Biology Reference
In-Depth Information
Chapter 1
Plant Proteomics Methods and Protocols
Jesus V. Jorrin-Novo
Abstract
In this fi rst, introductory chapter, it is intended to summarize from a methodological point of view the
state of the art in plant proteomics, focusing on mass spectrometry-based strategies. Thus, this chapter is
mainly directed at beginners or at those trying to get into the fi eld, rather than at those with real experi-
ence or a long trajectory in plant proteomics research. The different alternative workfl ows, methods,
techniques, and protocols from the experimental design to the data analysis will be briefl y commented,
with cross references to previous monographs and reviews, as well as to the rest of the topic chapters. The
diffi culty of working with proteins, together with the power, limitations, and challenges of the approach
will also be briefl y discussed.
Proteins, as molecular entities, and the cell proteome, as a whole, are much more complex than what
we thought in the past and can be studied in a single experiment. Because of that, fractionation and
complementary strategies are required for its study. The MS analysis of complex samples may result in up
to 100,000-peptide spectra that cannot be easily analyzed with standard procedures. Therefore, pro-
teomics, more than other -omics, needs a dry lab, time, and an effort in data mining.
As main conclusion, it can be stated that proteomics is in its beginnings. It is starting to make impor-
tant contributions to a proper gene annotation, identifi cation, and characterization of gene products or
protein species and to the knowledge of living organisms, having also an enormous application potential
to translational research. However, and despite its great potential, and as in any other experimental
approach, it is far from being a Pandora's Box. In the case of plant research, the full potential of proteomics
is quite far from being totally exploited, and second-, third-, and fourth-generation proteomics techniques
are still of very limited use. Most of the plant proteomics papers so far published belong to the descriptive,
subcellular, and comparative proteomics subgroup, mainly using a few experimental model systems—those
whose genome has been sequenced—and being from a biological point of view quite descriptive and
speculative. From now on we should put more emphasis on the study of posttranslational proteomics and
interactomics, and move to targeted, hypothesis-driven approaches. Furthermore, and even more impor-
tant, we should move to data validation through other -omics or classical biochemical strategies, in an
attempt to get a deeper, real, and more accurate view and understanding of cell biology. In the modern
Systems Biology concept, proteomics must be considered as a part of a global, multidisciplinary approach.
Making biological sense of a proteomics experiment requires a proper experimental design, data validation,
interpretation, and publication policy.
Key words
Plant proteomics, Proteomics workfl ows, Descriptive proteomics, Comparative
proteomics, Plant systems biology
