Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.

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

SUBMITTER: Birklbauer MJ 

PROVIDER: S-EPMC11659399 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature