ReviewProteomes2021
Proteome Discoverer-A Community Enhanced Data Processing Suite for Protein Informatics.
Review in Proteomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 185 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
185 citing papers in PubMed.
- Differential protein expression analysis of quantitative mass spectrometry data using DEqMS.Nature protocols · 2026Review
- Estimating protein isoform abundances with [Formula: see text].Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structure of NO16, a marine non-tailed vibriophage with an unusual symmetry-mismatched vertex arrangement.PLoS pathogens · 2026Article
- XunZi, an AI biologist, reveals disease-modifying targets.Nature biomedical engineering · 2026Article
- Application of Proteogenomic Approaches for Refinement of the Entamoeba histolytica Reference Genome Using High Resolution Mass-Spectrometry Data.Acta parasitologica · 2026Article
- Calcium and phosphorylation coordination is a novel mechanism that stabilises protein-complexes during HIV assembly.Journal of biomedical science · 2026Article
- Endurance exercise elicits temporal and sexual dimorphic multi-omics remodeling of liver metabolism revealed by MoTrPAC.Cell reports · 2026Article
- A decline in skeletal muscle NOX4 abrogates exercise-induced adaptive homeostasis and exacerbates biological aging.Science advances · 2026Article
- Metformin Redirects Autophagy from Bulk Turnover to Mitochondrial Clearance.bioRxiv : the preprint server for biology · 2026Article
- Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2.Molecular & cellular proteomics : MCP · 2026Article
- Article
- Hepatic ketogenic insufficiency blunts exercise-induced energy expenditure and alters mitochondrial proteins in skeletal muscle.Function (Oxford, England) · 2026Article
- Review
- Proteomic and degradomic signatures of extracellular matrix remodeling in calcific aortic valve stenosis.Molecular medicine (Cambridge, Mass.) · 2026Article
- Peptide-to-Protein Data Aggregation Using Fisher's Method Improves Target Identification in Chemical Proteomics.Analytical chemistry · 2026Article
- Phosphoproteomic and kinase networks reveal partial EMT and stress-adaptive growth programs in pediatric Peutz-Jeghers polyps.Pediatric research · 2026Article
- Transcriptomic and proteomic profiling of piroplasmosis resistance in Yunnan humped cattle.BMC genomics · 2026Article
- Prebiotic intervention changes host and microbe proteomes in plasma extracellular vesicles of Parkinson's disease.Scientific reports · 2026Article
- Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data.bioRxiv : the preprint server for biology · 2026Article
125 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
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers have defaulted to the vendor software Proteome Discoverer. Over the fourteen years since the initial release of the software, it has evolved in parallel with the increasingly complex demands faced by proteomics researchers. Today, Proteome Discoverer exists in two distinct forms with both powerful commercial versions and fully functional free versions in use in many labs today. Throughout the 11 main versions released to date, a central theme of the software has always been the ability to easily view and verify the spectra from which identifications are made. This ability is, even today, a key differentiator from other data analysis solutions. In this review I will attempt to summarize the history and evolution of Proteome Discoverer from its first launch to the versions in use today.
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.