Crosslinking mass spectrometry enables the structural analysis of proteins and protein complexes and serves as a powerful tool in protein-protein interaction studies, however, the data analysis of large non-cleavable crosslink studies remains challenging. Here, the authors report an algorithm MS Annika 3.0 for proteome-wide identification of non-cleavable crosslinks showing high sensitivity, accurate FDR estimation and computational performance, uncovering the structure of the C. elegans Box C/D complex.
- Micha J. Birklbauer
- Fränze Müller
- Viktoria Dorfer
