Datasets:

dsadd4
/

UltraMS-MSnLib-Benchmark

# VERIFY — UltraMS MSnLib formula-level split (split A)

This document records **what was checked, how, and with which exact values** for the
`msnlib_split_a_v1` tables. The split is a frozen benchmark definition: every spectrum of a
molecular formula lies in exactly one fold. All numbers below were re-derived from the
source `MSnLib.csv` and the shipped tables; nothing was written on the remote side.

## 1. Environments

| side | runtime |
| --- | --- |
| isolated data-preparation environment (read-only access) | Linux, Python 3.10.12, RDKit 2026.03.5, NumPy 2.2.6 |
| local post-processing (gzip twins, auxiliary voting table, cross-checks) | macOS, Python 3.13.11, NumPy 2.4.4, pandas 3.0.3, RDKit 2026.03.3 |

The molecular formula and the frozen fold assignment do not depend on the RDKit patch
release. The canonical isomeric SMILES strings were frozen with RDKit **2026.03.5**; other
patch releases can serialise the same molecule differently (see §7).

## 2. Inputs

| input | identity |
| --- | --- |
| `MSnLib.csv` | 560,084 data rows, 560,085 physical lines (no embedded newlines), 752,707,651 bytes, SHA-256 `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07`, columns `mzs,intensities,smiles,precursor_mz,adduct,collision_energy,fold` |
| MSnLib original release | 18 per-file MS2 JSONL releases; 560,084 records in total (equal to the CSV data-row count); CC BY 4.0, Zenodo record 10.5281/zenodo.11163380 |
| historical per-fold CSV files (cross-check only) | `MSnLib_test.csv` (57,437 rows) and `MSnLib_val.csv` (55,980 rows) in the same data workspace |
| `MSnLib_with_rt.csv` (retention-time source) | 755,984,910 bytes, SHA-256 `a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964`; columns `mzs,intensities,smiles,precursor_mz,adduct,collision_energy,fold,rt` |

Access to the data workspace was read-only: `MSnLib.csv` and the original JSON records
were streamed out, the tables were computed in memory, and nothing was written or modified
on the remote side.

## 3. Definition replayed

1. For every data row, parse `smiles` with `Chem.MolFromSmiles` and compute the neutral
   molecular formula with `rdMolDescriptors.CalcMolFormula`.
2. Read the frozen `fold` label of the row.
3. Require that the fold is a function of the formula only: every formula occurs in exactly
   one fold.
4. Export the tables. `row_formula_fold.csv` is the authoritative row → formula → fold
   mapping for all 560,084 spectra.

## 4. Counts — expected versus observed (all match)

| quantity | expected | observed | status |
| --- | ---: | ---: | --- |
| data rows | 560,084 | 560,084 | PASS |
| unique molecular formulas | 21,107 | 21,107 | PASS |
| formulas train / validation / test | 16,885 / 2,110 / 2,112 | 16,885 / 2,110 / 2,112 | PASS |
| spectra train / validation / test | 446,667 / 55,980 / 57,437 | 446,667 / 55,980 / 57,437 | PASS |
| formulas occurring in more than one fold | 0 | 0 | PASS |
| RDKit SMILES parse failures | 0 | 0 | PASS |
| test spectra | 57,437 | 57,437 | PASS |
| validation spectra | 55,980 | 55,980 | PASS |
| voting groups, official (MSnLib source SMILES) | 5,002 | 5,002 | PASS |
| voting spectra, official (MSnLib source SMILES) | 57,436 | 57,436 | PASS |
| voting groups, canonical view | 4,888 | 4,888 | PASS |
| voting spectra, canonical view | 57,436 | 57,436 | PASS |

The formula-level proportions are 16,885 / 2,110 / 2,112 formulas (80.00 % / 10.00 % /
10.01 %) and 446,667 / 55,980 / 57,437 spectra (79.75 % / 9.99 % / 10.25 %).

