ArticleThe Plant cell2021
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
- Identification of the plant mitochondrial OrfX protein: A mass spectrometry approach.FEBS letters · 2026Article
- AData in brief · 2026Article
- The Effects of Rapid Mitochondrial Gene Loss on Organellar Proteomes.Genome biology and evolution · 2026Article
- Article
- Exploring specialized metabolic pathways in medicinal plants with single-cell and spatial omics.Acta pharmaceutica Sinica. B · 2026Review
- Impact of alternative splicing on Arabidopsis proteome.Nucleic acids research · 2026Article
- A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs.Scientific data · 2026Article
- Quantitative western blotting adapted for expanded sample capacity with non-linear curve fitting.Journal of plant research · 2026Article
- TheJournal of proteome research · 2026Article
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- LanthMS: A Computational Tool for the Structure Elucidation of Lanthipeptides from Tandem Mass Spectrometry Data.Protein and peptide letters · 2026Article
- AI-integrated digital breeding for crop improvement.Frontiers in plant science · 2026Review
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- With or without a CaPlanta · 2025Article
- Impact of alternative splicing on Arabidopsis proteome.bioRxiv : the preprint server for biology · 2025Article
- Plant MutS2 proteins function in plastid ribosome quality control.bioRxiv : the preprint server for biology · 2025Article
- High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.bioRxiv : the preprint server for biology · 2025Article
- A spatio-temporal transcriptomic and proteomic dataset of developing Brassica napus seeds.Scientific data · 2025Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.
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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.