Getting into the rhythm with large-scale profiling of the plasma proteome.

Plasma is a powerful reservoir of disease biomarkers for diagnostic, prognostic, and predictive purposes, flowing through each tissue in the body and accumulating vital information about the pathological state of the individual. As such, untargeted proteomics represents one of the most powerful ways to mine the plasma proteome in a hypothesis-generating manner. However, the current state-of-the art suffers from limitations in terms of low protein identification rates and throughput, limiting its utility in large-scale clinical investigations.

Here, Gaun et al. use IonOpticks Aurora Series columns to perform in-depth, and high-throughput, quantitative profiling of the plasma proteome. Utilising the increased performance obtained by these columns in combination with their multiplexed proteome profiling platform (AutoMP3), they were able to quantify more than 40 proteins/min/sample from a single injection, doubling the previously published rates and demonstrating the significant advantage that it may offer to large-scale biomarker studies that require the analysis of thousands of plasma samples.

The application of this method was exemplified in plasma obtained from naked-mole rats and mice, evaluating changes in the plasma proteome as a function of circadian rhythm and in response to UV exposure. In doing so, they noted only modest changes in the abundance acute phase proteins (APPs) in naked-mole rats following UV exposure, which was instead highly evident in mice. Importantly, these findings shed new light on the adaptive cellular mechanisms that may help protect against UV damage in this species of rodent.

Read the full paper
Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice.
J Proteome Res. 2021 Feb 5;20(2):1280-1295.
doi: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00681. Epub 2021 Jan 26. PMID: 33499602.

Gaun A, Lewis Hardell KN, Olsson N, O’Brien JJ, Gollapudi S, Smith M, McAlister G, Huguet R, Keyser R, Buffenstein R, McAllister FE.

Commentary by Andrew Webb, PhD.

About the Author
Andrew has over 15 years’ experience in the field of chromatography and mass spectrometry. He is the lead innovator and inventor at IonOpticks, working closely with the team to test, refine and develop cutting edge techniques to support higher quality outputs and analytics from MS instruments. Andrew is also the Lab Head of the Walter and Eliza Hall Institute of Medical Research’s Proteomics Research Laboratory.