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. 2022 Jul 8;13:3975. doi: 10.1038/s41467-022-31701-w

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — A Average crosslink numbers using DSSO after acquisition using a stepped HCD MS2 method. Applied to the main library using the algorithms MeroX²⁶, MS Annika²⁴, XlinkX²⁷, pLink 2²⁸, MaxLynx²⁵ or xiSearch^{36, 44} for analysis. All results were obtained at 1% estimated FDR (solid line bars) and corrected by applying a post-score cutoff to reach an experimentally validated FDR < =1 (dashed line bars). The experimentally validated FDR is shown as callout, error-bars indicate standard deviations of average values, n = 3 independent samples acquired on different days. B Overlap of crosslinks identified in each replicate using MS Annika. C Overlap of cross links identified in replicate 3 after analysis using MS Annika or an alternative algorithm as given. B, C: Experimentally validated FDRs for commonly found and exclusively found links are given. Source data are provided as a Source Data file.