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Use of Linear Ion Traps in Data-Independent Acquisition Methods Benefits Low-Input Proteomics.

The need for a better understanding of cellular heterogeneity has pushed mass spectrometry technologies to the analysis of single-cell and single-cell-type proteomes, although several challenges still limit their widespread implementation. Among the efforts toward single-cell and low-input analyses, there is the adoption of data-independent acquisition methods to increase analytical sensitivity. Here, we revisited the use of linear ion traps mass analyzers in data-independent acquisition methods and demonstrate their benefits to boost peptide and protein identifications in low-input proteomes.