LinX: A Software Tool for Uncommon Cross-Linking Chemistry

0542387 - MBÚ 2022 RIV US eng J - Článek v odborném periodiku
Kukačka, Zdeněk - Rosůlek, Michal - Jelínek, Jan - Slavata, Lukáš - Kavan, Daniel - Novák, Petr
LinX: A Software Tool for Uncommon Cross-Linking Chemistry.
Journal of Proteome Research. Roč. 20, č. 4 (2021), s. 2021-2027. ISSN 1535-3893. E-ISSN 1535-3907
Grant CEP: GA ČR(CZ) GA19-16084S; GA MŠMT(CZ) LH15010; GA MŠMT(CZ) LQ1604; GA MŠMT(CZ) LD15089; GA MŠMT(CZ) ED1.1.00/02.0109
GRANT EU: European Commission(XE) 731077 - EU_FT-ICR_MS
Institucionální podpora: RVO:61388971
Klíčová slova: mass spectrometry * high resolution * chemical cross-linking * proteins
Obor OECD: Biochemistry and molecular biology
Impakt faktor: 5.370, rok: 2021
Způsob publikování: Open access
https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00858

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 N-14/N-15, including their ratio or crosslinks 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.
Trvalý link: http://hdl.handle.net/11104/0319810