Evaluating cPILOT Performance on Orbitrap Instruments

A global cPILOT assay developed on an Orbitrap Velos instrument was transitioned to an Orbitrap Fusion Lumos instrument. Parameters such as the LC gradient, m/z isolation window, dynamic exclusion, targeted mass analyses, and SPS-N were optimized. The number of proteins identified on the Fusion Lumos (1848) without fractionation are close to those identified to the Orbitrap Velos (2199) with sample pre-fractionation. Additionally, including sample fractionation with the Fusion Lumos optimized parameters resulted in the identification of 4968 proteins, of which 1234 were quantified in each tissue type and genotype (N=5 or 6). Combined, the various experiments described herein informed of system-wide changes in brain, heart, and liver proteins from a late-stage amyloid precursor protein/presenilin-1 (APP/PS-1) human transgenic double knock – in mouse model of AD.