bioRxivBioinformaticsPreprint
Cleavable crosslinkers redefined by novel MS3-trigger algorithm
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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