Biology Reference
In-Depth Information
CHAPTER
systems biology approaches
3
Andreas Otto
*
,J¨ rg Bernhardt
*
, Michael Hecker
*
, Uwe V ¨ lker
{
,D¨ rte Becher
*
,1
⁎
Ernst-Moritz-Arndt-University Greifswald, Institute for Microbiology, Greifswald, Germany
{
Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute for Genetics
and Functional Genomics, Greifswald, Germany
1
Corresponding author. e-mail address: dbecher@uni-greifswald.de
Proteomics: From relative to
absolute quantification for
Abbreviations
2DE
two-dimensional gel electrophoresis
LC-MS/MS
liquid chromatography coupled with tandem mass spectrometry
PTM
post-translational modification
SRM
selected reaction monitoring
1
INTRODUCTION
1.1
'Omics' techniques in systems biology approaches
In systems biology, the generation of large-scale interdependent data requires the
performance of 'omics' type studies (
Ideker
et al.
, 2001
). Genome, transcriptome,
proteome and metabolome level data are combined to provide a comprehensive
set of descriptive data for the biological system under investigation (
Kitano,
2002
). Even though each individual 'omics' level data reveals unique information
and targets different levels of biological regulation, the analysis of the proteome
leads to particularly valuable information due to the nature of proteins as the effec-
tors of cellular metabolism and structural determinants throughout all kingdoms of
life (
Chuang
et al.
, 2010
). Modern proteomics approaches can be grouped into
two different workflows addressing the analysis of complex proteome data, namely,
gel-based and gel-free proteomics techniques.
1.2
Gel-based proteomics
Gel-based studies rely on two-dimensional gel electrophoresis (2DE) for the resolu-
tion of complex protein mixtures according to the
p
I and molecular weight (MW) of
the individual proteins in a sample (
Neidhardt, 2011
). A major asset of gel-based
proteomics is the analysis of intact protein species providing direct access to
