Chemical cross-linking mass spectrometry has become a popular tool in structural biology. Although several algorithms exist that efficiently analyze data-dependent mass spectrometric data, the algorithm to identify and quantify intermolecular cross-links located at the interaction interface of homodimer molecules was missing. The algorithm in LinX utilizes high mass accuracy for ion identification. In contrast with standard data-dependent analysis, LinX enables the elucidation of cross-linked peptides originating from the interaction interface of homodimers labeled by 14N/15N, including their ratio or cross-links from protein-nucleic acid complexes. The software is written in Java language, and its source code and a detailed user's guide are freely available at https://github.com/KukackaZ/LinX or https://ms-utils.org/LinX. Data are accessible via the ProteomeXchange server with the data set identifier PXD023522.

Department of Biochemistry Faculty of Science Charles University Albertov 6 12800 Prague 2 Czech Republic

Department of Software Engineering Faculty of Mathematics and Physics Charles University Ke Karlovu 3 12000 Prague 2 Czech Republic

Institute of Microbiology v v i The Czech Academy of Sciences Videnska 1083 Prague 14220 Czech Republic

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