Additional structure:

| quantity | value |
| --- | --- |
| unique source SMILES strings (all adducts) | 48,597 |
| unique canonical isomeric SMILES (all adducts) | 47,662 |
| canonical molecules with more than one source SMILES variant | 935 |
| spectra per formula: min / median / mean / max | 1 / 15 / 26.535 / 627 |
| formulas with exactly one spectrum | 25 |
| test formulas | 2,112 |
| test unique source SMILES / canonical molecules | 5,003 / 4,889 |
| validation unique source SMILES / canonical molecules | 4,883 / 4,786 |
| adducts present in the test / validation folds | 11 / 11 |

Test-fold adduct distribution: `[M+H]+` 31,763, `[M-H]-` 13,824, `[M+FA]-` 5,884,
`[M+Cl]-` 2,403, `[M+H-H2O]+` 1,252, `[M+NH4]+` 1,189, `[M+Na]+` 583, `[M]+` 287,
`[M+H-2H2O]+` 169, `[M-H2O]+` 59, `[M]-` 24. Collision energies: 15 (4,264), 20 (30,383),
30 (6,041), 45 (3,289), 60 (13,429) and 75 eV (31).

## 5. Cross-checks against independent sources

### 5.1 Historical per-fold CSV files

The exported test and validation spectra tables were compared row by row (same order) with
`MSnLib_test.csv` and `MSnLib_val.csv` on `smiles`, `precursor_mz`, `adduct` and
`collision_energy`:

| file | rows | mismatches | status |
| --- | ---: | ---: | --- |
| `MSnLib_test.csv` | 57,437 | 0 | PASS |
| `MSnLib_val.csv` | 55,980 | 0 | PASS |

### 5.2 `formula` field of the MSnLib original JSON records

The MSnLib original release records carry an independent `formula` field. For every one of
the 18 original files, the RDKit formula of the **first** record equals the recorded
`formula` (18/18). Two complete files were streamed and compared record by record:

| file | records | RDKit formula ≠ recorded formula |
| --- | ---: | ---: |
| `20241003_enammol_neg_ms2.json` | 12,825 | 0 |
| `20241003_enammol_pos_ms2.json` | 24,352 | 0 |

For the sample formula **C10H10BrN5O2**, three original records were located and checked;
the recorded `formula` equals the RDKit formula of the recorded SMILES in all three. Two of
them are different molecules that share the formula, which is exactly what the formula-level
split groups together:

| file | line | smiles | adduct |
| --- | ---: | --- | --- |
| `20241003_mcescaf_pos_ms2.json` | 9,998 | `O=C1CNC(=O)N1C1CN(c2ncc(Br)cn2)C1` | `[M+H]+` |
| `20250828_mcediv_50k_sub_neg_ms2.json` | 23,736 | `O=C1CNC(=O)N1C1CN(c2ncc(Br)cn2)C1` | `[M-H]-` |
| `20250828_mcediv_50k_sub_pos_ms2.json` | 2,551 | `COc1ccc(Br)cc1C(=O)Nc1nnn(C)n1` | `[M+H]+` |

`MSnLib.csv` contains **23** spectra with formula C10H10BrN5O2, all in the **train** fold
(so the sample formula does not leak into test).

### 5.3 Multiple-spectrum voting table of the UltraMS repository

The repository summary
`benchmarks/molecular_identification/data/multiple_spectrum_voting_summary.csv` reports
`n_molecules = 5002` for the multiple-spectrum voting task. The per-group table
`multiple_spectrum_voting_per_group.csv.gz` (5,002 groups, 57,436 spectra) was compared
with our groupings:

| comparison | result |
| --- | --- |
| repository groups vs. the **official** grouping by MSnLib source SMILES string (`test_molecules_voting.csv`) | **identical** member sets and group sizes (5,002 groups, 57,436 spectra) |
| repository group strings vs. test-fold source SMILES set | all 5,002 repository strings are source SMILES strings of the test fold |
| repository groups vs. grouping by RDKit canonical isomeric SMILES | **not identical**: the canonical grouping merges 114 of the repository groups into 4,888 chemically identical molecules |

This is the only definition difference found; it is documented in §7 and in
`REPORT.json` → `anomalies`.

