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tooluniverse-proteomics-analysis
维护者 FreedomIntelligence · 最近更新 2026年4月1日
tooluniverse-proteomics-analysis：分析 mass spectrometry proteomics data ，涵盖 protein quantification，differential expression，post-translational modifications (PTMs)，、 protein-protein interactions。 Processes MaxQuant，Spectronaut，DIA-NN，、 other MS 平台 outputs。 适合在analyzing proteomics data，comparing protein abundance bet…时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-proteomics-analysis
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Comprehensive analysis of mass spectrometry-based proteomics data ，面向 protein identification through quantification，differential expression，post-translational modifications，、 systems-level interpretation。
- User has proteomics data (MS output files)。
- Questions about protein abundance 或 expression。
- Differential protein expression analysis requests。
- PTM analysis (phosphorylation，acetylation，ubiquitination)。
原始文档
SKILL.md 摘录
Core Capabilities
| Capability | Description |
|---|---|
| Data Import | MaxQuant, Spectronaut, DIA-NN, Proteome Discoverer, FragPipe outputs |
| Quality Control | Missing value analysis, intensity distributions, sample clustering |
| Normalization | Median, quantile, TMM, VSN normalization methods |
| Imputation | MinProb, KNN, QRILC for missing values |
| Differential Expression | Limma, DEP, MSstats for statistical testing |
| PTM Analysis | Phospho-site localization, PTM enrichment, kinase prediction |
| Protein-RNA Integration | Correlation analysis, translation efficiency |
| Pathway Enrichment | Over-representation and GSEA for protein sets |
| PPI Analysis | Protein complex detection, interaction networks via STRING/IntAct |
| Reporting | Comprehensive reports with volcano plots, heatmaps, pathway diagrams |
Phase 1: Data Import & Quality Control
Objective: Load proteomics data and assess data quality.
Supported input formats:
MaxQuant (most common):
proteinGroups.txt- Protein-level quantificationevidence.txt- Peptide-level dataPhospho (STY)Sites.txt- Phosphorylation sitesmodificationSpecificPeptides.txt- Other PTMs
Spectronaut:
*_Report.tsv- Protein/peptide quantification- DIA-based quantification
DIA-NN:
report.tsv- Protein groupsreport.pr_matrix.tsv- Protein matrix
Proteome Discoverer:
*_Proteins.txt*_PSMs.txt
Data loading:
Quality Control:
-
Missing value assessment:
-
Intensity distribution:
-
Sample correlation:
-
PCA:
Phase 2: Preprocessing & Normalization
Objective: Clean data and normalize across samples for fair comparison.
Filtering:
Missing value imputation:
Normalization:
适用场景
- User has proteomics data (MS output files)。
- Questions about protein abundance 或 expression。
- Differential protein expression analysis requests。
- PTM analysis (phosphorylation，acetylation，ubiquitination)。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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