Commit 48be5a75 authored by Filippo Rusconi's avatar Filippo Rusconi
Browse files

Another progress.

parent cbeb36e8
......@@ -228,7 +228,7 @@ xml:id="chap_main-program-window" version="5.0">
<para>
<guilabel>Run X!Tandem identifications</guilabel>. See <xref
linkend="chap_running-xtandem-identifications"/>.
linkend="sec_running-xtandem-identifications"/>.
</para>
......@@ -240,7 +240,7 @@ xml:id="chap_main-program-window" version="5.0">
<guilabel>Load identification results (mzIdentML, pepXML,
X!Tandem)</guilabel>. See <xref
linkend="chap_loading-identification-results"/>.
linkend="sec_loading-identification-results"/>.
</para>
......@@ -614,7 +614,9 @@ xml:id="chap_main-program-window" version="5.0">
linkend="fig_xtpcpp-main-program-window"/>). From there, it is possible to
open the &xtandem; results file located in the output directory configured
above. There are as many output files (XML-based format, and xml
extension) as there were mass spectrometry data files to process.
extension) as there were mass spectrometry data files to process. The
loading of the results files is described in <xref
linkend="sec_loading-identification-results"/>.
</para>
......@@ -622,5 +624,51 @@ xml:id="chap_main-program-window" version="5.0">
</sect1>
<sect1 xml:id="sec_loading-identification-results">
<title>Loading identification results</title>
<para>
The loading of identification results comes with a minimal set of
configuration required to instruct &xtpcpp; on the way to handle contaminant
proteins, for example. This process is pictured in <xref
linkend="fig_xtpcpp-load-identification-results-window"/> and described in this
section.
</para>
<figure xml:id="fig_xtpcpp-load-identification-results-window">
<title>&xtandem; presets configuration window</title>
<mediaobject>
<imageobject role="fo">
<imagedata fileref="print-xtpcpp-load-identification-results-window.png" format="PNG" scale="80"/>
</imageobject>
<imageobject role="html">
<imagedata fileref="web-xtpcpp-load-identification-results-window.png" format="PNG" scale="100"/>
</imageobject>
<caption>
<para>
Loading identification results comes with some configuration that is
described in the text.
</para>
</caption>
</mediaobject>
</figure>
</sect1>
</chapter>
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