ArticlePloS one2009
Empirical Bayes analysis of quantitative proteomics experiments.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
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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.
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Who cites it
35 citing papers in PubMed, 50 citations in OpenAlex.
- Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells.Nature communications · 2025Article
- Oxidative Stress Induced Dysfunction of Protein Synthesis in 661W Mice Photoreceptor Cells.Proteomes · 2023Article
- Identification and characterization of the mediator kinase-dependent myometrial stem cell phosphoproteome.F&S science · 2021Article
- Sex Differences in the Ventral Tegmental Area and Nucleus Accumbens Proteome at Baseline and Following Nicotine Exposure.Frontiers in molecular neuroscience · 2021Article
- Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections.Frontiers in genetics · 2021Review
- Amyloid-beta peptide neurotoxicity in human neuronal cells is associated with modulation of insulin-like growth factor transport, lysosomal machinery and extracellular matrix receptor interactions.Neural regeneration research · 2020Article
- Comparison of Statistical Tests and Power Analysis for Phosphoproteomics Data.Journal of proteome research · 2020Article
- Association between phospholipid metabolism in plasma and spontaneous preterm birth: a discovery lipidomic analysis in the cork pregnancy cohort.Metabolomics : Official journal of the Metabolomic Society · 2020Article
- DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling.Bioinformatics (Oxford, England) · 2019Article
- Upregulation of Proteolytic Pathways and Altered Protein Biosynthesis Underlie Retinal Pathology in a Mouse Model of Alzheimer's Disease.Molecular neurobiology · 2019Article
- Amyloid β Induces Early Changes in the Ribosomal Machinery, Cytoskeletal Organization and Oxidative Phosphorylation in Retinal Photoreceptor Cells.Frontiers in molecular neuroscience · 2019Article
- IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Specificity of Phosphorylation Responses to Mitogen Activated Protein (MAP) Kinase Pathway Inhibitors in Melanoma Cells.Molecular & cellular proteomics : MCP · 2018Article
- Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules.Cell · 2018Article
- Corticotropin-releasing factor overexpression gives rise to sex differences in Alzheimer's disease-related signaling.Molecular psychiatry · 2017Article
- An IonStar Experimental Strategy for MS1 Ion Current-Based Quantification Using Ultrahigh-Field Orbitrap: Reproducible, In-Depth, and Accurate Protein Measurement in Large Cohorts.Journal of proteome research · 2017Article
- Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields.PloS one · 2017Article
- Classification-based quantitative analysis of stable isotope labeling by amino acids in cell culture (SILAC) data.Computer methods and programs in biomedicine · 2016Article
- Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics.Cell reports · 2016Article
- Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics.Journal of proteome research · 2015Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundAdvances in mass spectrometry-based proteomics have enabled the incorporation of proteomic data into systems approaches to biology. However, development of analytical methods has lagged behind. Here we describe an empirical Bayes framework for quantitative proteomics data analysis. The method provides a statistical description of each experiment, including the number of proteins that differ in abundance between 2 samples, the experiment's statistical power to detect them, and the false-positive probability of each protein. METHODOLOGY/PRINCIPAL
findingsWe analyzed 2 types of mass spectrometric experiments. First, we showed that the method identified the protein targets of small-molecules in affinity purification experiments with high precision. Second, we re-analyzed a mass spectrometric data set designed to identify proteins regulated by microRNAs. Our results were supported by sequence analysis of the 3' UTR regions of predicted target genes, and we found that the previously reported conclusion that a large fraction of the proteome is regulated by microRNAs was not supported by our statistical analysis of the data. CONCLUSIONS/SIGNIFICANCE: Our results highlight the importance of rigorous statistical analysis of proteomic data, and the method described here provides a statistical framework to robustly and reliably interpret such data.
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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.