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CORE SERVICE

Unlock Actionable Biomarkers

Unlock actionable biomarkers hidden in exosomes. Our Exosome Proteomics Services deliver high-depth, quantitative protein profiling from complex biofluids, enabling reliable biomarker discovery and mechanistic insights even from low-input samples. Backed by advanced mass spectrometry and proven workflows, we help researchers generate reproducible data that supports confident biological conclusions.

High-depth detection: DIA and 4D-DIA workflows capture low-abundance exosomal proteins with robust quantification
Flexible strategies: Label-free, labeled, PTM, and targeted PRM/MRM analyses tailored to your study goals
Authoritative analysis: Advanced bioinformatics and expert interpretation grounded in published standards and large-scale project experience

Creative Proteomics' exosome proteomics services.

Figure 1. Exosome biogenesis involves multiple stages (Singh M, et al. 2025).

What Is Exosome Proteomics?

Exosome proteomics is the systematic analysis of proteins carried by exosomes, small extracellular vesicles secreted by cells into biological fluids. Exosomes play a crucial role in intercellular communication, carrying a rich molecular cargo that includes proteins, nucleic acids, lipids, and metabolites. By profiling exosomal proteins, researchers can gain insights into cellular physiology, pathological states, and disease progression.

Exosome proteomics utilises advanced mass spectrometry–based detection techniques, enabling both qualitative and quantitative profiling of proteins. With rich experience, Creative Proteomics offers high-quality exosome proteomics services, providing valuable insights into your protein research.

Why Exosomes Are Targets for Proteomic Detection

Exosomes are found in nearly all biological fluids, including blood, urine, saliva, and cerebrospinal fluid. Their small size (30–150 nm) and lipid bilayer structure allow them to transport proteins, nucleic acids, and metabolites stably between cells. This makes them excellent candidates for the discovery of non-invasive biomarkers.

Because exosomes reflect the physiological and pathological state of their parent cells, analyzing their proteomes can reveal disease-specific signatures, including cancer markers, neurodegenerative disease indicators, or immune-modulating proteins. In addition, exosomes provide access to molecular information that is difficult to obtain from tissue biopsies or other cell-derived samples, enabling real-time, minimally invasive disease monitoring.

Proteomic Detection Techniques for Exosomes

LC–MS/MS

Peptides (protein fragments) are separated by tiny-scale chromatography, then measured by a mass spectrometer. Good chromatography increases the number of proteins that can be detected and reduces interference from contaminating proteins.

DIA/4D-DIA

DIA systematically fragments all peptides across defined mass ranges, so it captures low-abundance peptides more reliably across many samples. DIA gives more reproducible quantification for cohort studies and is often our default for biomarker discovery. Adding ion-mobility reduces overlap between peptides, increases depth, and speeds up throughput.

Targeted (MRM/PRM)

For hypothesis-driven studies or biomarker verification, we offer targeted proteomics using PRM or MRM methods. These techniques focus on predefined proteins and measure them with high sensitivity and precision. They are ideal for confirming candidate exosomal markers.

Standardized Workflow for Exosome Proteomics

1. Exosome isolation and characterization: Using ultracentrifugation, size-exclusion chromatography, or commercial kits. Characterization via TEM, NTA, and immunoblotting.

2. Protein extraction and enzymatic digestion: Proteins are extracted and digested into peptides, with desalting and concentration.

3. Mass spectrometry analysis: Analysis using LC-MS/MS, DIA, or 4D-DIA platforms.

4. Bioinformatics analysis: Protein identification, quantification, function annotation, and pathway analysis.

5. Results interpretation: Comprehensive reports with statistical analyses.

Sample Requirements for Exosome Proteomics

Sample Type	Volume / Input	Notes
Plasma / Serum	≥ 200 μL	≥ 1×10¹⁰ particles/mL (NTA-based)
Urine	≥ 5–10 mL	Concentration dependent on donor variability
Cerebrospinal Fluid	≥ 200 μL	As available; low-input workflows applicable
Cell Culture Supernatant	≥ 10–50 mL	Dependent on cell density and culture conditions
Isolated Exosomes	≥ 50–100 μg	BCA-quantified protein input; ≥ 0.25 μg/μL

Demo: Urinary Exosomes in Alzheimer's Disease

The authors isolated EVs from human Alzheimer's disease (AD) brain tissue and applied quantitative proteomics to compare AD vs control EV protein cargo. Their analysis identified disease-associated proteomic alterations in brain-derived EVs and used machine-learning approaches to prioritize candidate markers.

Figure 2. Comparison of the proteomics analysis by hierarchical cluster and gene ontology (Song Z, et al., 2020).

Figure 3. Comparison of the proteomics analysis by KEGG pathway and PPI network analysis.

Figure 4. PPI analysis the target proteins from control and 5XFAD mice (Song Z, et al., 2020).

CASE STUDY

Urinary Exosomes in Colorectal Cancer (CRC)

CRC Research Case

Background & Purpose

Urinary exosomes reflect the physiological state of their cells of origin and carry protein cargo with diagnostic potential. This study aimed to isolate urinary exosomes from CRC patients and characterize their protein contents using label‑free LC–MS/MS to identify potential protein biomarkers for disease detection and staging.

Methods

Density gradient ultracentrifugation was used to isolate high‑purity urinary exosomes (~30–100 nm). Proteins were extracted and analyzed using label‑free LC–MS/MS for high‑sensitivity identification. Differential protein expression was assessed across samples and correlated with clinical staging.

Results Overview

The study successfully isolated urinary exosomes from both CRC patients and healthy controls. Several exosomal proteins showed statistically significant differential abundance between CRC and control groups, and some varied across clinical disease stages.

Figure 5. The characterization of EVs isolated from urine.

Figure 6. Proteomic profiling and comparison of urinary exosomes from different CRC groups.

Figure 7. Bioinformatics analysis of differentially expressed proteins identified from the urinary exosomes.

Conclusion

These findings demonstrate that urinary exosome proteomics can identify candidate biomarkers for colorectal cancer detection and staging, supporting their potential use in non-invasive diagnostics and personalized monitoring strategies.

Frequently Asked Questions

Q1: How do different exosome isolation methods impact proteomic results?

Different isolation methods (e.g., ultracentrifugation, size‑exclusion chromatography, immunoaffinity capture) influence the purity, yield, and proteome composition. High-purity methods, such as SEC, reduce co-isolation of soluble proteins that can confound MS analysis.

Q2: What controls should be included in exosome proteomics experiments?

Robust controls include non‑exosomal protein controls, spike‑in standards for quantification, and technical replicates. Particle characterization (NTA, TEM) and marker verification (CD9, CD63) are essential before MS analysis.

Q3: Can exosome proteomic profiles reflect the tissue of origin?

Yes. Because exosomes carry cell-specific proteins, their profiles can reflect the origin tissue. For example, serum-derived exosomes have shown placenta-associated proteins in pre-eclampsia.

Q4: Why is standardisation important in exosome proteomics?

Standardisation ensures reproducibility and comparability. Without standardized isolation, data interpretation is less reliable. Reference materials and consensus protocols help validate sample purity and detection sensitivity.

Q5: How does protein abundance affect exosome proteomic sensitivity?

Sensitivity is limited by low protein concentrations. Advanced MS techniques (like 4D-DIA) and optimized preparation can enhance detection, but limited input material remains a challenge requiring expert handling.

References

Nauwynck, Hans, et al. "Cell biological and molecular characteristics of pseudorabies virus infections in cell cultures and in pigs witd emphasis on tde respiratory tract." Veterinary Research 38.2 (2007): 229-241.
Wu, C‐Y., et al. "Enhancing expression of tde pseudorabies virus glycoprotein E in yeast and its application in an indirect sandwich ELISA." Journal of Applied Microbiology 123.3 (2017): 594-601.
Cheng, Ting-Yu, et al. "Detection of pseudorabies virus antibody in swine oral fluid using a serum whole-virus indirect ELISA." Journal of Veterinary Diagnostic Investigation 32.4 (2020): 535-541.

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