ArticleJournal of proteome research2019
Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.Nature methods · 2024Article
- Multidimensional Cross-Linking and Real-Time Informatics for Multiprotein Interaction Studies.Journal of proteome research · 2024Article
- Article
- Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Selenoprotein S Interacts with the Replication and Transcription Complex of SARS-CoV-2 by Binding nsp7.Journal of molecular biology · 2023Article
- Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows.Nature communications · 2022Article
- Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.Journal of proteome research · 2022Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Reliable identification of protein-protein interactions by crosslinking mass spectrometry.Nature communications · 2021Article
- Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS).Biomolecules · 2021Review
- Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data.Journal of proteome research · 2021Article
- Parallel Detection of Fundamental and Sixth Harmonic Signals Using an ICR Cell with Dipole and Sixth Harmonic Detectors.Journal of the American Society for Mass Spectrometry · 2020Article
- MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity.Molecular & cellular proteomics : MCP · 2020Article
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Authors and funding
4 authors.
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Abstract
Chemical cross-linking and mass spectrometry is of growing use for establishment of distance constraints on protein conformations and interactions. Whereas intraprotein cross-links can arise from proteins in isolation, interprotein cross-links reflect proximity of two interacting proteins in the sample. Prediction of expected ratios of the number of interprotein to intraprotein cross-links is hindered by lacking comprehensive knowledge on the interactome network and global occupancy levels for all interacting complex subunits. Here we determine the theoretical number of possible inter- and intraprotein cross-links in available PDB structures of proteins bound in complexes to predict a maximum expected fraction of interprotein cross-links in large scale in vivo cross-linking studies. We show how the maximum fraction can guide interpretation of reported interprotein fractions with respect to the extent of sample protein binding, comparing whole cell and lysate cross-linked samples as an example. We also demonstrate how an observation of interprotein cross-link fractions greater than the maximum value can result from the presence of false positive cross-links which are predominantly interprotein, their number estimable from the observed surplus fraction of interprotein cross-links.
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