a, b, Comparison of DDA and DIA data for individual peptides under each experimental condition. For both DDA and DIA data, intensities for all charge and modification states were summed together for each amino acid sequence. For both DDA and DIA data, MS1 intensities for each condition were normalized by dividing the intensity of each peptide by the sum of all measured peptide intensities. The duplicates (DDA) or triplicates (DIA) were averaged together, then the data was log 10-transformed. a, Relationship between DDA and DIA data. Each of the 64,796 points corresponds to the DDA and DIA results for one amino acid sequence under one experimental condition (cochlea vs. utricle; GFP- vs. GFP+; P0, P4, or P7). The log-transformed data were fit with y=mx+b (red line; m=1.050±0.003, b=0.24±0.01); the unity line is also displayed (grey dashed line). , Distribution of DDA and DIA values. Binned data were fit with single Gaussian functions. b c, Comparison of fragment-ion area (intensity) and MS1 area (intensity) for manually-extracted myosins data. For 1639 combinations of peptide and sample, the log 10 of the fragment-ion area was compared to the log 10 of the MS1 area. On average, the slope was 0.78, suggesting that MS1 area was lower than fragment-ion area. For ten high-abundance peptides (indicated with coloured points and linear fits), slopes ranged from 0.73 to 1.22, reflecting a substantial peptide-to-peptide variation.