Proteolytic ¹⁸O-labeling strategies for quantitative proteomics

Abstract

A number of proteomic techniques have been developed to quantify proteins in biological systems. This review focuses on the quantitative proteomic technique known as “proteolytic ¹⁸O-labeling.” This technique utilizes a protease and H₂¹⁸O to produce labeled peptides, with subsequent chromatographic and mass spectrometric analysis to identify and quantify (relative) the proteins from which the peptides originated. The technique determines the ratio of individual protein's expression level between two samples relative to each other, and can be used to quantitatively examine protein expression (comparative proteomics) and post-translational modifications, and to study protein–protein interactions. The present review discusses various aspects of the ¹⁸O-labeling technique, including: its history, the advantages and disadvantages of the proteolytic ¹⁸O-labeling technique compared to other techniques, enzymatic considerations, the problem of variable incorporation of ¹⁸O atoms into peptides with a discussion on recent advancements of the technique to overcome it, computational tools to interpret the data, and a review of the biological applications. © 2006 Wiley Periodicals, Inc., Mass Spec Rev 26:121–136, 2007