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What is Cell Surface Proteins?
The cell-surface proteins (CSPs) are a group of proteins that traverse or are anchored/embedded in the plasma membrane, playing a crucial role in various essential and distinct cellular functions along the plasma membrane, which mediates intercellular communication and regulating cellular interactions with the extracellular milieu, including nutrient and ion transportation, intercellular interactions, receptor-mediated signaling transduction, enzymatic reactions, and immune recognition. According to Almen et al., they classified CSPs into four categories: (i) transporters, including channels, solute carriers, and active transporters; (ii) receptors, such as G protein-coupled receptors, receptor type tyrosine kinases, receptors of the immunoglobulin superfamily and related, and scavenger receptors and related; (iii) enzymes, which include oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases; and (iv) miscellaneous, such as ligands, other proteins, structural/adhesion proteins and proteins of unknown function. Due to their critical biological function and unique subcellular location, CSPs have been proposed as valuable resource for the identification of targets in immune and targeted therapy. Additionally, they have been served as informative biomarkers for assays related to early disease detection, diagnosis, and prediction. Therefore, it is essential to employ cell surface proteomics strategies for identifying and quantifying the complete repertoire of CSPs, as well as investigating their functional roles.
Our Cell Surface Proteomics Service
With advancements in quantitative proteomics and shotgun proteomics based on LC-MS/MS analysis, it is now capable of characterizing and quantifying complex protein mixtures with high throughput, exclusive accuracy, and specificity. The initial step in studying CSPs involves the isolation of these proteins from the whole cells. Various strategies can be employed for the enrichment of CSPs, including (i) differential centrifugation, (ii) density gradient centrifugation, (iii) affinity-based enrichment methods such as streptavidin-biotinylation, antibody-antigen, and lectin-glycan, and (iv) hydrazide chemistry. Combining centrifugation with affinity or chemical enrichment techniques is a favorable approach to effectively remove abundant cytosolic proteins and enhance selectivity towards CSPs. The second critical step is to dissolve the CSPs, usually using agents such as detergents (SDS, RapiGest, etc.), denaturants (Urea, etc.), extreme pH (Na2CO3, etc.), high ionic strength (KCl, NaCl, etc.), organics (CH3OH, CHCl3, etc.) to dissolution CSPs. The proteomics technology is undoubtedly the most crucial step for deep and accurate identification and quantification of CSPs. The field of quantitative proteomics has witnessed the establishment of various well-established techniques, including SILAC, iTRAQ/TMT, label-free, DIA and target quantification proteomics such as (SRM/MRM, PRM). Most importantly, the methods mentioned above have been thoroughly mastered by Creative Proteomics. With over a decade of experience in the field of proteomics, we possess exceptional proficiency in executing Cell Surface Proteomics Projects. We are capable of supporting diverse sample types and can even assist in cell culturing for SILAC quantitative proteomics.
Figure 1. Biotinylation enrichment methods for cell surface proteomics [3].
Advantages of Cell Surface Proteomics Service
- Professional detection and analysis capability: Experienced technical team, strict quality control system, together with ultra-high resolution detection system and professional data pre-processing and analysis capability, ensure reliable and accurate data.
- High specificity and purification: Optimization of experimental design and methods.
- High stability and reproducible: Obtain consistent and reproducible inter- and intra- assay results for data analysis.
- High throughput: LC-MS/MS can identify and quantify thousands of proteins simultaneously.
- High resolution and sensitivity: Triple TOF 5600, Q-Exactive, Q-Exactive HF, Orbitrap Fusion™ Tribrid™, etc.
- High selectivity: We can provide a wide range of multi-technological services and efficiently handle various types of samples, while remaining cost-effective and ensuring short turnaround times for your projects.
Results Delivery
- Detailed report, including experiment procedures, parameters, etc.
- Raw data and data analysis results (e.g. identified proteins and peptides, and optional downstream bioinformatics analysis, such as volcano plot, PCA, GO, KEGG, Protein Interaction Networks, etc.)
Sample Requirements for Cell Surface Proteomics
| Sample Type | Description | Recommended Sample Amount |
|---|---|---|
| Adherent Cell Lines | Cultured cells that attach to the substrate. | 1 x 106 cells (approx. 0.1 g) |
| Suspension Cell Lines | Cultured cells that do not attach to the substrate. | 1 x 107 cells (approx. 0.5 g) |
| Primary Cells | Isolated from tissues; can be adherent or suspension. | 1 x 106 to 1 x 107 cells |
| Tissue Samples | Fresh or frozen tissue samples (e.g., liver, muscle). | 100-500 mg |
| Plasma/Serum Samples | Liquid biopsies from blood; may contain cell surface proteins. | 1-5 mL |
| Biopsies | Small tissue samples taken for diagnostic purposes. | 50-100 mg |
| Microbial Cells | Bacterial or fungal cultures for surface protein study. | 1 x 108 cells |
| Cell Membrane Fractions | Isolated membrane fractions from any cell type. | 50-100 mg |
| Exosomes | Small vesicles from cell cultures or biological fluids. | 10-50 mL of source fluid |
| Organelles | Isolated organelles such as membranes or cytoplasmic vesicles. | 50-100 mg |
How to place an order
The provision of comprehensive support tailored to your specific requirements for Cell Surface Proteomics is our area of expertise. Please feel free to contact us via email whenever you need to discuss your specific requirements. Our customer service representatives are available 24 hours a day, from Monday to Sunday.
