Metabolomics Creative Proteomics

Targeted Metabolomics Analysis Service

Unlock the Power of Absolute Quantification and High Sensitivity for Your Biomarker Studies, Drug Development, and Advanced Research.

Creative Proteomics offers high-sensitivity targeted metabolomics to quantify specific metabolites, reveal pathway insights, and support biomarker research.

Key Advantages:

  • Ultra-precise quantification with LC-MS/MS and GC-MS/MS
  • Custom targeted panels tailored to your research
  • Biological interpretation beyond raw data
  • Minimal sample requirements
  • Rigorous quality control for reliable results
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What is Targeted Metabolomics?

Targeted metabolomics is a highly precise analytical approach focused on the absolute or relative quantification of a specific set of known metabolites. Unlike untargeted metabolomics—which profiles the global metabolome—targeted analysis delivers quantitative data for metabolites of interest, with exceptional sensitivity and reproducibility. This precision is critical for biomarker validation, pharmacokinetic studies, regulatory submissions, and mechanistic research.

Whether you’re monitoring key metabolic pathways, verifying hypotheses, or ensuring regulatory compliance, targeted metabolomics empowers you to achieve robust, actionable insights with unparalleled confidence.

Why Choose Targeted Metabolomics for Your Research?

Targeted metabolomics is the right choice when your research requires:

  • Precise Quantification
    You need accurate, absolute concentrations of specific metabolites for biomarker validation, clinical studies, or regulatory submissions.
  • Detection of Low-Abundance Compounds
    Some key metabolites exist at trace levels and demand high sensitivity and selectivity for reliable detection.
  • Focused Pathway Analysis
    Your project targets specific metabolic pathways linked to diseases, biological processes, or treatment effects.
  • Reproducibility Across Batches
    Consistent, comparable data is essential for multi-sample or multi-center studies.
  • Minimal Sample Volumes
    Your samples are precious or limited, requiring efficient analysis without compromising quality.

Targeted metabolomics helps transform these research needs into actionable insights, supporting decision-making across biomedical research, drug development, nutrition, and other fields.

How We Help You Achieve Reliable Results

Our Targeted Metabolomics Service is designed around your needs, helping you move from data to discovery with confidence and clarity.

Here’s how we support your research:

  • Precision and Reproducibility
    We use advanced LC-MS/MS and GC-MS/MS platforms, along with carefully optimized protocols, to deliver consistent, high-quality data you can rely on.
  • High Sensitivity for Low-Abundance Metabolites
    Our methods can detect metabolites present at very low levels, enabling accurate measurement of biomarkers or pathway-specific compounds that might otherwise go unnoticed.
  • Biological Interpretation Included
    We provide more than just raw numbers. Our reports connect your quantitative results to biological pathways, trends, and potential implications for your study.
  • Minimal Sample Requirements
    Our workflows are optimized for small sample volumes, helping you conserve valuable material without compromising data quality.
  • Custom Panels for Your Goals
    We can tailor metabolite panels to your research focus—whether you’re investigating specific pathways, disease mechanisms, or particular classes of metabolites.
  • Rigorous Quality Control
    Every project includes thorough checks for accuracy, consistency, and data integrity, ensuring you receive trustworthy results.
  • Expert Support at Every Step
    Our team is available to discuss your goals, recommend optimal strategies, and help interpret your results to keep your project moving forward.

List of Detected Metabolites

Targeted metabolomics detectable substances include but are not limited to:

Targeted Metabolomics Technical Details & Coverage

Our targeted metabolomics services employ industry-standard instruments and methods to deliver precise, reliable data for a wide range of research and industrial applications. Here’s a quick guide to help you choose the optimal platform for your specific needs:

