UltraMS SpectraVerse dataset
Version 1.0.0 · 2026-11-04 · license CC BY 4.0 · Zenodo DOI 10.5281/zenodo.23964105 (see NOTICE.md)
A frozen, molecule-disjoint conversion of the SpectraVerse tandem mass spectral library, released by UltraMS. This is a data resource, not a standalone benchmark. The manuscript uses it in two roles:
- as the spectrum source of the negative-ion structure-family evaluation (Figure 2c: 661 molecule-spectrum pairs after negative-ion selection and exclusion of molecules present in the MoNA adaptation data set), and
- as one of the three structure-annotated sources (together with MassSpecGym and MSnLib) for the contrastively enhanced UltraMS training, the chemical-class evaluation and the UltraAtlas reference spectra.
1. The table
| item | value |
|---|---|
| file | Spectraverse.csv |
| rows | 464,346 spectra |
| bytes | 707,447,509 |
| SHA-256 | 06e084501e91f92cc642c3d60de2863266ff3d0db958354a011e32851bef3976 |
| columns | mzs, intensities, smiles, precursor_mz, adduct, collision_energy, fold |
| peak format | comma-separated strings, one spectrum per row |
The fold column is the frozen train / validation / test assignment:
| fold | spectra | unique exact SMILES |
|---|---|---|
| train | 370,362 | 33,846 |
| validation | 47,825 | 4,231 |
| test | 46,159 | 4,231 |
| total | 464,346 | 42,308 |
2. Split definition
- The split unit is the exact SMILES string (molecule level): every spectrum of a given SMILES string falls in exactly one fold, and no exact SMILES occurs in more than one fold (0 crossing strings out of 42,308).
- The partition is 8:1:1 at the molecule (exact-SMILES) level: 33,846 / 4,231 / 4,231 unique SMILES.
- This split is not formula-disjoint. Structural isomers share a molecular formula, and molecular formulas do recur across folds in this library. Downstream work must describe the partition as molecule/SMILES-disjoint, not as a formula-disjoint partition.
The frozen assignment is distributed as
splits/spectraverse_compound_split.csv
(42,308 rows: smiles, fold, n_spectra), so the data can be used without reconstructing
the assignment.
3. Usage
import pandas as pd
base = "https://huggingface.co/datasets/dsadd4/UltraMS-Spectraverse-Dataset/resolve/v1.0.0/"
spectra = pd.read_csv(base + "Spectraverse.csv")
split = pd.read_csv(base + "splits/spectraverse_compound_split.csv")
test = spectra[spectra.fold == "test"]
assert split.groupby("smiles").fold.nunique().max() == 1
The UltraMS repository consumes this table in
benchmarks/spectral_properties/prepare_library_spectra.py --dataset spectraverse
(published size/SHA-256 and fold counts are verified before use).
4. Provenance and licence
The spectra are the public SpectraVerse library (SpectraVerse v1.0.1, Zenodo 10.5281/zenodo.17870921, CC BY 4.0; Gupta, Qiang, Chung, Herbst and Skinnider). UltraMS contributed the CSV representation, the frozen molecule-level train / validation / test split and its distribution. See NOTICE.md for the full attribution.
5. Files
README.md, NOTICE.md, SHA256SUMS, VERIFY.md, stats.json
Spectraverse.csv (hosted with the release; not duplicated in the archive)
splits/spectraverse_compound_split.csv(.gz)
hf_dataset_card.md, hf_upload_commands.sh, zenodo_metadata.json