ArticleJournal of proteome research2020
EPIFANY: A Method for Efficient High-Confidence Protein Inference.
Article in Journal of proteome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The Peptonizer2000: Bringing Confidence to Metaproteomics.Journal of proteome research · 2026Article
- IsoBayes: a Bayesian approach for single-isoform proteomics inference.Bioinformatics (Oxford, England) · 2025Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer.bioRxiv : the preprint server for biology · 2024Article
- Integrative Multi-Omics Analysis of Oncogenic EZH2 Mutants: From Epigenetic Reprogramming to Molecular Signatures.International journal of molecular sciences · 2023Article
- PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores.Bioinformatics (Oxford, England) · 2023Article
- ProInfer: An interpretable protein inference tool leveraging on biological networks.PLoS computational biology · 2023Article
- Overview and considerations in bottom-up proteomics.The Analyst · 2023Review
- Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups.Molecular & cellular proteomics : MCP · 2022Article
- MetaLP: An integrative linear programming method for protein inference in metaproteomics.PLoS computational biology · 2022Article
- Enhanced protein isoform characterization through long-read proteogenomics.Genome biology · 2022Article
- Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs.PloS one · 2022Article
- Proteomic analysis of the umbilical cord in fetal growth restriction and preeclampsia.PloS one · 2022Article
- Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy.Journal of proteome research · 2021Article
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Authors and funding
6 authors.
Funding
Abstract
Accurate protein inference in the presence of shared peptides is still one of the key problems in bottom-up proteomics. Most protein inference tools employing simple heuristic inference strategies are efficient but exhibit reduced accuracy. More advanced probabilistic methods often exhibit better inference quality but tend to be too slow for large data sets. Here, we present a novel protein inference method, EPIFANY, combining a loopy belief propagation algorithm with convolution trees for efficient processing of Bayesian networks. We demonstrate that EPIFANY combines the reliable protein inference of Bayesian methods with significantly shorter runtimes. On the 2016 iPRG protein inference benchmark data, EPIFANY is the only tested method that finds all true-positive proteins at a 5% protein false discovery rate (FDR) without strict prefiltering on the peptide-spectrum match (PSM) level, yielding an increase in identification performance (+10% in the number of true positives and +14% in partial AUC) compared to previous approaches. Even very large data sets with hundreds of thousands of spectra (which are intractable with other Bayesian and some non-Bayesian tools) can be processed with EPIFANY within minutes. The increased inference quality including shared peptides results in better protein inference results and thus increased robustness of the biological hypotheses generated. EPIFANY is available as open-source software for all major platforms at https://OpenMS.de/epifany.
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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 Socratic graph.