| --- |
| pretty_name: UltraMS MSnLib benchmark (formula-level split A + strict-adduct molecule-level split B) |
| license: cc-by-4.0 |
| language: |
| - en |
| size_categories: |
| - 100K<n<1M |
| task_categories: |
| - other |
| configs: |
| - config_name: split_A_formula_split |
| data_files: split_A_full_msnlib/formula_split.csv |
| - config_name: split_A_row_formula_fold |
| data_files: split_A_full_msnlib/row_formula_fold.csv |
| - config_name: split_A_test_spectra |
| data_files: split_A_full_msnlib/test_spectra.csv |
| - config_name: split_A_val_spectra |
| data_files: split_A_full_msnlib/val_spectra.csv |
| - config_name: split_A_test_molecules_voting_official |
| data_files: split_A_full_msnlib/test_molecules_voting.csv |
| - config_name: split_A_test_molecules_voting_canonical_view |
| data_files: split_A_full_msnlib/test_molecules_voting_canonical_view.csv |
| - config_name: split_A_msnlib_rt |
| data_files: split_A_full_msnlib/msnlib_rt.csv.gz |
| - config_name: split_B_pos_compound_split |
| data_files: splits/pos_compound_split.csv |
| - config_name: split_B_neg_compound_split |
| data_files: splits/neg_compound_split.csv |
| - config_name: split_B_pos_val_queries |
| data_files: queries/pos_val_queries.csv |
| - config_name: split_B_pos_test_queries |
| data_files: queries/pos_test_queries.csv |
| - config_name: split_B_neg_val_queries |
| data_files: queries/neg_val_queries.csv |
| - config_name: split_B_neg_test_queries |
| data_files: queries/neg_test_queries.csv |
| - config_name: split_B_pos_val_library |
| data_files: libraries/pos_val_library.csv |
| - config_name: split_B_pos_test_library |
| data_files: libraries/pos_test_library.csv |
| - config_name: split_B_neg_val_library |
| data_files: libraries/neg_val_library.csv |
| - config_name: split_B_neg_test_library |
| data_files: libraries/neg_test_library.csv |
| tags: |
| - chemistry |
| - mass-spectrometry |
| - metabolomics |
| - small-molecules |
| - tandem-ms |
| - spectrum-library-search |
| - molecule-retrieval |
| - benchmark |
| - ultraMS |
| --- |
| |
| # UltraMS MSnLib benchmark |
|
|
| Zenodo DOI: [10.5281/zenodo.23963489](https://doi.org/10.5281/zenodo.23963489) |
|
|
| Two frozen, independent benchmark splits of the [MSnLib](https://doi.org/10.1038/s41592-025-02813-0) |
| tandem mass spectral library, released by UltraMS. The splits are different objects: |
|
|
| * **Split A — UltraMS MSnLib formula-level split** (all 560,084 spectra, all adducts): |
| 21,107 molecular formulas, split 16,885 / 2,110 / 2,112 formulas and |
| 446,667 / 55,980 / 57,437 spectra into train / validation / test. Formula-disjoint. Test |
| fold: 57,437 spectra, 2,112 formulas, 5,003 source SMILES / 4,889 canonical molecules. |
| Population for single-spectrum candidate ranking, multiple-spectrum voting, label-blind |
| grouping, fingerprint prediction and embedding analyses (Figure 2b/2j, 3a/3b/3d/3g, |
| 3a_sp_4, 3a_sp_5, single-spectrum baselines). The **official multiple-spectrum voting |
| units are the 5,002 MSnLib source-SMILES groups covering 57,436 spectra** |
| (`test_molecules_voting.csv`); a canonical-SMILES alternative view (4,888 groups) is also |
| provided (`test_molecules_voting_canonical_view.csv`). Per-spectrum retention times |
| (`row_index, rt` in seconds) are in `msnlib_rt.csv.gz` for the label-blind grouping and |
| multiple-spectrum voting analyses. |
| * **Split B — strict-adduct molecule-level split** (`[M+H]+` and `[M-H]-` only): 41,348 / |
| 21,293 compounds and 301,636 / 140,193 preprocessed spectra, split 70/15/15 per polarity |
| by RDKit canonical isomeric SMILES, with frozen queries and libraries for |
| spectrum-to-spectrum library search. Population for Figure 3e/3f/3h, 3h_sp_1 and the |
| cross-collision-energy task (6,161 positive / 2,999 negative queries). |
|
|
| | split-B task | queries | library spectra | queries with an exact-adduct library positive | |