Platform Typical Instruments Suitable Metabolites LOD / LOQ Common Applications
LC-MS/MS - Agilent 6495C Triple Quad
- SCIEX 6500+ Triple Quad
- Thermo TSQ Altis
Amino acids, bile acids, organic acids, lipids, steroids < 1–2 ng/mL Biomarker quantification, clinical studies, pharmacokinetics, targeted pathway analysis
GC-MS/MS - Agilent 7890B + 5977A MSD Organic acids, sugars, volatile metabolites, FAMEs < 10 ng/mL Organic acid profiling, food safety, environmental analysis
UHPLC-QTOF-MS - Agilent 6546 Q-TOF
- Waters Xevo G2-XS
Lipids, polyphenols, flavonoids, complex metabolites ~ ng/mL – low pg/mL High-resolution targeted profiling, structural elucidation, confirmation of unknowns
HPLC (LC) - Agilent 1260 Infinity II
- Waters ACQUITY UPLC
Chromatographic separation of diverse metabolites N/A (non-MS detection) Sample preparation, method development, pre-MS separation
NMR - Bruker AVANCE III HD 600 MHz
- JEOL ECZ Series
Central carbon metabolites, sugars, lipids ~ 1–10 μM Broad-spectrum metabolic profiling, comparative studies without internal standards

How to Choose?

  • Need ultra-sensitive quantification of biomarkers? → LC-MS/MS
  • Working with volatile metabolites like organic acids or sugars? → GC-MS/MS
  • Interested in high-resolution profiles and structural information? → UHPLC-QTOF-MS
  • Seeking robust, label-free profiling with minimal prep? → NMR
  • Need solid separation before MS analysis? → HPLC (LC)
SCIEX Triple Quad™ 6500+

SCIEX Triple Quad™ 6500+ (Figure from Sciex)

Agilent 7890B-5977A

Agilent 7890B-5977A (Figure from Agilent)

Waters Xevo TQ-s

Waters Xevo TQ-s (Figure from Waters)

Agilent 6495 Triple Quadrupole LC/MS Coupled with the Agilent 1290 Infinity II LC System

Workflow for Targeted Metabolomics Service

1

Project Consultation

  • Understand your research goals and target metabolites.
  • Recommend suitable panels and analytical methods.
  • Advise on sample types and required volumes.
2

Sample Preparation & QC

  • Apply optimized extraction methods for each matrix.
  • Add internal standards for precise quantification.
  • Check sample quality and preparation efficiency.
3

Instrumental Analysis

  • LC-MS/MS → polar & semi-polar compounds
  • GC-MS/MS → volatile or derivatized compounds
  • UHPLC-QTOF-MS → high-resolution profiling
4

Data Processing & Interpretation

  • Quantify metabolites using validated software.
  • Perform statistical analyses (e.g., PCA, group comparisons).
5

Reporting

  • Raw data files
  • Concentration tables
  • Visualizations (heatmaps, plots)
  • Biological interpretation
 Targeted Metabolomics Analysis Process

Sample Requirements for Targeted Metabolomics Analysis

Sample Type Recommended Volume/Amount Storage Temperature Notes
Plasma / Serum ≥ 50 µL -80°C Collect in EDTA or heparin tubes; avoid hemolysis
Urine ≥ 200 µL -80°C Midstream collection preferred; avoid preservatives
Tissue ≥ 20 mg -80°C Snap-freeze in liquid nitrogen; store dry
Cell Pellets ≥ 1 million cells -80°C Wash with PBS, remove media before freezing
Cell Culture Supernatant ≥ 500 µL -80°C Collect at desired time points; avoid repeated freeze-thaw
Feces / Stool ≥ 50 mg -80°C Store in airtight containers; minimize air exposure
Plant Material ≥ 50 mg -80°C Freeze immediately after harvest; dry if necessary

How Targeted Metabolomics Supports Your Research and Development

Biomarker Validation and Research

  • Validate biomarkers discovered in research studies.
  • Measure absolute metabolite levels for biological insights.
  • Support research models exploring disease mechanisms.

Pharmacokinetics and Drug Development

  • Monitor metabolic pathways affected by drug candidates.
  • Study drug metabolism and potential toxicity.
  • Analyze endogenous and exogenous metabolites in research contexts.

Nutrition and Health Research

  • Quantify metabolites linked to diet and metabolism.
  • Investigate metabolic shifts from nutritional interventions or supplements.

Plant and Agricultural Studies

  • Analyze plant metabolites related to stress, growth, and quality traits.
  • Explore bioactive compounds and natural products.

