~500k MS2 spectra with 70k SMILES, InChIKey, NPC & ClassyFire annotations

# Harmonized GNPS + MassSpecGym MS/MS spectra with NPClassifier and ChemOnt labels

This dataset contains zstd-compressed MGF spectra from GNPS public libraries andMassSpecGym, harmonized with canonical SMILES, InChIKey, molecular formula,NPClassifier labels, and ChemOnt/ClassyFire labels. It is intended forbenchmarking and modelling structure-aware MS/MS classification. Labels arecomputational annotations, not experimentally curated ground truth.

## Annotations

NPClassifier labels were predicted with NPClassifier.rs `Faithful`, CUDA f32,batch size `2048`. Coverage:

- NPClassifier: `7` pathways, `75` superclasses, `503` classes- ChemOnt: `2` kingdoms, `20` superclasses, `303` classes, `734` subclasses, `1,580` direct parents

Each MGF record includes source provenance, `SMILES`, `INCHIKEY`, `FORMULA`,`SPLASH`, NPC labels/scores, and ChemOnt labels.

## Processing

Spectra were parsed and serialized with `mascot-rs`. SMILES were canonicalizedwith `smiles-parser`; RDKit `2024.03.3` was used for tautomer-canonical SMILESand InChIKeys. Filters retained valid organic structures with non-zero precursorm/z, non-zero charge, `3-60` peaks, no post-top60 duplicate SPLASH collision,complete NPC labels, and no `(SPLASH, PEPMASS)` NPC/ChemOnt disagreement group.

## Fixed Compared To The Previous Version

- Updated to latest `mascot-rs`: `e9641034f75d019279a63f99d767d83a3bed55d1`.- Regenerated from GNPS and MassSpecGym sources instead of reusing the older corrupted MGF.- Did not patch contradictory metadata; records rejected by current `mascot-rs` were dropped.- Removed charge/ionmode conflicts: final mismatch count is `0`.- Added a final strict `mascot-rs` accept/reject pass; `282` harmonized records failed validation and were excluded.- Final file fully loads with current `mascot-rs`: `439,403` validated records.