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Significance Scientists have developed many affinity pulldown methods to characterize protein networks. Three persistent challenges with current approaches are capturing labile interactions, isolating insoluble DNA-bound complexes, and preserving modifications potentially important for binding specificity. This report presents a cross-linked affinity approach to meet these challenges and effectively capture interactions that otherwise may be intractable with native affinity techniques. We isolate severalDrosophila and human protein complexes to demonstrate the technique’s scalability across a range of initial cell amounts and sources, and we develop the ability to identify the breadth of associated histone and nonhistone modifications in parallel. Our results indicate that cross-linked affinity pulldowns should be broadly useful for comprehensive analyses of chromatin networks.

Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry