ArticleJournal of proteome research2013
When target-decoy false discovery rate estimations are inaccurate and how to spot instances.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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.
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Who cites it
8 citing papers in PubMed.
- Workflow enhancement of TurboID-mediated proximity labeling for SPY signaling network mapping.bioRxiv : the preprint server for biology · 2024Article
- MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts.Mass spectrometry reviews · 2019Review
- Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides.Molecular & cellular proteomics : MCP · 2016Article
- New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets.Analytical chemistry · 2014Article
- Proteomics for systems toxicology.Computational and structural biotechnology journal · 2014Review
- MS-viewer: a web-based spectral viewer for proteomics results.Molecular & cellular proteomics : MCP · 2014Article
- Matching cross-linked peptide spectra: only as good as the worse identification.Molecular & cellular proteomics : MCP · 2014Article
- Lessons in de novo peptide sequencing by tandem mass spectrometry.Mass spectrometry reviewsReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
To address problems with estimating the reliability of proteomic search engine results from mass spectrometry fragmentation data, the use of target-decoy database searching has become the de facto approach for estimating a false discovery rate. Several articles have been written about the effects of different ways of creating the decoy database, effects of the search engine scoring, or effects of search parameters on whether this approach provides an accurate estimate, not all agreeing with each other's conclusions. Hence, there may be some confusion about how effective this approach is and how broadly it can be applied. Although it is generally very effective, in this article I will try to emphasize some of the pitfalls and dangers of using the target-decoy approach and will indicate tell-tale signs that something may be amiss. This information will hopefully help researchers become more astute in their assessment of search results.
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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.