### 5.4 Retention-time export

`msnlib_rt.csv.gz` was exported from `MSnLib_with_rt.csv` in the data-preparation
environment. Two files were read in parallel and compared row by row:

| check | result |
| --- | --- |
| headers | 7-column `MSnLib.csv` header vs 8-column with-RT header, prefix identical | PASS |
| rows compared | 560,084 / 560,084 | PASS |
| first seven columns identical at every row | 0 mismatches | PASS |
| extra rows at the end of either file | 0 / 0 | PASS |
| unparsable RT values | 0 / 560,084 | PASS |
| distinct RT strings | 8,369 (RT is not constant) | PASS |

Because the row order and the first seven columns are identical, `row_index` alone is a
complete join key to `MSnLib.csv`. The exported table is

`msnlib_rt.csv.gz` — 1,483,069 bytes, SHA-256
`994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8`, 560,084 data rows,
columns `row_index,rt`, gzipped only (no plain twin) to keep the package compact.

## 6. Frozen table hashes

SHA-256 of the plain CSV files (the `.csv.gz` twins decompress to exactly these bytes):

| file | rows | bytes | SHA-256 |
| --- | ---: | ---: | --- |
| `formula_split.csv` | 21,107 | 424,350 | `fcc44d1996d25306c884a6f8da30c1447fbe74f93c6fa12a3f271c0475a704b8` |
| `row_formula_fold.csv` | 560,084 | 13,351,630 | `ac6113867fdda683304533f097fc7287c13271a2deac8e792d1316dcf00264ff` |
| `test_spectra.csv` | 57,437 | 7,751,575 | `f2a870ba8ac9a54a36feaf1ecc12929ad9250ade2d082dc31454028c4b66b548` |
| `val_spectra.csv` | 55,980 | 7,421,554 | `f4fa5e0f8875991bf9df2bcb67a05437271ee18c317f33d9108f3ec28a887a82` |
| `test_molecules_voting.csv` | 5,002 | 276,185 | `edad6ec7d6b6f9fc4763deac5245207aee767c78661532621c87acc5a9b1ee07` |
| `test_molecules_voting_canonical_view.csv` | 4,888 | 269,502 | `9fcd16ff4159e665833ea145848f94bee7c44115f4a858dd75fe486f15e92bd0` |

Gzipped-only companion: `msnlib_rt.csv.gz` — 560,084 rows, 1,483,069 bytes, SHA-256
`994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8`.

## 7. Voting-unit definitions: official 5,002 source-SMILES groups vs 4,888 canonical groups

The **official** multiple-spectrum voting unit is the MSnLib source SMILES string. The test
fold contains 5,003 distinct source SMILES strings and 4,889 distinct RDKit canonical
isomeric molecules:

* grouping by the **source SMILES string** gives **5,002 groups** with ≥2 spectra covering
  **57,436 spectra** (one source string occurs in only one spectrum), and this grouping is
  **member-for-member identical** to the published repository table that defines
  `n_molecules = 5002`; it is shipped as `test_molecules_voting.csv`;
* grouping by **RDKit canonical isomeric SMILES** gives **4,888 groups** covering the same
  57,436 spectra, leaving exactly one single-spectrum molecule
  (`CC(C)(C)OC(=O)NCC1(CC(=O)O)CCCCC1`); it is shipped as
  `test_molecules_voting_canonical_view.csv` and is an **alternative chemical-deduplication
  view, not the official voting unit**.

The difference is a property of the source library: 114 canonical molecules are written with
more than one SMILES string among their test spectra. No data was altered to force either
count.

## 8. Replay from `MSnLib.csv`

`build_split_a.py` replays the complete split (formula computation, frozen fold assignment,
all six tables) from `MSnLib.csv`. It was run **read-only in the isolated data-preparation environment**
(RDKit 2026.03.5) without an output directory:

```bash
python3 build_split_a.py --csv datasets/MSnLib/MSnLib.csv
```