Toxicology and Safety Assessment

  • Detect metabolic changes associated with chemical exposures.
  • Profile metabolites as indicators of safety or adverse effects.

Systems Biology and Multi-Omics Integration

  • Integrate metabolomics with genomics, proteomics, or transcriptomics.
  • Reveal comprehensive biological pathway dynamics.

What Results Will You Receive from Targeted Metabolomics?

Quantitative Data Tables

Detailed tables showing absolute or relative concentrations of each targeted metabolite, enabling precise comparisons across your samples and groups.

Quality Control Reports

Information on internal standards, calibration curves, and QC samples to demonstrate the reliability and consistency of your results.

Data Visualizations

Clear charts and plots, such as heatmaps, volcano plots, or PCA plots, to help you quickly identify trends, significant changes, and metabolic patterns.

Biological Interpretation

Expert analysis connecting metabolite changes to biological pathways, helping you understand the potential implications of your data.

Raw Data Files

Access to raw instrument files (e.g., .raw, .wiff, .d) if you wish to perform your own analysis or data integration.

Mass spectrometry spectrum with peaks labeled by m/z values for targeted metabolomics.

Simulated mass spectrum demonstrating characteristic m/z peaks for metabolites detected in targeted metabolomics.

Heatmap of metabolite intensities showing variations between samples.

Heatmap visualizing relative abundance patterns of targeted metabolites across multiple samples.

Volcano plot illustrating log2 fold change versus negative log10 p-values for metabolites.

Volcano plot displaying significant changes in metabolite levels, highlighting fold change and statistical significance.

PCA scatter plot showing sample separation and group clustering in targeted metabolomics.

PCA plot illustrating sample clustering in targeted metabolomics, with confidence ellipses distinguishing experimental groups.

Targeted Metabolomics Supports Discovery of Methyl Donor Benefits in Neurodegeneration


Journal: Journal of Neurochemistry

Published: August 2023

DOI: https://doi.org/10.1111/nan.12931


Background

A leading neuroscience research team investigating neurodegenerative tauopathies sought to determine how methyl donor supplementation—specifically L-methylfolate, choline, and betaine—affects one-carbon metabolism and tau pathology in a transgenic mouse model (TAU58/2 mice).

Challenge:

The researchers required:

  • Accurate quantification of low-abundance metabolites linked to one-carbon metabolism and oxidative stress.
  • Data sensitive and reproducible enough for correlating metabolic changes with tau pathology.
  • Fast turnaround to align with behavioral testing timelines in their animal study.

Our Solution

Creative Proteomics developed a customized targeted metabolomics panel tailored to the client's experimental goals. The panel included:

  • One-carbon metabolism markers: betaine, choline, 5-methyltetrahydrofolate (5-MTHF), total plasma homocysteine (tHcy).
  • Antioxidant markers: glutathione (GSH).
  • Neurotransmitters: acetylcholine (Ach).

Leveraging HPLC-MS/MS on the Agilent 1290 UHPLC coupled with the Sciex 4000 QTRAP mass spectrometer, our team delivered:

  • Highly sensitive and precise quantification via multiple reaction monitoring (MRM).
  • Triplicate measurements for statistical robustness.
  • Timely data delivery that matched the researchers' project schedule.

Results & Findings

Through our targeted metabolomics analysis, the client discovered:

  • A ~1.5-fold increase in betaine, ~1.3-fold increase in choline, and ~2.4-fold increase in 5-MTHF in mice receiving methyl donor supplementation.
  • A significant ~20% reduction in total plasma homocysteine levels.
  • Dramatically elevated glutathione levels in the supplemented group, suggesting improved antioxidant defenses.

These metabolic changes were directly associated with reduced pathological phosphorylation of tau and improved motor and learning performance in the tauopathy mouse model. The data provided critical biochemical insights supporting the therapeutic potential of methyl donors in neurodegenerative diseases.

