Fig. 2

Performance of digestion methods for the analysis of histone PTMs from  low-abundance samples. a Number of differentially modified peptides quantifiable from samples digested using the four in-gel or the Arg-C in-solution digestion protocols, at decreasing peptide amounts. After digestion and prior to MS analysis, the peptides were subjected to 1:5 serial dilutions, from an approximate starting amount of 3 µg to 5 ng (1:625 dilution). The PRO-PIC samples were quantified either manually (light red), or with the EpiProfile 2.0 software, followed by manual validation (dark red). b Heatmap display of the log₂ of ratios obtained for the indicated histone PTMs in MDA-MB-468 cells left untreated or treated with the HDAC inhibitor Panobinostat at 15 nM. The peptides were subjected to 1:5 serial dilutions, as described in (a). Grey: not quantified. c and d Correlation matrix based on Pearson correlation coefficients of L/H ratios (c) and principal component analysis (PCA,  d) for histone PTMs quantified from the MDA-MB-468 samples shown in (b)