The CNS myelin proteome: Deep profile and persistence after post-mortem delay

We revisited the proteome of myelin biochemically purified from the brains of healthy c56Bl/6N-mice utilizing complementary proteomic approaches for deep qualitative and quantitative coverage. A data-independent acquisition (DIA) workflow with alternating low and elevated energy (MSE) provided the high dynamic range required for correct quantification of highest-abundance proteins. According to this analysis, the most abundant myelin proteins PLP, MBP, CNP and MOG constitute 38%, 30%, 5% and 1% of the total myelin protein, respectively. Combined with data from an ion mobility-enhanced version of the MSE mode (referred to as UDMSE) and from 1D-gel-based proteomic approaches, we provide the most comprehensive proteome resource of CNS myelin so far and correlate it with published datasets on mRNA and protein abundance profiles of myelin and oligodendrocytes. Using dynamic range enhancement (DRE)-UDMSE as a dedicated data acquisition mode for routine differential myelin proteome profiling, we also establish that the myelin proteome displays only minor changes if assessed after a post mortem-delay of six hours. Together, these data provide a basis for addressing proteomic heterogeneity of myelin in mouse models and human patients with white matter disorders.