REVIEW: Quantitative Proteomics and Its Applications for Systems Biology

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S. Ivakhno^1* and A. Kornelyuk²

¹University of Edinburgh, School of Informatics, Appleton Tower, Crichton Str., Edinburgh, EH8 9LE, Scotland, UK; fax: (44) 131-651-1426; E-mail: s0567096@sms.ed.ac.uk

²Institute of Molecular Biology and Genetics, Department of Protein Engineering, 150 Academician Zabolotny Str., Kiev 03143, Ukraine; fax: (38) 044-526-0759; E-mail: kornelyuk@imbg.org.ua

^* To whom correspondence should be addressed.

Received September 6, 2005; Revision received January 8, 2006

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Here we discuss the current state of research in the rapidly growing field of quantitative proteomics and its applications to systems biology. Quantitative proteomics can be successfully used for characterizing alterations in protein abundance, finding novel protein-protein and protein-peptide interactions, investigating formation of large macromolecular complexes, and elucidating temporal changes in organellar protein composition and phosphorylation in signal transduction cascades. Further, quantitative proteomics can directly compare activation of entire signaling networks in response to individual stimuli and discover critical differences in their circuits that account for alterations of cell response. Maturation of proteomic bioinformatics applications and continuous improvements in proteomics and related genomics and transcriptomics technologies now allows us to investigate cellular mechanisms at the integrative system level.

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KEY WORDS: quantitative proteomics, stable isotope labeling, tandem mass spectrometry, proteome informatics, systems biology, protein interactions, DNA microarray

DOI: 10.1134/S0006297906100026

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