Biology Reference
In-Depth Information
extracellular fl uids) as products of in vitro synthesis from mRNA or
being chemically synthesized.
Proteomics comprises well-established methods of classical
protein chemistry/biochemistry used before the term “proteome”
was coined, including techniques for protein extraction, purifi ca-
tion (gel electrophoresis and liquid chromatography-based meth-
ods), labeling, identifi cation (Western blot), and sequencing
(EDMAN sequencing). Nonetheless, it is true that these methods
are being continuously improved, but also need to be improved
and optimized for different experimental systems, as well as for the
objectives of the research (descriptive, comparative, PTMs, inter-
actions) Although EDMAN sequencing is still valid, its use has
decreased dramatically [
23
], as it cannot be used in a high through-
put way. Western blot can also be useful since it can increase the
confi dent identifi cation of candidate proteins or PTMs [
24
].
Mass spectrometry is the analytical method that defi nes pro-
teomics, and differentiates it from classical protein biochemistry,
being in the core of this approach. It allows the identifi cation and
quantifi cation from hundreds to thousands proteins in a single
experiment. Advances in proteomics and its applicability to all areas
of the life sciences are continuously driven by the introduction of
new mass spectrometric tools with improved performances (
see
Chapter
6
)
[
25
]. The ability of the new instrumentation to pro-
duce huge volumes of data has emphasized the need for adequate
data analysis tools, which are nowadays often considered the main
bottleneck for proteomics development [
26
], together with the
availability of well-annotated protein sequence databases or mass
spectra atlas. Large volumes of proteomic data have been accumu-
lated in recent years, as with genomic data. These proteomic data
have been integrated and organized in databases that enable us to
retrieve, leverage and share public data through up-to-date com-
putational technology, such as the latest data management systems
and Web-interface techniques (
see
Chapter
3
)
.
Most of the works published on plant proteomics, and pre-
sented here in the different chapters, belongs to the group of in
vitro analysis of cell extracts or extracellular fl uids (
see
, as an exam-
ple, Chapters
28
,
29
,
38
,
39
)
, with the aim of identifying, quanti-
fying, and characterizing protein species present in a biological
unit (cellular compartment, cell, tissue, organ, individual, geno-
type, population, ecosystem) in specifi c time-space coordinates
(development and growth) and with specifi c external factors
(responses to the environment). The exception to this generality is
the new mass spectrometry imaging technique (
see
Chapter
17
)
,
where the spatial distribution of metabolites and proteins can be
deciphered. In this methodology, tissue sections—instead of a pro-
tein/peptide preparation—are subjected to MS, MALDI-TOF
analysis. Other in vitro techniques, such as those of the so-called
wide genomics approaches, are less represented in the plant
proteomics literature, and tend to not be considered sensu strictus
