Central Carbon Metabolism Analysis Service —Targeted LC–MS/MS Panel

What Is Central Carbon Metabolism and Why Profile It?

Central carbon metabolism is the cellular hub that converts nutrients into energy, redox cofactors, and building blocks for macromolecules, including glycan precursors. Glycolysis, the TCA cycle, and the pentose phosphate pathway work together to control ATP supply, redox balance, and carbon skeletons that support growth and product quality.

Because these pathways respond rapidly to media, genetic changes, and process stress, shifts in central carbon flux often appear before titer, viability, or glycan profiles change. Quantitative central carbon metabolism analysis therefore provides an early, pathway-level view of how a system is adapting and where optimization is possible. Typical questions this profiling can address include:

• How do key pathways respond to nutrient shifts, engineering, or small-molecule treatment?
• Does a given cell line or strain favor glycolytic or mitochondrial routes under specific conditions?
• Which steps in central carbon metabolism constrain productivity or robustness in fermentation or culture?
• How does carbon routing affect pools of glycan-related precursors and other biosynthetic intermediates?

Our Central Carbon Metabolism Quantification and Profiling

Creative Proteomics offers a modular central carbon metabolism analysis platform that can be tailored to your experimental system. Typical service modules include:

• Targeted central carbon metabolite quantification: Absolute or relative quantitation of key intermediates in glycolysis, TCA cycle, pentose phosphate pathway, anaplerotic routes, and related shunts.
• Stable isotope–based pathway flux analysis: ¹³C-labeled substrates (for example, glucose, glutamine, acetate) combined with time-course sampling and model-based flux estimation.
• Glycan precursor and cofactor profiling: Quantification of UDP-sugars, sugar phosphates, and redox cofactors relevant to glycan biosynthesis and cellular energy balance.
• Nicotinate and nicotinamide metabolite analysis: Targeted profiling of nicotinic acid, nicotinamide, NAD⁺, NADH, NADP⁺, NADPH, and related intermediates.
• Extracellular metabolite and nutrient balance: Measurement of substrate uptake and byproduct secretion to support carbon and redox balance calculations.
• Custom method development: Extension of analyte panels or isotope labeling strategies to fit unique pathways, engineered routes, or non-standard substrates.

Each module can be combined into an end-to-end study, from cell culture sampling to integrated pathway interpretation.

Analyte Coverage: Central Carbon Metabolites and Related Compounds

This panel can be expanded with additional targets on request, for example pathway-specific intermediates or custom sugar nucleotides.

Advantages of Central Carbon Metabolism Quantitative Analysis

• High-precision calibration – Targeted LC–MS/MS with isotope-labeled internal standards; calibration curves typically reach R² ≥ 0.99.
• Robust quality control – Pooled QC samples and internal standards keep intra-batch CVs commonly ≤ 15%, supporting confident group comparisons.
• Broad dynamic range – Optimized MRM methods cover 3–4 orders of magnitude, capturing both low-abundance intermediates and high-abundance end products in one run.
• Pathway-focused coverage – A curated panel spanning glycolysis, the TCA cycle, and the pentose phosphate pathway provides contiguous central carbon readouts.
• Flux-ready methods – The same setup supports steady-state quantitation and ¹³C isotopologue profiling, enabling straightforward extension to flux analysis.
• Integration-ready outputs – Data are delivered with stable identifiers and pathway annotations, ready for direct import into R, Python, and pathway analysis tools

Analytical Platform for Central Carbon Metabolism LC–MS/MS

Central carbon metabolites are quantified on a targeted LC–MS/MS platform built around UPLC systems and triple quadrupole mass spectrometers. The setup is optimized for polar metabolites in glycolysis, the TCA cycle, and the pentose phosphate pathway, with robust retention, sensitivity, and throughput for routine project work.

Instrumentation Overview

Typical LC–MS/MS Settings for Central Carbon Metabolites

Targeted methods with isotope-labeled internal standards, multi-level calibration, and batch-level QC ensure that central carbon readouts are quantitative, reproducible, and suitable for downstream modeling and integration with other omics data.

Triple Quad™ 6500+ (Figure from Sciex)

Waters ACQUITY UPLC System (Figure from Waters)

Agilent 6495C Triple Quadrupole (Figure from Agilent)

Agilent 1260 Infinity II HPLC (Fig from Agilent)

Workflow for Central Carbon Metabolism LC–MS/MS Panel

1

Project Consultation & Panel Design

Clarify your model and key questions, then select or customize the central carbon panel (with optional ^13C tracing).

2

Sample Receipt & Pre-analytical QC

Check sample IDs, storage conditions, shipping records, and integrity; document any deviations before analysis.

3

Metabolite Extraction & Internal Standards

Perform rapid cold extraction of polar metabolites and spike isotope-labeled internal standards to control recovery and matrix effects.

4

UPLC–MS/MS Acquisition

Run targeted LC–MS/MS (MRM) for glycolysis, TCA, and PPP metabolites with embedded batch QC samples.

5

Data Processing, QC & Pathway Reporting

Process and QC-check data, then map significant changes onto central carbon pathways and deliver publication-ready tables and figures.

Sample Requirements for Nicotinate and Nicotinamide LC-MS/MS Analysis

For other matrices such as culture media, formulated products, or specialized biological fluids, tailored requirements can be defined during project setup.

Deliverables: What You Receive from Central Carbon Metabolism Analysis

Technical summary – Study design overview, sample list, and analytical methods used.

Raw data files – Original LC–MS/GC–MS instrument files for all samples and QC runs.

Processed data tables – Curated tables of metabolite intensities or concentrations, with sample IDs and normalization details.

Isotope tracing outputs (if applicable) – Isotopologue distributions and label fractions for tracer-based experiments.

Quality control report – Internal standard performance, calibration results, and batch QC metrics.

Pathway-level data views – Pathway-organized result tables or figures summarizing changes in central carbon and related metabolites.

Heatmap of central carbon metabolites across experimental conditions, showing pathway-organized clusters and treatment-induced shifts in glycolysis, TCA cycle, and the pentose phosphate pathway.

PCA scores plot of central carbon metabolite profiles demonstrating clear separation of Control, Treatment, and Recovery groups with 95% confidence ellipses.

Research Applications of Central Carbon Metabolism Profiling

Microbial metabolic engineering

Optimize precursor supply, redirect carbon flux, and improve yields or by-product profiles in engineered strains.

Bioprocess and cell culture optimization

Link central carbon fluxes to growth and productivity to refine media, feeding, and control strategies in cell factories and advanced cell cultures.

Cancer metabolism research

Characterize glycolysis, TCA, and PPP rewiring in tumor models to understand metabolic reprogramming and carbon routing.

Immunometabolism and innate immunity

Map central carbon shifts in macrophages and T cells during activation or polarization to link metabolic state with immune functions.

Plant stress and crop resilience studies

Profile central carbon and associated pathways under drought, heat, salinity, or nutrient stress to dissect metabolic adaptation in crops.

Systems biology, fluxomics, and database building

Generate model-ready flux and metabolite datasets for kinetic modeling, ¹³C-MFA, and curated flux databases.