IMSC: Facilitate Biomarker Discovery Using Integrated “Omics” Differential Analysis with High Resolution Accurate LC/MS

Význam tématu

Multi-omics approaches combining lipidomics, proteomics and glycoproteomics enable comprehensive molecular profiling of complex diseases such as type 2 diabetes. Integrated analysis of multiple biomolecule classes provides deeper insights into disease mechanisms, improves biomarker discovery and supports systems-level understanding of pathological processes.

Cíle a přehled studie / článku

This study aimed to develop and demonstrate high-resolution Orbitrap-based workflows for simultaneous analysis of lipid species, proteins and glycopeptides in plasma from Zucker diabetic fatty (ZDF) and lean control rats. The objective was to identify and quantify hundreds of molecular entities across the three omics domains and highlight differential features between diabetic and healthy animals.

Použitá metodika a instrumentace

• Sample preparation: EDTA-anticoagulated rat plasma; chloroform/methanol/water extraction for lipids; reduction, alkylation and tryptic digestion of proteins; TMT sixplex labeling; HyperSep Retain AX cartridges for glycopeptide enrichment.
• Lipidomics: Thermo Scientific Dionex UltiMate 3000 RSLC with C30 reversed-phase column; Q Exactive HF Orbitrap MS in positive/negative DDA mode; LipidSearch 4.1 for identification and quantitation.
• Proteomics: nanoflow RSLC EASY-nLC 1000; Orbitrap Fusion Lumos MS in HCD DDA mode; Proteome Discoverer with Protein Center for protein annotation.
• Glycoproteomics: nanoflow EASY-nLC; Orbitrap Fusion Lumos with EThcD and SPS-MS3 fragmentation; Byonic node in Proteome Discoverer for glycopeptide identification and quantitation.

Hlavní výsledky a diskuse

• Lipidomics: 750 molecular lipid species across 17 classes identified; 349 species showed significant concentration changes (p<0.05) between ZDF and lean plasma. Notable increases in triglycerides (TG) and phosphatidylcholine (PC) in ZDF; decreases in phosphatidylethanolamine (PE) subclasses; specific TG species (e.g. TG 8:1/16:0/18:1) contributed most to class-level changes.
• Proteomics: Over 400 proteins identified from unfractionated plasma; several proteins exhibited elevated abundance in ZDF compared to lean controls, including known acute-phase and metabolic regulators.
• Glycoproteomics: ~2000 glycopeptides identified; high-mannose glycoforms at key sites (e.g. N321 in alpha-1 inhibitor) increased 2–4-fold in ZDF without corresponding changes at the total protein level, indicating glycosylation remodeling in diabetes.

Přínosy a praktické využití metody

Integrated multi-omics workflows offer high confidence identification and precise quantitation across molecular classes, enabling unbiased biomarker discovery and mechanistic studies. The methods are applicable to preclinical and clinical samples, support comparative studies of disease models and can guide therapeutic target validation.

Budoucí trendy a možnosti využití

Advances in chromatography, mass spectrometry sensitivity and data processing will drive deeper coverage and throughput. Automation and standardized bioinformatics pipelines will facilitate large-scale multi-omics studies in clinical cohorts. Integration with metabolomics and transcriptomics will further enrich system-level insights and precision medicine applications.

Závěr

The developed Orbitrap-based workflows successfully enabled simultaneous lipidomic, proteomic and glycoproteomic profiling of rat plasma, revealing significant molecular differences in a type 2 diabetes model. These integrated methods provide a robust platform for biomarker discovery and pathophysiological investigations.

Reference

• No external literature was cited in the source document.