="fo">-->
<imagedata fileref="print-xtpcpp-x-tandem-presets-phosphoproteomics-residue-tab.png"
format="PNG" scale="100"/>
<!--<imagedata fileref="print-xtpcpp-x-tandem-presets-phosphoproteomics-residue-tab.png" -->
<!--format="PNG" scale="100"/>-->
</imageobject>
<!--</imageobject>-->
<imageobject role="html">
<!--<imageobject role="html">-->
<imagedata fileref="web-xtpcpp-x-tandem-presets-phosphoproteomics-residue-tab.png"
format="PNG" scale="80"/>
<!--<imagedata fileref="web-xtpcpp-x-tandem-presets-phosphoproteomics-residue-tab.png" -->
<!--format="PNG" scale="80"/>-->
</imageobject>
<!--</imageobject>-->
<caption>
<!--<caption>-->
<para>
<!--<para>-->
Setting the &xtandem; parameters for phosphoproteomics analyses
involves specifying the mass difference between unmodified and
modified residues and the nature of the residue that might bear
the modification. In the figure, potential modifications are a
phosphoryl group attached to a tyrosine (Y) residue, and also
the loss of a phosphoric acid molecule on either serine (S) or
threonine (T) residues.
<!--Setting the &xtandem; parameters for phosphoproteomics analyses-->
<!--involves specifying the mass difference between unmodified and-->
<!--modified residues and the nature of the residue that might bear-->
<!--the modification. In the figure, potential modifications are a-->
<!--phosphoryl group attached to a tyrosine (Y) residue, and also-->
<!--the loss of a phosphoric acid molecule on either serine (S) or-->
<!--threonine (T) residues. -->
</para>
<!--</para>-->
</caption>
<!--</caption>-->
</mediaobject>
<!--</mediaobject>-->
</figure>
<!--</figure>-->
<tip>
<!--<tip>-->
<para>
<!--<para>-->
The loss of a phosphoric acid molecule <emphasis>(not ion)</emphasis> is
called a <quote>neutral loss</quote>. By essence that molecule cannot be
detected, being uncharged. However, the search software may detect that
there might be a negative mass delta between calculated fragments
bearing a phoshoryl group and the measured mass of product ions. In this
eventuality, the software may deduce that the fragment was
phosphorylated before the fragmentation occurred.
<!--The loss of a phosphoric acid molecule <emphasis>(not ion)</emphasis> is-->
<!--called a <quote>neutral loss</quote>. By essence that molecule cannot be-->
<!--detected, being uncharged. However, the search software may detect that-->
<!--there might be a negative mass delta between calculated fragments-->
<!--bearing a phoshoryl group and the measured mass of product ions. In this-->
<!--eventuality, the software may deduce that the fragment was-->
<!--phosphorylated before the fragmentation occurred.-->
</para>
<!--</para>-->
</tip>
<!--</tip>-->
<para>
<!--<para>-->
The
</para>
<!--The -->
<!--</para>-->
<para>
<!--<para>-->
The mass spectrometer might be configured to monitor neutral phosphoric acid
loss, or not. In some instruments, that workflow is not available; however,
in these instruments a higher energy collisional
dissociation<footnote><para> In Orbitrap analyzer-based instrument, HCD
stands for <quote>higher-energy C-trap dissociation</quote>. However, a more
generic term is oft-used: <quote>higher energy collisional
dissociation</quote>.</para></footnote> process elicits two fragmentation
events: loss of a phosphoric acid molecule and peptide backbone
dissociation. In this case, the database searching engine (&xtandem;, for
us) is instructed to monitor the loss of phosphoric acid (that is, a neutral
loss) on the product ions of the y ion series. In the best cases (best
sequence coverage by the product ions), it is thus possible to locate the
phosphoryl group on the peptide.
<!--The mass spectrometer might be configured to monitor neutral phosphoric acid-->
<!--loss, or not. In some instruments, that workflow is not available; however,-->
<!--in these instruments a higher energy collisional-->
<!--dissociation<footnote><para> In Orbitrap analyzer-based instrument, HCD-->
<!--stands for <quote>higher-energy C-trap dissociation</quote>. However, a more-->
<!--generic term is oft-used: <quote>higher energy collisional-->
<!--dissociation</quote>.</para></footnote> process elicits two fragmentation-->
<!--events: loss of a phosphoric acid molecule and peptide backbone-->
<!--dissociation. In this case, the database searching engine (&xtandem;, for-->
<!--us) is instructed to monitor the loss of phosphoric acid (that is, a neutral-->
<!--loss) on the product ions of the y ion series. In the best cases (best-->
<!--sequence coverage by the product ions), it is thus possible to locate the-->
<!--phosphoryl group on the peptide.-->
</para>
<!--</para>-->
</sect2>
<!--</sect2>-->
</sect1>
</chapter>
<!ENTITY VERSION "0.4.42">
<!ENTITY VERSION "0.4.43">
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