Histone Coder counts the number of MS/MS ions in a given spectrum to determine the unambiguous localization of a post-translational modification (PTM). The software lists number and type of site determining ions found between the assigned PTM localization by Mascot (Matrix Science) and the closest other amino acids which can host the modification. The PTMs included in the script are phosphorylation (S,T,Y), acetylation (K), mono- and dimethylation (K,R) and trimethylation (K). From the interface it is possible to select filters for spectrum score, fragment ion types and MS/MS tolerance for the search. As additional feature, Histone Coder converts the Mascot output (xml) to the standard Brno nomenclature for PTMs (e.g. K4me3K14ac).