| | --- | ---: | ---: | ---: | |
| | `[M+H]+` test | 6,202 | 295,434 | 6,201 | |
| | `[M+H]+` validation | 6,202 | 250,424 | 6,194 | |
| | `[M-H]-` test | 3,193 | 137,000 | 3,160 | |
| | `[M-H]-` validation | 3,193 | 116,135 | 3,163 | |
|
|
| > **Disjointness.** Split A is formula-disjoint (no formula in two folds); split B is |
| > molecule-disjoint within each polarity (the train / validation / test compound sets are |
| > pairwise empty). The two splits must **not** be merged into a global-disjointness claim: |
| > about 41 % of split-B compounds lie in a different split-A fold, and a spectrum can be |
| > split-A test while its compound is split-B train. See the package |
| > `figures_mapping.md` §2 for the full cross-tabulation. |
| |
| ## Usage |
| |
| ```python |
| import pandas as pd |
| |
| base = "https://huggingface.co/datasets/dsadd4/UltraMS-MSnLib-Benchmark/resolve/main/" |
| |
| # split A — formula-level split of the full library |
| formulas = pd.read_csv(base + "split_A_full_msnlib/formula_split.csv") |
| rows = pd.read_csv(base + "split_A_full_msnlib/row_formula_fold.csv") # 560,084 rows |
| test = pd.read_csv(base + "split_A_full_msnlib/test_spectra.csv") # 57,437 rows |
| assert formulas.groupby("formula")["fold"].nunique().max() == 1 |
| |
| # split B — strict-adduct molecule-level library search |
| compound_split = pd.read_csv(base + "splits/pos_compound_split.csv") |
| queries = pd.read_csv(base + "queries/pos_test_queries.csv") |
| library = pd.read_csv(base + "libraries/pos_test_library.csv") |
| |
| positives = library.groupby("canonical_isomeric_smiles").size() |
| n_pos = queries["canonical_isomeric_smiles"].map(positives).fillna(0).astype(int) |
| denominator = int((n_pos > 0).sum()) # 6,201 |
| ``` |
| |
| With `datasets` (one config per table, see the YAML header): |
| |
| ```python |
| from datasets import load_dataset |
| queries = load_dataset("dsadd4/UltraMS-MSnLib-Benchmark", "split_B_pos_test_queries", split="train") |
| ``` |
| |
| Peak data are **not** part of the split tables. Every row is joined back to the spectra by |
| `row_index` / `msnlib_csv_data_row` / `first_msnlib_csv_data_row`, which point into |
| `MSnLib.csv`. `MSnLib.csv` and `MSnLib_candidates.json` are hosted in the same dataset; see |
| **Hosted files** below. |
|
|
| ## Columns |
|
|
| * `split_A_full_msnlib/formula_split.csv`: `formula, fold, n_spectra` |
| * `split_A_full_msnlib/row_formula_fold.csv`: `row_index, formula, fold` |
| * `split_A_full_msnlib/{test,val}_spectra.csv`: `row_index, smiles, precursor_mz, adduct, |
| collision_energy, fold, canonical_isomeric_smiles` |
| * `split_A_full_msnlib/test_molecules_voting.csv`: `group_id, smiles, n_spectra` — |
| **official** voting units: 5,002 MSnLib-source-SMILES groups covering 57,436 spectra, the |
| grouping of the published multiple-spectrum voting task (`n_molecules = 5002`) |
| * `split_A_full_msnlib/test_molecules_voting_canonical_view.csv`: `group_id, |
| canonical_isomeric_smiles, n_spectra` — alternative canonical view: 4,888 groups covering |
| the same 57,436 spectra |
| * `split_A_full_msnlib/msnlib_rt.csv.gz`: `row_index, rt` — per-spectrum retention time in |
| seconds, aligned 1:1 to the `MSnLib.csv` data rows (560,084 rows) |
| * `splits/*_compound_split.csv`: `polarity, compound_id, canonical_isomeric_smiles, split, |
| n_spectra, n_frozen_queries, n_raw_smiles_variants, first_msnlib_csv_data_row` |
| * `queries/*.csv`: `polarity, split, query_index, compound_id, canonical_isomeric_smiles, |
| adduct, msnlib_csv_data_row, msnlib_csv_line, precursor_mz, n_peaks, collision_energy, |
| source_smiles_raw, n_library_positives` |
| * `libraries/*.csv`: same as queries with `library_index` and `compound_split` instead of |
| `query_index`; row order is the frozen library order |
|
|
