Sample Size-comparable Spectral Library Enhances Data-Independent Acquisition-based Proteome Coverage of Low-input Cells

Despite advancement of data-independent acquisition mass spectrometry (DIA-MS) to provide comprehensive and reproducible quantitative proteome profiling, its utility in very low-input samples is limited. For low-input samples at microscale, the proteome composition and overall peptide ion patterns are different from the conventional sample size. Thus, the conventional LC-MS/MS acquisition and widely used large proteome-scale DIA libraries may not be suitable for the microscale sample. In this study, we report a sample size-comparable library-based DIA approach for enhanced proteome coverage of low-input samples at nanoscale to near single-cell levels (i.e. nanogram cells,~5-50 cells). With these spectral libraries made freely available, we envision that such single-shot DIA strategy and the DIA digital map will advance quantitative proteomics applications by enabling improved deep proteome profiling for mass-limited samples.