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Integrative Analysis of Proteomics and Metabolomics

Creative Proteomics provides comprehensive analysis services of proteomics and metabolomics to mine the correlation and mutual verification of proteome and metabolome levels; screen key proteins / metabolites / metabolic pathways from massive data to provide powerful insights into the mechanism of complex life activities evidence. Then analyze the development of biological system processes, explain the complexity and integrity of biological processes.

Why Do Integrative analysis of Proteomics and Metabolomics?

Proteomics is mainly based on mass spectrometry to conduct detailed research on the composition, activity rules and protein-protein interactions of intracellular proteins from the overall level of proteins. Metabolomics explores the metabolic mechanism of the whole organism by detecting the changes of metabolites in the organism after exogenous stimulation or genetic modification.

The integrated analysis of the omics data at the proteome and metabolome levels, on the one hand, combines the analysis results of the two omics to verify each other and improve the success rate of subsequent experimental verification; on the other hand, it also helps to complement each other and enable research is more systematic. Finally, a comprehensive understanding of the general trend and direction of biological changes is achieved, a molecular biology change mechanism model is proposed, and proteins or metabolites related to key metabolic pathways are screened out, thus providing a data basis for subsequent in-depth experiments and analysis.

Technical Advantages

  • Proteomics and metabolomics are mutually validated and complement each other.
  • The results are more comprehensive and reliable, and the data is richer.
  • Comprehensive analysis of biological problems.

Our Integrative Analysis Services of Proteomics and Metabolomics

Creative Proteomics provides you with one-stop proteome detection services and metabolome detection services. In addition, we offer integrative analysis services of proteomics and metabolomics to seamlessly connect your experiments upstream and downstream.

Bioinformatics Analysis

To obtain the set of relevant proteins and metabolites that have an impact on the sample grouping and to analyze their association characteristics, we performed the following analyses mainly based on the expression abundance and function of proteins and metabolites: multivariate statistical integration analysis of proteome-metabolome, KEGG metabolic pathway integration analysis of proteome-metabolome, and correlation analysis of proteome-metabolome.

Bioinformatics Analysis

Why Choose Us?

  • Excellent bioinformatics analysis - our bioinformatics center brings together many high-level information analysis talents from home and abroad, and has many years of practical experience in the field of bioinformatics research and development.
  • Rich data analysis content - standard analysis, advanced analysis, customized analysis.
  • In addition to excellent bioinformatics analysis, we also have an advanced experimental platform that supports sequencing and metabolome / proteome detection, etc., and we have many successful project experiences.
  • Cost-effective, short project cycle.

Case Study

Tissue-specific study across the stem of Taxus media identifies a phloem-specific TmMYB3 involved in the transcriptional regulation of paclitaxel biosynthesis

Journal: The Plant Journal
Impact factor: 6.141
Published: 2020


Taxus stem barks can be used for extraction of paclitaxel. However, the composition of taxoids across the whole stem and the stem tissue-specificity of paclitaxel biosynthesis-related enzymes remain largely unknown.

Materials & Methods

Proteomic and metabolomic analysis of cortical, bast, xylem and pith tissues of common yew PTX (paclitaxel), DAP (10-deacetylpaclitaxel), BAC (baccatin III) and 10-DAB (10-Deacetylbaccatin)

Proteomic analysis Metabolomic analysis Integrative analysis of Proteomics + Metabolomics
Distribution of differentially expressed proteins in different tissues: a total of 5604 proteins were identified, and 9 classical TFs were identified, among which MYB3, NAC25 and GATA9-like proteins mainly accumulated in the bast, suggesting their possible involvement in the regulation of paclitaxel accumulation in the bast. Differential distribution of metabolites in different tissues: A total of 5162 potential metabolites were identified and divided into four groups based on four tissue-specific differential metabolites (DAMs), with Cluster I- Cluster IV metabolites accumulating mainly in the cortex, phloem, medulla and cortex/phloem, respectively. A total of 12 key intermediate metabolites and 10 key enzymes were identified in the biosynthesis of paclitaxel, most of which were mainly produced in the phloem.


TmMYB3 is involved in paclitaxel biosynthesis by activating the expression of TBT and TS. Differences in the taxoid composition of different stem tissues suggest that the whole stem of T. media has potential for biotechnological applications. Phloem-specific TmMYB3 plays a role in the transcriptional regulation of paclitaxel biosynthesis, and may explain the phloem-specific accumulation of paclitaxel.

A model for the role of TmMYB3 in paclitaxel biosynthesis.Fig.1 A model for the role of TmMYB3 in paclitaxel biosynthesis. The phloem-specific TmMYB3 has a significant effect on paclitaxel biosynthesis by activating the expression of the TS and TBT genes. GGPP, geranylgeranyl diphosphate; MEP, 2-C-methyl-d-erythritol 4-phosphate; MRE, MYB recognition element; 10-DAB, 10-deacetylbaccatin III. (Yu C, et al., 2020)

Creative Proteomics relies on advanced platforms and cutting-edge technologies to provide omics services to customers around the world, and provide accurate and detailed analysis reports. In addition, we also provide multi-omics integrated analysis services. You can discuss with our technical engineers to customize solutions or build new methods to meet your specific needs. If you have any questions, you can tell us through the inquiry form, and our technicians will communicate with you. Please don't hesitate to contact us, Creative Proteomics can be trusted.


  1. Yu C, Luo X, Zhang C, Xu X, Huang J, Chen Y, Feng S, Zhan X, Zhang L, Yuan H, Zheng B, Wang H, Shen C. Tissue-specific study across the stem of Taxus media identifies a phloem-specific TmMYB3 involved in the transcriptional regulation of paclitaxel biosynthesis. Plant J. 2020 Jul;103(1):95-110. doi: 10.1111/tpj.14710. Epub 2020 Feb 21. PMID: 31999384.
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Creative Proteomics, your unparalleled center of excellence in sequencing, mass spectrometry, and bioinformatics analysis platforms, is elevating the landscape of research. Our seamless integration of these cutting-edge capabilities ensures that clients receive extraordinary multi-omics joint analysis services.

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