Graphs showing body weight and plasma metabolites in TAU58/2 mice fed methyl donor or control diets, highlighting levels of betaine, choline, 5-MTHF, acetylcholine, homocysteine, and glutathione.Impact of methyl donor supplementation on one-carbon metabolism in TAU58/2 mice. (A) Body weight unchanged between methyl donor (MD) and control diet (CD) groups. (B–G) Plasma levels of betaine, choline, 5-MTHF, acetylcholine, total homocysteine, and glutathione. Data: mean ± SD (n=6); *p < 0.05, **p < 0.01, ***p < 0.001, ***p < 0.0001.

Reference

  1. van Hummel, Annika, et al. " Methyl donor supplementation reduces phospho‐Tau, Fyn and demethylated protein phosphatase 2A levels and mitigates learning and motor deficits in a mouse model of tauopathy." Neuropathology and applied neurobiology 49.4 (2023): e12931.

Do you provide assistance in interpreting metabolomics results?

Yes. Our deliverables include not just raw data but also biological interpretation, helping you understand pathway implications, biomarker relevance, or trends related to your research goals.

How do you ensure data quality and reproducibility across batches?

We implement strict quality control (QC) procedures, including:

  • Internal standards
  • Calibration curves
  • QC samples throughout the batch
  • Re-analysis of suspect results

This ensures high consistency and reliability of your data.

Can I integrate targeted metabolomics data with other omics data?

Yes. Many clients integrate metabolomics with genomics, proteomics, or transcriptomics for a systems biology perspective. We can help align your data formats and assist in multi-omics interpretation.

Are stable isotope labeling experiments supported?

Yes. We support stable isotope tracing experiments for metabolic flux analysis, allowing precise tracking of pathway dynamics. Let us know your tracer compounds of interest.

Do you accept partially processed samples?

We prefer raw or minimally processed samples to maintain data integrity. However, we can sometimes work with extracts if details of prior processing are provided.

Can you quantify absolute concentrations, or is the data relative only?

We offer both absolute quantification (using calibration curves and internal standards) and relative quantification, depending on your study goals and metabolite targets.

How do you handle matrix effects in complex biological samples?

We use several approaches to minimize matrix effects:

  • Internal standards for correction
  • Careful sample cleanup and extraction
  • Calibration curves in matched matrices

This ensures reliable quantification even in complex samples.

Can targeted metabolomics detect isomers or structural variants?

Yes, but it depends on the metabolites. LC-MS/MS and GC-MS/MS can separate many isomers, but some compounds require high-resolution MS or specific chromatographic methods for clear differentiation.

Are all metabolites detected equally well in a single run?

No. Different metabolites vary in ionization efficiency, polarity, and stability. Targeted assays often split compounds into different methods optimized for specific classes.

How are internal standards selected?

We choose internal standards that:

  • Match chemical properties of target metabolites
  • Do not overlap with native compounds
  • Are isotopically labeled whenever possible

Can highly reactive or unstable metabolites be analyzed?

Some highly labile compounds are challenging. We minimize degradation by:

  • Fast processing
  • Low temperatures
  • Adding stabilizing agents if suitable

Do you perform method validation for custom assays?

Yes. For custom targets, we validate:

  • Linearity
  • Precision and accuracy
  • Limit of detection and quantification
  • Recovery rates

Validation ensures robust and reliable data.

How do you handle samples with low metabolite concentrations?

We can enhance sensitivity by:

  • Concentrating samples during prep
  • Using highly sensitive triple quadrupole instruments
  • Optimizing injection volumes and MS parameters

Still, some compounds may remain below detection limits in certain matrices.

Are carryover issues a concern in targeted metabolomics?

Potentially, especially for sticky compounds like lipids. We mitigate this by:

  • Optimized washing steps
  • Dedicated blank runs
  • Monitoring carryover signals

What happens if my sample volume is lower than the recommended amount?

We can sometimes adapt protocols for lower volumes, but:

  • Detection limits may increase
  • Some analytes might fall below quantifiable levels
  • Data reproducibility could be affected

Contact us to discuss options for your sample size.

Do you adjust methods for different species (human, animal, plant)?

Yes. Extraction protocols, matrices, and even chromatographic conditions may differ across species to account for unique biochemical backgrounds.

