Flux Ratio Analysis

Flux Ratio Analysis

Metabolic flux analysis (MFA) has become a key approach in metabolic engineering and systems biology. In the most commonly applied approaches, fluxes are calculated by global isotopomer balancing and iterative fitting to stationary ¹³C-labeling data. This approach requires a closed carbon balance, persistent metabolic steady state, and the detection of ¹³C patterns in a large number of metabolites. The metabolic flux ratio is a number that represents the relative fraction of a given metabolite that flows through a selected reaction or pathway. The flux ratio is estimated based on a stoichiometric model, knowledge of the ¹³C conformation of all relevant substrates, and the labeling pattern of the metabolite as measured by mass spectrometry (or NMR). Metabolic flux ratio analysis methodology relies heavily on the acquisition of ¹³C-labeling data that are dedicated to metabolites close to flux convergence nodes and local parameter estimation with a system of ordinary differential equations. Creative Proteomics has introduced a novel ¹³C-metabolic flux ratio analysis that allows rapid estimation of local relative fluxes from ¹³C labeling experiments without the need for a global isotopic equilibrium.

Figure 1. A novel flux ratio in central carbon metabolism of E. coli. (Kogadeeva, M.; et al. 2016)

Our Services

Creative Proteomics has developed a novel metabolic flux analysis platform to provide flux ratio analysis service in a competitive fashion. We can offer a wide range of services to support all research and development activities. We have developed a generic workflow of flux ratio analysis for data processing, modeling, parameter and error estimation considering the reaction type and the availability of mass spectrometry data on molecular ions or fragments.

• The overall degree of ¹³C labelling in the sample and the fraction of the labelled substrate are determined by analysis of the scalar coupling fine structure of leucine C
• We calculate the relative abundances of intact carbon fragments originating from a single molecule of glucose
• The experimental error is estimated from the signal-to-noise ratio of the ¹³C-¹H COSY spectra according to the Gaussian law of error propagation

Workflow for targeted flux ratio analysis

• Sample flux distributions
• Simulate ¹³C-labeling patterns
• Select available measurements
• Calculate the flux ratio

Figure 2. Optimizing experimental design to improve the estimation of three flux ratios in Bacillus subtilis central carbon metabolism. (Kogadeeva, M.; et al. 2016)

Advantages of Our Methods

• Our method has been demonstrated by analyzing three key nodes of converging fluxes in central metabolism
• The flux estimates we obtained are consistent with published results obtained from steady-state experiments, but reduces the time of the necessary ¹³C labeling experiments to less than one minute
• Our strategy is able to formally estimate relative pathway fluxes in a very short time scale, ignoring cellular carbon equilibrium
• This approach paves the way for targeted ¹³C-MFA in dynamic systems with multiple carbon sources and offers the possibility of enriched media

Figure 3. Workflow for targeted flux ratio analysis. (Kogadeeva, M.; et al. 2016)

Features of Our MFA Platform

• Developed based on the most updated knowledge of biology, bioinformatics and software development
• Widely applicable to a wide range of metabolic system
• Professional bioinformatics teams & personalized bioinformatics analysis services.
• Advanced instrument platform
• Integrated quantitative methodologies and comprehensive solutions for metabolomics

Based on high-performance quantitative techniques and advanced equipment, Creative Proteomics has constantly updating our metabolic flux analysis platform and is committed to offering professional, rapid and high-quality services of flux ratio analysis at competitive prices for global customers. Our personalized and comprehensive services can satisfy any innovative scientific study demands, please contact our specialists to discuss your specific needs. We are looking forward to cooperating with you!

Reference

1. Kogadeeva, M.; et al. SUMOFLUX: A Generalized Method for Targeted ¹³C Metabolic Flux Ratio Analysis. PLoS Computational Biology. 2016. 12(9): e1005109.