Friday, 24 April, 2026
Molecular Component
The molecular component of the Geochemistry module covers the 144 organic molecules in the catalog, divided into ten micropollutant families plus a marginal family of inorganics (oxyanions). This page describes the general operation of the component, the structure of molecular data within an IsoFind project, and the relationship between reference sheets, sample measurements, and advanced analysis.
Navigating the Component
Each molecule family has its own dedicated page detailing compounds, regulatory thresholds, tabulated degradation pathways, and available isotope fractionation data. Cross-functional pages cover CSIA isotopy, the reference database, and general degradation pathways.
Pesticides (38)
Triazines, organophosphorus, neonicotinoids, chloroacetamides, phenylureas, organochlorines.
PFAS (26)
PFCA C2 to C12, PFSA C4 to C10, FTS, FOSA, Cl-PFAS, next-generation substitutes.
PAH and Hydrocarbons (19)
16 priority EPA PAHs, methylated PAHs, diagnostic source ratios.
Chlorinated Solvents (16)
Chlorinated ethylenes (PCE, TCE, DCE, VC), chlorobenzenes, chlorinated methanes and ethanes.
CSIA Isotopy
Compound-Specific Isotope Analysis: principles, tabulated epsilons, Rayleigh equation, dual isotope.
Degradation Pathways
50 tabulated pathways with kinetics, primary metabolite, favorable conditions, and references.
Structure of Molecular Measurements
Molecular measurements for a sample are stored in dedicated tables accessible via the API /api/molecules/{sample_id}/mesures. Each measurement contains the raw value, the original unit, the normalized value in µg/L, the analytical uncertainty, and a compliance indicator calculated automatically based on the regulatory threshold.
| Measurement Field | Content |
|---|---|
| molecule_id | Link to the reference catalog |
| valeur, unite | Value as reported by the laboratory (value, unit) |
| valeur_ug_l | Normalized value in µg/L for threshold comparison |
| incertitude | Analytical uncertainty as a percentage or absolute value |
| mz_mesure | MS transition actually used |
| detecte, conforme | Calculated flags: detected above LOQ, threshold compliance |
| seuil_ref, unite_ref | Reference threshold and its unit, captured at the time of measurement |
| methode, laboratoire | Analytical method and issuing laboratory |
| matrice, date_analyse | Sample matrix, date of analysis |
Automatic Compliance
IsoFind automatically calculates the compliance of each measurement against the water matrix regulatory threshold. Normalization to µg/L allows for the comparison of measurements reported in ng/L, mg/L, or pg/L with standard thresholds.
| Original Unit | Conversion to µg/L |
|---|---|
| ng/L | × 0.001 |
| µg/L | × 1 (reference) |
| mg/L | × 1000 |
| pg/L | × 0.000001 |
Two dedicated endpoints allow for re-triggering compliance calculations at a global scale or for a specific molecule: POST /api/molecules/recalculer-conformite and POST /api/molecules/recalculer-conformite/{molecule_id}. These recalculations are useful after a regulatory update (new EU threshold) or a threshold correction in the catalog.
Compliance is a simple calculation (value vs. threshold), but it depends on the quality of both terms: correctly normalized measurement in µg/L and a correctly entered threshold in the catalog. The report blocks molecule_conformity and regulatory_compliance_forecast consume these results.
Data Entry and Import
There are four ways to enter molecular measurements into an IsoFind project.
| Method | Usage |
|---|---|
| Manual Entry | Single measurement via the Molecule tab form |
| CSV or Excel Import | Batch loading via the IsoFind import module |
| Batch API | POST /api/molecules/{sample_id}/mesures/batch for programmatic integration |
| Catalog Seed | Pre-filling from a reference family via POST /api/molecules/catalogue/seed/{family} |
Statistics
Two endpoints return aggregated statistics to populate report blocks and the user interface. These statistics are recalculated on-the-fly with each call, without caching, ensuring they are always up to date.
| Endpoint | Content |
|---|---|
| GET /api/molecules/stats/global | Number of measurements, distinct molecules, families covered, compliance rate |
| GET /api/molecules/stats/par-sample/{sample_id} | Detailed statistics for a given sample |
Isotopic Suggestions
For a given sample, IsoFind can suggest which isotopic measurements would provide the most information based on the detected molecules. The endpoint GET /api/molecules/ref-isotopes/suggest/{sample_id} returns an ordered list of suggestions with their rationale: source identification, degradation diagnostics, or process traceability.
These suggestions are generated from the ref_molecules_isotopes table, which associates molecules with relevant isotopic elements and their typical interpretation. They populate the molecule_suggestions report block.
Learn More
- Pesticides: the largest family in the catalog.
- PFAS: catalog for sum of 4 PFAS and 20 PFAS.
- CSIA Isotopy: bridge to the Nexus engine.
- Reference Database: catalog structure and enrichment.