ArticleJournal of proteome research2019
Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate.
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.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Query Mix-Max Method for FDR Estimation Supported by Entrapment Queries.Journal of proteome research · 2025Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Article
- HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search.Journal of proteome research · 2023Article
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Unveiling the Links Between Peptide Identification and Differential Analysis FDR Controls by Means of a Practical Introduction to Knockoff Filters.Methods in molecular biology (Clifton, N.J.) · 2023Article
- False discovery rate estimation using candidate peptides for each spectrum.BMC bioinformatics · 2022Article
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- Null-free False Discovery Rate Control Using Decoy Permutations.Acta mathematicae applicatae Sinica (English series) · 2022Article
- Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics.Journal of proteome research · 2021Article
- Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.Journal of proteome research · 2021Article
- Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments.Journal of proteome research · 2020Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed data set analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, data sets, or databases. The average TDC (aTDC) protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. We provide a tutorial introduction to aTDC, describe an improved variant of the protocol that offers increased statistical power, and discuss how to deploy aTDC in practice using the Crux software toolkit.
Indexed as
Identifiers
What OpenQuestion holds
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.