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Briefings in Functional Genomics and Proteomics Advance Access published online on January 16, 2009
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/eln055
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© The Author 2009. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

18O Stable Isotope Labeling in MS-based Proteomics

Xiaoying Ye, Brian Luke, Thorkell Andresson and Josip Blonder

Corresponding author. Dr Josip Blonder, Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick Inc., NCI at Frederick, P.O. Box B, Frederick, MD 21702-1201, USA. Tel: +1 301 846 7211; Fax: +1 301 846 6037; E-mail: blonder{at}ncifcrf.gov

A variety of stable isotope labeling techniques have been developed and used in mass spectrometry (MS)-based proteomics, primarily for relative quantitation of changes in protein abundances between two compared samples, but also for qualitative characterization of differentially labeled proteomes. Differential 16O/18O coding relies on the 18O exchange that takes place at the C-terminal carboxyl group of proteolytic fragments, where two 16O atoms are typically replaced by two 18O atoms by enzyme-catalyzed oxygen-exchange in the presence of H218O. The resulting mass shift between differentially labeled peptide ions permits identification, characterization and quantitation of proteins from which the peptides are proteolytically generated. This review focuses on the utility of 16O/18O labeling within the context of mass spectrometry-based proteome research. Different strategies employing 16O/18O are examined in the context of global comparative proteome profiling, targeted subcellular proteomics, analysis of post-translational modifications and biomarker discovery. Also discussed are analytical issues related to this technique, including variable 18O exchange along with advantages and disadvantages of 16O/18O labeling in comparison with other isotope-coding techniques.

Keywords: 18O labeling, enzyme-mediated isotope incorporation, stable isotope labeling, MS-based proteomics, relative protein quantitation, LC/MS/MS


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