DIA+: a data-independent acquisition method combining multiple precursor charges to improve peptide signal

Abstract

Data-independent acquisition methods that acquire fragment ions from virtually any peptide in a sample have expanded the benefits of low-throughput targeted proteomics to proteome-wide analyses. While these methods have increased the reproducibility of peptide quantification across multiple samples, their sensitivity is still limited, and the quantification of complete proteomes remains a challenge. Here we present DIA+, a DIA method that combines signals from identical peptides with different charge states, resulting in improved signal-to-noise, additional number of fragments, and therefore in a higher number of identified and quantified peptides in complex samples.