Exosome Proteomics and RNA Sequencing Service

Q: Q1: Can you process rare or low-volume samples (e.g., cerebrospinal fluid, small tumor tissue supernatants) for both proteomics and RNA sequencing?

A: Yes, we specialize in handling rare samples. We use an optimized "one-step method" to simultaneously extract proteins and RNA from the same exosome sample. This minimizes sample loss, making it ideal for low-volume samples like cerebrospinal fluid or trace tumor tissue supernatants. We also validate exosome purity and integrity (via Western blot, NTA, and electron microscopy) to ensure downstream analysis quality.

Q: Q2: What types of RNA can your exosome RNA sequencing service detect, and do you offer target-specific analysis (e.g., only miRNAs)?

A: Our RNA sequencing service covers multiple RNA types in exosomes, including mRNA, small RNAs (miRNA, piRNA, snoRNA), lncRNA, and circRNA. We provide both "comprehensive profiling" and "target-specific analysis" options: if you only need miRNA detection, we can optimize the library preparation protocol to focus on 18-30 nt small RNAs, with dedicated analysis (e.g., miRNA target gene prediction, differential expression screening) to meet your specific research goals.

Q: Q3: How do you ensure the reliability of "RNA-protein" joint analysis results?

A: We use a two-layer quality control (QC) system to guarantee reliability: Data QC: For proteomics, we use BSA peptide standards to verify detection sensitivity and include technical replicates; for RNA sequencing, we ensure RIN ≥7.0 and Q30 scores >90%. Joint Analysis QC: We validate the correlation between RNA expression (from sequencing) and protein abundance (from mass spectrometry) to exclude post-transcriptional regulation interference (e.g., miRNA-mediated translation inhibition). We also map differential RNA and proteins to the same pathways (e.g., KEGG) to confirm consistent regulatory trends, ensuring the "RNA-protein" interaction network and pathway integration results are scientifically rigorous.

Q: Q4: How long does the entire service take from sample submission to report delivery, and can it be accelerated for urgent projects?

A: The standard turnaround time for combined proteomics and RNA sequencing is 4-6 weeks (including sample processing, detection, analysis, and report preparation). For urgent projects, we offer an "expedited service" option: by prioritizing your sample in the experiment queue and streamlining the analysis process, we can shorten the cycle to 3-4 weeks. Please note that expedited services require advance confirmation to ensure resource availability.

Q: Q5: If I only need exosome isolation and not the full proteomics/RNA sequencing service, is that an option?

A: Absolutely. We offer standalone "exosome isolation and validation services" for clients who have their own downstream analysis capabilities. We use validated methods (ultracentrifugation, magnetic bead-based isolation, or size-exclusion chromatography) tailored to your sample type (e.g., serum, cell culture supernatant). The service includes full validation: Western blot (for CD63/CD81/TSG101 markers), NTA particle size analysis, and electron microscopy imaging, with a detailed isolation report delivered within 1-2 weeks.

Exosome proteomics and RNA sequencing technologies provide powerful tools for studying the composition, function, and role of exosomes in disease. Creative Biostructure offers professional exosome multi-omics integration analysis services, combining next-generation sequencing (NGS) and ultra-high-sensitivity mass spectrometry (MS) technologies to simultaneously analyze the RNA and protein composition of exosomes. We are committed to providing robust and reliable support for clients in basic research and preclinical studies by deeply elucidating the molecular composition of exosomes.

Why Integrate Exosome Proteomics and RNA-Seq?

Exosomes are nanoscale extracellular vesicles secreted by cells that carry a wealth of bioactive molecules such as proteins and RNA (e.g., miRNA, lncRNA, mRNA). They serve as key mediators of intercellular communication. Exosomes hold great potential in fields such as the discovery of disease diagnostic biomarkers, tumor microenvironment research, drug delivery system development, and regenerative medicine.

However, exosome research faces challenges such as the difficulty in detecting low-abundance molecules, limited sample availability, and interference from co-isolated impurities. Therefore, highly sensitive and precise multi-omics analysis technologies are crucial. Integrating proteomics with RNA sequencing can overcome the limitations of single-omics approaches, providing more systematic and in-depth scientific insights for research. The specific advantages are reflected in the following aspects:

Achieve "transcript-protein" linkage verification to enhance result reliability.
Uncover "RNA-protein" regulatory networks for in-depth molecular mechanism insights.
Expand biomarker screening dimensions and improve translational value.
Reduce sample consumption, lowering research costs and timelines.
Support multidimensional functional validation to accelerate the translation of research findings.

Our Exosome Proteomics and RNA Sequencing Service

Creative Biostructure relies on advanced technology platforms and professional teams to provide one-stop exosome proteomics and RNA sequencing analysis services to clients worldwide, covering the entire process from sample processing to data interpretation.

Exosome extraction and identification: We offer services for the separation and identification of exosomes from samples, supporting a variety of sample types (such as plasma, serum, tissue, etc.).
Exosome proteomics analysis: Identification and quantitative analysis of exosome proteins using liquid chromatography-mass spectrometry (LC-MS/MS) technology, providing detailed protein expression profiles and functional annotations.
Exosome RNA sequencing service: Includes deep sequencing of mRNA, miRNA, and lncRNA to reveal the role of exosomes in gene regulation.
Personalized analysis solutions: Provides customized analysis tailored to research needs, such as studies on exosomal drug delivery mechanisms and disease biomarker screening.

