LC-MS/MS-Based Exosome Proteomics Workflow: Isolation, Digestion, Acquisition, and Analysis

Exosome proteomics LC-MS/MS workflow cover

Exosome proteomics by LC-MS/MS links extracellular vesicle biology to biomarkers and disease pathways when isolation, digestion, acquisition, and annotation are aligned.

Key Takeaways

Sample type sets sensitivity and contamination risk.
Isolation trades purity, throughput, and yield.
Controlled digestion matters for low-input vesicle protein.
DDA, DIA, and PRM serve discovery, cohort quant, and validation.
Use ExoCarta/Vesiclepedia to support vesicle specificity.

Exosome workflow — Figure 1. Isolation quality drives data quality.

Related Services

Exosome Proteomics Service

Active Exosome Isolation Service

Animal Cell-derived Exosome Isolation and Development Service

Exosomal Peptidomics Detection Service

Protein Extraction through LC-MS/MS

Lyse, quantify, reduce/alkylate, trypsin digest, desalt, optional fractionation, nanoLC, then DDA, DIA, or PRM as study design requires.

DDA DIA PRM — Figure 2. Match acquisition to discovery, quantification, or validation.

Data Analysis

Search at <1% FDR; differential screening; GO/KEGG/PPI; ExoCarta and Vesiclepedia cross-checks.

Bioinformatics — Figure 3. Database validation supports exosomal specificity.

FAQ

Can exosome proteomics use DIA?

Yes, for reproducible multi-sample quantification with suitable libraries.

Conclusion

Document each workflow step to move from vesicle profiles to translational insight.

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