Protein array and proteome

Cahill, D. )., Nordhoee, E. (2003). Protein arrays and their role in proteomics. Adv. Biochem. Eng. Biotechnol. 83,177-187. 

The preceding studies suggest that some of the variability in correlating protein and transcript levels involve (1) sampling time after treatments (mRNA changes precede protein expression), (2) the high information density of DNA arrays and proteomic platform capacity for identified proteins (many transcripts compared to few proteins), (3) very different bioinformatic methods... 

Finally in this section, it must be emphasized that relative quantitative proteomics measurements currently use a range of methodologies other than those based on mass spectrometry. Recently (Unwin 2006) this range of techniques, including those summarized above plus protein arrays and flow cytometry, has been reviewed... 

J.S. Albala and I. Humphery-Smith, Protein Arrays, Biochips, and Proteomics, Chap. 3, Marcel Dekker Inc. (2003). 

This book picks up the array technology journey from the mid-1990s with the introduction of microarray-based gene expression analysis. The global analysis of genes by microarrays has provided a fresh and exciting view of the cellular process. More importantly, it enabled others to consider similar utility in various "omic" fields. Hence, we have witnessed the emergence of protein arrays to address proteomics. 

There are several important advantages RPMAs have over antibody arrays and other proteomic techniques such as immunohis-tochemistry or tissue arrays. Antibody arrays usually require a second specific antibody, made in a different species, for each captured protein to be visualized in a manner analogous to enzyme-linked immunosorbent assays (ELISA). Therefore, it becomes difficult to simultaneously optimize the antibody-antigen hybridization conditions for so many antibodies at once present on antibody arrays while minimizing nonspecific cross-reactivity and ensuring that proteins over a wide range of concentrations can be quantitated in a linear fashion (14). Antibody arrays also consume or require much higher inputs of protein than reverse phase arrays. With antibody arrays. 

The practice of protein analysis of whole proteomes relies on (i) two-dimensional gel electrophoresis for separation (ii) mass spectrometry for analysis and (iii) protein arrays for achieving massively parallel analysis. 

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