Fig. 3.

DIA-TMT accurately reflects cell type specifics with increased replicate overlap.A, intersection of transcriptome (FPKM) with DIA proteome data, top 300 and 60 proteins are colored according to cluster contributions or labeled, respectively. Venn Diagrams of unique peptide sequences identified across three technical replicates at indicated peptide input of (B) DIA and (C) DDA data (mix 1 = purple, mix 2 = gray, mix 3 = blue). D, peptide-based DDA (purple) and DIA (blue) or ID-independent DIA (turquoise) accumulation of nonoverlapping peptides or indexed MS/MS scans, respectively across 12 analytical runs at decreasing peptide input (i.e., 0.5, 1, 5, 10 ng).