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New Mass Spectrometer Technology Enables Unbiased Single-Cell 4D-Proteomics

Enabling single-cell epiproteomics through increased sensitivity and specificity

Scott D. Hanton, PhD

New mass spectrometry (MS) technology combining liquid chromatography, time-of-flight and trapped ion mobility MS, and improved automation software will enable significant improvements in efficiency for proteomic and epiproteomic analysis for the lab.

Epiproteomics expands proteomics to include all of the post translational modifications—the signaling mechanisms in a cell that tell proteins what to do. This new technology revolutionizes quantitative single-cell proteomics and opens the door for a much deeper understanding of the proteins that drive cell function. According to Rohan Thakur, managing director and executive VP of Bruker Daltonics, “proteomics at scale, with sensitivity and depth of coverage, will enable investigations into why one cell becomes cancerous and the other one doesn’t.”

The new MS technology takes advantage of the combination of high-resolution MS and ion mobility generated collisional cross sections (CCS). According to Thakur, “when signals are faint, ambiguity rises, and we check the ambiguity by harnessing minute differences in CCS.  It is an additional fingerprint prior to mass analysis.” Thakur adds that improvements in both sensitivity and specificity can increase productivity by an order of magnitude, from up to 10 runs per day to up to 100 runs per day. In addition, the new technology can analyze five to 20 times less sample per run, and the new hardware is also coupled with advanced new software, which improves the speed at which proteins are identified from the MS data.

The impact of the new technology is to open the quantitative study of single-cell proteomics. Professor Matthias Mann, research director at the Proteomics Program at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen says, “I always said that single-cell proteomics would not happen in my lifetime, but I’m happy to have been proven wrong.” The new MS tools will improve an understanding of the proteins that drive cellular function and have the potential to revolutionize the understanding of biology. Thakur adds that, “the next big thing is to get to 10,000 proteins.” He says the “evolution of technology will be even more sensitivity with specificity. Sensitivity has always driven MS technology.”

To take advantage of this new technology, Thakur suggests that “lab managers will need to change their way of thinking about sensitivity. It will require a mindset shift.” The significant improvements in MS sensitivity will need to drive an evolution of the supporting technology, including stepwise improvements in things like solvent purity, leaching from wetted surfaces, and liquid automation to handle nL sample preparation.



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