Tau is the primary protein studied in Alzheimer's disease (AD), and its post-translational modifications (PTMs) play a critical role in disease progression. However, conventional closed-search PTM workflows are limited to predefined modification types, which constrains the detection of unexpected Tau PTMs in AD. In this study, we generated a high-resolution delta-mass table by combining known PTMs from Open-pFind with a dense series of additional mass delta values and applied an open-search proteomics workflow to analyze Alzheimer's disease data. This approach identified 23 Tau PTM sites in AD, primarily involving ubiquitination (Ub) and deamidation (Asn → Asp). These characteristic PTM sites enabled more accurate discrimination of Braak stage V-VI samples not only from controls but also from earlier Braak stages. We further established a unified AD-identifying indicator based on ubiquitination, deamidation, and characteristic mass shifts, which accurately classified AD samples in data set PXD020517 & PXD020538 and was validated in PXD038901. In addition, we detected some previously unreported Tau PTMs and characteristic mass shifts through open-search analysis. In conclusion, we have successfully employed Open-pFind along with a high-resolution delta-mass table to achieve a comprehensive analysis of both known Tau PTMs and characteristic mass shifts to accurately distinguish Alzheimer's disease samples.
Guo et al. (Thu,) studied this question.