ArticleScientific data2022
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Bovine Corpus Luteum Proteomics during Different Reproductive and Physiological Stages.Scientific data · 2026Article
- Review
- Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow.Journal of proteome research · 2026Article
- Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration.Nucleic acids research · 2026Article
- Proteomic Analysis of Cerebrospinal Fluid: Toward the Identification of Biomarkers for Early Central Nervous System Infection.Infection and drug resistance · 2026Article
- An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.Proteomics · 2025Article
- Mouse Bone Marrow Neutrophil Extracellular Trap Proteomics by Microbial Stimuli.Scientific data · 2025Article
- Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets.Journal of proteome research · 2025Article
- The PRIDE database at 20 years: 2025 update.Nucleic acids research · 2025Article
- Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues.Journal of proteome research · 2024Article
- PMHeliyon · 2024Article
- Article
- Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine.Annual review of pharmacology and toxicology · 2024Review
- Expression Atlas update: insights from sequencing data at both bulk and single cell level.Nucleic acids research · 2024Article
- Article
- Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.Proteomics · 2023Article
- Integrated View of Baseline Protein Expression in Human Tissues.Journal of proteome research · 2023Article
- The ProteomeXchange consortium at 10 years: 2023 update.Nucleic acids research · 2023Article
- Article
- Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.PLoS computational biology · 2022Article
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Authors and funding
12 authors.
Funding
Abstract
The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.
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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.