| # UltraMS MSnLib formula-level split (split A) |
|
|
| Version **1.0.0** · 2026-11-04 · license **CC BY 4.0** |
|
|
| The frozen, **formula-disjoint** 80/10/10 train / validation / test split of the complete |
| MSnLib tandem mass spectral library (560,084 spectra, all adducts). This directory is also |
| shipped as `split_A_full_msnlib/` inside `ultrams_msnlib_benchmark_v1/`. |
|
|
| | | train | validation | test | total | |
| | --- | ---: | ---: | ---: | ---: | |
| | molecular formulas | 16,885 | 2,110 | 2,112 | 21,107 | |
| | spectra | 446,667 | 55,980 | 57,437 | 560,084 | |
|
|
| Every spectrum of a molecular formula lies in exactly one fold; no formula occurs in two |
| folds. The frozen assignment is the `fold` column of `MSnLib.csv` and the split is replayed |
| exactly by [`build_split_a.py`](build_split_a.py). |
|
|
| ## Files |
|
|
| | file | rows | content | |
| | --- | ---: | --- | |
| | `formula_split.csv(.gz)` | 21,107 | `formula, fold, n_spectra` — one row per molecular formula | |
| | `row_formula_fold.csv(.gz)` | 560,084 | `row_index, formula, fold` — authoritative row → formula → fold map for all spectra | |
| | `test_spectra.csv(.gz)` | 57,437 | `row_index, smiles, precursor_mz, adduct, collision_energy, fold, canonical_isomeric_smiles` | |
| | `val_spectra.csv(.gz)` | 55,980 | same schema for the validation fold | |
| | `msnlib_rt.csv.gz` | 560,084 | `row_index, rt` — compact per-spectrum retention time (seconds); gzipped only | |
| | `test_molecules_voting.csv(.gz)` | 5,002 | **official** multiple-spectrum voting units (Figure 3d / 3a voting): the test spectra grouped by the MSnLib source SMILES string, group size ≥ 2 (57,436 spectra); reproduces the published voting task's `n_molecules = 5002` grouping member-for-member | |
| | `test_molecules_voting_canonical_view.csv(.gz)` | 4,888 | alternative canonical view (not the official unit): the same test spectra grouped by RDKit canonical isomeric SMILES, group size ≥ 2 (57,436 spectra) | |
| | `REPORT.json` | | machine-readable report: counts, expected values, hashes, cross-checks, anomaly record | |
| | `VERIFY.md` | | full verification record (inputs, counts, cross-checks, replay transcript) | |
| | `build_split_a.py` | | replay from `MSnLib.csv` and SHA-256 check against the frozen tables | |
|
|
| `row_index` is the 0-based data row of `MSnLib.csv` (560,084 rows, 752,707,651 bytes, |
| SHA-256 `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07`; physical |
| line = data row + 2). Every `.csv` has a `.csv.gz` twin that decompresses to the identical |
| bytes. |
|
|
| ## Official voting units (Figure 3d / Figure 3a voting) |
|
|
| The official multiple-spectrum voting unit is the **MSnLib source SMILES string**. The |
| 57,437 test spectra contain 5,003 distinct source strings; one of them occurs in only one |
| spectrum, so `test_molecules_voting.csv` has **5,002 groups covering 57,436 spectra**. This |
| is the grouping of the published multiple-spectrum voting task and it is verified |
| member-for-member against the repository voting table (`n_molecules = 5002`). |
|
|
| For a chemically deduplicated view, `test_molecules_voting_canonical_view.csv` groups the |
| same spectra by RDKit canonical isomeric SMILES: 4,889 distinct molecules, of which |
| **4,888 groups cover the same 57,436 spectra**. 114 source-string groups merge into |
| chemically identical molecules, and the single excluded molecule is |
| `CC(C)(C)OC(=O)NCC1(CC(=O)O)CCCCC1`. The canonical view is an alternative, **not** the |
| official voting unit. See `VERIFY.md` §7. |
|
|
| ## Retention times (RT) |
|
|
| `msnlib_rt.csv.gz` is a compact companion table (1.4 MB gzipped, no 756 MB full CSV): |
| `row_index` is the 0-based `MSnLib.csv` data row (0 … 560,083) and `rt` is the retention time |
| in seconds, kept in the source text representation. It was exported from |
| `MSnLib_with_rt.csv` (755,984,910 bytes, SHA-256 |
| `a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964`, columns |
| `mzs,intensities,smiles,precursor_mz,adduct,collision_energy,fold,rt`) after verifying |
| row-by-row that its first seven columns are identical to `MSnLib.csv` in the same order |
| (560,084/560,084 rows, 0 mismatches). RT is source metadata from the MSnLib records |
| (CC BY 4.0; see `NOTICE.md` / the parent package `NOTICE.md`). |
|
|
| ```python |
| import gzip |
| import pandas as pd |
| |
| test = pd.read_csv("test_spectra.csv") |
| rt = pd.read_csv("msnlib_rt.csv.gz") # row_index, rt |
| test_rt = test.merge(rt, on="row_index", how="left") |
| assert test_rt["rt"].notna().all() |
| ``` |
|
|
| The table is needed by the label-blind grouping / multiple-spectrum voting analyses |
| (Figure 3d), which use RT as spectrum metadata. |
|
|
| ## Quick start |
|
|
| ```python |
| import pandas as pd |
| |
| formulas = pd.read_csv("formula_split.csv") |
| test = pd.read_csv("test_spectra.csv") |
| rows = pd.read_csv("row_formula_fold.csv") # 560,084 rows |
| |
| # formula-level disjointness: one fold per formula |
| assert formulas.groupby("formula")["fold"].nunique().max() == 1 |
| assert formulas["n_spectra"].sum() == 560_084 |
| ``` |
|
|
| ## Rebuild and verify |
|
|
| ```bash |
| # read-only replay + hash check (needs MSnLib.csv and RDKit 2026.03.5): |
| python3 build_split_a.py --csv /path/to/datasets/MSnLib/MSnLib.csv |
| |
| # write the tables (byte-identical with the frozen copies under RDKit 2026.03.5): |
| python3 build_split_a.py --csv /path/to/MSnLib.csv --output-dir replay_split_a |
| ``` |
|
|
| The split is **formula-disjoint, not molecule-disjoint**: different molecules can share a |
| formula and therefore a fold. The molecule-disjoint benchmark is split B |
| (strict-adduct 70/15/15) of `ultrams_msnlib_benchmark_v1/`; the two splits must never be |
| combined into a single global-disjointness claim. See `figures_mapping.md` in the parent |
| package for which manuscript panels use which split, and `NOTICE.md` for the MSnLib |
| attribution (Brungs et al., Zenodo 10.5281/zenodo.11163380, CC BY 4.0). |
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