Datasets:

dsadd4
/

UltraMS-MSnLib-Benchmark

This package is a derived benchmark manifest, not a re-release of the MSnLib spectra. It contains compound identities (raw and RDKit canonical SMILES), molecular formulas, source-row pointers into MSnLib.csv, precursor m/z, adduct, collision energy and the train / validation / test assignments of two independent, frozen benchmark splits. The manifest itself contains no mass spectra (mzs / intensities).

The Hugging Face dataset that mirrors this manifest additionally hosts two large source files, because every table points into them:

hosted file	bytes	SHA-256	content
`MSnLib.csv`	752,707,651	`be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07`	one row per MSnLib spectrum (560,084 rows), including the `mzs` / `intensities` peak lists
`MSnLib_candidates.json`	1,368,264,026	`125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc`	candidate SMILES lists behind the single-spectrum candidate-ranking task (JSON object: query SMILES → candidate SMILES list; 9,886 query entries)

Both hosted files derive from the MSnLib release and remain under CC BY 4.0 with attribution to the MSnLib authors; the candidate lists are derived from the MSnLib compound set by UltraMS.

Upstream resource: MSnLib

Brungs C., Schmid R., Pluskal T. MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries. Nature Methods (2025), doi:10.1038/s41592-025-02813-0.
Data release: MSnLib mass spectral libraries, Zenodo 10.5281/zenodo.11163380 (2024).
License: Creative Commons Attribution 4.0 International (CC BY 4.0). Attribution to the MSnLib authors is required for any reuse of the material derived from it, including the compound identities, formulas and metadata distributed here.

The 18 MSnLib original per-file MS2 JSONL releases contain exactly 560,084 records, equal to the number of data rows of the MSnLib.csv file this package indexes. MSnLib.csv is the UltraMS CSV conversion of those records (one row per spectrum; peaks stored as comma-separated strings; 752,707,651 bytes; SHA-256 be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07). It is not part of this manifest; it is hosted with the Hugging Face mirror (see README.md §8.1).

Retention times

split_A_full_msnlib/msnlib_rt.csv.gz contains the per-spectrum retention time (row_index, rt in seconds). RT is source metadata from the MSnLib records and remains under CC BY 4.0 with attribution to the MSnLib authors. The table was exported from MSnLib_with_rt.csv (755,984,910 bytes, SHA-256 a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964) after verifying that its row order and first seven columns are identical to MSnLib.csv (560,084 rows, 0 mismatches; see split_A_full_msnlib/VERIFY.md §5.4).

What UltraMS added (the original contribution of this package)

the CSV representation of the MSnLib release and the source-row pointers,
the frozen formula-level split A (all adducts: 21,107 formulas; 16,885 / 2,110 / 2,112 formulas and 446,667 / 55,980 / 57,437 spectra for train / validation / test),
the frozen strict-adduct molecule-level split B (70/15/15 by canonical isomeric SMILES, per polarity, with frozen query and library definitions),
the query / library / voting tables, row metadata, protocol arrays, rebuild scripts and verification artifacts derived from them.

The split assignments themselves are an original creation of this work and may be reused with attribution. The compound identities and metadata derived from MSnLib remain under CC BY 4.0.

UltraMS code (rebuild scripts only)

Li Y., Zhong Y., Liu P., Xia J. UltraMS. Apache License 2.0 (repository: https://github.com/Dsadd4/UltraMS).
rebuild/build_library_manifest.py and rebuild/baseline_common.py are byte-identical copies of files from the UltraMS public release (benchmarks/molecular_identification/source_code/original/). Their license text is reproduced in rebuild/LICENSE-APACHE-2.0.txt; the files keep their original copyright and attribution.
rebuild/verify_release.py and split_A_full_msnlib/build_split_a.py are original verifier / replay scripts of this release.

Recommended license for this package

CC BY 4.0. Rationale:

the largest share of the derived content (compound identities, molecular formulas, metadata, source-row pointers) comes from MSnLib under CC BY 4.0, so redistribution must keep at least that attribution requirement;
the split assignments and the derived tables added by UltraMS are released under the same permissive, attribution-preserving terms so that the whole package has one simple license;
a single license keeps the benchmark usable for academic and commercial research.

If you redistribute this package, keep NOTICE.md, README.md and SHA256SUMS, and cite MSnLib and UltraMS as described in README.md §12.

Third-party names

MSnLib, UltraMS, RDKit, Nature Methods and Zenodo are names/trademarks of their respective owners. Their use here is descriptive only and does not imply endorsement.