Biology Reference
In-Depth Information
proteomics so far published belong to the three fi rst categories,
being carried out with model experimental systems whose genome
has been sequenced, and that is well annotated or with a good
number of genomic or ESTs sequences available, with Arabidopsis
truncatula
(
see
Chapter
22
)
, and soybean (
see
Chapters
23
and
37
)
being in the top ranking group. In this regard, proteomics of
orphan and unsequenced organisms remains one of the main chal-
lenges in proteomics (
see
Chapters
24
and
39
)
. The interest in the
proteome analysis of the unicellular plant algae has just emerged,
as they offer the possibility of using single-celled photosynthetic
eukaryotes to address biological questions, together with their
potential as a source of biofuels [
5
]. Proteomics as an analytical
tool can be used for practical purposes, in areas such as food trace-
ability, substantial equivalence in transgenic, allergens and proteo-
typing, as the most representative examples (
see
Chapters
49
-
52
)
.
During the 1990s and early 2000s, proteomics generated a
great expectation. In this sense, B. Marte stated in the March 13th,
2003, Nature insight issue on Proteomics [
6
],
We are just beginning to appreciate the power and limitations of the
genomics revolution, yet hard on its heels proteomics promises an even
more radical transformation of biological research.
By 2013, 10 years later, we should realize and admit that the
reality is quite far from the original expectations. The results gained
over the last 15 years have shown that the dynamism, variability, and
behavior of proteins are more complex than what was thought. This
is concluded considering the number of protein species per gene as
a result of alternative splicing, reading frame, and posttranslational
modifi cations, traffi cking, turnover, and interactions (protein com-
plexes, rather than individual proteins, are the functional units of the
biological machines) [
7
]. Proteins, if compared to nucleic acids, are
molecular entities of the greatest diffi culty to work with. Indeed,
they are much more diverse in physicochemical properties, greater in
number, have a higher dynamic range and, if not enough, there is no
PCR for them. As proteins are the major functional component of
cells, knowledge of their cellular localization and turnover is crucial
to gain an understanding of the biology of multicellular organisms [
8
].
Because of the reasons mentioned above, it is almost impossible to
capture an important fraction of the whole proteome in just a single
experiment. For this reason, it is absolutely necessary to fractionate
the whole proteome at the subcellular or protein level, in order to
study subcellular proteomes or specifi c groups of physicochemical or
functional proteins. It is clear that there is no universal protocol or
recipe in proteomics, being necessary to optimize the methods to
the experimental system and objectives of the research. Each specifi c
protocol and its variants lead us to a specifi c fraction of the star fi r-
mament which is the complete proteome.
