ReviewNature communications2021
A proteomics sample metadata representation for multiomics integration and big data analysis.
Abstract readReview
In one paragraph
Review in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 2 of them syntheses that pooled it.
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74citing papers in PubMed, 2 pooled it
–field-weighted citation impact
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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.
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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
74 citing papers in PubMed, 2 syntheses or guidelines 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
- Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.Nature methods · 2023Guideline
- Standardized Annotation of Quantitative Proteomics Datasets Using SDRF-Proteomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Reviving Data Potential─The Reanalysis-Driven Metabolomics Data Repository MB-POST.Analytical chemistry · 2026Article
- Agentic AI-Assisted Coding Offers a Unique Opportunity to Instill Epistemic Grounding during Software Development.Journal of proteome research · 2026Article
- Temporal and Functional Profiling of the Microbiome of High and Low Nitrogen Content Barley Seed in Silo Storage.Food science & nutrition · 2026Article
- FRED enables standardized FAIR metadata generation and management for omics research.Scientific reports · 2026Article
- The need for standardization and improved open (meta)data practices in metaproteomics.Microbiome · 2026Article
- Article
- Rapid Histone Post-Translational Modification Analysis Using Alternative Proteases and Tandem Mass Tags.Analytical chemistry · 2026Article
- pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.Molecular & cellular proteomics : MCP · 2026Article
- Rapid Histone Post-Translational Modification Analysis Using Alternative Proteases and Tandem Mass Tags.bioRxiv : the preprint server for biology · 2026Article
- Review
- Semantic annotation of Glycomics and Glycoproteomics methods.Glycobiology · 2026Article
- Blood proteomics: insights from public data.Genome biology · 2026Review
- Semantic alignment of the German Human Genome-Phenome Archive metadata model in Europe's genomics field.Scientific data · 2026Article
- Unlocking the Next Decade of Proteomics with Standardized, Structured Metadata.Journal of proteome research · 2026Review
- TheJournal of proteome research · 2026Article
- BioSamples database: the global hub for sample metadata and multi-omics integration.Nucleic acids research · 2026Article
- EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025.Nucleic acids research · 2026Review
14 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
40 authors.
Chengxin DaiChongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China.
Anja FüllgrabeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.ORCID 0000-0002-8674-0039
Julianus PfeufferAlgorithmic Bioinformatics, Freie Universität Berlin, Berlin, Germany.
Elizaveta M SolovyevaMoscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.ORCID 0000-0002-3093-4774
Jingwen DengChongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China.
Pablo MorenoEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.ORCID 0000-0002-9856-1679
Selvakumar KamatchinathanEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Deepti Jaiswal KunduEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Nancy GeorgeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.ORCID 0000-0003-4183-8865
Silvie FexovaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Björn GrüningBioinformatics Group Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.ORCID 0000-0002-3079-6586
Melanie Christine FöllInstitute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
Johannes GrissDepartment of Dermatology, Medical University of Vienna, Vienna, Austria.ORCID 0000-0003-2206-9511
Marc VaudelDepartment of Clinical Sciences, University of Bergen, Bergen, Norway.ORCID 0000-0003-1179-9578
Enrique AudainDepartment of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany.ORCID 0000-0002-9201-7840
Marie Locard-PauletNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.ORCID 0000-0003-2879-9224
Michael TurewiczRuhr University Bochum, Medical Faculty, Medizinisches Proteom-Center, 44801, Bochum, Germany.ORCID 0000-0003-0737-1114
Martin EisenacherRuhr University Bochum, Medical Faculty, Medizinisches Proteom-Center, 44801, Bochum, Germany.ORCID 0000-0003-2687-7444
Julian UszkoreitRuhr University Bochum, Medical Faculty, Medizinisches Proteom-Center, 44801, Bochum, Germany.ORCID 0000-0001-7522-4007
Tim Van Den BosscheVIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.ORCID 0000-0002-5916-2587
Veit SchwämmleDepartment of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.ORCID 0000-0002-9708-6722
Henry WebelNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
Stefan SchulzeUniversity of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA.ORCID 0000-0002-4771-7987
David BouyssiéInstitute of Pharmacology and Structural Biology, University of Toulouse, CNRS, UPS, Toulouse, France.ORCID 0000-0002-0847-4759
Savita Jayaramnference Labs, Bengaluru, KA, 560017, India.
Vinay Kumar Duggineninference Labs, Bengaluru, KA, 560017, India.
Patroklos SamarasChair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany.ORCID 0000-0001-6042-1585
Mathias WilhelmChair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany.ORCID 0000-0002-9224-3258
Meena ChoiDepartment of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA.ORCID 0000-0002-6025-5035
Mingxun WangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
Oliver KohlbacherDepartment of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, 72076, Germany.ORCID 0000-0003-1739-4598
Alvis BrazmaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.ORCID 0000-0001-5988-7409
Irene PapatheodorouEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.ORCID 0000-0001-7270-5470
Nuno BandeiraSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0001-8385-3655
Eric W DeutschInstitute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
Juan Antonio VizcaínoEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.ORCID 0000-0002-3905-4335
Mingze BaiChongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China. baimz@cqupt.edu.cn.
Timo SachsenbergDepartment of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, 72076, Germany. timo.sachsenberg@uni-tuebingen.de.ORCID 0000-0002-2833-6070
Lev I LevitskyV.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia. lev.levitsky@phystech.edu.ORCID 0000-0002-4048-0876
Yasset Perez-RiverolEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK. yperez@ebi.ac.uk.ORCID 0000-0001-6579-6941
Funding
Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computingR01GM087221 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI DEUTSCH, ERIC, MORITZ, ROBERT L · 2010 to 2021
$6.0MMassIVE.quant: a curated and scalable community resource for quantitative proteomicsR01LM013115 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BANDEIRA, NUNO · 2019 to 2022
$1.3MAdvancing data and metadata standards for proteomics mass spectraR24GM127667 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI DEUTSCH, ERIC · 2017 to 2019
$1.2MNIGMS NIH HHS R01 GM087221NIGMS NIH HHS R24 GM127667NLM NIH HHS R01 LM013115Wellcome TrustWellcome Trust 208391/Z/17/Z
Abstract
The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.
Indexed as
Data AnalysisDatabases, ProteinMetadataProteomicsBig DataHumansReproducibility of ResultsSoftwareTranscriptome
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Textmetadata
LicenceCC BY
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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.