Result: all 12 count checks passed, all 6 table SHA-256 values matched the frozen files, and
the script exited 0. Transcript:

```text
[PASS] n_data_rows: 560,084 (expected 560,084)
[PASS] n_unique_formula: 21,107 (expected 21,107)
[PASS] n_formula_train: 16,885 (expected 16,885)
[PASS] n_formula_val: 2,110 (expected 2,110)
[PASS] n_formula_test: 2,112 (expected 2,112)
[PASS] n_spectra_train: 446,667 (expected 446,667)
[PASS] n_spectra_val: 55,980 (expected 55,980)
[PASS] n_spectra_test: 57,437 (expected 57,437)
[PASS] n_voting_groups_official: 5,002 (expected 5,002)
[PASS] n_voting_spectra_official: 57,436 (expected 57,436)
[PASS] n_voting_groups_canonical: 4,888 (expected 4,888)
[PASS] n_voting_spectra_canonical: 57,436 (expected 57,436)
[PASS] formula_split.csv: 424,350 bytes sha256 fcc44d1996d25306c884a6f8da30c1447fbe74f93c6fa12a3f271c0475a704b8
[PASS] row_formula_fold.csv: 13,351,630 bytes sha256 ac6113867fdda683304533f097fc7287c13271a2deac8e792d1316dcf00264ff
[PASS] test_spectra.csv: 7,751,575 bytes sha256 f2a870ba8ac9a54a36feaf1ecc12929ad9250ade2d082dc31454028c4b66b548
[PASS] val_spectra.csv: 7,421,554 bytes sha256 f4fa5e0f8875991bf9df2bcb67a05437271ee18c317f33d9108f3ec28a887a82
[PASS] test_molecules_voting.csv: 276,185 bytes sha256 edad6ec7d6b6f9fc4763deac5245207aee767c78661532621c87acc5a9b1ee07
[PASS] test_molecules_voting_canonical_view.csv: 269,502 bytes sha256 9fcd16ff4159e665833ea145848f94bee7c44115f4a858dd75fe486f15e92bd0
```

A local replay needs `MSnLib.csv` (752,707,651 bytes, SHA-256 as in §2) and RDKit
2026.03.5. With a different RDKit patch release, the tables that carry canonical
strings can differ textually while every count above still matches; the script reports that
as a `DIFF` with an explanatory message (or a warning under `--lenient-rdkit`) and the
formula tables are unaffected.

## 9. Simple structural checks

```bash
# rows
wc -l formula_split.csv row_formula_fold.csv test_spectra.csv val_spectra.csv \
      test_molecules_voting.csv test_molecules_voting_canonical_view.csv
# 21108 / 560085 / 57438 / 55981 / 5003 / 4889  (incl. header)
# gzip -dc msnlib_rt.csv.gz | wc -l   -> 560085 (incl. header)
# csv.gz twins are byte-identical after decompression
for f in *.csv; do cmp <(gzip -dc "$f.gz") "$f" || echo "MISMATCH $f"; done
# formula-level uniqueness
python3 - <<'PY'
import csv, collections
fold = {}
for r in csv.DictReader(open("formula_split.csv")):
    fold[r["formula"]] = r["fold"]
print(len(fold), collections.Counter(fold.values()))
PY
```

## 10. What could not be verified from this directory alone

* The actual peak arrays (`mzs`/`intensities`) are not shipped; they live in `MSnLib.csv`.
  The row pointers and the row → formula → fold mapping in `row_formula_fold.csv` are the
  authoritative link back to the spectra.
* The exact physical row order of `MSnLib.csv` (which follows the frozen UltraMS conversion
  of the MSnLib release records); the package depends on the row pointers, not on
  reconstructing that order from the release files.
* The historical Figure-3 analysis artifacts themselves; only the published repository
  voting-group table was cross-checked (§5.3).

## 11. Version

Split A release `1.0.0`, generated 2026-11-04. Any change to the tables, the fold
assignment or the formula computation invalidates the hashes above and requires a new
version directory.

	# VERIFY — UltraMS MSnLib formula-level split (split A)

	This document records what was checked, how, and with which exact values for the
	`msnlib_split_a_v1` tables. The split is a frozen benchmark definition: every spectrum of a
	molecular formula lies in exactly one fold. All numbers below were re-derived from the
	source `MSnLib.csv` and the shipped tables; nothing was written on the remote side.

