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--- name: tandem-mass-spectra-research description: >- Guides research comparison of tandem mass spectra and spectral-library evidence. Use when preparing MS/MS data, matching spectra or interpreting candidate compound identities. --- # Tandem mass spectra research 1. Record sample and acquisition provenance, instrument conditions, precursor and adduct metadata, collision settings, library identity and relevant quality flags. Preserve raw spectra and any conversion or preprocessing history. 2. Apply compatible preprocessing to query and reference spectra. Document peak filtering, mass-tolerance units and scoring settings; verify that precursor and ion-mode assumptions match the intended comparison. 3. Report candidate matches with their score, coverage, metadata agreement and library scope. A high spectral similarity is evidence for a candidate, not proof of compound identity; use suitable independent confirmation and report ambiguous matches. 4. Preserve identifiers, processing parameters and software environment for reproducibility. Library permissions and data rights are separate from the analysis software's license. This guidance was informed by the [upstream tandem-spectra skill](https://github.com/K-Dense-AI/scientific-agent-skills/blob/5f2bc0341354fd5590aef76a533ada1e1e5b4e62/skills/matchms/SKILL.md). Consult the selected method and library documentation for their exact assumptions and input contracts.