Extended Data Fig. 2: Evaluating Iseq-Kac in low-input samples.
From: Acetylation profiling by Iseq-Kac reveals insights into HSC aging and lineage decision
a-h, Peptides from trichostatin A (TSA)-treated HCT116 cells labeled with TMT129 and TMT131 were analyzed by Iseq-Kac. a,b, Venn diagrams showing the overlap of identified (a) and quantified (b) acetylated peptides between two replicates. c, Two-sided Pearson correlation analysis of acetylated peptide ratios (TSA/NC) between replicates. d, Comparison of quantitative results for histone acetylated peptides from Iseq-Kac, IP-MS, and immunoblotting. The immunoblotting data were quantified with ImageJ. e, Histone acetylation sites detected by immunoblotting. Representative western blots from n = 2 or 3 independent experiments. f, Bar graph showing the average number of identified (blue) and quantified (red) acetylated peptides from 100 to 10,000 (per channel) TSA-treated or untreated HCT116 cells. Data are presented as the mean ± s.e.m. of n = 3 independently performed experiments. g, Venn plots showing the overlap of quantified acetylated peptides across three replicates in experiments with 100 to 10,000 cells per channel. h, CV of overlapping acetylated peptides across three replicates using varying numbers of cells. i, Chord diagram showing the classes of proteins identified in different numbers of HCT116 cells. j, Bubble diagram comparing the quantitative results of histone acetylated peptides in different numbers of HCT116 cells. NBT-2015 represents data from Scholz et al.’s work, where acetylome data were obtained using an enrichment-based strategy with 20 mg of protein input.
