Performing large scale plasma profiling studies involving thousands of samples are challenging due to both lengthy sample preparation and long instrument time requirements. We present a fully Automated Multiplexed Proteome Profiling Platform (AutoMP3) that is capable of processing hundreds to thousands of samples. We combined 16-plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) and real-time search (RTS) to maximize protein depth in plasma. The concentration of plasma proteins spans a dynamic range of at least 12 orders of magnitude, resulting in poor protein identification depth. FAIMS Pro and RTS have been critical to enable deep coverage in single shot mass spectrometry runs.

We have applied this platform to multiple studies including naked mole rats treated with UV radiation, circadian rhythm samples, various mouse and human cohorts as well as diseased cohorts such as chronic kidney disease. We continue to improve the AutoMP3 workflow and extend its applications both in the sample type as well as post translational modification space and will present some of our recent efforts in these areas.