Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

H Mohammed, C Taylor, GD Brown, EK Papachristou… - Nature protocols, 2016 - nature.com
H Mohammed, C Taylor, GD Brown, EK Papachristou, JS Carroll, CS D'santos
Nature protocols, 2016nature.com
Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) is a method
that allows the study of protein complexes, in particular chromatin and transcription factor
complexes, in a rapid and robust manner by mass spectrometry (MS). The method can be
used in parallel with chromatin immunoprecipitation–sequencing (ChIP-seq) experiments to
provide information on both the cistrome and interactome for a given protein. The method
uses formaldehyde fixation to stabilize protein complexes. By using antibodies against the …
Abstract
Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) is a method that allows the study of protein complexes, in particular chromatin and transcription factor complexes, in a rapid and robust manner by mass spectrometry (MS). The method can be used in parallel with chromatin immunoprecipitation–sequencing (ChIP-seq) experiments to provide information on both the cistrome and interactome for a given protein. The method uses formaldehyde fixation to stabilize protein complexes. By using antibodies against the endogenous target, the cross-linked complex is immunoprecipitated, rigorously washed, and then digested into peptides while avoiding antibody contamination (on-bead digestion). By using this method, MS identification of the target protein and several dozen interacting proteins is possible using a 100-min LC-MS/MS run. The protocol does not require substantial proteomics expertise, and it typically takes 2–3 d from the collection of material to results.
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