Shortlist molecular identities from tandem mass spectra

Your decision and inputs

Compare formula-free retrieval configurations within a named split and shortlist size, then validate the intended instrument, chemistry and candidate database before selecting a workflow.

Who this is for

Metabolomics researchers shortlisting candidate molecular identities for experimental confirmation; Computational researchers choosing retrieval inputs, candidate pools and validation splits

Context

Research

Inputs

• MS/MS spectra with metadata sufficient to derive neutral molecular mass
• A frozen set of candidate molecular structures; the true identity must be present for the measured retrieval endpoint

Expected output

Split-specific Recall@1 and Recall@20 evidence for six exact configurations, plus candidate-pool and domain-shift limits.

Biological setting

MSAlign paper Table 3, MassSpecGym formula and MCES splits, formula-free inputs. Each source candidate pool contains 256 mass-matched PubChem structures. Formula and MCES splits remain distinct.

Outside this use case

• De novo molecular generation or cases where the true structure is absent from the candidate set
• Formula-conditioned retrieval, including MIST, FLARE and MSAlign+Filter
• Pooling split-specific results or transferring scores to different candidate database sizes
• Authenticated molecular identification and clinical diagnosis

Which evaluations inform this question?

Evidence is grouped by its protocol. Relevance refers to the stated endpoint and context; it is separate from clinical validation and from the review method.

What evidence is still missing?

• The correct structure must be in a 256-candidate mass-filtered pool. Scores do not transfer automatically to a larger database, a different pool-construction procedure or a missing true structure.
• MCES and formula splits impose different distribution shifts. The source authors favour formula splits for their deployment interpretation; that choice does not prove that formula-split performance represents every intended application.
• Reported methods are the paper implementations: DeepSets training was extended to 50 epochs. These are not interchangeable with original model-paper scores or current checkpoints.
• Exact test denominators, split-manifest hashes, checkpoint hashes and evaluator revisions remain unextracted or unreported in the catalogue. No uncertainty values or new independent reproduction are established.
• Candidate recall is not an authenticated metabolite identification, a clinical diagnosis or a calibrated probability. Human domain review remains outstanding.
• The four metric and split groups come from one paper and do not constitute independent replications.

Contribute evidence or propose a correction

Sources and review

Automated source review · 2026-09-28 · Codex research curation

Primary-source curation and separate automated cross-review checked exact evidence identities, comparator coverage, endpoint relevance and transfer limits. No new execution, human scientific review, independent replication or clinical validation.

• msalign: Primary paper PDF · Original source ↗Table 3, MassSpecGym MCES and formula blocks, formula-free columns, R@1 and R@20; Sections 4, 5.1 and 5.2