Metabolomics (service)

01Overview and value chain

Markers: [EC: In-vitro diagnostics & bioanalytical services | OECD: Genomics & bioinformatics | Regulator: FDA (US), EMA (EU), NMPA (China)]

Metabolomics-as-a-service profiles the full set of small-molecule metabolites — amino acids, organic acids, lipids, sugars — in a biological sample using complementary liquid- and gas-chromatography mass spectrometry, turning raw spectra into biomarker panels, drug-response readouts and bioprocess metabolic profiles for pharma, nutrition and industrial-fermentation clients. Metabolon operates one of the highest-coverage untargeted platforms in the industry, its HD4 platform and proprietary reference library underpinning both discovery-stage biomarker studies and pharmacometabolomic assessments of how patients respond to new drugs. Biocrates Life Sciences, based in Austria, sells validated absolute-quantification kits (its MxP Quant 500 panel covers several hundred metabolites) run to cGMP/GLP standards, letting a lab quantify a defined metabolite panel without building its own reference-standard library from scratch. Creative Proteomics runs an integrated multi-omics CRO out of the US offering deep central-carbon-metabolism and lipidomics panels alongside proteomics services. In Denmark, MS-Omics (founded 2014, based in Vedbæk) provides metabolomics services spanning agriculture, food and clinical applications. In China, Novogene — a Shenzhen Stock Exchange-listed (688315) genomics and multi-omics CRO founded in 2011, serving more than 7,300 clients across roughly 90 countries — offers untargeted metabolomics (GC-MS/LC-MS) services and filed a patent in November 2025 for a metabolite spectral-library construction method and database, directly relevant to improving metabolite identification accuracy.

The key directions of metabolomics as a service are:

1. Untargeted (discovery) metabolomics: unbiased LC-MS/GC-MS profiling of as many detectable metabolites as possible in a sample, used to discover novel biomarkers or characterize a broad metabolic shift.
2. Targeted (quantitative) metabolomics: absolute quantification of a defined metabolite panel using isotope-labeled internal standards and triple-quadrupole mass spectrometry in multiple-reaction-monitoring (MRM) mode.
3. Lipidomics: reversed-phase LC-MS profiling specifically of lipid species (phospholipids, fatty acids, sterols) using C8/C18 column chemistry suited to hydrophobic analytes.
4. Bioinformatic annotation and pathway analysis: matching measured mass spectra against reference databases (HMDB, METLIN) and running multivariate statistical models (PLS-DA, VIP scoring) to identify significant biomarkers from the raw peak table.

Sectoral value chain

[Sample collection & metabolic quenching] ──> [Extraction & protein precipitation] ──> [LC-MS / GC-MS analysis]
                                                                                                  │
                                                                                    (QC pool monitoring)
                                                                                                  │
     [Client biomarker/pathway report] <─── [Chemometric modeling (PLS-DA/VIP)] <─── [Peak annotation vs. HMDB/METLIN]

Value chain levels

Cross-cutting technologies of the sector:

• HILIC and reversed-phase LC-MS: hydrophilic-interaction chromatography for highly polar metabolites (amino acids, organic acids, sugars) paired with C8/C18 reversed-phase chromatography for lipids and hydrophobic species, together covering the full polarity range of the metabolome.
• GC-MS derivatization: a two-step chemical process (methoximation followed by MSTFA silylation) that converts polar, non-volatile metabolites into volatile trimethylsilyl derivatives suitable for gas-chromatographic separation.
• Triple-quadrupole MRM quantification: targeted mass spectrometry that filters for a specific precursor ion, fragments it, and detects a specific product ion, giving the high selectivity and sensitivity needed for absolute quantification.

02US

The United States hosts the industry’s highest-coverage untargeted metabolomics platform and integrated multi-omics CRO services.

Metabolon’s ultra-deep coverage platform, Creative Proteomics’ integrated multi-omics CRO, CLIA/CAP compliance

• Metabolon: operates its HD4 untargeted metabolomics platform alongside targeted panels (lipidomics, gut metabolites, oxidative stress), backed by a proprietary reference library, serving both discovery-stage biomarker research and pharmacometabolomic studies of drug response for pharma clients.
• Creative Proteomics: runs an integrated multi-omics CRO offering deep central-carbon-metabolism and lipidomics panels using triple-quadrupole and Orbitrap mass spectrometry alongside capillary-electrophoresis-MS, serving both academic and industrial clients.
• Regulatory context: US metabolomics labs serving clinical applications operate under CLIA/CAP diagnostic-laboratory standards, with FDA oversight extending to verification of the chemometric models used to generate clinical-grade biomarker calls.

03CN

China integrates metabolomics services into both pharmaceutical drug-response research and its distinctive traditional-Chinese-medicine research base, backed by a large domestic multi-omics CRO industry.

