ArticleJournal of proteome research2025
Impact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics.
Article in Journal of proteome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Fibroblast-Derived Decellularized Extracellular Matrix as a Bioactive Substrate for Osteoblast Activation.ACS omega · 2026Article
- Systematic Evaluation of Depletion and Enrichment Technologies for Platelet-Free Plasma Proteomics.Journal of proteome research · 2026Article
- Advancing DIA-Based Limited Proteolysis Workflows: Introducing DIA-LiPA.Analytical chemistry · 2026Article
- Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics.Journal of proteome research · 2025Article
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Authors and funding
6 authors.
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Abstract
Serum proteomics plays a crucial role in biomarker discovery and disease research, yet the selection of an optimal sample preparation method remains challenging. Evaluating the accuracy of protein quantitation is of major importance and a vital part of a benchmarking study in proteomics, since clinical studies are based on the differential expression of certain proteins that can be used as biomarkers or be indicative of a pathological state. In this study, we performed a direct comparison of 6 widely used serum proteomic sample preparation workflows: In-gel digestion (IGD), Single-Pot Solid-Phase-enhanced Sample Preparation (SP3), Top 14 Abundant Protein Depletion (Top 14), Isopropanol/Trichloroacetic Acid (IPA/TCA) precipitation, PreOmics ENRICH-iST (PreOmics), and Seer Proteograph XT (Seer). Seer and PreOmics demonstrated superior quantitative accuracy, especially for proteins with low abundance in serum, while the Seer enrichment approach provided the highest number of protein identifications (>2000) as measured by an Orbitrap Exploris 480. All methods had median CVs close to or below 20%. This comparative analysis provides a comprehensive resource for selecting the most appropriate serum sample preparation strategy based on specific experimental needs, facilitating human serum proteomic profiling for biomedical research.
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