Construction of the DIA assay library
The raw MS2 spectral library from data-dependent acquisition (DDA) LCMS2 data of all samples contained 16,306 proteins, 139,790 peptides, 154,426 precursors (different charge states of peptides), and 864,374 transitions (fragment ions) (Supplementary fig. 1. Applying the quality control (QC) filter steps resulted in a final DIA assay library comprised of a target list containing 68,586 transitions, 13,847 precursors (one per peptide), and 3024 proteins. Despite requiring each protein to be represented by at least two unique peptides in the raw spectral library, 27.3% (825) of the proteins are only represented by a single peptide (although multiple transitions) in the final DIA assay library because other peptides were excluded during DIA assay library construction if they did not meet the QC criteria in all filter steps.