ArticleMolecular & cellular proteomics : MCP2019
MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins.
Article in Molecular & cellular proteomics : MCP, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 50 citations in OpenAlex.
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- Targeting Inflammation by Pioglitazone and its R-Enantiomer Mitigates Pathological Myocardial Remodeling in Murine Hypertrophic Cardiomyopathy.JACC. Basic to translational science · 2026Article
- Ablation of ACSS2 drives alteration to cardiac and hepatic proteomic landscapes in a tissue- and sex-specific manner.Journal of proteomics · 2026Article
- From kidney injury to cardiac dysfunction: the central role of oxidative stress in diabetes and CKD.Basic research in cardiology · 2026Article
- Activation of the alpha 7 nicotinic acetylcholine receptor (CHRNA7) limits hypoxia-induced inflammatory responses and regulates collagens in cultured human granulosa cells†.Biology of reproduction · 2026Article
- NMR and proteomic analysis of Cornus officinalis extract reveals abundance of 5-hydroxymethylfurfural and induced expression of Nrf2 and superoxide dismutase-2 in 1.1B4 human pancreatic β-cells and murine islets.Molecular and cellular endocrinology · 2026Article
- Decoding adult murine pancreatic islet cell diversity through cell type-resolved proteomics and phosphoproteomics.Communications biology · 2025Article
- Metabolic control of glycosylation forms for establishing glycan-dependent protein interaction networks.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Increasing mass spectrometry throughput using time-encoded sample multiplexing.bioRxiv : the preprint server for biology · 2025Article
- Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE.Briefings in bioinformatics · 2025Article
- Contribution of hypoxia-inducible factor 1alpha to pathogenesis of sarcomeric hypertrophic cardiomyopathy.Scientific reports · 2025Article
- Oxidative stress initiates hemodynamic change in CKD-induced heart disease.Basic research in cardiology · 2024Article
- Multi-omics analysis of diabetic pig lungs reveals molecular derangements underlying pulmonary complications of diabetes mellitus.Disease models & mechanisms · 2024Article
- Single-nucleus proteomics identifies regulators of protein transport.bioRxiv : the preprint server for biology · 2024Article
- Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.Molecular & cellular proteomics : MCP · 2023Article
- Proteomics- and Metabolomics-Based Analysis of Metabolic Changes in a Swine Model of Pulmonary Hypertension.International journal of molecular sciences · 2023Article
- MS-DAP Platform for Downstream Data Analysis of Label-Free Proteomics Uncovers Optimal Workflows in Benchmark Data Sets and Increased Sensitivity in Analysis of Alzheimer's Biomarker Data.Journal of proteome research · 2023Article
- Proteomics and disease network associations evaluation of environmentally relevant Bisphenol A concentrations in a human 3D neural stem cell model.Frontiers in cell and developmental biology · 2023Article
- The hibernation-derived compound SUL-138 shifts the mitochondrial proteome towards fatty acid metabolism and prevents cognitive decline and amyloid plaque formation in an Alzheimer's disease mouse model.Alzheimer's research & therapy · 2022Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mass spectrometry based proteomics is the method of choice for quantifying genome-wide differential changes of protein expression in a wide range of biological and biomedical applications. Protein expression changes need to be reliably derived from many measured peptide intensities and their corresponding peptide fold changes. These peptide fold changes vary considerably for a given protein. Numerous instrumental setups aim to reduce this variability, whereas current computational methods only implicitly account for this problem. We introduce a new method, MS-EmpiRe, which explicitly accounts for the noise underlying peptide fold changes. We derive data set-specific, intensity-dependent empirical error fold change distributions, which are used for individual weighing of peptide fold changes to detect differentially expressed proteins (DEPs).In a recently published proteome-wide benchmarking data set, MS-EmpiRe doubles the number of correctly identified DEPs at an estimated FDR cutoff compared with state-of-the-art tools. We additionally confirm the superior performance of MS-EmpiRe on simulated data. MS-EmpiRe requires only peptide intensities mapped to proteins and, thus, can be applied to any common quantitative proteomics setup. We apply our method to diverse MS data sets and observe consistent increases in sensitivity with more than 1000 additional significant proteins in deep data sets, including a clinical study over multiple patients. At the same time, we observe that even the proteins classified as most insignificant by other methods but significant by MS-EmpiRe show very clear regulation on the peptide intensity level. MS-EmpiRe provides rapid processing (< 2 min for 6 LC-MS/MS runs (3 h gradients)) and is publicly available under github.com/zimmerlab/MS-EmpiRe with a manual including examples.
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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.