Biology Reference
In-Depth Information
1
Introduction
The term “proteome” was coined by M. Wilkins and fi rst used dur-
ing the Siena meeting, back in 1994 [
1
]. It was an adaptation of the
term genome, and simply referred to the PROTEin complement of
a genOME. Originally considered, and still being, as just an experi-
mental approach, it could be—at least I do—also considered as a
scientifi c discipline (the classical protein biochemistry in which mass
spectrometry and bioinformatics have been incorporated) with
focus on the proteome. Thus, the proteome should be understood
as the total set of protein species or gene products present in a bio-
logical unit (ecosystem, population, organism, organ, tissue, cell, or
organelle) at a specifi c developmental stage and under determined
external biotic and abiotic conditions. By using a proteomics
approach we aim to know “how,” “where,” “when,” and “what
for” are the several hundred thousand of individual protein species
produced in a cell, how they do interact with each other and with
other molecules to construct the cellular building, how they do
work in order to fi t in with programmed growth and development,
and to interact with their biotic and abiotic environments. Answering
all these questions is fi rstly the objective of Proteomics and secondly
of Systems Biology (
see
Chapter
2
)
.
After the completion of the genome sequence of over 1,000
organisms (4,069, 15,581, and 1,879, complete, incomplete,
and targeted projects, respectively; GOLD database,
http://
2013), proteomics is or will become a research priority in any
biological project. As proof of that, mass spectrometry-based
proteomics, and specifi cally that of targeted proteomics (called
single or multiple reaction monitoring) [
3
], has been chosen by
the journal Nature Methods as the Method of the Year 2012.
The relevance of proteomics nowadays is supported by a number
of international initiatives recently appeared, either general or
focused on plants. We should mention, among others, HUPO-
iMOP (
http://www.hupo.org/
-
http://www.hupo.org/
research/imop/
-), EuPA-, COST-FA0603 (
http://www.
y&layout=blog&id=1&Itemid=194
), INPPO (
http://www.
inppo.com/
)
, and AOAPO (
http://aoapo.org/
). In the last 5
years, plant proteomics special issues have been published in plant
sciences and proteomics journals, including Journal of Proteomics,
Proteomics, Journal of Proteome Research, Phytochemistry,
Journal of Experimental Botany, and some others. As a very rep-
resentative example, I must mention the special issue devoted to
Plant Proteomics in Europe—COST action [
2
]. Within the
Humana Press Methods in Molecular Biology collection, quite a
number of monographs on proteomics have been published, with
