Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice

• DOI: 10.1021/acs.jproteome.0c00681
• Publication Date: 2021-01-27T01:19:41Z
• Authors: Aleksandr Gaun; Kaitlyn N. Lewis ...; Niclas Olsson; Jonathon J. O’Brien; Sudha Gollapudi; Megan Smith; Graeme McAlister; Romain Huguet; Robert Keyser; Rochelle Buffenstein; Fiona E. McAllister
• Keywords: Proteome; Ion-mobility spectrometry

Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully automated multiplexed platform (AutoMP3) using the Hamilton Vantage liquid handling robot capable of preparing hundreds thousands samples. To maximize protein depth in single-shot runs, we combined 16-plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) real-time search (RTS). quantified over 40 proteins/min/sample, doubling previously published rates. applied AutoMP3 investigate naked mole-rat both as function circadian cycle response ultraviolet (UV) treatment. In keeping lack synchronized rhythms mole-rats, find few patterns proteins course 48 h. Furthermore, quantify many disparate changes between mice mole-rats at h one week after UV exposure. These species differences temporal responses could contribute pronounced cancer resistance observed mole-rats. The mass proteomics data have been deposited ProteomeXchange Consortium via PRIDE [1] partner repository dataset identifier PXD022891.