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Cited by 8Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsClick Chemistry and Applications

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Trioxane-based MS-cleavable cross-linking mass spectrometry for profiling multimeric interactions of cellular networks

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Yu, Clinton, Novitsky, Eric, Balasubramani, Sree Ganesh, Wang, Xiaorong, Shen, Xiyu, Yang, Qin, Rychnovsky, Scott, Echeverria, Ignacia, Huang, Lan·2025·Nature Communications
DOI 10.1038/s41467-025-60642-3PMC PMC12215968

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Abstract

Cross-linking mass spectrometry (XL-MS) is a powerful technology for mapping protein-protein interactions (PPIs) at the systems level. While bivalent cross-links are effective for defining protein interactions and structures, multivalent cross-links offer enhanced spatial resolution to facilitate characterization of heterogeneous protein complexes. However, their identification remains challenging due to fragmentation complexity and the vast expansion of database search space. Here, we present tris-succinimidyl trioxane (TSTO), a novel trioxane-based, MS-cleavable homotrifunctional cross-linker capable of targeting three proximal lysines simultaneously. TSTO’s unique MS-cleavability enables concurrent release of cross-linked peptide constituents during collision-induced dissociation, permitting their unambiguous identification. The TSTO-based XL-MS platform is effective for mapping cellular networks from intact cells and tissues, illustrating its versatility for complex biological systems. Trimeric interactions captured by TSTO reveal structural details inaccessible to bifunctional reagents, enhancing modeling accuracy and precision. Furthermore, this development opens a new avenue for designing multifunctional MS-cleavable cross-linkers to further advance structural systems biology.

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Metadata

Authors
Yu, C., Novitsky, E., Balasubramani, S. G., Wang, X., Shen, X., Yang, Q., Rychnovsky, S., Echeverria, I., & Huang, L.
Affiliations
  • University of California, Irvine (US)
  • University of California, San Francisco (US)
Corresponding author
Huang, Lan
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-07-01
Volume
16
Issue
1
Pages
5585-5585
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-60642-3
PMC
PMC12215968
OpenAlex
W4411886858
Cited by
8
References
2
Citations by year
2026: 7 · 2025: 1
FWCI
2.02
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35GM145249, 35GM151256)
  • U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (R01CA290875)
  • U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (R01DK136940, R01DK121146)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
Keywords
cross-linking mass spectrometry, protein-protein interaction, protein complexes, lysine cross-linking, cellular networks

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