High Levels of Oxidative Stress Early after HSCT Are Associated with Later Adverse Outcomes

Cook, E., Langenberg, L., Luebbering, N., Ibrahimova, A., Sabulski, A., Lake, K. E., ... & Davies, S. M.

Journal: Transplantation and Cellular Therapy

Year: 2024

DOI: https://doi.org/10.1016/j.jtct.2023.12.096

Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content

Badoni, S., Pasion-Uy, E. A., Kor, S., Kim, S. R., Tiozon Jr, R. N., Misra, G., ... & Sreenivasulu, N.

Journal: Proceedings of the National Academy of Sciences

Year: 2024

DOI: https://doi.org/10.1073/pnas.2410598121

The Brain Metabolome Is Modified by Obesity in a Sex-Dependent Manner

Norman, J. E., Milenkovic, D., Nuthikattu, S., & Villablanca, A. C.

Journal: International Journal of Molecular Sciences

Year: 2024

DOI: https://doi.org/10.3390/ijms25063475

UDP-Glucose/P2Y14 Receptor Signaling Exacerbates Neuronal Apoptosis After Subarachnoid Hemorrhage in Rats

Kanamaru, H., Zhu, S., Dong, S., Takemoto, Y., Huang, L., Sherchan, P., ... & Zhang, J. H.

Journal: Stroke

Year: 2024

DOI: https://doi.org/10.1161/STROKEAHA.123.044422

Pan-lysyl oxidase inhibition disrupts fibroinflammatory tumor stroma, rendering cholangiocarcinoma susceptible to chemotherapy

Burchard, P. R., Ruffolo, L. I., Ullman, N. A., Dale, B. S., Dave, Y. A., Hilty, B. K., ... & Hernandez-Alejandro, R.

Journal: Hepatology Communications

Year: 2024

DOI: https://doi.org/10.1097/HC9.0000000000000502

Comparative metabolite profiling of salt sensitive Oryza sativa and the halophytic wild rice Oryza coarctata under salt stress

Tamanna, N., Mojumder, A., Azim, T., Iqbal, M. I., Alam, M. N. U., Rahman, A., & Seraj, Z. I.

Journal: Plant‐Environment Interactions

Year: 2024

DOI: https://doi.org/10.1002/pei3.10155

Teriflunomide/leflunomide synergize with chemotherapeutics by decreasing mitochondrial fragmentation via DRP1 in SCLC

Mirzapoiazova, T., Tseng, L., Mambetsariev, B., Li, H., Lou, C. H., Pozhitkov, A., ... & Salgia, R.

Journal: iScience

Year: 2024

DOI: https://doi.org/10.1016/j.isci.2024.110132

Physiological, transcriptomic and metabolomic insights of three extremophyte woody species living in the multi-stress environment of the Atacama Desert

Gajardo, H. A., Morales, M., Larama, G., Luengo-Escobar, A., López, D., Machado, M., ... & Bravo, L. A.

Journal: Planta

Year: 2024

DOI: https://doi.org/10.3390/antiox9111098

A personalized probabilistic approach to ovarian cancer diagnostics

Ban, D., Housley, S. N., Matyunina, L. V., McDonald, L. D., Bae-Jump, V. L., Benigno, B. B., ... & McDonald, J. F.

Journal: Gynecologic Oncology

Year: 2024

DOI: https://doi.org/10.1016/j.ygyno.2023.12.030

Glucocorticoid-induced osteoporosis is prevented by dietary prune in female mice

Chargo, N. J., Neugebauer, K., Guzior, D. V., Quinn, R. A., Parameswaran, N., & McCabe, L. R.

Journal: Frontiers in Cell and Developmental Biology

Year: 2024

DOI: https://doi.org/10.3389/fcell.2023.1324649

Proteolytic activation of fatty acid synthase signals pan-stress resolution

Wei, H., Weaver, Y. M., Yang, C., Zhang, Y., Hu, G., Karner, C. M., ... & Weaver, B. P.

Journal: Nature Metabolism

Year: 2024

DOI: https://doi.org/10.1038/s42255-023-00939-z

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