Proteome profile of myelin in the zebrafish brain

While the myelin proteome is well characterized in mice, much less is known about the protein composition of myelin in non-mammalian species such as zebrafish (Danio rerio), despite its increasing popularity as model organism for myelin biology. Here, we assess the proteome of myelin biochemically purified from the brains of adult zebrafish by 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 predominant Ig-CAM myelin protein zero (MPZ/P0), myelin basic protein (MBP) and the short chain dehydrogenase 36K constitute 12%, 8% and 6% 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 zebrafish myelin so far, correlate it with previously established mRNA-abundance profiles, and demonstrate both similarities and heterogeneity of myelin composition between teleost fish and rodents.