ArticleJournal of proteome research2024
A Framework for Quality Control in Quantitative Proteomics.
Article in Journal of proteome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- MCOD: a memory-constrained deep learning framework for robust outlier detection in quantitative proteomics.Briefings in bioinformatics · 2026Article
- DIA proteomics of FFPE renal biopsies reveals two molecular subtypes of lupus nephritis and identifies APOL1 as candidate biomarker for stratification.Lupus science & medicine · 2026Article
- Label-Free Targeted Proteomics Data Analysis Workflow Selection - Benchmarking AI-based and Data-Driven Approaches.Molecular & cellular proteomics : MCP · 2026Article
- Circulating extracellular vesicles in plasma carry accessible molecular signatures of aging in mice.bioRxiv : the preprint server for biology · 2026Article
- Identification and characterization of a novel aldehyde metabolite of WIN18,446 and associated WIN18,446-ALDH1A2 protein adducts using mass spectrometry.Drug metabolism reviews · 2026Article
- A quantitative proteomics dataset for assessment and prediction of low dose X-ray radiation exposure in mice.bioRxiv : the preprint server for biology · 2026Article
- Proteomic profiling of human omental and subcutaneous adipose tissue in individuals with a broad range of BMI.Scientific data · 2026Article
- Is Protein Quantification and Physical Normalization Always Necessary in Proteomics?bioRxiv : the preprint server for biology · 2026Article
- Development of Highly Multiplex Targeted Proteomics Assays in Biofluids Using a Nominal Mass Ion Trap Mass Spectrometer.Molecular & cellular proteomics : MCP · 2026Article
- Gas Chromatography-Mass Spectrometry (GC-MS) in the Plant Metabolomics Toolbox: GC-MS in Multi-Platform Metabolomics and Integrated Multi-Omics Research.International journal of molecular sciences · 2026Review
- Proteomic Profiling of Human Omental and Subcutaneous Adipose Tissue in Individuals with a Broad Range of BMI.bioRxiv : the preprint server for biology · 2026Article
- Proteomics Approaches to Ecoimmunology: New Insights into Wildlife Immunity and Disease.Integrative and comparative biology · 2025Review
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Development and Validation of a Novel LC-MS/MS-Based Proteomics Method for Quantitation of Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR).Journal of proteome research · 2025Article
- QSample: An Automated System for Rapid Monitoring of Quality Indicators in Proteomics Samples.Journal of proteome research · 2025Article
- Development and Validation of a Novel LC-MS/MS Based Proteomics Method for Quantitation of Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR).bioRxiv : the preprint server for biology · 2025Article
- Part A: Implementing an Analyte Panel and Sampling Protocol for Quality Control in Mass Spectrometry Imaging.Rapid communications in mass spectrometry : RCM · 2025Article
- A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities.Journal of proteome research · 2025Article
- Advancements in Mass Spectrometry-Based Targeted Metabolomics and Lipidomics: Implications for Clinical Research.Molecules (Basel, Switzerland) · 2024Review
- Calculating and Reporting Coefficients of Variation for DIA-Based Proteomics.Journal of proteome research · 2024Review
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17 authors.
Funding
Abstract
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at the protein and peptide levels allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and ProteomeXchange under the identifier PXD051318.
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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.