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False discovery rate estimation and heterobifunctional cross-linkers

By Lutz Fischer, Juri Rappsilber

Posted 28 Dec 2017
bioRxiv DOI: 10.1101/239715 (published DOI: 10.1371/journal.pone.0196672)

False discovery rate (FDR) estimation is a cornerstone of proteomics that has recently been adapted to cross-linking/mass spectrometry. Here we demonstrate that heterobifunctional cross-linkers, while theoretically different from homobifunctional cross-linkers, need not be considered separately in practice. We develop and then evaluate the impact of applying a correct FDR formula for use of heterobifunctional cross-linkers and conclude that there are minimal practical advantages. Hence a single formula can be applied to data generated from the many different non-cleavable cross-linkers.

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