Figure → split mapping
This package contains the two frozen MSnLib splits behind the UltraMS manuscript. They are different objects and answer different questions:
- Split A — UltraMS MSnLib formula-level split (
split_A_full_msnlib/): the complete MSnLib library (560,084 spectra, all adducts) split by molecular formula into 16,885 / 2,110 / 2,112 formulas and 446,667 / 55,980 / 57,437 spectra (train / validation / test). Formula-disjoint, not molecule-disjoint. Test fold: 57,437 spectra, 2,112 formulas, 5,003 source SMILES / 4,889 canonical molecules. - Split B — strict-adduct molecule-level split (
splits/,queries/,libraries/): the strict[M+H]+and[M-H]-subsets (447,956 source rows) re-split 70/15/15 at the level of RDKit canonical isomeric SMILES, separately per polarity, with frozen queries and libraries for spectrum-to-spectrum library search. Molecule-disjoint within each polarity. Test tasks: 6,202 positive and 3,193 negative queries against 295,434 and 137,000 library spectra.
1. Panel mapping
| figure panel | split | evaluation population / task |
|---|---|---|
| Figure 2b — ionization-polarity recognition | A | polarity prediction over the split-A evaluation population (A test fold; A train / validation used for fitting and reference). |
| Figure 2j — peak-token embedding chemical atlas | A | peak-token embedding visualization/analysis over the split-A test fold with split-A reference spectra; colours are chemical properties, not a model output. |
| Figure 3a — single-spectrum candidate ranking (Hit@1/5/20) | A | 57,437 split-A test spectra as queries, ranked against the per-formula candidate tables used by the manuscript (candidate ranking tables are part of the UltraMS repository, not of this split package). |
| Figure 3b — score/rank density and cumulative Top-k | A | same 57,437 split-A test queries and their candidate rankings. |
| Figure 3d — multiple-spectrum voting | A | 57,437 split-A test spectra grouped into the official voting units: 5,002 MSnLib source-SMILES groups covering 57,436 spectra (split_A_full_msnlib/test_molecules_voting.csv); the alternative canonical-isomeric-SMILES view (4,888 groups, same 57,436 spectra) is split_A_full_msnlib/test_molecules_voting_canonical_view.csv; the retention times used by this analysis are split_A_full_msnlib/msnlib_rt.csv.gz (row_index, rt). See the parent README.md §4.3/§4.5. |
| Figure 3g — empirical rank CDF | A | 57,437 split-A test queries. |
| Figure 3a_sp_4 — label-blind consensus grouping | A | split-A test fold, label-blind grouping of same-molecule spectra. |
| Figure 3a_sp_5 — promoted MSnLib fingerprint analysis | A | split-A fingerprint-prediction evaluation population (split-A train / validation for fitting). |
| baselines — single-spectrum Top-1 table | A | 57,437 split-A test queries, one ranking per method. |
| Figure 3e — strict-adduct library search, FDR–recall | B | strict [M+H]+: 6,202 test queries vs 295,434 library spectra (recall denominator 6,201); strict [M-H]-: 3,193 vs 137,000 (denominator 3,160). Validation tasks: 6,202 / 250,424 and 3,193 / 116,135. |
| Figure 3f — cross-polarity molecular retrieval | B | molecule-level split-B compounds; one polarity's spectra query the other polarity's library. |
| Figure 3h — seven-method strict-adduct FDR–recall (unused figure) | B | same split-B query / library sets as Figure 3e. |
| Figure 3h_sp_1 — FDR threshold transfer | B | split-B validation/test query identities; 200 paired molecule-disjoint calibration/held-out assignments over those identities. |
| cross-collision-energy search | B | split-B test queries that have at least two collision energies: 6,161 positive and 2,999 negative cross-CE queries (from 6,202 / 3,193 split-B test queries). |
| NPLIB1 and MassSpecGym comparison panels | not this dataset | NPLIB1 (3,699 test molecules) and MassSpecGym are independent external benchmarks with their own splits and libraries; they are not derived from MSnLib and are not covered by this package. |
| Figure 3c / Figure 3i case studies | neither | case-study panels use specific MSnLib spectra and MAGMa peak annotations; they are not defined by either split table. |
2. Cross-split inconsistency: split A (formulas) vs split B (compounds)
The two splits are built on different units (formula vs canonical molecule) and different
populations (all adducts vs strict [M+H]+/[M-H]-), so their fold labels disagree for a
large share of compounds. The tables below are computed by mapping every split-B compound
to its molecular formula through msnlib_csv_data_row → split_A_full_msnlib/row_formula_fold.csv.