	## 1. Environments

	\| side \| runtime \|
	\| --- \| --- \|
	\| isolated data-preparation environment (read-only access) \| Linux, Python 3.10.12, RDKit 2026.03.5, NumPy 2.2.6 \|
	\| local post-processing (gzip twins, auxiliary voting table, cross-checks) \| macOS, Python 3.13.11, NumPy 2.4.4, pandas 3.0.3, RDKit 2026.03.3 \|

	The molecular formula and the frozen fold assignment do not depend on the RDKit patch
	release. The canonical isomeric SMILES strings were frozen with RDKit 2026.03.5; other
	patch releases can serialise the same molecule differently (see §7).

	## 2. Inputs

	\| input \| identity \|
	\| --- \| --- \|
	\| `MSnLib.csv` \| 560,084 data rows, 560,085 physical lines (no embedded newlines), 752,707,651 bytes, SHA-256 `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07`, columns `mzs,intensities,smiles,precursor_mz,adduct,collision_energy,fold` \|
	\| MSnLib original release \| 18 per-file MS2 JSONL releases; 560,084 records in total (equal to the CSV data-row count); CC BY 4.0, Zenodo record 10.5281/zenodo.11163380 \|
	\| historical per-fold CSV files (cross-check only) \| `MSnLib_test.csv` (57,437 rows) and `MSnLib_val.csv` (55,980 rows) in the same data workspace \|
	\| `MSnLib_with_rt.csv` (retention-time source) \| 755,984,910 bytes, SHA-256 `a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964`; columns `mzs,intensities,smiles,precursor_mz,adduct,collision_energy,fold,rt` \|

	Access to the data workspace was read-only: `MSnLib.csv` and the original JSON records
	were streamed out, the tables were computed in memory, and nothing was written or modified
	on the remote side.

	## 3. Definition replayed

	1. For every data row, parse `smiles` with `Chem.MolFromSmiles` and compute the neutral
	molecular formula with `rdMolDescriptors.CalcMolFormula`.
	2. Read the frozen `fold` label of the row.
	3. Require that the fold is a function of the formula only: every formula occurs in exactly
	one fold.
	4. Export the tables. `row_formula_fold.csv` is the authoritative row → formula → fold
	mapping for all 560,084 spectra.

	## 4. Counts — expected versus observed (all match)

	\| quantity \| expected \| observed \| status \|
	\| --- \| ---: \| ---: \| --- \|
	\| data rows \| 560,084 \| 560,084 \| PASS \|
	\| unique molecular formulas \| 21,107 \| 21,107 \| PASS \|
	\| formulas train / validation / test \| 16,885 / 2,110 / 2,112 \| 16,885 / 2,110 / 2,112 \| PASS \|
	\| spectra train / validation / test \| 446,667 / 55,980 / 57,437 \| 446,667 / 55,980 / 57,437 \| PASS \|
	\| formulas occurring in more than one fold \| 0 \| 0 \| PASS \|
	\| RDKit SMILES parse failures \| 0 \| 0 \| PASS \|
	\| test spectra \| 57,437 \| 57,437 \| PASS \|
	\| validation spectra \| 55,980 \| 55,980 \| PASS \|
	\| voting groups, official (MSnLib source SMILES) \| 5,002 \| 5,002 \| PASS \|
	\| voting spectra, official (MSnLib source SMILES) \| 57,436 \| 57,436 \| PASS \|
	\| voting groups, canonical view \| 4,888 \| 4,888 \| PASS \|
	\| voting spectra, canonical view \| 57,436 \| 57,436 \| PASS \|

	The formula-level proportions are 16,885 / 2,110 / 2,112 formulas (80.00 % / 10.00 % /
	10.01 %) and 446,667 / 55,980 / 57,437 spectra (79.75 % / 9.99 % / 10.25 %).

