title: Quirks of Error Estimation in Cross-Linking/Mass Spectrometry.
abstract: Cross-linking/mass spectrometry is an increasingly popular approach to obtain structural information on proteins and their complexes in solution. However, methods for error assessment are under current development. We note that false-discovery rates can be estimated at different points during data analysis, and are most relevant for residue or protein pairs. Missing this point led in our example analysis to an actual 8.4% error when 5% error was targeted. In addition, prefiltering of peptide-spectrum matches and of identified peptide pairs substantially improved results. In our example, this prefiltering increased the number of residue pairs (5% FDR) by 33% (n = 108 to n = 144). This number improvement did not come at the expense of reduced accuracy as the added data agreed with an available crystal structure. We provide an open-source tool, xiFDR ( https://github.com/rappsilberlab/xiFDR ), that implements our observations for routine application. Data are available via ProteomeXchange with identifier PXD004749.
authors.affiliation: Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom.
authors.forename: Lutz
authors.identifier: 0000-0003-4978-0864
authors.initials: L
authors.lastname: Fischer
authors.affiliation: Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom.|Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany.
authors.forename: Juri
authors.identifier: 0000-0001-5999-1310
authors.initials: J
authors.lastname: Rappsilber