ArticleEuPA open proteomics2015
Detecting Significant Changes in Protein Abundance.
Article in EuPA open proteomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 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
190 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Flimma: a federated and privacy-aware tool for differential gene expression analysis.Genome biology · 2021Pooled it
- Comparison of tear proteomic and neuromediator profiles changes between small incision lenticule extraction (SMILE) and femtosecond laser-assisted in-situ keratomileusis (LASIK).Journal of advanced research · 2021Trial
- High-throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers.Molecular oncology · 2021Trial
- Differential protein expression analysis of quantitative mass spectrometry data using DEqMS.Nature protocols · 2026Review
- PiProteline: An R Package for Integrated Proteomics Data Analysis, from Label-Free Quantitation to Systems Biology.Biology · 2026Article
- Adjunctive nebulization of Idursulfase to intravenous treatment enhances cardiac proteome adaptations in IDS-KO mice.bioRxiv : the preprint server for biology · 2026Article
- Proteasome-dependent protein degradation shapes developmental tempo in mouse and human neural progenitors.Developmental cell · 2026Article
- Neuroproteasomes regulate endogenous tau paired helical filament formation in an APOE genotype- and age-dependent manner.Nature neuroscience · 2026Article
- Stress granules formed during infections with RNA viruses have significant virus-specific differences in generation and composition.PLoS biology · 2026Article
- A journey through the molecular networks of endomyocardial biopsies to explore ATTR and ALiScience · 2026Article
- Ground Truth-Based Evaluation of False Discovery Rate and Statistical Power in DIA Proteomics.bioRxiv : the preprint server for biology · 2026Article
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- Integrated transcriptomic and proteomic analyses identify novel biomarkers of bladder outlet obstruction.bioRxiv : the preprint server for biology · 2026Article
- Computational proteomics to enhance personalized treatment of COVID-19 and Long COVID.Clinical proteomics · 2026Review
- Covalent Protein Inhibitors via Tyrosine and Tryptophan Conjugation with Cyclic Imine Mannich Electrophiles.Angewandte Chemie (International ed. in English) · 2026Article
- Engineered GM1 Intersects Between Mitochondrial and Synaptic Pathways to Ameliorate ALS Pathology.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Bumped Kinase Inhibitor BKI-1708 Interferes in Cytokinesis and Drives Baryzoite Conversion in the Cyst-Forming Apicomplexan ParasitesInternational journal of molecular sciences · 2026Article
- Deciphering Stiffness-Driven Changes in Colorectal Cancer by Proteomics.Molecular & cellular proteomics : MCP · 2026Article
- Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8.Nucleic acids research · 2026Article
- 3D Visualization and Proteomic Analysis of Human Cardiac Transthyretin Amyloidosis Tissue Reveals Microangiopathy and Capillary Occlusion.bioRxiv : the preprint server for biology · 2026Article
130 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
4 authors.
Funding
Abstract
We review and demonstrate how an empirical Bayes method, shrinking a protein's sample variance towards a pooled estimate, leads to far more powerful and stable inference to detect significant changes in protein abundance compared to ordinary t-tests. Using examples from isobaric mass labeled proteomic experiments we show how to analyze data from multiple experiments simultaneously, and discuss the effects of missing data on the inference. We also present easy to use open source software for normalization of mass spectrometry data and inference based on moderated test statistics.
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.