Fig. 1.

Comparison of in-gel digestion methods for MS-based histone PTM analysis. a Schematic representation of the protocols used to in-gel digest histones. b Average chromatographic retention time drifts for peptides obtained from the digestion of MDA-MB-468 cells with the four methods, as compared with the D3-Ac method. Two different gradients were tested for the PRO-PIC method (see Additional file 1: Fig. S4). c List of peptides identified and quantified from MDA-MB-468 cells using the four different in-gel or the Arg-C in-solution digestion protocols, which were performed in technical triplicates. The lighter blue color indicates isobaric peptides that could not be quantified individually. d and e Elution profiles of the differentially acetylated forms of the H3 27–40 peptides (d) and H4 peptide 4–17 (e) for samples digested in-gel using the D3-Ac or the PRO-PIC protocol. f Correlation matrix based on Pearson correlation coefficients of L/H ratios (light channel: MDA-MB-468 cells; heavy channel: spike-in standard) for histone PTMs quantified from samples processed in technical triplicates through the four in-gel digestion protocols