Untargeted Metabolomics

Technical Specifications

TECHNICAL SPECIFICATIONS

Item	Details
Platform	Q Exactive HF-X high-resolution MS · polarity-switching acquisition
Identification Strategy	Dual matching against public databases and in-house libraries, covering polar and non-polar metabolites
Applicable Matrices	Blood (serum/plasma) · tissue · cells · urine and other matrices
Differential Screening	Default FC ≥ 1.5 and p < 0.05; or VIP ≥ 1 and q ≤ 0.05 (strategy auto-selected based on permutation-test results)

Analysis Workflow

ANALYSIS WORKFLOW

Data Preprocessing

Peak picking · alignment · normalization

Quality Control

PCA · QC correlation

Univariate Stats

FC · t-test / Wilcoxon

Multivariate Stats

OPLS-DA · permutation test

Differential Screening

FC + p or VIP + q

Abundance Analysis

Clustering · correlation · Z-score

Functional annotation

KEGG · HMDB / SMPDB

Biomarkers & Disease

ROC · AUC · Venn

Workflow: consultation (goals / study design) → proposal & quote (timeline / agreement) → sample intake (cold chain / pre-check / labeling) → experiment (acquisition / QC) → delivery (data + report + interpretation).

Bioinformatics Analyses (9 Modules)

BIOINFORMATIC MODULES

Module	Core Methods & Metrics	Key Outputs
Data Preprocessing	Peak picking, retention-time correction and alignment in Compound Discoverer; TIC normalization, missing-value filtering and imputation, Pareto scaling	Metabolic-feature quantification matrix
Quality Control	Global PCA / PLS-DA, QC-sample correlations (generally > 0.99) and pairs plots, sample-intensity boxplots, HMDB level-3 classification statistics	QC figure sets, classification statistics tables
Univariate Stats	Fold change; Welch's t-test / Wilcoxon test; BH-adjusted p-values (padj)	Volcano plots, classified volcano plots, full metabolite statistics tables
Multivariate Stats	PCA / PLS-DA / OPLS-DA modeling; 200 permutation tests; VIP score calculation	Score plots, permutation-test plots, VIP Top-25 bar charts
Differential Screening	Default FC ≥ 1.5 and p < 0.05; or VIP ≥ 1 and q ≤ 0.05 (strategy auto-selected based on permutation-test results)	Differential metabolite lists, up/down-regulation counts
Abundance Analysis	Hierarchical clustering; complex heatmap of top-50 significant metabolites; abundance analysis; Spearman correlation; Z-score normalization	Cluster heatmaps, correlation plots, abundance plots
Functional annotation	KEGG level 1–3 annotation and enrichment; Sankey diagrams, differential abundance score (DA Score), pathway-impact topology analysis, chord / donut plots / regulatory networks	KEGG enrichment figure sets and result tables
HMDB / SMPDB	HMDB and SMPDB enrichment; single-metabolite pathway analysis; pathway–metabolite networks	SMPDB enrichment figure sets and result tables
Disease & Biomarkers	Metabolite–disease association enrichment; ROC curves and AUC ranking; Venn overlap analysis of differential metabolites for multi-group comparisons	ROC plots, AUC ranking tables, Venn diagrams

Example Results

SELECTED FIGURES FROM ACTUAL REPORTS

Total Ion Chromatogram (TIC)

One chromatogram per polarity mode showing base-peak overlap of QCs and all samples, assessing chromatographic separation and instrument-response stability.

Global PCA

All samples including QCs projected together; tight QC clustering indicates a stable system, while clear group separation indicates distinct metabolic profiles.

QC Sample Correlation

Pairwise Pearson correlation heatmap of QC samples; values generally > 0.99 indicate reliable, batch-comparable data.

Sample Intensity Boxplot

Comparison of metabolite intensity distributions across groups, revealing outliers and normalization quality.

Metabolite Classification Donut

Composition of identified metabolites by HMDB Super Class, profiling the chemical classes of the dataset.

OPLS-DA Score Plot

Clearer separation after orthogonal signal correction, used to screen the most discriminating metabolites between groups.

QC Correlation Pairs Plot

Pairwise scatter, distribution and correlation coefficients of QC samples, assessing injection stability and data reproducibility.

Differential Metabolite Radar Chart

Radar chart of fold changes for differential metabolites, intuitively comparing magnitude and pattern of changes across groups.

Volcano Plot

log2(FC) on the x-axis and −log10(P) on the y-axis, presenting fold change and statistical significance together.

Volcano Plot (Classified)

Colored by HMDB chemical superclass, with the top-15 most significant known differential metabolites labeled.

Significant Pathway Chord Diagram

Mapping between differential metabolites and significant pathways (Level 1 / Level 2), colored by regulation direction and log2(FC).

Hierarchical Clustering Heatmap

Rows are metabolites and columns are samples — red high, blue low; dendrograms show clustering, revealing intergroup patterns and within-group reproducibility.

Applications

APPLICATIONS

Disease Biomarker DiscoveryDrug Mechanism & EfficacyNutrition & PhenotypingPlant / Microbial MetabolismToxicology & Exposure Assessment

FAQ

How long does a Untargeted Metabolomics project take?

Mature targeted panels typically take 1-3 weeks; untargeted projects take 2-4 weeks (counted from sample receipt and QC approval). The exact timeline is confirmed in writing before project start, and progress is trackable on the OmicsHub cloud platform.

What if my sample amount is below the recommendation?

Please do not dilute your samples. Low-input samples can often be accommodated by adjusting the preparation workflow — tell us the actual amount and our technical team will assess feasibility and note adjustments in the study plan.

Can I add targets to an existing panel?

Yes. Mature panels support on-demand additions; novel analytes outside the list can be implemented through custom method development (requires standards and extra validation time) — see our Custom Targeted Metabolomics service.

What samples do you need for Untargeted Metabolomics?

Serum/plasma ≥100 μL (fasting, no haemolysis), tissue ≥50 mg (snap-frozen), cells ≥1×10⁶ (medium washed off), urine ≥200 μL. Keep fasting time consistent, aliquot into single-use volumes and avoid freeze–thaw. Full guidance: Technical Resources → Sample Guide.