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The term `proteome' was first introduced in 1995 by Marc Wilkins from the University
of Sydney to represent the `proteins expressed by a particular genome'. Later, in the
post-genomic era, the term was expanded as the time- and cell-specific protein
complement of the genome, so as to encompass all proteins that are expressed in a cell at one
time, including isoforms and post-translational modifications (Pandey and Mann, 2000).
Currently, there are three widely accepted divisions of proteomics: 1) Clinical proteomics
for investigating disease biomarkers; 2) Structural proteomics for analyzing and
understanding the properties of cellular proteins; and 3) Functional proteomics for investigating
cell signaling mechanisms. A new research field, which may be called
`developmental proteomics' or `embryo proteomics', is now emerging from the interface between
proteomics and developmental biology. Embryo proteomics may be defined as the systematic
analysis of cohorts of proteins expressed during development, aided by large-scale proteomic
methods. However, in a broad sense, embryo proteomics can also include all
high-throughput approaches such as 2DE, protein microarray, in silico proteomics and
activity-based profiling.
Embryo proteomics will be essential for the completion of a whole proteome
catalog because expressions of some proteins are restricted to early embryonic developmental
stages and are not expressed in somatic cells and tissues (Ko, 2001; and Gao et al., 2004). However, embryonic samples are rare materials that are difficult to obtain for ethical and
technical reasons. The difficulty in obtaining early embryonic material is reflected in the
current publicly available papers in which < 1000 embryos were used for whole proteomic
analysis that could identify < 50 proteins and mainly consisted of high abundant proteins. So
far, application of Matrix-Assisted Laser-Desorption Ionization Time-of-Flight
(MALDI-TOF) approach of Mass Spectrometry (MS) combined with two-dimensional gel electrophoresis
(2-DE) for separation of protein mixtures has enabled the identification and
differential expression of 35 proteins during in
vitro maturation of porcine oocytes (Ellederova et al., 2004), 24 proteins in porcine somatic nuclei exposed to oocyte extract system (Novak et al., 2004), 40 proteins during in
vitro maturation of bovine oocytes (Bhojwani et al., 2006), 12 proteins in vitro maturation of mouse oocytes (Vitale et al., 2007) and 39 (Chae et al., 2006) to 43 (Lee et al., 2007c) proteins in extraembryonic tissue from cloned
porcine embryos. More recently, Surface-Enhanced Laser-Desorption and Ionization
Time-of-Flight (SELDI-TOF) of MS has surfaced as a potential proteomic tool for biomarker discovery
in limited amount of embryonic samples (Katz-Jaffe et al., 2005). This approach enabled the proteomic expression profiling of single human embryos (Katz-Jaffe et al., 2006a) and of proteins secreted by human and mouse embryos during in vitro culture (Katz-Jaffe et al., 2006b). However, SELDI-TOF only produces a pattern of peptides and small proteins
that might be useful for discovering biomarkers of embryo quality but not for protein
identification and quantification. Thus, although the use of SELDI-TOF in limited embryo samples
is tantalizing, the reliability and reproducibility of data has been the subject of debate,
given its limited sensitivity for low-abundance components and the limited robustness of
the bioinformatics analysis (Baggerly et al., 2004; and Combelles and Racowsky, 2006). |
