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Abstract
DIA strategies are based on the acquisition of fragment-ion information for all precursor ions within a certain range of m/z values (DIA MS2 spectra), as exemplified by the sequential window acquisition of all theoretical mass spectra (SWATH) approach. The prevalent approach for DIA analysis is currently the targeted extraction of quantitative information from the acquired DIA data with the use of libraries containing retention- time and fragmentation information for the desired peptide species(peptide-centric matching approach; Fig. 1b). Library generation is a current limitation of this strategy: either time and sample must be consumed to generate libraries with the same samples and instrument, or libraries can be obtained independently but with the caveat that fragmentation patterns and retention times may differ across experimental conditions. Additionally, DIA MS1 information (precursor peptide measurement scans) has not been systematically incorporated into DIA scoring so far, and the lack of an accurate precursor mass leads to ambiguity in data interpretation, especially for peptides coisolated in the same DIA window and sharing fragment-ion peaks.