Wide-Targeted Metabolomics: Bridging Non-Targeted and Targeted for High-Coverage, Reproducible Quantification

Metabolomics serves as a core omics technology in medicine, agricultural research and systems biology. As the downstream readout of genetic, transcriptional and protein regulatory networks, metabolite changes are more closely linked to phenotypic outcomes. Among available approaches, wide-targeted metabolomics (also known as pseudotargeted metabolomics) represents a powerful hybrid strategy that combines the unbiased coverage of high-resolution mass spectrometry (HRMS) with the high sensitivity and reproducibility of multiple reaction monitoring (MRM) quantification. BMKGENE offers wide-targeted metabolomics services, tailored to meet the diverse needs of researchers across medical, plant, animal, and agricultural fields.

What Is Wide-Targeted Metabolomics?

Wide-targeted metabolomics employs a hybrid workflow designed to overcome the limitations of both non-targeted and targeted metabolomics.

1)Database Construction (Non-Targeted HRMS)

Perform UHPLC-HRMS (Q-TOF/Orbitrap) on pooled sample mixtures under positive/negative ionization and multiple collision energies to capture comprehensive MS1 and MS2 spectra. Use bioinformatics tools to extract peaks, annotate features, and select optimal precursor→product ion pairs (MRM transitions) for each metabolite. In addition to information generated from sample, data from authenticated standard compounds are also integrated to form the local database.

2)Quantification (Targeted TQ-MS)

Curated MRM transition to a triple quadrupole (QQQ) mass spectrometer, then analyze all biological samples in MRM mode, delivering high sensitivity, excellent reproducibility relative quantification.

This approach allows simultaneous detection of thousands of metabolites, without relying on a predefined limited target list, hence the term “wide-targeted.”

Key Differences: Non-Targeted vs. Wide-Targeted vs. Targeted Metabolomics

To clarify positioning, we compare the three core strategies (aligned with Zheng et al., 2020):

When to Choose Wide-Targeted Metabolomics?

Wide-targeted is the optimal choice when you need both breadth and reliability—avoiding the tradeoffs of pure non-targeted or targeted approaches. BMKGENE recommends this solution for:

1.Medical Research: Biomarker discovery in large cohorts, using plasma, serum, cerebrospinal fluid, or tissue samples.

2.Plant Research: Studies on crop stress response (drought, salinity, heat), plant development (seed germination, fruit ripening), secondary metabolite biosynthesis (flavonoids, alkaloids), and variety screening. Ideal for identifying metabolic markers of stress resistance and quality traits.

3.Animal Research: Profiling of animal serum, milk, tissues, or feces to study nutrition metabolism, disease mechanisms, breed differences, and product quality.

4.Microbial Research: Metabolic profiling of microbial strains, functional metabolism analysis, microbe–host interactions, fermentation metabolism, and environmental microbial metabolic characteristics.

5.Multi-Omics Integration: Combined analysis with transcriptomics, proteomics, or genomics to uncover phenotype-associated regulatory networks.

If your research requires absolute quantification or focused validation of differential metabolites, and involves only a limited number of known target metabolites, targeted metabolomics is the more appropriate choice.

BMKGENE’s Wide-Targeted Metabolomics Service: Your Trusted Partner

With over 16 years of experience in multi-omics research and service, BMKGENE has optimized the wide-targeted metabolomics workflow to support high-quality, cross-field research globally.

Service Advantages: 

• Comprehensive In-house Database: Integrates more than 70,000 metabolites from authentic reference standards and high-confidence spectral libraries, including 70K for plant metabolites and 9K for animal metabolites.

• Cross-Sample Compatibility: Optimized protocols for multiple sample types: human (plasma, serum, tissues), plant (leaves, roots, seeds, fruits), animal (serum, milk, tissues, feces), microorganism, etc.

• Advanced Platforms: Equipped with state-of-the-art UHPLC-Q-TOF (Waters Xevo G2) and UHPLC-QQQ (Sciex Triple Quad 7500), delivering high sensitivity (detection down to pg/ml level) and accuracy.

• Professional Bioinformatics Support: Expert in-house analysis team providing annotation, differential expression analysis, pathway enrichment, visualization, etc.

• Standardized Workflows: Rigorous quality control procedures implemented throughout the process to ensure data reliability and repeatability.

• Extensive Experience: Long-standing experience in metabolomic profiling and multi-omics integration.

References

Zheng, F., Zhao, X., Zeng, Z., et al. Development of a plasma pseudotargeted metabolomics method based on ultra-high-performance liquid chromatography–mass spectrometry. Nature Protocols, 2020, 15(7): 2221–2247. https://doi.org/10.1038/s41596-020-0341-5