Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 77

MudPIT
The multidimensional protein identification technology (MudPIT) consists of a
combination of different separation methods described before, in atypical 'shotgun
approach'. MudPIT is especially suitable for the analysis of proteins that are diffi-
cult to separate by 2-DE, as well as for high-volume analysis by automated analyti-
cal instruments now in common use (Yates et al. 2009 ).
FT-ICR MS
Fourier transformation ion cyclotron resonance mass spectrometry (FT-ICR MS)
possesses high resolution, high sensitivity, high dynamic range and high mass
measurement accuracy. The high resolution and precision of FT-ICR MS allows
researchers to carry out 'top-down proteomics', similar to a 'shotgun approach'
in which an intact protein mixture is analysed directly, without separation and/or
purification of the proteins (Bogdanov and Smith 2005 ).
QuantitativeProteomics
Quantification of the abundance of proteins identified is important for a better un-
derstanding of protein dynamics and kinetics, in response to cellular activities and
environmental changes. A quantitative proteome approach also plays a crucial role
in the discovery of key proteomic changes, including expression, repression, inter-
action and modification of proteins that are associated with genetic variations and/
or phenotypic changes in organisms (Gstaiger and Aebersold 2009 ).
DIGE
Difference gel electrophoresis (DIGE) is now a popular method for differential dis-
play of proteins for quantitative protein comparisons. In DIGE, protein samples
are labelled with different fluorescent dyes before 2-D electrophoresis, enabling
accurate determination of differences in protein abundance between samples (Ros-
signol et al. 2006 ). This method is effective in minimising and even negatinggel to
gel variation while significantly increasing accuracy and reproducibility of samples.
There are a number of commercial suppliers of 2D DIGE based gels available and
ready for proteomic studies.
iCAT (iTRAQ)
Isotope-coded affinity tags (ICATs) and isobaric tags for relative and absolute quan-
tification and comparison in basic regulation of proteins (iTRAQ), are other impor-
tant methods in proteomics.