Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 78

SILAC
Stable isotope labelling with amino acids in cell cultures (SILAC) is a method used
for protein differential display using stable isotope labelling (Jorrin-Novo et al.
2009 ). Super SILAC technology is available from suppliers, and well suited for
plant cell and tissue culture comparisons.
MS-MS Analysis (Differential Isotopes)
Using a single MS/MS analysis, corresponding peptides from each sample are dif-
ferentially detected based on mass shifts caused by the different isotopes used; and
this type of analysis allows comparison of relative protein and polypeptide abun-
dance between samples.
LC-MS/MS
Recently, label-free quantitative techniques have been developed to facilitate high-
throughput comparisons specific for proteomic expression. For example, label-free
quantification in the proteomes from each of two samples are separately analysed
using liquid chromatography (LC)-MS/MS. Then, each MS spectrum is aligned to
calculate relative protein abundance and changes based on ion intensity differences,
such as peptide peak areas or peak heights in the chromatograms. Finally, MS/MS
analysis is used to identify the peptides of interest (Gstaiger and Aebersold 2009 ).
SubcellularProteomics(Organelles)
Accurate and quick proteome analysis of cell organelles has become very important
for understanding the various enzymatic activities within cell organelles, the com-
partmentalisation of metabolites and metabolic pathways, cellular logistics such as
protein targets, their movement and regulation; and it has become very important to
understand proteomic dynamics at the subcellular level (Andersen and Mann 2006 ;
Chen and Harmon 2006 ; Baginsky 2009 ). A number of different approaches listed
below have been applied to analyse the proteome of organelles and subcellular com-
partments of plant cells. Studies so far have included cell organelles and compart-
ments like the chloroplasts, etioplasts, amyloplasts, chromoplasts, mitochondria,
vacuoles, plasma membrane, nucleus, peroxisomes, cytosolic ribosomes and cell
walls (Baginsky 2009 ).