Prenylation Analysis – Systematic LC-MS/MS Characterization of Prenylated Proteins

Prenylation is a process in which hydrophobic isoprenoid groups, such as farnesyl or geranylgeranyl, are covalently attached to specific cysteine residues. This modification plays a key role in protein localization to membranes, signaling pathways, and regulation of the cardiovascular system. Creative Proteomics offers high-precision prenylation research services with a focus on identifying and quantifying prenylated proteins and their modifications.

Comprehensive detection: Identify and quantify prenylated proteins and specific amino acid modifications.
Advanced technology: Use of metabolic labeling combined with LC-MS/MS to ensure accuracy and depth of analysis.
Functional insights: Integration of bioinformatics tools to analyze motifs, pathways, and networks.
Research impact: Clarify the regulatory roles of prenylation in signaling pathways and provide new insights into the mechanisms and therapeutic targets of cardiovascular disease.

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What Is Prenylation?

Prenylation is a covalent post-translational modification in which a farnesyl (C15) or geranylgeranyl (C20) group is transferred from its pyrophosphate donor (FPP or GGPP) to a cysteine residue within a C-terminal CAAX motif of target proteins. This process is catalyzed by enzymes such as farnesyltransferase (FTase) or geranylgeranyltransferases (GGTase-I/II). It involves multiple steps including transfer of the prenyl group, proteolytic cleavage of the "AAX" residues, and methylation of the modified cysteine. This increases the protein's hydrophobicity, enabling membrane localization and proper subcellular placement. Prenylation plays crucial roles in cellular signaling, vesicle trafficking, and protein interactions by regulating small GTPases like Ras, Rho, and Rab. Dysregulation of prenylation has been linked to conditions such as cancer, metabolic disorders, and cardiovascular and neurodegenerative diseases^[1].

Prenylation Service at Creative Proteomics

Given the biological importance and site-specific nature of prenylation, it is not only a fundamental regulatory mechanism but also a promising target for therapeutic and biotechnological applications. Therefore, identifying prenylated proteins and their sites in cells is essential. We offer comprehensive prenylation proteomics services, including high-resolution mass spectrometry, site-specific identification, quantitative profiling, and advanced bioinformatics analysis. Our services help researchers investigate prenylated proteins systematically, explore their pathway associations, and uncover their clinical and therapeutic significance.

Prenylation Research Platforms

Thermo Fisher Easy-nLC 1000 and Thermo Fisher LTQ Obitrap ETD
(Figure from Thermo Scientific)

Workflow of Prenylation Analysis

Advantages Our Prenylation Service

Professional detection and analysis capability: Our experienced research team and well-established techniques ensure reliable results.
High specificity and accuracy: We use skilled quantification proteomics techniques along with PTMs enrichment methods.
High stability and reproducibility: Our methods produce consistent and reproducible data across different runs.
Advanced analytical platforms: We use high-sensitivity mass spectrometry and the latest tools to ensure precise and repeatable results.
End-to-end support: We provide a full range of services from design to data interpretation, with ongoing technical assistance throughout the research process.

Applications of Prenylation

Cancer

Prenylation affects tumor metabolic reprogramming and epigenetic alterations by regulating histone function and non-histone activity, and can serve as a tumor diagnostic marker and therapeutic target^[2].

Metabolic diseases

Protein prenylation plays a critical role in metabolic disorders such as obesity, diabetes, and fatty liver disease by regulating insulin secretion, lipid metabolism, and cellular signaling pathways, highlighting its potential as a therapeutic target and biomarker^[3].

Neurodegenerative disease

Abnormal protein phenylation is associated with neurodegenerative processes: regulating the prenylation pathway can provide new targets for the treatment of neurological diseases and the development of biomarkers^[4].

Cardiometabolic health

Protein prenylation is closely involved in cardiovascular diseases by modulating endothelial function, vascular inflammation, and smooth muscle cell signaling, thereby influencing processes such as atherosclerosis, hypertension, and cardiac remodeling, and serving as a potential therapeutic target^[5].

Demo Result of Prenylation Service

PCA plot

Heat map

GO analysis

Heatmap

The plot is used to show the enrichment of prenylated proteins in different pathways.

KEGG analysis

The protein-protein interaction network demonstrated the interactions between all prenylated differential proteins.

PPI

FAQs of Prenylation Service

Which sample types are accepted by the service？

We only accept samples of cell. We recommend that customers provide fresh or frozen samples, which should avoid repeated freezing and thawing, and we will be responsible for subsequent protein extraction and pretreatment.

Whether the sample needs pretreatment？

If you need this service, please contact us before cell culture. We will provide the probes for co-incubation with cells and the labeling methods.

Learn about other Q&A.

