Targeted Organic Acids Quantification by LC–MS/MS

What Are Organic Acids and Why Analyze Them?

Organic acids are small, acidic metabolites with one or more carboxyl groups, including citric, malic, lactic, fumaric, succinic, and acetic acids. They are central nodes in energy and carbon metabolism rather than peripheral by-products.

In metabolism, organic acids mainly act as:

• TCA-cycle intermediates (citric, malic, fumaric, succinic, oxaloacetic acids) that reflect mitochondrial flux and ATP production.
• Glycolytic and fermentation products (lactate, pyruvate, acetic, butyric acids) that report on oxygen status, mitochondrial function, and microbial fermentation.
• Signaling metabolites such as itaconic acid that influence immune activation and inflammatory pathways.

In food and agriculture, organic acids are key markers of taste, acidity, freshness, fermentation progress, and product authenticity.

Because they sit close to core metabolic flux, small changes in organic acid profiles can indicate major pathway shifts. High-quality organic acid data help you:

• Link gene or protein changes to real metabolic outcomes.
• Separate on-target metabolic effects from off-target toxicity.
• Track how diet, microbiota, environment, or treatments reshape metabolic networks.

Targeted LC–MS/MS organic acids analysis provides the sensitivity and selectivity needed to capture these changes across complex matrices such as plasma, urine, tissues, feces, cell extracts, foods, and environmental samples.

What Questions Can Organic Acids Analysis Answer?

Organic acids profiling is most informative when it is linked to clear biological or product questions. Our organic acids analysis service commonly supports projects such as:

Energy metabolism & mitochondrial function

Evaluate how compounds, genetic perturbations, or stressors reshape TCA-cycle intermediates and mitochondrial function, and relate organic acid shifts to ATP, ROS, or cell viability readouts.

Metabolic disease & energy homeostasis

Profile organic acids in obesity, diabetes, NAFLD and related models to quantify changes in central carbon flux, detect pathway bottlenecks, and support translational metabolomics studies.

Immunometabolism & cancer metabolism

Profile lactate, pyruvate, succinate, itaconate and related acids to support proposed immunometabolic mechanisms and investigate metabolic reprogramming in tumor or immune cells.

Gut microbiota & SCFA-driven effects

Quantify short-chain fatty acids and fermentation acids in feces, plasma, or culture systems to link microbiome changes with host metabolic and inflammatory phenotypes.

Food quality, authenticity & processing

Use organic acid fingerprints to characterize flavor, acidity, freshness, batch consistency, and geographical origin in juices, wines, dairy products, and fermented foods.

Soil, plant & environmental assessments

Monitor root exudates and soil or water organic acids to study plant stress responses, nutrient dynamics, and environmental impact.

Targeted Organic Acids Panel and Pathway Coverage

Our targeted organic acids panel is organized by pathway and application so you can quickly check whether your metabolites of interest are covered.

*The panel is periodically optimized. Additional organic acids can be included or added as custom targets upon request.

Why Choose Creative Proteomics for Organic Acids Analysis?

• Pathway-centered organic acids panel: Coverage across TCA cycle, central carbon metabolism, SCFAs, plant/food acids, and signaling metabolites.
• Advanced LC–MS/MS platform: High-sensitivity QTRAP®-based workflows with optimized MRM methods for organic acids.
• Matrix experience across biology, food, and environment: Proven protocols for plasma, urine, tissues, feces, foods, beverages, and environmental samples.
• Robust QC and method validation: Calibration, QC samples, and internal standards to ensure reproducible quantification.
• Integration with broader metabolomics strategies: Organic acids panels that can be combined with other targeted or untargeted metabolomics services.
• Project-driven data interpretation: Reports and visualizations tailored to your experimental design and decision points, not just generic output.

Analytical Platform for LC–MS/MS Organic Acids Quantification

Core Instrumentation

LC–MS/MS system – High-performance triple quadrupole platform (e.g., AB Sciex QTRAP® 6500 or equivalent) with electrospray ionization and optimized MRM methods for organic acids.

UHPLC system – Binary or quaternary UHPLC with precise autosampler injection for stable gradients and low carryover in polar metabolite analysis.

LC columns – Reversed-phase C18 and/or HILIC columns selected to retain and separate highly polar and isomeric organic acids.

Sample preparation tools – Refrigerated centrifuges, vortex mixers, and homogenizers enabling cold protein precipitation and extraction under controlled conditions.

Data processing & QC – Vendor LC–MS/MS software combined with in-house pipelines for MRM integration, calibration, QC tracking, and downstream statistical and pathway analysis.

Key Analytical Parameters

Triple Quad™ 6500+ (Figure from Sciex)

Agilent 6495C Triple Quadrupole (Figure from Agilent)

Agilent 1260 Infinity II HPLC (Fig from Agilent)

LC–MS/MS Workflow for Organic Acids Quantification

1

Step 1 – Project consultation and panel design

We clarify your study goals, sample types, and target pathways, then recommend an organic acids panel, sample size, and provide a quotation.

2

Step 2 – Sample preparation and shipment

You prepare and ship samples according to our guidelines (matrix, volume, storage, labeling). We perform intake QC to confirm identity, condition, and suitability.

3

Step 3 – Extraction and LC–MS/MS acquisition

We carry out cold extraction/protein precipitation with internal standards, then run targeted LC–MS/MS (MRM) for the selected organic acids.

4

Step 4 – QC review and data processing

Calibration, blanks, and pooled QC samples are used to verify system performance. We integrate peaks, apply calibration, and generate concentration tables.

5

Step 5 – Reporting and follow-up

You receive a report package with data tables, key figures, and a concise interpretation. If needed, we arrange a follow-up discussion to review results and plan next steps.

How to Prepare and Submit Your Samples

Notes: For unusual matrices (fermented foods, environmental samples, plant exudates), send extra aliquots for method adaptation.

Project Deliverables for Organic Acids Analysis

• Sample receipt sheet (sample IDs, matrix, received volume and condition).
• LC–MS/MS method summary (organic acids panel used, matrix type, key settings and QC design).
• Result table for all quantified organic acids (per-sample concentrations with units, Excel/CSV).
• Calibration and QC summary (calibration range and R², QC sample results).
• Standard result report (key tables and basic comparison figures, in PDF/Word).
• Raw LC–MS/MS data files (provided if agreed in advance).

Representative LC-MS/MS chromatograms of targeted organic acids

(A) Standard mixture, (B) human plasma and (C) fecal extract, showing baseline separation and high signal-to-noise for key organic acids across matrices.

Calibration and quantitative performance of the LC–MS/MS organic acid assay

(A) Standard curve with linear regression and R². (B) LLOQ and linear range for representative organic acids. (C) QC %CV at low, mid and high levels, demonstrating robust linearity and precision.