ArticleJournal of proteome research2022
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation.
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 32 papers, 3 of them syntheses that pooled it.
What it found
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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
32 citing papers in PubMed, 3 syntheses or guidelines pooled it, 39 citations in OpenAlex.
- 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
- Integrative Proteomic Analysis Implicates Inhibition of Intracellular Protein Trafficking in Therapy-Induced Migrastasis in Prostate Cancer.Proteomes · 2026Article
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- Contemporary design of small-molecule kinase modulators: orthosteric, allosteric and induced-proximity strategies.Nature reviews. Drug discovery · 2026Review
- An AI-enabled structural atlas decodes kinase specificity across the human proteome.Nature biotechnology · 2026Article
- Evolution-guided prioritization identifies a tissue-specific phosphorylation switch on herpes simplex virus 1 UL7 regulating viral replication and pathogenicity.Journal of virology · 2026Article
- A Landscape Analysis of Human SUMOylation.Molecular & cellular proteomics : MCP · 2026Article
- A comprehensive proteome and phosphoproteome atlas across nine organs of the Chinese hamster.Animal models and experimental medicine · 2026Article
- Post-translational modifications as a regulatory code for tau function in health and disease.Frontiers in dementia · 2026Review
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- Are you having a LaPh? Diverse roles of Labile Phosphorylation in mammalian cells.Biochemical Society transactions · 2025Review
- Unraveling Stuttering Through a Multi-Omics Lens.Life (Basel, Switzerland) · 2025Article
- Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance.Journal of proteome research · 2025Article
- Theoretical evaluation of the biological activity of hydrogen.Medical gas research · 2025Review
- Searching for Sulfotyrosines (sY) in a HA(pY)STACK.Journal of proteome research · 2025Article
- High-throughput approaches for the identification of ribosome heterogeneity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research.Scientific data · 2024Article
- The fitness cost of spurious phosphorylation.The EMBO journal · 2024Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
Abstract
Public phosphorylation databases such as PhosphoSitePlus (PSP) and PeptideAtlas (PA) compile results from published papers or openly available mass spectrometry (MS) data. However, there is no database-level control for false discovery of sites, likely leading to the overestimation of true phosphosites. By profiling the human phosphoproteome, we estimate the false discovery rate (FDR) of phosphosites and predict a more realistic count of true identifications. We rank sites into phosphorylation likelihood sets and analyze them in terms of conservation across 100 species, sequence properties, and functional annotations. We demonstrate significant differences between the sets and develop a method for independent phosphosite FDR estimation. Remarkably, we report estimated FDRs of 84, 98, and 82% within sets of phosphoserine (pSer), phosphothreonine (pThr), and phosphotyrosine (pTyr) sites, respectively, that are supported by only a single piece of identification evidence─the majority of sites in PSP. We estimate that around 62 000 Ser, 8000 Thr, and 12 000 Tyr phosphosites in the human proteome are likely to be true, which is lower than most published estimates. Furthermore, our analysis estimates that 86 000 Ser, 50 000 Thr, and 26 000 Tyr phosphosites are likely false-positive identifications, highlighting the significant potential of false-positive data to be present in phosphorylation databases.
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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.