Biology Reference
In-Depth Information
robustness of the technique made a quantum leap that is still
enjoyed today. Moreover, this parallelization of the technique is
also a very strong advantage when multiple comparisons, and not
only binary ones, must be performed [
27
].
3
Effi ciency of 2D Gel-Based Proteomics
Nowadays, Edman sequencing for protein identifi cation has been
almost completely replaced by mass spectrometry-based protein
identifi cation, which is much more sensitive and much faster.
However, mass spectrometers are expensive and delicate instru-
ments, and the machine time is often considered as precious.
In this frame, shotgun proteomic techniques often represent
a waste of machine time. In many comparative experiments,
which represent most of the proteomic experiments, most of the
proteins do not change between the various conditions tested.
Thus, the mass spectrometer is analyzing again and again a very
high number of peptides from proteins that have no interest in
the biological question studied.
Oppositely, 2D gel-based proteomics makes an optimal use of
mass spectrometer time, because most of what is carried out within
the mass spectrometer in shotgun proteomics is carried out upfront
at the 2D gel stage in 2D gel-based proteomics. In fact, the mod-
ern gel staining techniques [
28
-
30
], allow to perform a sensitive
and linear detection of the protein spots on the gels. Then, image
analysis [
31
,
32
] coupled with statistical analysis [
33
], allow to per-
form a quantitative analysis of all protein spots and to determine
which spots are worth identifying. These spots are then the only
ones that need to be processed by the mass spectrometer.
When fi nancial resources are scarce, which is often the case in
academic research, this allows to build a “hub and spokes” model,
where a central hub hosting the mass spectrometry platform is able
to serve very effi ciently several biology-oriented laboratories, each
using 2D gel electrophoresis and image analysis to select the rele-
vant proteins within their respective research projects.
With plant proteomics usually less funded than medicine-
oriented proteomics, and this situation even harder for the pro-
teomics of traditional crops, this effi ciency factor cannot be
neglected in the research landscape.
4
Interface with Biochemical Techniques
Within this section, the focus will be shifted from classical, quantita-
tive proteomics, where the name of the game is to fi nd differences in
expression on total extracts, to more focused proteomics experiments
where the interest is centered on subclasses of proteins. In many
