ArticleAnalytical chemistry2017
Quirks of Error Estimation in Cross-Linking/Mass Spectrometry.
Article in Analytical chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
96 citing papers in PubMed.
- Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.Nature communications · 2026Article
- Quantitative interactome mapping of skeletal muscle insulin resistance.Molecular systems biology · 2026Article
- Mapping the architecture of protein complexes inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation.Nature communications · 2026Article
- Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.Nucleic acids research · 2026Article
- Phosphorylation-dependent tuning of mRNA deadenylation rates.Nature structural & molecular biology · 2026Article
- Thianthrenium Chemistry for Identification of Protein-Protein Interactions in Cells.Journal of the American Chemical Society · 2025Article
- Nucleosome interaction of the CPC secures centromeric chromatin integrity and chromosome segregation fidelity.The EMBO journal · 2025Article
- Conformational plasticity of a BiP-GRP94 chaperone complex.Nature structural & molecular biology · 2025Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
- MORC2 is a phosphorylation-dependent DNA compaction machine.Nature communications · 2025Article
- Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA.Molecular cell · 2025Article
- Article
- Structural insights into distinct mechanisms of RNA polymerase II and III recruitment to snRNA promoters.Nature communications · 2025Article
- Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.Communications chemistry · 2024Article
- Kinetic principles of chemical cross-link formation for protein-protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.Nature methods · 2024Article
- Modelling protein complexes with crosslinking mass spectrometry and deep learning.Nature communications · 2024Article
- Rescuing error control in crosslinking mass spectrometry.Molecular systems biology · 2024Article
- Structural basis for Mis18 complex assembly and its implications for centromere maintenance.EMBO reports · 2024Article
36 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
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.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.