Proteome and Metabolome Integration Analysis



Proteome is a new subject in the era of functional genomics, which studies the composition and activity of proteins in cells as well as the interaction between different proteins on the overall level. At present, the research of proteomics is mainly based on the proteomics of mass spectrometry. Metabolome is a newly developed subject in the field of systems biology after relaying genome and proteome. It explores the metabolic mechanism of the entire organism by detecting the changes of the metabolites in the organism after exogenous stimulation or genetic modification.

The integrated analysis of the omics data of the two molecular levels of the proteome and the metabolome can be combined with the analysis results of the two omics to perform mutual verification and improve the success rate of subsequent experimental verification. On the other hand, it is also helpful to complement each other, and make research more systematic. Finally, it can help us achieve a comprehensive understanding of the general trend and direction of biological changes, propose a molecular biology change mechanism model, and screen out proteins or metabolites related to key metabolic pathways, so as to provide a data basis for subsequent in-depth experiments and analysis.

Metabolic and Proteomic Profiling Reveals Distinct Changes in L-Arginine Metabolism in Activated Human T Cells.Figure 1. Metabolic and Proteomic Profiling Reveals Distinct Changes in L-Arginine Metabolism in Activated Human T Cellsr. (Roger G, et al. 2016)


The main applications of proteome and metabolome integration analysis in biomedicine are:

  • Basic medicine, clinical diagnosis-including biomarkers, disease mechanism, disease classification, personalized treatment and other research directions.
  • Biomedicine research on drug action mechanism, drug efficacy evaluation, drug development, etc.

What We Offer

As one of the experienced bioinformatics data analysis providers, we offer established, cost-efficient, rapid turnaround, and one-stop analysis services for proteome and metabolome integration analysis. We provide our clients with the following data analysis services:

  • Data analysts evaluate and filter the data.
  • Formulate the optimal analysis plan.
  • Perform data analysis, including develop a personalized analysis plan or a personalized chart summarizing the results.
  • Provide a comprehensive report and report interpretation services.
  • Fast project analysis cycle.

Data Analysis Technical Route

A flow chart showing our proteome and metabolome integration analysis. - CD Genomics.Fig 2. A flow chart showing our proteome and metabolome integration analysis.

An Example Analysis Content Includes:

The main content of proteome and metabolome integration analysis: normalize the batch data from the two biomolecular levels of the proteome and metabolome, perform statistical analysis such as comparative analysis and correlation analysis, and establish data relationships between different levels of molecules. At the same time, combined with GO function analysis, metabolic pathway enrichment, molecular interaction and other biological function analysis, systematically and comprehensively analyze the biological molecular functions and regulatory mechanisms.

  • Comparative analysis of PCA between proteome and metabolome.
  • Correlation analysis between proteome and metabolome
  • Correlation coefficient matrix heat map, correlation analysis hierarchical clustering heat map, correlation coefficient control network analysis.
  • Integrated analysis of KEGG metabolic pathways of proteome and metabolome: including O2PLS correlation analysis, OPLS related variables screening
  • Multivariate statistical integration analysis of proteome and metabolome.
  • Mining key protein or metabolite information.

Data Ready

Before data analysis, the first thing is to get your data ready. The input data can be obtained from the following channels:

Channels of proteome and metabolome raw data. - CD Genomics.

The raw input proteome and metabolome data can be produced from a range of platforms including LC-MS/MS, NMR, GC-MS etc. In addition, we are able to receive various formats of data for analysis such as raw data files, or other intermediate data formats. In order to process data more efficiently, we prefer to receive data files in the raw format, but we also accept pre-normalized files.

What's More

For proteome and metabolome integration analysis, if you don’t have the raw data, CD Genomics can also provide you with a series of spectrometers with high resolution, high-quality accuracy, and good stability to detect proteins and metabolites. In addition, we also provide services to obtain raw data from public databases.

CD Genomics is happy to work with you at every stage of the research to ensure the best results for your research. For proteome and metabolome integration analysis, if you have any questions, please feel free to contact us. We have a professional technical support team to provide you with services and look forward to working with you.


  1. Roger G, et al. L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity[J]. Cell, (2016),

* For research use only. Not for use in clinical diagnosis or treatment of humans or animals.

Online Inquiry

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