Proteins are involved in almost all cellular processes. They are organized through extensive networks of interactions, regulating the working mechanisms of the cell with high fidelity and precision. However, characterization of the protein interactome has been an extremely challenging task due to the lack of highly confident and efficient technology. To address this issue, we describe a major leap forward in cross-linking mass spectrometry demonstrating a new integrated workflow that robustly identifies cross-links from proteome samples. Our approach is based on the application of a cleavable cross-linker, sequential CID and ETD MS2 acquisitions of peptide fragmentation spectra of cross-linked peptides, and a dedicated search engine termed XlinkX. We applied this novel XL-MS strategy to several highly complex samples, including various cell lysates as well intact organelles such as the mitochondrion. The XL-MS-based method not only reveals protein partnerships systematically but also provides insights into subcellular protein localizations, protein conformations, and binding interfaces within protein complexes. These diverse capabilities were demonstrated in detail by our recent study on the protein interactome of mouse heart mitochondria.
Biography of Fan Lui
Dr. Liu is an independent group leader as well as the head of the Mass Spectrometry and Proteomics Core Facility at the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP, Berlin, Germany) since 2017. She completed her undergraduate study in the Department of Life Sciences at Fudan University (Shanghai, China) and obtained a PhD degree in Biochemistry at North Carolina State University (North Carolina, the USA). She joined Prof. Albert Heck’s lab at the Utrecht University (Utrecht, the Netherlands) as a postdoctoral fellow in 2013.