Biology Reference
In-Depth Information
Proteomics is making important contributions to the biologi-
cal knowledge of plants, despite its diffi culties and limitations, as it
has an enormous applicability to translational research [
9
].
Moreover, although it is usually not considered, plant systems may
represent an invaluable tool for our efforts to understand molecu-
lar mechanisms in human diseases. Although Arabidopsis and
humans diverged 1.6 billion years ago, recent studies have demon-
strated a remarkable conservation of protein function and cellular
processes between these two distant species [
10
].
On the long and dark way between genotype and phenotype,
proteins are closest to the last, so the information provided goes
beyond the possibilities of genomic studies. In addition, there are
aspects of cell research that can only be approached by proteomics,
such as posttranslational modifi cations and protein interactions. In
these two areas, proteomics is on the frontier of knowledge, and
here is where proteomics can make important contributions.
Unfortunately, works within this category on plant proteomics are
more the exception than the rule. It can be stated that up to now
most of the proteomics works published is descriptive and there-
fore speculative from a biological perspective. We can only get a
deeper, realistic view of the cell molecular biology by validating our
proteomics data with other techniques together with complemen-
tary classical and -omics approaches, in the direction of modern
System Biology (
see
Chapter
2
)
. Proteomics will grow in parallel
with other areas, nourishing and being nourished by them. The
integration of genotyping, pheno/morphotyping and the analysis
of the molecular phenotype using metabolomics, proteomics and
transcriptomics will reveal a novel understanding of plant biology
and its interaction with the environment [
11
].
This introductory chapter does not aim to deepen the numer-
ous studies on plant biological processes approached by pro-
teomics, from growth and development, to responses to the
environment, as it has been periodically reviewed by us and others
[
12
-
22
]. Instead, and in agreement with the focus of this topic, it
is intended to summarize from a methodological point of view the
state of the art in plant proteomics, focusing on mass spectrometry-
based strategies. This chapter is mainly directed at beginners or at
those trying to get into the fi eld, rather than at those with real
experience or a long trajectory in plant proteomics research.
2
Methodologies and Workfl ows
In the broadest sense, and from a methodological point of view,
proteomics includes techniques utilized in the study of proteins
and peptides, from structure to location and function, either in
vivo, in vitro or
in silico
experiments, and whether the protein or
peptide samples are extracted from living organisms (intracellular,