	Additional structure:

	\| quantity \| value \|
	\| --- \| --- \|
	\| unique source SMILES strings (all adducts) \| 48,597 \|
	\| unique canonical isomeric SMILES (all adducts) \| 47,662 \|
	\| canonical molecules with more than one source SMILES variant \| 935 \|
	\| spectra per formula: min / median / mean / max \| 1 / 15 / 26.535 / 627 \|
	\| formulas with exactly one spectrum \| 25 \|
	\| test formulas \| 2,112 \|
	\| test unique source SMILES / canonical molecules \| 5,003 / 4,889 \|
	\| validation unique source SMILES / canonical molecules \| 4,883 / 4,786 \|
	\| adducts present in the test / validation folds \| 11 / 11 \|

	Test-fold adduct distribution: `[M+H]+` 31,763, `[M-H]-` 13,824, `[M+FA]-` 5,884,
	`[M+Cl]-` 2,403, `[M+H-H2O]+` 1,252, `[M+NH4]+` 1,189, `[M+Na]+` 583, `[M]+` 287,
	`[M+H-2H2O]+` 169, `[M-H2O]+` 59, `[M]-` 24. Collision energies: 15 (4,264), 20 (30,383),
	30 (6,041), 45 (3,289), 60 (13,429) and 75 eV (31).

	## 5. Cross-checks against independent sources

	### 5.1 Historical per-fold CSV files

	The exported test and validation spectra tables were compared row by row (same order) with
	`MSnLib_test.csv` and `MSnLib_val.csv` on `smiles`, `precursor_mz`, `adduct` and
	`collision_energy`:

	\| file \| rows \| mismatches \| status \|
	\| --- \| ---: \| ---: \| --- \|
	\| `MSnLib_test.csv` \| 57,437 \| 0 \| PASS \|
	\| `MSnLib_val.csv` \| 55,980 \| 0 \| PASS \|

	### 5.2 `formula` field of the MSnLib original JSON records

	The MSnLib original release records carry an independent `formula` field. For every one of
	the 18 original files, the RDKit formula of the first record equals the recorded
	`formula` (18/18). Two complete files were streamed and compared record by record:

	\| file \| records \| RDKit formula ≠ recorded formula \|
	\| --- \| ---: \| ---: \|
	\| `20241003_enammol_neg_ms2.json` \| 12,825 \| 0 \|
	\| `20241003_enammol_pos_ms2.json` \| 24,352 \| 0 \|

	For the sample formula C10H10BrN5O2, three original records were located and checked;
	the recorded `formula` equals the RDKit formula of the recorded SMILES in all three. Two of
	them are different molecules that share the formula, which is exactly what the formula-level
	split groups together:

	\| file \| line \| smiles \| adduct \|
	\| --- \| ---: \| --- \| --- \|
	\| `20241003_mcescaf_pos_ms2.json` \| 9,998 \| `O=C1CNC(=O)N1C1CN(c2ncc(Br)cn2)C1` \| `[M+H]+` \|
	\| `20250828_mcediv_50k_sub_neg_ms2.json` \| 23,736 \| `O=C1CNC(=O)N1C1CN(c2ncc(Br)cn2)C1` \| `[M-H]-` \|
	\| `20250828_mcediv_50k_sub_pos_ms2.json` \| 2,551 \| `COc1ccc(Br)cc1C(=O)Nc1nnn(C)n1` \| `[M+H]+` \|

	`MSnLib.csv` contains 23 spectra with formula C10H10BrN5O2, all in the train fold
	(so the sample formula does not leak into test).

	### 5.3 Multiple-spectrum voting table of the UltraMS repository

	The repository summary
	`benchmarks/molecular_identification/data/multiple_spectrum_voting_summary.csv` reports
	`n_molecules = 5002` for the multiple-spectrum voting task. The per-group table
	`multiple_spectrum_voting_per_group.csv.gz` (5,002 groups, 57,436 spectra) was compared
	with our groupings:

	\| comparison \| result \|
	\| --- \| --- \|
	\| repository groups vs. the official grouping by MSnLib source SMILES string (`test_molecules_voting.csv`) \| identical member sets and group sizes (5,002 groups, 57,436 spectra) \|
	\| repository group strings vs. test-fold source SMILES set \| all 5,002 repository strings are source SMILES strings of the test fold \|
	\| repository groups vs. grouping by RDKit canonical isomeric SMILES \| not identical: the canonical grouping merges 114 of the repository groups into 4,888 chemically identical molecules \|

	This is the only definition difference found; it is documented in §7 and in
	`REPORT.json` → `anomalies`.

