Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry

Shama P. Mirza, Michael Olivier
2008 Physiological Genomics  
Mirza SP, Olivier M. Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry. Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at
more » ... given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins. quantitative proteomics; isotopic labeling; phosphoproteomics Comprehensive Proteomic Characterization A typical standard mass spectral analysis of a complex protein sample involves an initial fragmentation step, a separation methodology to fractionate the complex mixture, and a subsequent mass spectral analysis of the resulting fractions. Commonly, proteins in a complex mixture are fragmented with proteolytic enzymes such as trypsin. Upon treatment, a typical Article published online before print. See web site for date of publication
doi:10.1152/physiolgenomics.00292.2007 pmid:18162499 pmcid:PMC2771641 fatcat:kwpqxwd5qre5fmahjiqc423vjm