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- W2885161888 abstract "Abstract Recent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the density and coverage of protein-protein interaction maps can be significantly improved through the use of multiple proteases. In addition, the use of sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching. Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems." @default.
- W2885161888 created "2018-08-22" @default.
- W2885161888 creator A5055053315 @default.
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- W2885161888 creator A5079952504 @default.
- W2885161888 date "2018-08-17" @default.
- W2885161888 modified "2023-09-26" @default.
- W2885161888 title "Optimized cross-linking mass spectrometry for in situ interaction proteomics" @default.
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- W2885161888 doi "https://doi.org/10.1101/393892" @default.
- W2885161888 hasPublicationYear "2018" @default.
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