Compound counts are split-B compounds (a compound belongs to one polarity and one split-B
fold).
[M+H]+ — 41,348 compounds
| split B ↓ / split A → | train | validation | test | total |
|---|---|---|---|---|
| train | 23,059 | 2,901 | 2,984 | 28,944 |
| validation | 4,924 | 647 | 631 | 6,202 |
| test | 4,922 | 626 | 654 | 6,202 |
| total | 32,905 | 4,174 | 4,269 | 41,348 |
Same-fold compounds: 24,360 / 41,348 (58.9 %). Of the 6,202 split-B positive test compounds only 654 (10.5 %) are split-A test compounds; 4,922 (79.4 %) are split-A train compounds.
[M-H]- — 21,293 compounds
| split B ↓ / split A → | train | validation | test | total |
|---|---|---|---|---|
| train | 12,035 | 1,447 | 1,425 | 14,907 |
| validation | 2,552 | 307 | 334 | 3,193 |
| test | 2,541 | 349 | 303 | 3,193 |
| total | 17,128 | 2,103 | 2,062 | 21,293 |
Same-fold compounds: 12,645 / 21,293 (59.4 %). Of the 3,193 split-B negative test compounds only 303 (9.5 %) are split-A test compounds.
Spectra-level view
The split-B tables cover all 441,829 preprocessed strict-adduct spectra (301,636 positive + 140,193 negative); each maps to exactly one split-A fold:
[M+H]+ — 301,636 preprocessed spectra:
| split B ↓ / split A → | train | validation | test | total |
|---|---|---|---|---|
| train | 168,804 | 20,917 | 22,024 | 211,745 |
| validation | 35,535 | 4,604 | 4,742 | 44,881 |
| test | 35,716 | 4,490 | 4,804 | 45,010 |
| total | 240,055 | 30,011 | 31,570 | 301,636 |
[M-H]- — 140,193 preprocessed spectra:
| split B ↓ / split A → | train | validation | test | total |
|---|---|---|---|---|
| train | 79,644 | 9,523 | 9,234 | 98,401 |
| validation | 16,760 | 1,981 | 2,186 | 20,927 |
| test | 16,609 | 2,263 | 1,993 | 20,865 |
| total | 113,013 | 13,767 | 13,413 | 140,193 |
The spectra-level matrix is computed from the frozen protocol/ row metadata (each
preprocessed row → its compound → its split-B fold) and split_A_full_msnlib/row_formula_fold.csv;
the per-split totals equal the split-B split_spectra_counts of the frozen manifest
(211,745 / 44,881 / 45,010 positive and 98,401 / 20,927 / 20,865 negative).
(Recompute with rebuild/verify_release.py, which rebuilds both matrices from the shipped
tables.)
Relation of the split-A test fold to split B
- 57,437 split-A test spectra in total;
- 31,570 (55.0 %) are strict
[M+H]+spectra of the split-B tables, 13,413 (23.3 %) are strict[M-H]-spectra; 44,983 (78.3 %) therefore lie inside split B; - the remaining 12,454 split-A test spectra carry other adducts (
[M+FA]-,[M+Cl]-,[M+Na]+,[M+NH4]+,[M+H-H2O]+, …) and never occur in split B.
What this means — and what must not be claimed
- Split A is formula-disjoint only; split B is compound-disjoint within each polarity. Each property holds only inside its own split.
- The two splits cannot be merged into a global-disjointness claim: about 41 % of the split-B compounds are in a different split-A fold, and the same spectrum can be a test spectrum in split A while belonging to a train compound in split B (e.g. 4,922 of the 6,202 positive split-B test compounds are split-A train compounds).
- A score computed on an split-A test spectrum whose compound is split-B train must not be reported as a "held-out molecule" result, and vice versa. Train and evaluate within one split only; if a cross-split experiment is unavoidable, state explicitly which split defines the training population and which defines the test population.