Biology Reference
In-Depth Information
Chapter 7
Analytical Bioinformatics
for Proteomics
Patricia M. Palagi and Frédérique Lisacek
1. Introduction
Proteomics was originally defined as the combination of protein separa-
tion techniques, such as two-dimensional gel electrophoresis (2-DE) or
liquid chromatography (LC), with mass spectrometry (MS). Analysis of
these experimental data encompasses the identification and quantification
of proteins, as well as the determination of their localization, modifications,
interactions, activities, and, ultimately, function. Proteomes — complete
sets of proteins expressed by a genome, cell, tissue, or organism — are now
routinely compared under different conditions (time, temperature, pH,
pathological conditions, etc.). This comparison is both qualitative and
quantitative, and it depends heavily on computers.
The Proteome Informatics Group (PIG) at the Swiss Institute of
Bioinformatics (SIB) focuses its activities on the development of software
tools and databases for proteomics, and targets research projects in three
domains: proteome imaging, protein identification and characterization
with MS data, and proteomics knowledge integration and databases.
As shown in Fig. 1, these domains are chronologically integrated in the
proteomics workflow. Some of the derived projects have been ongoing
since 1984, long before the SIB was created in 1998. The state of the art
of the three topics is detailed in this chapter, whilst the contributions of
the PIG are highlighted.
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