Case Study

Article

Publications

Here are some publications in Proteomics research from our clients:

Epithelial WNT2B and Desert Hedgehog are necessary for human colonoid regeneration after bacterial cytotoxin injury. 2018. https://doi.org/10.1101/434639
In Vitro Identification of Phosphorylation Sites on TcPolβ by Protein Kinases TcCK1, TcCK2, TcAUK1, and TcPKC1 and Effect of Phorbol Ester on Activation by TcPKC of TcPolβ in Trypanosoma cruzi Epimastigotes. 2024. https://doi.org/10.3390/microorganisms12050907
Hyperactivation of the proteasome core particle in Caenorhabditis elegans protects against proteotoxic stress and extends lifespan. 2021. https://doi.org/10.21203/rs.3.rs-960676/v1
Immunoproteomics characterization of Leishmania panamensis proteins for potential clinical diagnosis of mucosal Leishmaniasis. 2021. https://doi.org/10.1111/pim.12824
Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein. 2016. https://doi.org/10.1186/s12867-016-0066-8

More Publications

Prenylation Service Sample Requirements

Sample	Sample Quantity
Cell	suspension cell	> 3x10⁸
Cell	adherent cell	> 3x10⁸

References

R. Surana, K., B. Pawar, R., A. Khairnar, R., & K. Mahajan, S. (2024). Protein Prenylation and Their Applications. IntechOpen. doi: 10.5772/intechopen.104700.
Wang, J., Yao, X., & Huang, J. (2017). New tricks for human farnesyltransferase inhibitor: cancer and beyond. MedChemComm, 8(5), 841–854. https://doi.org/10.1039/c7md00030h.
Wu, X., Xu, M., Geng, M., Chen, S., Little, P. J., Xu, S., & Weng, J. (2023). Targeting protein modifications in metabolic diseases: molecular mechanisms and targeted therapies. Signal transduction and targeted therapy, 8(1), 220. https://doi.org/10.1038/s41392-023-01439-y
Jeong, A., Cheng, S., Zhong, R., Bennett, D. A., Bergö, M. O., & Li, L. (2021). Protein farnesylation is upregulated in Alzheimer's human brains and neuron-specific suppression of farnesyltransferase mitigates pathogenic processes in Alzheimer's model mice. Acta neuropathologica communications, 9(1), 129. https://doi.org/10.1186/s40478-021-01231-5
Shi, W., Chen, Y., Zhang, X., Lou, L., Wang, P., Jiang, R., Liu, S., Sok, T., Zhang, Q., Guo, X., & Yang, J. (2025). Research advances in protein prenylation in cardiovascular diseases. European journal of pharmacology, 1005, 178093. https://doi.org/10.1016/j.ejphar.2025.178093

Proteomics Sample Submission Guidelines

Ensure your samples are prepared and submitted correctly by downloading our comprehensive Proteomics Sample Submission Guidelines. This document provides detailed instructions and essential information to facilitate a smooth submission process. Click the link below to access the PDF and ensure your submission meets all necessary criteria.

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* For Research Use Only. Not for use in diagnostic procedures.

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From Our Clients

"I recently used their proteomics service for a project analyzing protein interactions in yeast models. The team was very responsive and helped clarify the methodology they employed, which made me feel confident in the results. The data quality was solid, with clear identification of several key proteins involved in our study. Their thorough analysis enabled me to pinpoint specific interactions that I hadn't considered before, which significantly improved the direction of my research. I appreciate their professionalism and support throughout the process."

Sarah Thompson, University of California, Berkeley

"Our lab collaborated with them on a project studying cancer biomarkers. The proteomics analysis provided was detailed and focused, specifically highlighting the differential expression of proteins between healthy and tumor samples. Their clear explanations of the data helped my team understand the biological implications. I also appreciated their willingness to revise the reports based on our feedback, ensuring that we had everything we needed for our publication. This collaborative spirit was invaluable."

Emily Rodriguez, Stanford University

"Our lab worked with them on a project studying the effects of diet on gut microbiota using proteomics. They used a label-free quantification method to analyze proteins in fecal samples before and after dietary intervention. The results showed significant changes in protein expression linked to microbial activity. This was pivotal for our hypothesis about diet-microbiota interactions. The clarity of their data presentation made it easy for our team to integrate these findings into our ongoing research."

Dr. Lisa Wong, University of Toronto

"My experience with Creative Proteomics during the mass spectrometry analysis was excellent. We sent in human saliva and mouse brain tissue samples, which they expertly analyzed using both LC-MS and GC-MS techniques. The results were invaluable, revealing key metabolites in the saliva and identifying biomarkers linked to brain function in the brain tissue."

Dr. Emily Carter, Senior Research Scientist

"The overall service from Creative Proteomics was outstanding. They made the entire process seamless and efficient, allowing us to focus on our research. We worked with leaf and root samples from various Arabidopsis genotypes for targeted metabolomics analysis. Their thorough profiling of primary and secondary metabolites gave us important insights into how the plants respond metabolically to environmental stress."

Dr. Laura Henderson, Plant Physiologist

"We had a pleasant collaboration with Creative Proteomics on mass spectrometry analysis of lipids. They conducted a detailed analysis of lipid species, providing us with important insights into lipid metabolism and its relationship with metabolic syndrome disease states."

Dr. Sarah Mitchell, Research Scientist

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