Biology Reference
In-Depth Information
the number 355—appearing in 2007—devoted to plants (Plant
Proteomics. Methods and Protocols, edited by H. Thiellement,
M. Zivi, C. Damerval, and V. Mechin). The great advances made
in the last 5 years within the fi eld justifi ed the reedition of this
topic in which last advancements, dispersed in the original litera-
ture, have been compiled and organized in just a single topic.
Proteomics can be thought as a holistic or as a targeted
approach, depending on the initial hypothesis, fi rstly from the
most general (proteins are responsible for the phenotypic differ-
ences among biological samples) and secondly to the most specifi c
ones (specifi c proteins or gene products, or groups of proteins
according to their physicochemical or biological properties that are
involved in the biological phenomenon studied). At the method-
ological level, proteomics research was originally based on 2-DE
protein separation coupled to MS analysis of spots (fi rst genera-
tion), moving then to LC-based shotgun strategies (second gen-
eration), and later to quantitation approaches including label and
label-free variants (third generation). Selected or multiple reaction
monitoring (SRM, MRM) hypothesis-driven approaches consti-
tute the last, fourth generation. Innovation in proteomics, impli-
cating a change in the paradigm research within the fi eld, allows
researchers to apply the scientifi c method [
3
].
Proteomics should be considered as a young discipline, so it is
not surprising the daily appearance of some novelty. Advances in
proteomics have been made possible due to continuous improve-
ments in protein extraction, purifi cation and separation, mass spec-
trometry analysis and equipment, developments of bioinformatics
tools and algorithms for data analysis, protein identifi cation, quan-
tifi cation and characterization. It resulted in the creation and
establishment of quite a number of databases and repositories
where information on the proteome of a number of plant species is
stored and updated (
see
Chapter
3
)
. The advances in MS, without
any doubt, have mainly led to the big progress of the fi eld (
see
Chapter
6
)
. As summarized by JJ Thelen and JA Miernyk [
4
]
recent improvements in sensitivity, mass accuracy, and fragmentation
have led to achievements previously only dreamed of, including whole-
proteome identifi cation, and quantifi cation and extensive mapping of
specifi c PTMs (posttranslational modifi cations); with such capabilities
at present, one might conclude that proteomics has already reached its
zenith; however, 'capability' indicates that the envisioned goals have
not yet been achieved.
Proteomics, depending on the research objectives, can be
divided in subareas, being the more relevant: descriptive (
see
(
see
Chapters
37
-
39
)
, posttranslational (
see
Chapters
40
-
45
)
,
interactomics (
see
Chapters
46
and
47
), proteinomics (
see
Chapter
