biostudies-literatureBirklbauer MJÖsterreichische ForschungsförderungsgesellschaftAustrian Science Fund FWFÖsterreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)Vienna Science and Technology Fund300https://www.ebi.ac.uk/biostudies/studies/S-EPMC11659399biostudies-literatureUnknown7(1)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 Communications chemistryProteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.PMC11659399LS20-079ESP566AT-SCPSFB F 8805-BP35045-BBirklbauer MJGeetha SSMuller FMechtler KDorfer VMatzinger MfalseProteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.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 2024-01-01T00:00:00Z2024 Dec2026-06-01T17:38:10.957Z2025-04-04T02:46:50.285ZS-EPMC116593993970246310.1038/s42004-024-01386-x