The invention relates to the use of recombinant/semi-synthetic nucleosomes carrying histone and/or DNA modifications as a reference standard for quantification of covalently modified (on the histone proteins or wrapping DNA), variant, or mutant nucleosomes (collectively “modified nucleosomes” or “nucleosome modifications”) from a biological sample. The invention further relates to methods of using the assay to accurately quantify single or combinatorial nucleosome modifications as biomarkers of disease.