3. Quantitative Proteome:
The Isobaric Tags for
Relative and Absolute
Quantitation (iTRAQ)
Yi-Hsuan Wu and Hsueh-Fen Juan∗
Institute of Molecular and Cellular Biology,
National Taiwan University, Taipei, Taiwan
∗[email protected]- Introduction to the methods for quantitative proteome
The term “proteome” was first introduced in 1996 in analog to genome
with a definition of the entire complements of proteins expressed in a
specific state of a cell, tissue or an organism.^1 Despite the similarity among
genome, transcriptome and proteome, the proteomic profiling of a subject
cannot be directly transferred from its genome or transcriptome. The events
of gene regulation, alternative splicing variants, post-transcriptional and
post-translational modifications are responsible for the diverse profiling of
proteome that are distinct from genome or transcriptome. The field of
proteomics not only identifies and quantifies proteins but also encompasses
the dimensions of protein subcellular localizations, post-translational modi-
fications, temporal changes in expression and interactions.^2
The development of mass spectrometry (MS) greatly drives the advance-
ment of proteomic studies. Different from single-stage MS measuring the
mass of polypeptides, tandem mass spectrometry (MS/MS) contains the
determination of mass as single-stage MS and a fragmentation of selected
peptides by collision for further analysis. In most cases, MS/MS is performed
to determine additional structure information of the peptides including
amino acid sequence.^3 Shotgun proteomics, coined in 1998, refers to the
MS-based proteomics that determines proteins by measuring the peptides
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