Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry.
Matthew M MakowskiCathrin GräweBenjamin M FosterNhuong V NguyenTill BartkeMichiel VermeulenPublished in: Nature communications (2018)
Interaction proteomics studies have provided fundamental insights into multimeric biomolecular assemblies and cell-scale molecular networks. Significant recent developments in mass spectrometry-based interaction proteomics have been fueled by rapid advances in label-free, isotopic, and isobaric quantitation workflows. Here, we report a quantitative protein-DNA and protein-nucleosome binding assay that uses affinity purifications from nuclear extracts coupled with isobaric chemical labeling and mass spectrometry to quantify apparent binding affinities proteome-wide. We use this assay with a variety of DNA and nucleosome baits to quantify apparent binding affinities of monomeric and multimeric transcription factors and chromatin remodeling complexes.
Keyphrases
- mass spectrometry
- liquid chromatography
- label free
- binding protein
- high resolution
- capillary electrophoresis
- circulating tumor
- transcription factor
- high performance liquid chromatography
- single molecule
- protein protein
- dna binding
- cell free
- gas chromatography
- amino acid
- gene expression
- high throughput
- single cell
- dna damage
- stem cells
- tandem mass spectrometry
- magnetic resonance imaging
- dna methylation
- computed tomography
- cell therapy
- mesenchymal stem cells
- simultaneous determination
- circulating tumor cells