AlterLab MatchMS
技能 已验证 活跃Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.
To enable researchers to compare mass spectra, compute similarity scores, and identify unknown compounds from spectral libraries for metabolomics research.
功能
- Import and export mass spectrometry data
- Filter and process spectral data
- Calculate spectral similarities
- Build reproducible processing pipelines
- Manage metadata and chemical annotations
使用场景
- Comparing mass spectra for identification
- Computing spectral similarity scores
- Identifying unknown compounds from spectral libraries
- Building metabolomics analysis workflows
非目标
- Full LC-MS/MS proteomics pipelines
- Replacing pyopenms for complex proteomics workflows
工作流
- Load spectra from various file formats (MGF, mzML, MSP, JSON, Pickle).
- Apply default and custom filters for metadata harmonization, peak processing, and quality control.
- Calculate spectral similarities using various metrics (CosineGreedy, ModifiedCosine, FingerprintSimilarity).
- Build and execute reproducible processing pipelines.
- Enrich spectra with chemical annotations and validate identifications.
Scope
- info:Tool surface sizeThe underlying library exposes numerous functions, but the skill itself integrates a focused subset, making the effective 'tool surface' manageable for the agent.
安装
npx skills add AlterLab-IEU/AlterLab-Academic-Skills通过 npx 运行 Vercel skills CLI(skills.sh)— 需要本地安装 Node.js,以及至少一个兼容 skills 的智能体(Claude Code、Cursor、Codex 等)。前提是仓库遵循 agentskills.io 格式。
质量评分
已验证类似扩展
Matchms
99Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
PyTDC (Therapeutics Data Commons)
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PyOpenMS
95Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms. Part of the AlterLab Academic Skills suite.
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