| # UltraMS SpectraVerse dataset |
|
|
| Version **1.0.0** · 2026-11-04 · license **CC BY 4.0** · Zenodo DOI **10.5281/zenodo.23964105** |
| (see [NOTICE.md](NOTICE.md)) |
|
|
| A frozen, molecule-disjoint conversion of the |
| [SpectraVerse](https://doi.org/10.5281/zenodo.17870921) tandem mass spectral library, |
| released by UltraMS. **This is a data resource, not a standalone benchmark.** The |
| manuscript uses it in two roles: |
|
|
| 1. 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 |
| 2. 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`](splits/spectraverse_compound_split.csv) |
| (42,308 rows: `smiles, fold, n_spectra`), so the data can be used without reconstructing |
| the assignment. |
|
|
| ## 3. Usage |
|
|
| ```python |
| 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](https://doi.org/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](NOTICE.md) for the full attribution. |
|
|
| ## 5. Files |
|
|
| ```text |
| 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 |
| ``` |
|
|