Exosome Proteomics and RNAseq Analysis Workflow

We offer a service workflow that combines customization and standardization to deliver tailored solutions based on clients' research objectives.

Our standard workflow includes the following key steps:

1

Sample pretreatment and exosome isolation

For client-provided original samples (e.g., cell culture supernatant, serum/plasma, urine, cerebrospinal fluid, saliva), we offer validated exosome isolation services (utilizing ultracentrifugation, magnetic bead-based methods, size-exclusion chromatography, etc.). The purity and integrity of exosomes are verified through Western blot (CD63/CD81/TSG101), nanoparticle tracking analysis (NTA), and transmission electron microscopy to ensure high-quality samples for downstream analysis.

2

Protein/RNA Extraction

We employ an optimized "one-step" method to simultaneously extract both proteins and RNA from the same exosome sample, effectively preventing sample loss during repeated processing. This approach is particularly suited for rare clinical specimens (e.g., cerebrospinal fluid, supernatants from micro tumor tissues).

3

Data Analysis and Interpretation

In addition to basic data (including protein identification lists, RNA expression matrices, and differential molecule screening results), we provide multidimensional in-depth analysis.

Single-omics analysis
Proteomics analysis	GO/KEGG functional enrichment, protein-protein interaction (PPI) network, and modified protein site analysis.
RNA sequencing	Differential gene expression screening (DESeq2/edgeR), functional enrichment analysis (GO/KEGG/GSEA), and RNA target gene prediction (miRNA-target interactions, lncRNA-protein interactions).
Integrated RNA-protein analysis
Transcription - Verification of protein expression correlation (excluding post-transcriptional regulatory interference).
RNA - Construction of protein interaction networks (such as miRNA-target protein, lncRNA-protein complexes).
Integration of multi-omics pathways (such as mapping differentially expressed RNA and proteins to the same metabolic/signaling pathways to elucidate regulatory mechanisms).

Workflow for exosomal proteomics and RNA sequencing. Figure 1. Exosome proteomics and RNAseq analysis workflow. (Creative Biostructure)

Supported Sample Types

Body fluids: Serum, plasma, saliva, urine, cerebrospinal fluid, breast milk, etc. (≥1mL).
Cell culture supernatant: Conditioned medium (≥10mL).
Special samples: Tissue exudate, ascites, etc.

Deliverables

We ultimately deliver a comprehensive report, which specifically includes:

Experimental workflow and quality control report (sample processing records, exosome identification results, mass spectrometry/sequencing quality control data such as Q30 scores, protein/RNA extraction concentrations).
Core results file (protein/RNA identification list, quantification matrix, differential molecule screening thresholds and results).
Visualization charts (volcano plots, heatmaps, pathway enrichment plots, interaction network plots).

Advantages of Our Exosome Proteomics and RNA Sequencing Service

In-depth coverage: Leading mass spectrometry and sequencing platforms ensure in-depth identification of RNA and proteins.
Strict quality control: Quality control measures are implemented throughout the entire process, from sample collection to data analysis, to ensure the reliability of results.
Integrated analysis: A unique bioinformatics pipeline provides integrated analysis of RNA and proteins to uncover deeper biological patterns.
Professional support: Project scientists provide full-cycle support, from scheme design to report interpretation.

Case Study

Case: Serum Exosome Biomarkers Diagnose Lung Cancer Brain Metastas

Background

Brain metastasis occurs in 40-50% of lung cancer patients and is associated with poor prognosis. This study aimed to identify potential exosomal biomarkers for the early detection of brain metastasis in lung cancer using a comprehensive multi-omics approach.

Methods

Using a lung cancer mouse model, which develops brain metastasis, we collected serum samples at different stages (control, 6 weeks for lung cancer, and 10 weeks for brain metastasis).
The contents of serum-derived exosomes using small RNA sequencing and LC-MS/MS proteomic analysis, and assessed the clinical relevance of candidate biomarkers using publicly available patient datasets.

Conclusion

RNA sequencing identified 11 differentially expressed miRNAs across disease progression, with miR-206-3p showing significant upregulation during brain metastasis.
Proteomic analysis revealed 77 proteins specifically upregulated in the brain metastasis stage, with vinculin (VCL) emerging as a promising marker.

Proteomic profiling of differentially expressed exosomal proteins. Figure 2. Proteomic analysis of differentially expressed exosomal proteins. (Lim J, et al., 2025)

At Creative Biostructure, we not only provide exosome proteomics and RNA sequencing services, but are also committed to tailoring end-to-end solutions for our client's unique research objectives. Whether you are investigating exosome-mediated cellular communication, screening for clinical biomarkers, or elucidating disease mechanisms, our integrated workflow (from sample isolation to combined proteomics-RNA sequencing analysis) ensures consistency, reliability, and efficiency, saving you time on sample preparation and data troubleshooting. Contact us today to discuss your project details, share your sample type or research focus, and receive a personalized solution that aligns with your timeline, budget, and scientific objectives.

References

Lim J, Kang M, Ahn Y H, et al. Comprehensive Profiling of Serum Exosomes by a Multi-Omics Approach Reveals Potential Diagnostic Markers for Brain Metastasis in Lung Cancer. Cancers. 2025, 17(12): 1929.

Frequently Asked Questions

For any inquiries, our support team is ready to help you get technical support for your research and maximize your experience with Creative Biostructure.

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