Method Evaluation of Liquid Biopsy Proteomics for Limited Plasma Volume
Abstract
One of the biggest challenges in plasma proteomics is to reduce the dynamic range of plasma proteins to capture the expression of low-abundance proteins. Although abundant protein depletion and proximity extension assay are widely used for human samples, the application to animal species in non-clinical assessment remains limited. Here, we evaluated the Mag-Net and ENRICH-iST methods using 20 μl of plasma from both healthy and type 2 diabetes model rats. By combining with the optimized LC-MS method, Mag-Net identified more proteins than ENRICH-iST with high precision, although both methods identified over 5000 proteins. Using integrative proteomics and analytical approaches, including extracellular vesicle (EV) database comparison, Gene Ontology analysis, Simple Western, nanoparticle tracking analysis, and contamination assessments, we demonstrated in rat plasma that Mag-Net preferentially enriches EV proteins, whereas ENRICH-iST more evenly captures low-abundance proteins, including EV proteins. Regardless of the protein enrichment method employed, more than half of the tissue-specific proteins were classified as being specific to either the liver or the brain tissues. Whereas, several liver-specific proteins involved in protein-protein interactions, including Proz/Serpina10 and Ambp/Itih1/Itih2, were identified as exhibiting over a ten-fold increase in mean quantification values in the Mag-Net method compared to ENRICH-iST, suggesting enhanced enrichment of protein-protein…
Read the paper
Related studies
- Antioxidant efficacy and the upregulation of Nrf2-mediated HO-1 expression by (+)-lariciresinol, a lignan isolated from Rubia philippinensis, through the activation of p38
- Anti-influenza virus activity of green tea by-products in vitro and efficacy against influenza virus infection in chickens
- Therapeutic Potential of Mesenchymal Stem Cells (MSCs) and MSC-Derived Extracellular Vesicles for the Treatment of Spinal Cord Injury
- The intratumoral administration of ferucarbotran conjugated with doxorubicin improved therapeutic effect by magnetic hyperthermia combined with pharmacotherapy in a hepatocellular carcinoma model
- Enhanced anticancer efficacy of TRAIL-conjugated and odanacatib-loaded PLGA nanoparticles in TRAIL resistant cancer
- In vivo tracking of bioorthogonally labeled T-cells for predicting therapeutic efficacy of adoptive T-cell therapy
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.