ArticleJournal of proteome research2020
Toward a Sample Metadata Standard in Public Proteomics Repositories.
Article in Journal of proteome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of published cerebrospinal fluid proteomics data identifies and validates metabolic enzyme panel as Alzheimer's disease biomarkers.Cell reports. Medicine · 2023Pooled it
- Fragment-level FAIRness: annotating scientific data and its provenance using data fragment selectors.Journal of integrative bioinformatics · 2026Article
- FRED enables standardized FAIR metadata generation and management for omics research.Scientific reports · 2026Article
- Review
- Blood proteomics: insights from public data.Genome biology · 2026Review
- The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration.Journal of mass spectrometry : JMS · 2025Article
- Metabolomics in neonatal sepsis: A critical appraisal of current evidence.Computational and structural biotechnology journal · 2025Review
- What is the real value of omics data? Enhancing research outcomes and securing long-term data excellence.Nucleic acids research · 2024Article
- Ten simple rules for starting FAIR discussions in your community.PLoS computational biology · 2023Article
- SMetaS: A Sample Metadata Standardizer for Metabolomics.Metabolites · 2023Article
- Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.Scientific data · 2022Article
- A knowledge graph to interpret clinical proteomics data.Nature biotechnology · 2022Article
- The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.Nucleic acids research · 2022Article
- A proteomics sample metadata representation for multiomics integration and big data analysis.Nature communications · 2021Review
- Sharing biological data: why, when, and how.FEBS letters · 2021Article
- The European Bioinformatics Institute: empowering cooperation in response to a global health crisis.Nucleic acids research · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Metadata is essential in proteomics data repositories and is crucial to interpret and reanalyze the deposited data sets. For every proteomics data set, we should capture at least three levels of metadata: (i) data set description, (ii) the sample to data files related information, and (iii) standard data file formats (e.g., mzIdentML, mzML, or mzTab). While the data set description and standard data file formats are supported by all ProteomeXchange partners, the information regarding the sample to data files is mostly missing. Recently, members of the European Bioinformatics Community for Mass Spectrometry (EuBIC) have created an open-source project called Sample to Data file format for Proteomics (https://github.com/bigbio/proteomics-metadata-standard/) to enable the standardization of sample metadata of public proteomics data sets. Here, the project is presented to the proteomics community, and we call for contributors, including researchers, journals, and consortiums to provide feedback about the format. We believe this work will improve reproducibility and facilitate the development of new tools dedicated to proteomics data analysis.
Indexed as
Identifiers
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.