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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. 5 — A Average number of unique crosslinks from the DSSO crosslinked main library after acquisition using a stepped HCD MS2 strategy with separate FDR calculation for inter- and intra-crosslinked peptides set on or off. Although synthetic peptides were used for crosslinking their sequences are based on ribosomal protein sequences. “Intraprotein” are defined as homomeric links and “interprotein” are heteromeric links based on the proteins the synthetic peptides correspond to. B Average number of crosslinks from the DSSO linked main library identified with MS Annika at 1% estimated FDR when filtering for crosslinked peptides of the given length (meaning the length of the shorter peptide within the crosslinked sequence). A and B Error bars indicate standard deviations of average values, experimentally validated FDR is shown as callout or in table format under the x-axis, n = 3 independent samples acquired on different days. Source data are provided as a Source Data file.