Abstract
Purification of small, native chromatin regions for proteomic identification of specifically bound proteins and histone posttranslational modifications is a powerful approach for studying mechanisms of chromosome metabolism. Here we detail a Chromatin Affinity Purification with Mass Spectrometry (ChAP-MS) approach for affinity purification of 1 kb regions of chromatin for targeted proteomic analysis. This approach utilizes quantitative, high resolution mass spectrometry to categorize proteins and histone posttranslational modifications co-enriched with the given chromatin region as either "specific" to the targeted chromatin or "nonspecific" contamination. In this way, the ChAP-MS approach can help define and redefine mechanisms of chromatin-templated activities.