Integrated Proteomics and Metabolomics Analysis

Service Details
Case Study

Proteomes are all proteins that can be expressed by a certain organism. Proteomics, as the executioner of the function of life activities, is the study of protein composition, activity patterns and protein interactions within the cell at a holistic level. Changes in protein content play an important role in the growth of organisms, environmental stress, and disease development. Metabolome is the collection of all metabolites of a cell at a certain point in time, referring to the small molecules that act as substrates and products in different metabolic processes. It can explain the physiological state of the cell at the time of sampling, regulate protein interactions, change enzyme activities, change protein stability, and thus regulate the metabolism of the organism. Integrated proteomic and metabolomic analysis can screen out key proteins and metabolites and metabolic pathways by comparing the differential expression of proteins or metabolites. At the same time, the results of the respective proteomic and metabolomic analyses can also be cross-validated, which can help to more systematically and comprehensively study the regulatory mechanisms of physiological and pathological processes, and discover new biological markers, and provide an effective research strategy for describing the metabolic regulatory network of biological organisms.

Creative Proteomics has many years of experience in multi-omics integration services. Based on our advanced analysis services, we aim to provide one-stop integrated proteomics and metabolomics analysis service for our clients.

The perturbed proteins and metabolites corresponding metabolic pathways related to Shikonin treatment by integrating the proteome and metabolome data sets.（Chen Y, et al. 2020）

What are the main analyses we provide?

Differential metabolites bioinformatics analysis.
Metabolic pathway-based protein metabolic integration analysis.
Differential protein integration analysis based on metabolite-related enzymes.
Differential protein bioinformatics analysis.

Integrating proteomic and metabolomic analysis has two main aspects

Integrated analysis based on pathway level. Analyze proteomic and metabolomic data through the KEGG Metabolic Pathway to find proteins and metabolites that undergo significant changes in the same biological process (KEGG Pathway), and quickly target key proteins and metabolites. Integrate enrichment analysis and KEGG Pathway coloring to visualize association results.
Integrated analysis based on expression level. Integrate the expression data of differentially expressed proteins and metabolites to find out the differentially changed proteins and metabolites with synchronous change rules, and then combine them with correlation coefficient matrix heatmap, correlation analysis clustering heatmap, and correlation coefficient regulatory network map to carry out personalized analysis.

Applications of integrated proteomics and metabolomics analysis

Biomedical research. Disease pathogenesis research, disease diagnosis and typing research, clinical diagnosis, biomarkers, etc.
Pharmaceutical research. Drug action mechanisms, efficacy evaluation, drug development, etc.
Agricultural research. Plant growth and development regulation mechanism, plant important quality traits, plant resistance regulation mechanism, etc.
Microbiology research. Pathogenesis, drug resistance mechanisms, etc.
Food and nutrition research. Optimization of food storage and processing conditions, identification of food components and quality, functional food development, food safety testing, etc.

Our service workflow

Our service advantages

Comprehensively reveal the distribution of expression levels in organisms at the protein and metabolite levels, enabling full spectrum analysis of biological expression regulation.
Exploiting proteomic and metabolomic data to explore the interaction mechanism from "cause" to "effect".
We have rich experience in multi-omics correlation analysis and have completed many cases of multi-omics joint analysis for our clients.

Creative Proteomics has rich experience in multi-omics co-analysis. The integrated proteomics and metabolomics analysis services we provide are designed to help researchers to find differential proteins and differential metabolites that share a certain type of metabolic pathway or have the same trend of change, to systematically characterize the molecular regulatory mechanisms in the organism and to provide a data basis for subsequent experimental validation and analysis. If you are interested in us, please feel free to contact us.

Reference

Chen Y,Ni J,Gao Y, et al. Integrated proteomics and metabolomics reveals the comprehensive characterization of antitumor mechanism underlying Shikonin on colon cancer patient-derived xenograft model. Sci Rep. 2020;10 (1):14092.

Integrated Proteomics and Metabolomics Analysis Highlights Correlative Metabolite-Protein Networks in Soybean Seeds Subjected to Warm-Water Soaking

Journal: J Agric Food Chem

Published: 2020

Abstract

Soaking soybean seeds is a prerequisite for the production of soybean food products, and it has been shown that the degree of water uptake under different swelling conditions directly affects the quality of subsequent soybean seed products in an unknown way, but the mechanism is still unclear. To elucidate the molecular changes in soybean seeds at different soaking temperatures, the authors performed proteomic and metabolomic analyses of seeds soaked at different temperatures and found that high-temperature (55°C) soaking could improve the nutritional value of soybean seeds by reducing the content of some common antinutrients.

Results

Proteomic analyses showed that several enzymes related to carbohydrate and protein hydrolysis were activated in soybean seeds during water immersion at 55°C ( Figure 1).

Figure 1

The results obtained in the combined proteomics and metabolomics study showed changes in various metabolites, including isoflavones, amino acids, and sugars, that were positively correlated with proteomic changes after 55°C soaking. Proteomics analysis showed that various enzymes associated with carbohydrate and protein hydrolysis were activated in 246 soybean seeds during water immersion at 55°C. These findings suggest a positive correlation with the production of free sugars such as glucose or galactose ( Figure 2).

Figure 2

In addition, soaking soybean seeds at 55°C resulted in the degradation of indigestible anti-nutrients such as raffinose oligosaccharides (Figure 3).

Figure 3

Conclusion

In this article, the authors analyze soybeans under different temperatures of soaking by integrating proteomic and metabolomic data. Findings that soaking of soybean seeds at 55°C will removes anti-nutrients including raffinose, and stachyose and results in an accumulation of essential amino acids and isoflavone aglycones, thereby increasing the nutritional quality of soybean seeds.

Reference

Min CW,Hyeon H,Gupta R, et al. Integrated Proteomics and Metabolomics Analysis Highlights Correlative Metabolite-Protein Networks in Soybean Seeds Subjected to Warm-Water Soaking. J Agric Food Chem. 2020;68 (30):8057-8067.

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

Our customer service representatives are available 24 hours a day, 7 days a week. Inquiry

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

Online Inquiry

Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to for inquiries.

Great Minds Choose Creative Proteomics