Omicser — Omics Engineer

Omics field

Metabolomics

Metabolomics is the comprehensive study of small-molecule metabolites and the chemical fingerprint they leave in a cell, tissue or biofluid. It reports the downstream chemistry of a biological system at the moment of sampling.

Questions this field can answer

  • Which metabolites differ between conditions, and by how much?
  • Which pathways are plausibly affected by a treatment or state?
  • How confidently is a given feature annotated as a specific compound?
  • Does the measured chemistry reflect biology, diet, drugs or sample handling?
  • Can a candidate marker be reproduced in an independent public study?

Method

Research workflow

Established practice, from framing a question to depositing data others can reuse.

  1. 01

    Study design

    Decide targeted versus untargeted, fix the platform, and randomise sample order across the run. Plan QC pool injections before you start.

  2. 02

    Sampling

    Quench metabolism fast and standardise collection, fasting state, time of day, tube type and freezing. Metabolite levels shift within minutes.

  3. 03

    Assay and data generation

    Extract with a documented protocol including internal standards, then acquire by LC-MS, GC-MS (usually with derivatisation) or NMR.

  4. 04

    Quality control

    Run extraction blanks, solvent blanks and pooled QC samples at fixed intervals. Track internal standard response, retention-time drift and QC coefficient of variation.

  5. 05

    Analysis

    Peak-pick and align features, remove blank-associated and poorly reproducible features, correct for drift and batch, then normalize before statistics.

  6. 06

    Interpretation

    Report annotation confidence explicitly. A matching mass alone is a putative annotation, not an identification, and pathway enrichment is hypothesis generating.

  7. 07

    Reproducibility

    Record instrument, column, gradient, polarity, software versions and every filtering threshold, plus the spectral library used.

  8. 08

    Deposition

    Deposit raw and processed data with study metadata in MetaboLights and cite the MTBLS accession.

Practice

Samples, technologies and what can go wrong

Method choice sets the ceiling on what an analysis can show. Limitations are part of the method, not an afterthought.

Sample types

  • Plasma and serum
  • Urine, highly variable and usually creatinine-normalised
  • Tissue extracts, requiring fast quenching
  • Cell extracts and spent culture medium
  • Faecal samples for gut-microbial metabolites
  • Saliva, sweat and other accessible biofluids

Major technologies

LC-MS
Broadest coverage of polar and semi-polar metabolites; sensitive, but ion suppression and matrix effects are real.
GC-MS
Excellent chromatographic resolution and reproducible spectral libraries for volatile and derivatised compounds.
NMR
Highly reproducible, quantitative and non-destructive, with lower sensitivity and less coverage than MS.
Targeted panels
Absolute quantification of a defined compound list using authentic standards and calibration curves.
Untargeted profiling
Measures thousands of features without prior selection, at the cost of uncertain annotation.

Limitations

  • Most untargeted features are never confidently identified.
  • One mass matches many possible formulas and isomers.
  • Coverage depends strongly on extraction chemistry and platform.
  • Absolute concentration needs standards; untargeted data give relative intensity.
  • Metabolite levels are highly sensitive to time, diet and medication.

Common confounders

  • Instrument drift and carry-over across a long acquisition batch.
  • Fasting state, diet, exercise and medication before sampling.
  • Haemolysis, tube additives and delayed processing.
  • Storage temperature and repeated freeze–thaw cycles.
  • Sample order correlated with study group — always randomise.

Live data

Search the public record

Read-only searches against public databases. Madomic presents and explains the records; the databases named below remain their source and owner.

Madomic Research Explorer

Look up a compound in PubChem

Live, read-only compound lookup by name through PubChem PUG REST. Identifiers and properties come directly from PubChem; Madomic only formats and explains them.

Requests are throttled below PubChem's documented five-per-second policy. Nothing you type is stored.

Reference

Glossary

Essential terms, in plain English.

Feature
A detected mass-to-charge and retention-time pair, not yet a named compound.
Annotation confidence
The evidence level behind naming a feature, from formula match to a matched authentic standard.
Internal standard
A known compound added to every sample to monitor extraction and instrument response.
QC pool
An aliquot mixture of all samples, injected repeatedly to measure technical reproducibility.
Batch drift
Systematic signal change across an acquisition sequence, corrected using QC injections.
Ion suppression
Loss of signal when co-eluting matrix components compete for ionisation.
InChIKey
A hashed, fixed-length chemical structure identifier used to match compounds across databases.
ChEBI ID
A stable identifier for a chemical entity of biological interest.
MTBLS accession
The public identifier of a study deposited in MetaboLights.

For students

Learning path and a practical activity

Everything below uses public data only. No samples, credentials or paid services are needed.

Learning path

  1. 01Learn what a metabolite is and why levels change on a minute scale.
  2. 02Compare targeted and untargeted designs and their trade-offs.
  3. 03Understand LC-MS, GC-MS and NMR coverage differences.
  4. 04Learn the QC framework: blanks, pools, internal standards, randomisation.
  5. 05Learn annotation confidence levels and never over-claim an identification.
  6. 06Practise looking up compounds by name, formula and InChIKey.
  7. 07Read a MetaboLights study and audit its metadata completeness.

Activity — from a compound to a public study

  1. 01Look up a metabolite in the explorer below, for example “glucose”, “citrate” or “caffeine”.
  2. 02Record the PubChem CID, molecular formula, molecular weight and InChIKey.
  3. 03Find the same compound in ChEBI and note its ChEBI ID and any biological role annotations.
  4. 04Search MetaboLights for a study involving that compound or its pathway, and record the MTBLS accession, organism and platform.
  5. 05Audit the study metadata: is sample collection, QC design, extraction and instrument method described well enough to repeat?
  6. 06Write a short note stating which facts came from PubChem, ChEBI or MetaboLights, and which parts are your own interpretation.

Attribution

Research resources

Authoritative public resources. Omicser is independent of each of them and links to the official source.

MetaboLights

Maintained by EMBL-EBI

Open repository for metabolomics studies, raw and processed data, and standardised study metadata.

ChEBI

Maintained by EMBL-EBI

Curated dictionary of chemical entities of biological interest, with ontology, roles and stable identifiers.

PubChem

Maintained by NCBI, US National Library of Medicine

Very large public chemistry database of compounds, substances, properties and bioassays.

PubChem PUG REST documentation

Maintained by NCBI

The official programmatic interface and usage policy — the source used by the explorer on this page.

Research and education use only. This page is not a clinical diagnosis, medical advice or a laboratory result. Verify every finding in the originating database and in the peer-reviewed literature before drawing conclusions.