	### 5.4 Retention-time export

	`msnlib_rt.csv.gz` was exported from `MSnLib_with_rt.csv` in the data-preparation
	environment. Two files were read in parallel and compared row by row:

	\| check \| result \|
	\| --- \| --- \|
	\| headers \| 7-column `MSnLib.csv` header vs 8-column with-RT header, prefix identical \| PASS \|
	\| rows compared \| 560,084 / 560,084 \| PASS \|
	\| first seven columns identical at every row \| 0 mismatches \| PASS \|
	\| extra rows at the end of either file \| 0 / 0 \| PASS \|
	\| unparsable RT values \| 0 / 560,084 \| PASS \|
	\| distinct RT strings \| 8,369 (RT is not constant) \| PASS \|

	Because the row order and the first seven columns are identical, `row_index` alone is a
	complete join key to `MSnLib.csv`. The exported table is

	`msnlib_rt.csv.gz` — 1,483,069 bytes, SHA-256
	`994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8`, 560,084 data rows,
	columns `row_index,rt`, gzipped only (no plain twin) to keep the package compact.

	## 6. Frozen table hashes

	SHA-256 of the plain CSV files (the `.csv.gz` twins decompress to exactly these bytes):

	\| file \| rows \| bytes \| SHA-256 \|
	\| --- \| ---: \| ---: \| --- \|
	\| `formula_split.csv` \| 21,107 \| 424,350 \| `fcc44d1996d25306c884a6f8da30c1447fbe74f93c6fa12a3f271c0475a704b8` \|
	\| `row_formula_fold.csv` \| 560,084 \| 13,351,630 \| `ac6113867fdda683304533f097fc7287c13271a2deac8e792d1316dcf00264ff` \|
	\| `test_spectra.csv` \| 57,437 \| 7,751,575 \| `f2a870ba8ac9a54a36feaf1ecc12929ad9250ade2d082dc31454028c4b66b548` \|
	\| `val_spectra.csv` \| 55,980 \| 7,421,554 \| `f4fa5e0f8875991bf9df2bcb67a05437271ee18c317f33d9108f3ec28a887a82` \|
	\| `test_molecules_voting.csv` \| 5,002 \| 276,185 \| `edad6ec7d6b6f9fc4763deac5245207aee767c78661532621c87acc5a9b1ee07` \|
	\| `test_molecules_voting_canonical_view.csv` \| 4,888 \| 269,502 \| `9fcd16ff4159e665833ea145848f94bee7c44115f4a858dd75fe486f15e92bd0` \|

	Gzipped-only companion: `msnlib_rt.csv.gz` — 560,084 rows, 1,483,069 bytes, SHA-256
	`994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8`.

	## 7. Voting-unit definitions: official 5,002 source-SMILES groups vs 4,888 canonical groups

	The official multiple-spectrum voting unit is the MSnLib source SMILES string. The test
	fold contains 5,003 distinct source SMILES strings and 4,889 distinct RDKit canonical
	isomeric molecules:

	* grouping by the source SMILES string gives 5,002 groups with ≥2 spectra covering
	57,436 spectra (one source string occurs in only one spectrum), and this grouping is
	member-for-member identical to the published repository table that defines
	`n_molecules = 5002`; it is shipped as `test_molecules_voting.csv`;
	* grouping by RDKit canonical isomeric SMILES gives 4,888 groups covering the same
	57,436 spectra, leaving exactly one single-spectrum molecule
	(`CC(C)(C)OC(=O)NCC1(CC(=O)O)CCCCC1`); it is shipped as
	`test_molecules_voting_canonical_view.csv` and is an **alternative chemical-deduplication
	view, not the official voting unit**.

	The difference is a property of the source library: 114 canonical molecules are written with
	more than one SMILES string among their test spectra. No data was altered to force either
	count.

