%0 Journal Article %A Zhuo A. Chen %A Lutz Fischer %A Salman Tahir %A Jimi-Carlo Bukowski-Wills %A Paul N. Barlow %A Juri Rappsilber %T Quantitative Cross-Linking/Mass Spectrometry Reveals Subtle Protein Conformational Changes %D 2016 %R 10.1101/055418 %J bioRxiv %P 055418 %X We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found that small local conformational changes affect the yields of cross-linking residues that are near in space while larger conformational changes affect the detectability of cross-links. Distinguishing between minor and major changes required robust analysis based on replica analysis and a label-swapping procedure. By providing workflow, code of practice and a framework for semi-automated data processing, we lay the foundation for QCLMS as a tool to monitor the domain choreography that drives binary switching in many protein-protein interaction networks.BS3Bis[sulfosuccinimidyl] suberateCLMSCross-linking/mass spectrometryFDRFalse discovery rateHCDHigher energy collision induced dissociationLC-MS/MSLiquid chromatography tandem mass spectrometryLTQLinear trap quadrupoleMS2Tandem mass spectrometryQCLMSQuantitative cross-linking/mass spectrometrySCXStrong cation exchange %U https://www.biorxiv.org/content/biorxiv/early/2016/05/25/055418.full.pdf