Current trends in quantitative proteomics – an update

Abstract

In the Biomarker era, quantitative proteomics has become one of the most important tools for the discovery and validation of protein biomarkers in complex biological samples. The challenge has become how to reproducibly identify and accurately quantify the protein/peptide targets at low concentrations, and distinguish real signals from noise. The past 7 years have witnessed the development of new instrumentation and quantitation technologies such as Parallel Reaction Monitoring (PRM) and Sequential Window Acquisition of all THeoretical fragment ion mass spectra (SWATH). New sampling formats such as dried blood spot (DBS) and MALDI imaging, have evolved, as well as new sample derivatization techniques (the TMT 10-plex). In this perspective special feature, Christoph Borchers and colleagues discus these innovations and give critical insights on the future of the field. Dr. Borchers is the director of the University of Victoria-Genome British Columbia Proteomics Centre (Victoria, BC, Canada). His prime research interests are centered on technology development for protein identification and characterization, quantitative proteomics for biomarker discovery and validation, and bioinformatics.