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Integrated Proteomics and Metabolomics Analysis

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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.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 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.


  1. 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


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.


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 1Figure 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 2Figure 2

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

Figure 3Figure 3


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.


  1. 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.
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