Biology Reference
In-Depth Information
Chapter 2
From Proteomics to Systems Biology: MAPA, MASS
WESTERN, PROMEX, and COVAIN as a User-Oriented
Platform
Wolfram Weckwerth , Stefanie Wienkoop , Wolfgang Hoehenwarter,
Volker Egelhofer , and Xiaoliang Sun
Abstract
Genome sequencing and systems biology are revolutionizing life sciences. Proteomics emerged as a funda-
mental technique of this novel research area as it is the basis for gene function analysis and modeling of
dynamic protein networks. Here a complete proteomics platform suited for functional genomics and sys-
tems biology is presented. The strategy includes MAPA (mass accuracy precursor alignment;
http://www.
univie.ac.at/mosys/software.html
) as a rapid exploratory analysis step; MASS WESTERN for targeted
proteomics; COVAIN (
http://www.univie.ac.at/mosys/software.html
) for multivariate statistical analy-
sis, data integration, and data mining; and PROMEX (
http://www.univie.ac.at/mosys/databases.html
)
as a database module for proteogenomics and proteotypic peptides for targeted analysis. Moreover, the
presented platform can also be utilized to integrate metabolomics and transcriptomics data for the analysis
of metabolite-protein-transcript correlations and time course analysis using COVAIN. Examples for the
integration of MAPA and MASS WESTERN data, proteogenomic and metabolic modeling approaches for
functional genomics, phosphoproteomics by integration of MOAC (metal-oxide affi nity chromatography)
with MAPA, and the integration of metabolomics, transcriptomics, proteomics, and physiological data
using this platform are presented. All software and step-by-step tutorials for data processing and data min-
ing can be downloaded from
http://www.univie.ac.at/mosys/software.html
.
Key words
MAPA, MOAC, COVAIN, PROMEX, MASS WESTERN
1
Introduction
Proteins are the active part of life, and life is centered on proteins.
They perform and control all processes from gene regulation to
physiology leading to a balance of a thermodynamically open and
susceptible system. Eventually the system collapses and imbalance
leads to death. Even this process is controlled by proteins involved
in programmed cell death (PCD). As a consequence of the discov-
ery of the chemical-physical principles of life in the middle of the
