Chemical cross-linking in combination with mass spectrometry (XL-MS) has established itself as an important technology for the structural analysis of protein complexes. The improved sensitivity of the current generation of mass spectrometers and sophisticated bioinformatics tools for data analysis have recently provided insight into large assemblies including proteasomes, ribosomes and chromatin remodelers. In order to make XL-MS more gener(ic)ally applicable and an accepted tool for structural biologists, we have developed an integrated workflow for the routine generation of structural information from protein complexes that includes a step-by-step protocol and open source, open access software (1,2).
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