Biology Reference
In-Depth Information
fi xed to a subcellular fraction is far from being real, with protein
traffi cking being one of the issues to be studied in depth. Membrane
proteins, and especially microdomains, are quite recalcitrant and
elusive to standard protocols (
see
Chapter
33
). For PTM analysis,
an enrichment step prior to MS analysis tends to be required,
depending the success of the experiment on the type of modifi ca-
tion (lability of the bound), stoichiometry and behavior of the
modifi ed protein species in MS (
see
Chapters
40
-
45
)
. While the in
vitro analysis of PTMs is straightforward, the in vivo studies and the
identifi cation of the specifi c modifi ed peptides are quite challenging
(
see
Chapters
41
and
42
)
.
The chapters have been written by worldwide recognized sci-
entists, leaders in the fi eld, and include reviews and original papers.
They have been organized in nine sections, starting with a general
one in which the fi eld is being reviewed, both from a biological and
methodological perspective. Section II is devoted to specifi c meth-
odologies, with emphasis on second-, third-, and fourth-genera-
tion techniques (those of gel-free, label or label-free, imaging, and
targeted approaches). Applications of these techniques to the study
of experimental model systems, crops, and orphan species (section
III), organs (section IV), subcellular fractions (section V), and
responses to stresses (section VI) are also included. Sections VII
and VIII are devoted to the study and analysis of PTMs, protein
interactions, and specifi c families of proteins. Section IX has been
dedicated to the use of proteomics in translational research, with
chapters on proteotyping, beverage trazeability, and allergens.
The last, but not least, Chapter
53
has been included due to it
deals with the standards required in proteomics publications. It
includes standards for proteomics data representation, as well as
guidelines that set the minimum information to be included when
reporting a proteomics experiment (MIAPE). These standards are
also listed in the “instruction to authors” of the journals of the fi eld.
As editor and referee I have noticed with surprise the high number
of manuscripts submitted from authors that ignore such standards,
and even the number of published papers that do not fi t in them.
References
1. Bini L, Pallini V, Hochstrasser DF et al (2007)
From genome to proteome: back to the future.
Proteomics 7:1561-1563, Editorial
2. Renaut J, Jorrin-Novo J, Panis B, Svensson B,
guest editors (2011) Plant proteomics in
Europe. J Proteomics 74:1161-1164
3. Picotti P, Bodenmiller B, Aebersold R (2013)
Proteomics meets the scientifi c method. Nat
Methods 1:24-27
4. Thelen JJ, Miernyk JA (2012) The proteomic
future: where mass spectrometry should be
taking us. Biochem J 444:169-181
5. Uhrig G, Moorhead GB (2013) Plant pro-
teomics: current status and future prospects. J
Proteomics (On line advanced) doi:10.1016/j.
jprot.2013.01.018
6. Marte B (2003) Introduction proteomics.
Nature 422:191
7. Jungblut PR, Schluter H (2011) Towards the
analysis of protein species: an overview about
strategies and methods. Amino Acids
41:219-222
8. Petricka JJ, Schauer MA, Megraw M et al
(2012) The protein expression landscape of
