Deep Characterization of Isomerization in the Human Eye Lens Proteome by Crystallin‐Depleted Data‐Independent Acquisition

The eye lens is a unique tissue optimized for light transmission and refraction, necessitating dissolution of all organelles in mature fiber cells. This absence of organelles prevents protein turnover and leads to the accumulation of many spontaneous modifications over time. One modification that is oft overlooked is isomerization, despite its known impact on protein structure, interference with enzymatic activity, and association with disease. Prior analysis of isomerization in the lens has been limited to a small number of targets, consisting primarily of the highly abundant crystallin proteins. Proteomic coverage can be greatly increased by first depleting the crystallins and then employing state-of-the-art data-independent acquisition (DIA) mass spectrometry (MS). However, this approach has not been combined with data analysis methods capable of identifying isomers. By so doing, we identified hundreds of previously unreported, noncrystallin Asp isomer sites. To a lesser extent, isomerization was also detected at serine and glutamic acid, consistent with previous reports of relative isomerization propensities. Interestingly, we also identify histidine isomerization sites in a select number of peptides associated with metal adduction. We further analyzed our results according to primary sequence and secondary structure to explore factors potentially influencing isomerization. Finally, we found that while isomerization percents for individual proteins are modestly accurate predictor of age, inclusion of multiple isomerized sites affords a more accurate prediction of age, which may be useful for applications in forensics.