Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 73

the ChIP-Seq platform. A chromatin ChIP-Seq assay is also available from Illumina
using the chromatin immunoprecipitation approach (Farrer et al. 2009 ).
Protein (Proteomics)
Genome sequencing projects for several organisms have been completed, but pro-
teome analysis, which is the detailed investigation of the function, modification
network and 3D structure of proteins, has gained increase attention (De Filippis and
Magel 2012 ; Memon 2012 ). Large-scale proteome information can be an important
resource for a better understanding of protein function in cellular systems, which
are controlled primarily by polypeptides and proteins. Protein dynamic properties
reflect cell and organ differences in terms of growth, development and response to
biotic and abiotic stress. The primary objective of plant proteomics has tradition-
ally been to simply identify all (or most of) the proteins in cells, organs and tissues.
Recent rapid technical advances in proteomics (e.g. protein separation and purifica-
tion, advances in mass spectrometry and methodological development in protein
quantification and identification) have lead scientists into the second stage of pro-
teomics, including quantitative proteomics, subcellular proteomics, modifications
of proteins and protein-metabolite interactions (Rose et al. 2004 ; Rossignol et al.
2006 ; Baginsky 2009 ; Yates et al. 2009 ).
ResourcesinProteomics
The different Web-accessible plant proteome-related databases are summarized
on the proteomics subcommittee home web page of the Multinational Arabidopsis
Steering Committee (MASCP); under the heading of 'Proteomic Databases and Re-
sources'. A summary of the information in various basic and advance proteomics
sites and databases is given in Table 2.6 , including their relevant URL.
ProteomeProfiling
A typical experimental research pathway for protein profiling can be summa-
rized as; (i) sample preparation of impure plant protein mixtures, (ii) separation
and purification of the proteins, (iii) detection of proteins and/or polypeptides, and
(iv) identification of fractionated or ionised proteins and polypeptides. Various
technical advances for each step of the process above have greatly increased the
overall performance, efficiency and cost effectiveness of plant proteomics research
(Rose et al. 2004 ; Jorrin-Novo et al. 2009 ; Uauy et al. 2009 ).