ArticleJournal of proteome research2015
Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Ketogenic Metabolism in Neurodegenerative Diseases: Mechanisms of Action and Therapeutic Potential.Metabolites · 2025Review
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- Query Mix-Max Method for FDR Estimation Supported by Entrapment Queries.Journal of proteome research · 2025Article
- Ion entropy and accurate entropy-based FDR estimation in metabolomics.Briefings in bioinformatics · 2024Article
- Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier.PLoS computational biology · 2023Article
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- Considerations for constructing a protein sequence database for metaproteomics.Computational and structural biotechnology journal · 2022Review
- Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen.Nature communications · 2021Article
- Proteome Analysis of Molecular Events in Oral Pathogenesis and Virus: A Review with a Particular Focus on Periodontitis.International journal of molecular sciences · 2020Review
- MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts.Mass spectrometry reviews · 2019Review
- Learning Concave Conditional Likelihood Models for Improved Analysis of Tandem Mass Spectra.Advances in neural information processing systems · 2018Article
- A Matter of Time: Faster Percolator Analysis via Efficient SVM Learning for Large-Scale Proteomics.Journal of proteome research · 2018Article
- Controlling the FDR in imperfect matches to an incomplete database.Journal of the American Statistical Association · 2018Article
- Gradients of Generative Models for Improved Discriminative Analysis of Tandem Mass Spectra.Advances in neural information processing systems · 2017Article
- Significance estimation for large scale metabolomics annotations by spectral matching.Nature communications · 2017Article
- Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2017Article
- LipidFinder: A computational workflow for discovery of lipids identifies eicosanoid-phosphoinositides in platelets.JCI insight · 2017Article
- Fuzzy-FishNET: a highly reproducible protein complex-based approach for feature selection in comparative proteomics.BMC medical genomics · 2016Article
- Faster and more accurate graphical model identification of tandem mass spectra using trellises.Bioinformatics (Oxford, England) · 2016Article
- Tandem Mass Spectrum Identification via Cascaded Search.Journal of proteome research · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interpreting the potentially vast number of hypotheses generated by a shotgun proteomics experiment requires a valid and accurate procedure for assigning statistical confidence estimates to identified tandem mass spectra. Despite the crucial role such procedures play in most high-throughput proteomics experiments, the scientific literature has not reached a consensus about the best confidence estimation methodology. In this work, we evaluate, using theoretical and empirical analysis, four previously proposed protocols for estimating the false discovery rate (FDR) associated with a set of identified tandem mass spectra: two variants of the target-decoy competition protocol (TDC) of Elias and Gygi and two variants of the separate target-decoy search protocol of Käll et al. Our analysis reveals significant biases in the two separate target-decoy search protocols. Moreover, the one TDC protocol that provides an unbiased FDR estimate among the target PSMs does so at the cost of forfeiting a random subset of high-scoring spectrum identifications. We therefore propose the mix-max procedure to provide unbiased, accurate FDR estimates in the presence of well-calibrated scores. The method avoids biases associated with the two separate target-decoy search protocols and also avoids the propensity for target-decoy competition to discard a random subset of high-scoring target identifications.
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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.