ArticleNature methods2024
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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
34 citing papers in PubMed.
- MCOD: a memory-constrained deep learning framework for robust outlier detection in quantitative proteomics.Briefings in bioinformatics · 2026Article
- pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.Molecular & cellular proteomics : MCP · 2026Article
- Unpaired data as a first-order challenge in single-cell and spatial proteomics.Nature biotechnology · 2026Article
- Development of PROTACs for targeted degradation of oncogenic TRK fusions.RSC chemical biology · 2026Article
- Extensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs.Journal of neuroinflammation · 2026Article
- Blood proteomics: insights from public data.Genome biology · 2026Review
- Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow.Journal of proteome research · 2026Article
- Navigating the conjugated metabolome.bioRxiv : the preprint server for biology · 2026Article
- EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025.Nucleic acids research · 2026Review
- BioSamples database: the global hub for sample metadata and multi-omics integration.Nucleic acids research · 2026Article
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms.Nucleic acids research · 2026Article
- Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.BMC bioinformatics · 2026Article
- Proteomics Approaches to Ecoimmunology: New Insights into Wildlife Immunity and Disease.Integrative and comparative biology · 2025Review
- Characterisation of human in vitro tumour-associated macrophage models to define translational relevance.Scientific reports · 2025Article
- Genomic, Proteomic, and Biochemical Study ofJournal of agricultural and food chemistry · 2025Article
- Facilitating analysis and dissemination of proteomics data through metadata integration in MaxQuant.Nature communications · 2025Article
- Integration of multi-omics approaches in exploring intra-tumoral heterogeneity.Cancer cell international · 2025Review
- Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.Journal of proteome research · 2025Article
- The evolution of analytical techniques for multiplex analysis of protein biomarkers.Expert review of proteomics · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
The volume of public proteomics data is rapidly increasing, causing a computational challenge for large-scale reanalysis. Here, we introduce quantms ( https://quant,ms.org/ ), an open-source cloud-based pipeline for massively parallel proteomics data analysis. We used quantms to reanalyze 83 public ProteomeXchange datasets, comprising 29,354 instrument files from 13,132 human samples, to quantify 16,599 proteins based on 1.03 million unique peptides. quantms is based on standard file formats improving the reproducibility, submission and dissemination of the data to ProteomeXchange.
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.