Commit 69ced454 authored by Filippo Rusconi's avatar Filippo Rusconi
Browse files

Add new file for stuff not ready but that I want to advance.

parent aacd8228
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE chapter [
<!ENTITY % entities SYSTEM "pappso-user-manuals.ent">
%entities;
<!ENTITY % xtpcpp-entities SYSTEM "xtpcpp-entities.ent">
%xtpcpp-entities;
<!ENTITY % sgml.features "IGNORE">
<!ENTITY % xml.features "INCLUDE">
<!ENTITY % dbcent PUBLIC "-//OASIS//ENTITIES DocBook Character Entities V4.5//EN" "/usr/share/xml/docbook/schema/dtd/4.5/dbcentx.mod">
%dbcent;
]>
<chapter xmlns="http://docbook.org/ns/docbook"
xmlns:xlink="http://www.w3.org/1999/xlink"
xml:id="chap_stuff-awaiting-inclusion" version="5.0">
<info>
<title>Stuff awaiting inclusion </title>
</info>
<para>
<itemizedlist>
<listitem>
<para>
<guilabel>Checked</guilabel>: If checked, then the peptide is accounted
for in the grouping process;
</para>
</listitem>
<listitem>
<para>
<guilabel>Group</guilabel>: Identity of the group that the current
peptide belongs to;
</para>
</listitem>
<listitem>
<para>
<guilabel>Accession</guilabel>: Unambiguous identification of the
protein identified through the current peptide. This identification
comes from the protein database files;
</para>
</listitem>
<listitem>
<para>
<guilabel>Description</guilabel>: Description of the protein in the
protein database file.
</para>
</listitem>
<listitem>
<para>
<guilabel>log(E-value)</guilabel>&thinsp;:
</para>
</listitem>
<listitem>
<para>
<guilabel>E-value</guilabel>: Expectation value of the current peptide
that is computed like so: .
</para>
</listitem>
<listitem>
<para>
<guilabel>Spectra</guilabel>: Number of spectra that contain
</para>
</listitem>
<listitem>
<para>
<guilabel>Specific spectra</guilabel>: Number of spectra that contain
</para>
</listitem>
<listitem>
<para>
<guilabel>Sequences</guilabel>:
</para>
</listitem>
<listitem>
<para>
<guilabel>Specific sequences</guilabel>:
</para>
</listitem>
<listitem>
<para>
<guilabel>Coverage</guilabel>:
</para>
</listitem>
<listitem>
<para>
<guilabel>MW</guilabel>:
</para>
</listitem>
<listitem>
<para>
PAI: <quote>Protein abundance index</quote>. This index was defined as the
<quote>number of peptides identified divided by the number of
theoretically observable tryptic peptides</quote>. See <link
xlink:href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC186633/"/>.
</para>
</listitem>
<listitem>
<para>
emPAI: <quote>Exponentially modified protein abundance index</quote>. This
index was defined as
emPAI = 10<superscript>PAI</superscript>&nbsp;&nbsp;1. See <link
xlink:href="https://pubmed.ncbi.nlm.nih.gov/15958392/"/>.
</para>
</listitem>
</itemizedlist>
</para>
</chapter>
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