Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM-DIA, and Untargeted DIA

Data-independent acquisition (DIA) is an emerging technology for quantitative proteomics. Current DIA focusses on the identification and quantitation of fragment ions that are generated from multiple peptides contained in the same selection window of several to tens of m/z. An alternative approach is WiSIM-DIA, which combines conventional DIA with wide-SIM (wide selected-ion monitoring) windows to partition the precursor m/z space to produce high-quality precursor ion chromatograms. However, WiSIM-DIA has been underexplored; it remains unclear if it is a viable alternative to DIA. We demonstrate that WiSIM-DIA quantified more than 24 000 unique peptides over five orders of magnitude in a single 2 h analysis of a neuronal synapse-enriched fraction, compared to 31 000 in DIA. There is a strong correlation between abundance values of peptides quantified in both the DIA and WiSIM-DIA datasets. Interestingly, the S/N ratio of these peptides is not correlated. We further show that peptide identification directly from DIA spectra identified >2000 proteins, which included unique peptides not found in spectral libraries generated by DDA.