Multiplexing our understanding of health and disease - Tandem Mass Tags and the coming decade of proteomics

Understanding biology is complicated! There are six major types of molecules (DNA, RNA, Proteins, Lipids, Glycans, Metabolites) that all work in concert to define whether a biological system is healthy or diseased. To truly understand health and disease we need quantitative maps of all of these molecules and how they relate to each other in terms of presence and abundance at any given time. We are still a long way from delivering on this holistic level, but significant progress in the development of analytical and quantitative methods for all of these molecular entities, led of course by nucleic acid research, have delivered major improvement in the breadth and depth of quantitation available.

Comprehensive analysis of the Proteome has been a long time in the making since the first mass spectrometry methods for peptide sequencing were introduced in the 1990s, and is hampered by our inability to amplify proteins and the sheer complexity created by post-translational changes. This complexity creates challenges in stochastic sampling high levels of missing data that dramatically impacts on the numbers of features quantified in unbiased proteomics studies. Several strategies have been introduced to reduce ‘missingness’ and this talk will focus on the particular role that Tandem Mass Tags® (TMT® & TMTpro™) are playing in the large-scale quantitation of proteins, peptides and post-translational modifications.

The underlying principle of isobaric mass tagging was invented by Dr. Andrew Thompson in the mid-1990s and Proteome Sciences acquired the technology in 2002 when Dr. Thompson also joined the Company. We have developed both TMT® reagents, starting at 6-plex and moving up to 11-plex, and then the TMTpro™ reagents to deliver even higher multiplexing with our 18plex set being the largest set of commercially available tags. Being able to mix samples after digestion gives greater throughput and the option to perform extensive fractionation for deep profiling, whilst retaining quantitative precision. We have also used the power of isobaric tagging to develop new workflows for enhanced biomarker discovery in biofluids and accurate quantification using internal calibration curves with parallel reaction monitoring assays. Others have used similar approaches to develop single-cell proteomics methods able to quantify >1,500 proteins.

Whilst we may still be some way from knowing what the whole proteome really is, the breadth and depth of quantification achievable with 18plex TMTpro™ is driving a better understanding of complex biological questions in basic research, drug development and diagnostic biomarker discovery. Whilst the last two decades have been the era of genomics, the 2020’s are shaping up to be the decade of multiplex proteomics.