Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.01.26.525676v1?rss=1
Authors: Kolbowski, L., Fischer, L., Rappsilber, J.
Abstract:
Crosslinking MS is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable crosslinkers could substantially reduce the associated search space expansion by allowing an MS3-based approach for identifying crosslinked peptides. However, MS2-based approaches currently outperform approaches utilising MS3. We show here that MS3-trigger sensitivity and specificity were hampered algorithmically. Our four-step MS3-trigger algorithm greatly outperformed currently employed methods and comes close to reaching the theoretical limit.
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