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.