Chemical Strategies for Functional Proteomics

Abstract

With complete genome sequences now available for several prokaryotic and eukaryotic organisms, biological researchers are charged with the task of assigning molecular and cellular functions to thousands of predicted gene products. To address this problem, the field of proteomics seeks to develop and apply methods for the global analysis of protein expression and protein function. Here we review a promising new class of proteomic strategies that utilizes synthetic chemistry to create tools and assays for the characterization of protein samples of high complexity. These approaches include the development of chemical affinity tags to measure the relative expression level and post-translational modification state of proteins in cell and tissue proteomes. Additionally, we discuss the emerging field of activity-based protein profiling, which aims to synthesize and apply small molecule probes that monitor dynamics in protein function in complex proteomes. Molecular & Cellular Proteomics 1:781-790, 2002.

Advances in proteomics data analysis and display using an accurate mass and time tag approach

“…A variety of chemical, enzymatic, and metabolic labeling techniques that utilize stable isotopes have been developed to facilitate relative quantitation for comparative analysis of proteome samples from different biological states (Adam, et al, 2002. A number of these different stable isotope labeling techniques for quantifying protein abundances and post-translational modifications have already been extensively reviewed , Sechi & Oda, 2003, Tao & Aebersold, 2003.…”

The Lipolytic Proteome of Mouse Adipose Tissue

“…1). Basically an activity label is a molecule consisting of (i) a recognition site targeting a certain enzyme species, (ii) a properly positioned reactive site that forms a covalent bond with the target, and (iii) a tag for visualization and/or purification of the covalently bound target (13)(14)(15)(16). The active site for lipases and esterases typically consists of a catalytic triad formed by Ser-His-(Asp/ Glu), which is common for most serine hydrolases (17).…”

Update on Proteomics in Arabidopsis. Where Do We Go From Here?

“…Because ionization efficiency is affected by a number of factors, peak intensities of the same peptide from separate LC-MS/MS experiments are difficult to compare. One solution to this problem is the use of isotope-coded affinity tags (ICAT; for review, see Adam et al, 2002). This method relies on covalent modification of Cys residues with chemically identical biotinylated tags that differ only in mass because of inclusion of heavy and light isotopes.…”