Increasing proteome coverage using cysteine-specific DIA Mass spectrometry - Cys-DIA

We report a Data Independent Analysis (DIA) mass spectrometric method for quantitative proteomics based on cysteine-containing peptides derived by tryptic digestion from biological samples (termed Cys-DIA). This technology significantly increases the coverage of the identifiable and quantifiable proteome in DIA/SWATH analyses by >35% compared to the conventional DIA/SWATH methods. The strategy was applied here to illustrate the quantitative difference in the proteome between isogenic human cancer cell lines with different metastatic capabilities.