ArticleBioinformatics (Oxford, England)2019
Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Interactome Quantitation Reveals Non-Energetic Mitochondrial Roles in Cell Type Specialization in Murine Kidney.Molecular & cellular proteomics : MCP · 2025Article
- Rescuing error control in crosslinking mass spectrometry.Molecular systems biology · 2024Article
- Intra-organ cell specific mitochondrial quantitative interactomics.bioRxiv : the preprint server for biology · 2024Article
- Studying Protein-Ligand Interactions by Protein Denaturation and Quantitative Cross-Linking Mass Spectrometry.Analytical chemistry · 2023Article
- Skeletal muscle mitochondrial interactome remodeling is linked to functional decline in aged female mice.Nature aging · 2023Article
- Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart.Nature cardiovascular research · 2022Article
- Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.Journal of proteome research · 2022Article
- Upregulation of mitochondrial ATPase inhibitory factor 1 (ATPIF1) mediates increased glycolysis in mouse hearts.The Journal of clinical investigation · 2022Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx.Analytical chemistry · 2022Article
- Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs.Molecular omics · 2021Article
- Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data.Journal of proteome research · 2021Article
- Isobaric Quantitative Protein Interaction Reporter Technology for Comparative Interactome Studies.Analytical chemistry · 2020Article
- Cellular Interactome Dynamics during Paclitaxel Treatment.Cell reports · 2019Article
- Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.Journal of proteome research · 2019Article
- Tools for 3D Interactome Visualization.Journal of proteome research · 2019Article
- Development of R7BP inhibitors through cross-linking coupled mass spectrometry and integrated modeling.Communications biology · 2019Article
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Authors and funding
3 authors.
Funding
Abstract
motivationPeptides crosslinked with cleavable chemical crosslinkers are identified with mass spectrometry by independent database search of spectra associated with the two linked peptides. A major challenge is to combine together the evidence of the two peptides into an overall assessment of the two-peptide crosslink.
resultsHere, we describe software that models crosslink specific information to automatically validate XL-MS cleavable peptide crosslinks. Using a dataset of crosslinked protein mixtures, we demonstrate that it computes accurate and highly discriminating probabilities, enabling as many as 75% more identifications than was previously possible using only search scores and a predictable false discovery rate. AVAILABILITY AND IMPLEMENTATION: XLinkProphet software is freely available on the web at http://brucelab.gs.washington.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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