Fig. 6.

MS‐based histone PTM quantitation strategies. Simplified scheme depicting the most common histone PTM quantitation methods in bottom‐up MS approaches. In label‐free experiments, unlabeled samples are acquired in distinct runs and then compared. When using labeling strategies, different samples are labeled, combined, and acquired in a single run, from which the information regarding the abundance of distinct samples can be extracted. Labeling can be achieved by growing cells in media containing isotope‐encoded amino acids, a method known as SILAC. Unlabeled samples can also be compared with an internal standard, which can be SILAC‐labeled histones purified from cell lines, or synthetic isotope‐labeled peptides. Alternatively, peptides can be chemically modified after digestion, using TMT or iTRAQ. Up to 16 samples can be labeled using different tags, which have the same chemical structures and mass, but contain isotopes that allow them to be distinguished at the MS2 level.