| ## Split-B evaluation protocol |
|
|
| 1. Score every query against the complete library of its task (no candidate short list). |
| 2. Correct = the top-1 library spectrum has the same canonical compound identity. |
| 3. Empirical FDR = `(accepted − correct) / accepted`; identification recall = |
| `correct / n_queries_with_library_positive` (6,201 / 3,160 for the two test tasks). |
| Queries without a library positive enter the FDR denominator but not the recall |
| denominator; `n_library_positives` is provided per query. |
| 4. The test library contains all preprocessed spectra of the polarity except the selected |
| test queries; the validation library contains train and validation compounds only. |
| 5. Validation is for model selection only; evaluate the test fold once. |
|
|
| ## Hosted files |
|
|
| The dataset hosts the complete manifest plus two large source files. Every file of the |
| manifest is checksummed in `SHA256SUMS`; the two large files are kept in a separate upload |
| step (see `hf_upload_commands.sh`, dry-run by default). |
|
|
| | hosted file | bytes | SHA-256 | purpose | |
| | --- | ---: | --- | --- | |
| | manifest: `split_A_full_msnlib/`, `splits/`, `queries/`, `libraries/`, `protocol/`, `rebuild/`, docs (59 files) | ≈ 185.2 MiB | see `SHA256SUMS` | the two benchmark splits, verifier, docs | |
| | `split_A_full_msnlib/msnlib_rt.csv.gz` | 1,483,069 | `994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8` | compact per-spectrum retention time (`row_index, rt` in seconds), aligned 1:1 to `MSnLib.csv`; used by the label-blind grouping analysis | |
| | `MSnLib.csv` | 752,707,651 | `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07` | full source CSV: one row per MSnLib spectrum (560,084 rows); every row pointer in the split tables resolves here | |
| | `MSnLib_candidates.json` | 1,368,264,026 | `125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc` | candidate SMILES lists behind the single-spectrum candidate-ranking task: a JSON object mapping a query SMILES string to its candidate SMILES list (9,886 query entries) | |
|
|
| `MSnLib.csv` is the UltraMS CSV conversion of the MSnLib original release (Zenodo |
| 10.5281/zenodo.11163380, CC BY 4.0), whose 18 per-file MS2 JSONL record lists contain the |
| same 560,084 spectra. `MSnLib_candidates.json` contains candidate SMILES lists derived from |
| the MSnLib compound set; both files carry the MSnLib attribution. |
|
|
| ## Provenance, verification, license |
|
|
| * Source rows: `MSnLib.csv` (560,084 rows) converted from the MSnLib original release |
| (Brungs et al., CC BY 4.0; Zenodo 10.5281/zenodo.11163380). |
| * Hosted source files: `MSnLib.csv` (752,707,651 bytes, SHA-256 `be54b330…`) and |
| `MSnLib_candidates.json` (1,368,264,026 bytes, SHA-256 `125a1cdc…`). |
| * Frozen split-B manifest, seeds 42 / 43, query seed 119; frozen split-A fold assignment |
| from the `fold` column of `MSnLib.csv`. |
| * `SHA256SUMS` covers every file; `rebuild/verify_release.py` is a self-contained verifier |
| that re-checks every count, ordering hash, disjointness statement, cross-split statistic |
| and checksum offline. |
| * License **CC BY 4.0**, with attribution to MSnLib (CC BY 4.0); Apache-2.0 for the two |
| UltraMS producer scripts. See the package `NOTICE.md`. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @misc{ultrams_msnlib_benchmark_2026, |
| title = {UltraMS MSnLib benchmark: full-library formula-level split and strict-adduct molecule-level library-search split}, |
| author = {Li, Yifan and Zhong, Yunhua and Liu, Pan and Xia, Jun}, |
| year = {2026}, |
| note = {Derived from MSnLib (Brungs, Schmid, Pluskal; CC BY 4.0, Zenodo 10.5281/zenodo.11163380)}, |
| howpublished = {Hugging Face / Zenodo dataset, version 1.0.0} |
| } |
| ``` |
|
|
| Please also cite MSnLib (doi:10.1038/s41592-025-02813-0) and the UltraMS manuscript. |
|
|
