ArticleCommunications chemistry2024
Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.
Article in Communications chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 6 papers.
What it found
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Who cites it
6 citing papers in PubMed.
- U1 snRNP and RNA polymerase II interaction is predominantly mediated by Prp40 rather than U1-70K in yeast.Nucleic acids research · 2026Article
- Red blood cells serve as a primary glucose sink to improve glucose tolerance at altitude.Cell metabolism · 2026Article
- Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral.Nature communications · 2025Article
- Click-linking: a cell-compatible protein crosslinking method based on click chemistry.Nature communications · 2025Article
- In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies.Communications chemistry · 2025Article
- Developing a new cleavable crosslinker reagent for in-cell crosslinking.Communications chemistry · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
The field of crosslinking mass spectrometry has seen substantial advancements over the past decades, enabling the structural analysis of proteins and protein complexes and serving as a powerful tool in protein-protein interaction studies. However, data analysis of large non-cleavable crosslink studies is still a mostly unsolved problem due to its n-squared complexity. We here introduce an algorithm for the identification of non-cleavable crosslinks implemented in our crosslinking search engine MS Annika that is based on sparse matrix multiplication and allows for proteome-wide searches on commodity hardware. We compare our algorithm to other state-of-the-art crosslinking search engines commonly used in the field and conclude that MS Annika unifies high sensitivity, accurate FDR estimation and computational performance, outperforming competing tools. Application of this algorithm enabled us to employ a proteome-wide search of C. elegans nuclei samples, where we were able to uncover previously unknown protein interactions and conclude a comprehensive structural analysis that provides a detailed view of the Box C/D complex. Moreover, our algorithm will enable researchers to conduct similar studies that were previously unfeasible.
Identifiers
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Registered trials
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