References
- Almén MS, Nordström KJ, Fredriksson R, et al. Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol. 2009 Aug 13;7:50.
- Sun B. Proteomics and glycoproteomics of pluripotent stem-cell surface proteins. Proteomics. 2015 Mar;15(5-6):1152-63.
- Kalxdorf M, Gade S, Eberl HC, et al. Monitoring Cell-surface N-Glycoproteome Dynamics by Quantitative Proteomics Reveals Mechanistic Insights into Macrophage Differentiation. Molecular Cell Proteomics. 2017 May;16(5):770-785.
Bar Chart of Total Protein Identification
2D PCA Plot of Sample Grouping
3D PCA Plot of Sample Grouping
Pearson Correlation Analysis
Sample Hierarchical Clustering
Volcano Plot of Differential Proteins
Bar Chart of GO Enrichment for Candidate Proteins
KEGG Pathway Enrichment of Candidate Proteins
Cell-Surface Proteomics Identifies Differences in Signaling and Adhesion
Protein Expression between Naive and Primed Human Pluripotent Stem Cells
Journal: Stem Cell Reports
Published: 2020
Main technologies: Cell Surface Proteomics, TMT quantitative proteomics, Cell proliferation assay, Flow cytometry, Immunofluorescence microscopy, Western Blot, Quantitative RT-PCR
Abstract
Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified 1,715 plasma membrane proteins (74% specificity), including those involved in cell adhesion, signaling, and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signaling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signaling pathway activity and has identified new markers to define human pluripotent states.
Figure 1. Cell-Surface Proteomics of Naive and Primed Human Pluripotent Stem Cells.
How are cell surface proteins isolated from other cellular components?
Isolation of cell surface proteins (CSPs) involves several enrichment strategies. Common methods include differential centrifugation to separate membrane proteins from cytosolic proteins, density gradient centrifugation, and affinity-based techniques such as biotinylation followed by streptavidin capture. Each method has its advantages, and often, a combination of techniques is employed to enhance selectivity for CSPs while reducing the presence of abundant cytosolic proteins.
How do you handle the data analysis for cell surface proteomics?
Data analysis in cell surface proteomics is conducted using a combination of bioinformatics tools and statistical approaches. After raw data acquisition via LC-MS/MS, we perform rigorous data processing, including peak identification and quantification. Our analysis pipeline includes bioinformatics applications for downstream analysis such as protein-protein interaction networks, pathway analysis (e.g., KEGG, GO), and comparative analysis between different sample groups. Detailed reports are generated to summarize the findings, and we also offer custom analysis options based on client needs.
What are the potential applications of cell surface proteomics in biomedical research?
Cell surface proteomics has a wide array of applications in biomedical research, including:
- Identifying potential biomarkers for early disease detection and diagnosis.
- Studying immune responses and the interactions of immune cells with pathogens.
- Investigating tumor microenvironments and the roles of CSPs in cancer progression.
- Understanding cellular responses to therapeutic agents and drug resistance mechanisms.
- Exploring plant-microbe interactions in agricultural research.
What precautions should be taken regarding sample composition before submission?
It is crucial to ensure that submitted samples are free from nucleic acids, lipids, polysaccharides, detergents, and denaturants, as these components can interfere with protein extraction and analysis. We recommend informing our team about the buffer composition used in protein solutions to allow for proper processing and to avoid any adverse reactions that could affect the integrity of the analysis.
Learn about other Q&A about proteomics technology.
Quantitative proteomic analysis of cellular responses to a designed amino acid feed in a monoclonal antibody producing Chinese hamster ovary cell line.
Torkashvand, Fatemeh, et al.
Journal: Iranian Biomedical Journal
Year: 2018
Variability in probiotic formulations revealed by proteomics and physico-chemistry approach in relation to the gut permeability.
Razafindralambo, H., Correani, V., Fiorucci, S., & Mattei, B.
Journal: Probiotics and antimicrobial proteins
Year: 2020
Untargeted proteomics and stage-specific Huntington's disease reveal biological pathways, and potential protein biomarkers.
Papanicolaou, E. Z., Christodoulou, C., & Demetriou, C.
Journal: Research Square
Year: 2024
Impaired phagocytosis of photoreceptor outer segments by RPE in CLN3 disease is a consequence of altered sphingolipid metabolism.
KUMAR, L. K., Han, J., Dalvi, S., Foley, N., Subedi, Y., & Singh, R.
Journal: Investigative Ophthalmology & Visual Science
Year: 2024
Quantitative proteomic analysis of cellular responses to a designed amino acid feed in a monoclonal antibody producing Chinese hamster ovary cell line.
Torkashvand, F., Mahboudi, F., Vossoughi, M., Fatemi, E., Basri, S. M. M., Heydari, A., & Vaziri, B.
Journal: Iranian Biomedical Journal
Year: 2018
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