Biology Reference
In-Depth Information
Chapter 1
Proteomic Analysis of Cellular Systems
Marco Y. Hein, Kirti Sharma, J ยจ rgen Cox and Matthias Mann
Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
Chapter Outline
Introduction
3
Large-Scale Determination of Post-Translational
Modifications
MS-Based Proteomics Workflow
4
15
Computational Proteomics
7
Outlook and Future Challenges
18
Deep Expression Proteomics
11
References
19
Interaction Proteomics
13
INTRODUCTION
A prerequisite for a system-wide understanding of cellular
processes is a precise knowledge of the principal actors
involved, which are biomolecules such as oligonucleotides,
proteins, carbohydrates and small molecules. Ever more
sophisticated methods to measure the identity and amount
of such biomolecules were an integral component of most
of the biological breakthroughs of the last century. At the
level of the genome, DNA sequencing technology can now
give us a complete inventory of the basic set of genetic
instructions of any organism of interest. Furthermore,
recent breakthroughs in next-generation sequencing are
promising to allow large-scale comparison of the genomes
of individuals. However, genomic sequences and their
variations between individuals are completely unin-
terpretable without knowledge of the encoded genes as well
as the biological processes in which they are involved.
Therefore, the growing ability to obtain genetic data
provides an increasing need and impetus to study the
functions of gene products individually (classic molecular
biology) and at a large scale (systems biology). The first
such system-wide studies were performed at the level of
mRNA ('transcriptomics'). They enable an unbiased and
increasingly comprehensive view of which parts of the
genome are actually expressed in a given situation. Tran-
scriptomics also revealed that the relationship between the
genomic coding sequences and their corresponding RNA
molecules can be exceedingly complex. However, in terms
of cellular function, the transcriptome still represents only
a middle layer of information transmission, with no or little
function of its own. The actual 'executives' of the cell are
the proteins, which perform myriad roles, from orches-
trating gene expression to catalyzing chemical reactions,
directing the information flow of the cell and performing
structural roles in cells and organisms. This crucial role of
proteins is also underlined by the fact that diseases always
involve malfunctioning proteins, and that drugs are almost
invariably directed against proteins or modify their
expression levels.
Unfortunately, given the central importance of proteins,
until recently there were no methods of protein measure-
ment that were comparable to the powerful sequencing,
hybridization or amplification-based methods to charac-
terize oligonucleotides. This is finally beginning to change
owing to the introduction of mass spectrometry, first in
protein science and later for the large-scale study of
proteins, a field called mass spectrometry (MS)-based
proteomics
[1]
.
The proteome of a cell designates the totality of all
expressed proteins in a given biological situation, and is
therefore a dynamic entity. It encompasses not only the
identity and amount of all proteins but also their state of
modification, their turnover, location in the cell, interaction
partners and
their structures and
functions. Clearly, the proteome of the cell is the most
complex and functionally most relevant level of cellular
regulation and function.
Accordingly, in systems biology it is usually the pro-
teome that is the object of modeling. Typically only very
small subsets of all proteins
by some definitions
e
e
those participating in
e
a defined function of interest
are included in these
models. Even then, reliable and relevant information on
e
