ArticleJournal of proteome research2022
Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 3 of them syntheses that pooled it.
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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
23 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- An AI-Ready Phosphorylation Meta-Analysis forJournal of proteome research · 2026Pooled it
- Phosphorylation in theJournal of proteome research · 2024Pooled it
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
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- A Landscape Analysis of Human SUMOylation.Molecular & cellular proteomics : MCP · 2026Article
- TheJournal of proteome research · 2026Article
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- The functional landscape of the human ubiquitinome.bioRxiv : the preprint server for biology · 2025Article
- Article
- The PRIDE database at 20 years: 2025 update.Nucleic acids research · 2025Article
- Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research.Scientific data · 2024Article
- Pyro(phospho)mania.Nature chemical biology · 2024Article
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome.bioRxiv : the preprint server for biology · 2023Article
- Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond.Chemical communications (Cambridge, England) · 2023Review
- Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis.Journal of cell communication and signaling · 2023Article
- Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets.Journal of proteome research · 2023Article
- Principles of phosphoproteomics and applications in cancer research.The Biochemical journal · 2023Article
- Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.Journal of proteome research · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Phosphoproteomic methods are commonly employed to identify and quantify phosphorylation sites on proteins. In recent years, various tools have been developed, incorporating scores or statistics related to whether a given phosphosite has been correctly identified or to estimate the global false localization rate (FLR) within a given data set for all sites reported. These scores have generally been calibrated using synthetic datasets, and their statistical reliability on real datasets is largely unknown, potentially leading to studies reporting incorrectly localized phosphosites, due to inadequate statistical control. In this work, we develop the concept of scoring modifications on a decoy amino acid, that is, one that cannot be modified, to allow for independent estimation of global FLR. We test a variety of amino acids, on both synthetic and real data sets, demonstrating that the selection can make a substantial difference to the estimated global FLR. We conclude that while several different amino acids might be appropriate, the most reliable FLR results were achieved using alanine and leucine as decoys. We propose the use of a decoy amino acid to control false reporting in the literature and in public databases that re-distribute the data. Data are available via ProteomeXchange with identifier PXD028840.
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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.