	## 8. Replay from `MSnLib.csv`

	`build_split_a.py` replays the complete split (formula computation, frozen fold assignment,
	all six tables) from `MSnLib.csv`. It was run read-only in the isolated data-preparation environment
	(RDKit 2026.03.5) without an output directory:

	```bash
	python3 build_split_a.py --csv datasets/MSnLib/MSnLib.csv
	```

	Result: all 12 count checks passed, all 6 table SHA-256 values matched the frozen files, and
	the script exited 0. Transcript:

	```text
	[PASS] n_data_rows: 560,084 (expected 560,084)
	[PASS] n_unique_formula: 21,107 (expected 21,107)
	[PASS] n_formula_train: 16,885 (expected 16,885)
	[PASS] n_formula_val: 2,110 (expected 2,110)
	[PASS] n_formula_test: 2,112 (expected 2,112)
	[PASS] n_spectra_train: 446,667 (expected 446,667)
	[PASS] n_spectra_val: 55,980 (expected 55,980)
	[PASS] n_spectra_test: 57,437 (expected 57,437)
	[PASS] n_voting_groups_official: 5,002 (expected 5,002)
	[PASS] n_voting_spectra_official: 57,436 (expected 57,436)
	[PASS] n_voting_groups_canonical: 4,888 (expected 4,888)
	[PASS] n_voting_spectra_canonical: 57,436 (expected 57,436)
	[PASS] formula_split.csv: 424,350 bytes sha256 fcc44d1996d25306c884a6f8da30c1447fbe74f93c6fa12a3f271c0475a704b8
	[PASS] row_formula_fold.csv: 13,351,630 bytes sha256 ac6113867fdda683304533f097fc7287c13271a2deac8e792d1316dcf00264ff
	[PASS] test_spectra.csv: 7,751,575 bytes sha256 f2a870ba8ac9a54a36feaf1ecc12929ad9250ade2d082dc31454028c4b66b548
	[PASS] val_spectra.csv: 7,421,554 bytes sha256 f4fa5e0f8875991bf9df2bcb67a05437271ee18c317f33d9108f3ec28a887a82
	[PASS] test_molecules_voting.csv: 276,185 bytes sha256 edad6ec7d6b6f9fc4763deac5245207aee767c78661532621c87acc5a9b1ee07
	[PASS] test_molecules_voting_canonical_view.csv: 269,502 bytes sha256 9fcd16ff4159e665833ea145848f94bee7c44115f4a858dd75fe486f15e92bd0
	```

	A local replay needs `MSnLib.csv` (752,707,651 bytes, SHA-256 as in §2) and RDKit
	2026.03.5. With a different RDKit patch release, the tables that carry canonical
	strings can differ textually while every count above still matches; the script reports that
	as a `DIFF` with an explanatory message (or a warning under `--lenient-rdkit`) and the
	formula tables are unaffected.

	## 9. Simple structural checks

	```bash
	# rows
	wc -l formula_split.csv row_formula_fold.csv test_spectra.csv val_spectra.csv \
	test_molecules_voting.csv test_molecules_voting_canonical_view.csv
	# 21108 / 560085 / 57438 / 55981 / 5003 / 4889 (incl. header)
	# gzip -dc msnlib_rt.csv.gz \| wc -l -> 560085 (incl. header)

	# csv.gz twins are byte-identical after decompression
	for f in *.csv; do cmp <(gzip -dc "$f.gz") "$f" \|\| echo "MISMATCH $f"; done

	# formula-level uniqueness
	python3 - <<'PY'
	import csv, collections
	fold = {}
	for r in csv.DictReader(open("formula_split.csv")):
	fold[r["formula"]] = r["fold"]
	print(len(fold), collections.Counter(fold.values()))
	PY
	```

	## 10. What could not be verified from this directory alone

	* The actual peak arrays (`mzs`/`intensities`) are not shipped; they live in `MSnLib.csv`.
	The row pointers and the row → formula → fold mapping in `row_formula_fold.csv` are the
	authoritative link back to the spectra.
	* The exact physical row order of `MSnLib.csv` (which follows the frozen UltraMS conversion
	of the MSnLib release records); the package depends on the row pointers, not on
	reconstructing that order from the release files.
	* The historical Figure-3 analysis artifacts themselves; only the published repository
	voting-group table was cross-checked (§5.3).

	## 11. Version

	Split A release `1.0.0`, generated 2026-11-04. Any change to the tables, the fold
	assignment or the formula computation invalidates the hashes above and requires a new
	version directory.