Novogene’s multi-omics CRO scale, metabolite spectral-library patent, TCM mechanism research

• Novogene: a Shenzhen Stock Exchange-listed (688315) genomics and multi-omics CRO founded in 2011, headquartered in Beijing’s Zhongguancun Life Science Park with labs across China, the US, UK, Germany, Singapore, Thailand, Korea and Japan, serving more than 7,300 clients in roughly 90 countries; the company offers untargeted metabolomics (GC-MS/LC-MS) services and filed a patent in November 2025 for a metabolite spectral-library construction method and database.
• Traditional Chinese medicine (TCM) research: a distinctive national application is using metabolomics to scientifically characterize the mechanisms of multi-component TCM herbal formulas, tracking shifts in arachidonic-acid, lipid-metabolism and TCA-cycle pathways in patient serum before and after treatment.
• Regional cluster support: provincial biomedical-cluster funding in regions such as Zhejiang and Guangdong has supported local mass-spectrometry infrastructure investment to serve domestic metabolomics CROs and startups.

04EU

The European Union’s metabolomics service sector is closely tied to gut-microbiome research and strict analytical validation standards.

Biocrates’ validated quantification kits, MS-Omics’ microbiome-associated services, ISO 17025 validation

• Biocrates Life Sciences (Austria): sells validated absolute-quantification kits — its MxP Quant 500 panel covers several hundred metabolites — run to cGMP/GLP standards, letting a lab quantify a defined metabolite panel using triple-quadrupole mass spectrometry without building its own reference library.
• MS-Omics (Denmark, founded 2014): provides metabolomics services spanning agricultural, food and clinical applications from its Vedbæk base, part of a broader European specialization in short-chain-fatty-acid and bile-acid profiling relevant to gut-microbiome and functional-nutrition clients.
• ISO 17025 validation standard: European metabolomics labs operate under strict ISO 17025 accreditation, requiring detailed validation of accuracy, linearity and detection limits for every extraction and measurement method used.

05Leading companies and research institutes

06Tech stack and innovations

The metabolomics-service stack pairs complementary chromatographic separation modes with mass-spectrometric detection strategies suited to the metabolome’s extreme chemical diversity:

1. HILIC and reversed-phase LC-MS separation:
   • Hydrophilic-interaction chromatography resolves highly polar metabolites (amino acids, nucleotides, TCA-cycle organic acids) while C8/C18 reversed-phase columns separate lipids and hydrophobic species, together covering the metabolome’s full polarity range in a single analytical workflow.
2. GC-MS derivatization chemistry:
   • A two-step methoximation-then-MSTFA-silylation process converts polar, non-volatile metabolites into volatile trimethylsilyl derivatives, making them separable by gas chromatography on a long capillary column.
3. Triple-quadrupole MRM targeted quantification:
   • Filtering for a specific precursor ion (Q1), fragmenting it in a collision cell (q2), and detecting a specific product ion (Q3) gives the selectivity and sensitivity needed for absolute quantification against isotope-labeled internal standards.

07Value chains and production pipelines

Industrial pipeline for untargeted metabolomic profiling of industrial bioreactor culture broth

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. Sample collection &     │ ───> │ 2. Metabolite extraction & │
│    metabolic quenching         │      │    protein precipitation     │
└───────────────────────────┘      └───────────────────────────┘
                                                 │
                                                 ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. LC-MS/MS measurement   │ <─── │ 3. Drying & derivatization/│
│    with QC pool monitoring    │      │    reconstitution              │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. Peak annotation &      │ ───> │ 6. Chemometric modeling &  │
│    database matching          │      │    B2B report delivery       │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: Sample collection and metabolic quenching

The culture broth is rapidly filtered or centrifuged, the supernatant is instantly chilled in liquid nitrogen, and a mixture of isotope-labeled internal standards is added to freeze the metabolic profile in place before it can shift.

Stage 2: Metabolite extraction and protein precipitation

Cold 80% methanol is added to the sample, vortexed and incubated to precipitate interfering proteins, then centrifuged at high speed to yield a clarified metabolite-containing supernatant.

Stage 3: Drying and derivatization/reconstitution

The extract is dried in a vacuum concentrator; for LC-MS analysis the dried residue is reconstituted in starting mobile phase, while for GC-MS analysis it undergoes methoximation followed by MSTFA silylation to make the metabolites volatile.

Stage 4: LC-MS/MS measurement with QC pool monitoring

The prepared sample is injected into the LC-MS/MS system (HILIC mode for polar fractions), high-resolution mass spectra are collected in both positive and negative ionization modes, and pooled quality-control samples are periodically measured to track instrument drift.

Stage 5: Peak annotation and database matching

Raw spectra undergo peak picking and retention-time alignment in XCMS, and detected accurate masses (MS1) and fragmentation spectra (MS2) are matched against the HMDB reference database while filtering out salt adducts and other artifacts.

Stage 6: Chemometric modeling and B2B report delivery

The annotated feature table is analyzed with multivariate statistical models (PLS-DA, VIP scoring) to identify significant biomarkers, and the results are compiled into a client-facing pathway and biomarker report.