ArticleEMBO molecular medicine2025
Pre-analytical drivers of bias in bead-enriched plasma proteomics.
Article in EMBO molecular medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Nanoparticle-enriched mass spectrometry proteomics in British South Asians identifies links between genetic variants, plasma protein levels and disease risk.Nature genetics · 2026Article
- Proteomic Biomarker Discovery in Breast Cancer: Advances, Challenges, and Translational Prospects.Journal of biochemical and molecular toxicology · 2026Review
- Translational bottlenecks in blood-based proteomics.EMBO molecular medicine · 2026Article
- Development and Validation of a Streamlined Workflow for Proteomic Analysis of Proteins and Post-translational Modifications from Dried Blood.Journal of proteome research · 2026Article
- Leveraging nanoparticle protein corona to advance plasma proteome profiling.Nature communications · 2026Review
- Benchmarking Plasma Proteomics Workflows and Their Correlation to Clinical Routine Protein Assays.Journal of proteome research · 2026Article
- Systematic Evaluation of Depletion and Enrichment Technologies for Platelet-Free Plasma Proteomics.Journal of proteome research · 2026Article
- Method Evaluation of Liquid Biopsy Proteomics for Limited Plasma Volume.Molecular & cellular proteomics : MCP · 2026Article
- Deeper is not always better in plasma proteomics.Nature biotechnology · 2026Article
- Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery.Journal of proteome research · 2026Article
- Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies.bioRxiv : the preprint server for biology · 2026Article
- Blood proteomics: insights from public data.Genome biology · 2026Review
- Defining the reference proteomes for small extracellular vesicles and non-vesicular components.Nature cell biology · 2026Article
- Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics.Journal of proteome research · 2026Article
- Qoppa as a New Pan-Tumor Synthetic Parameter Derived from Tumor-Associated Biomarkers for Identifying Oncology Patients at High Risk of Metastasis: A Prospective Pilot Study.Journal of clinical medicine · 2026Article
- Blood Matrices and Sample Preparation Influence Blood Marker Discovery.Journal of proteome research · 2026Article
- Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics.EMBO molecular medicine · 2026Article
- Machine learning-guided deconvolution of plasma protein levels.Molecular systems biology · 2025Article
- Evaluation of Nanoparticle-Based Plasma Enrichment on Individuals with Primary and Metastatic Pancreatic Cancer.Cancers · 2025Article
- Development and validation of a streamlined workflow for proteomic analysis of proteins and post-translational modifications from dried blood.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Bead-based enrichment is a promising strategy to improve depth in plasma proteomics by overcoming the dynamic range barrier. However, its robustness against pre-analytical variation has not been sufficiently characterized. Here, we systematically evaluate five plasma proteomics workflows, including three bead-based methods, a neat workflow, and a precipitation protocol using spike-ins of low-abundance proteins and defined cellular contaminants. We find that bead-based approaches enhance detection of low-abundance proteins but can be highly susceptible to systematic bias from platelet and PBMC contamination. This can inflate results by thousands of proteins, potentially explaining some of the high literature-reported numbers. A perchloric acid-based workflow shows resistance to erythrocyte and platelet-derived contamination. We investigate how centrifugation conditions, anticoagulant choice, and buffer-bead combinations modulate contamination profiles and demonstrate that bias can be mitigated by optimized sample handling. Altogether, we identify more than 13,000 different protein groups, including cellular components from the circulating proteome. Our results provide a quantitative framework for assessing workflow performance under variable sample quality and offer guidance for both biomarker discovery and quality control in clinical proteomics studies.
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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 Socratic graph.