BI
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipid…
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数据与复现
BI
bio-proteomics-ptm-analysis
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic data or other modification-enriched samples.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-proteomics-ptm-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
- Python：pyopenms ，用于 PTM-aware search，scipy ，用于 site-level statistics。
- CLI：MaxQuant ，支持 variable modifications ，用于 enrichment-based PTM analysis。
- 分析 phosphorylation sites ，面向 my proteomics data" → Identify 、 quantify post-translational modifications ，涵盖 phosphorylation，acetylation，、 ubiquitination ，支持 site localization 、 motif analysis. Python：pyopenms ，用于 PTM-aware search，scipy ，用于 site-level statistics CLI：MaxQuant ，支持 variable modifications ，用于 enrichment-based PTM analysis。
- phospho = pd.read_csv('Phospho (STY)Sites.txt'，sep='\t'，low_memory=False)。
原始文档
SKILL.md 摘录
Processing MaxQuant PTM Output
Goal: Extract high-confidence phosphorylation sites from MaxQuant output with proper filtering and site annotation.
Approach: Load the Phospho(STY)Sites table, remove reverse hits and contaminants, filter by localization probability, and construct gene-level site identifiers.
import pandas as pd
import numpy as np
## Filter valid sites
phospho = phospho[
(phospho['Reverse'] != '+') &
(phospho['Potential contaminant'] != '+')
]
## Filter by localization probability
phospho_confident = phospho[phospho['Localization prob'] >= 0.75]
print(f'Confident sites (prob >= 0.75): {len(phospho_confident)}')
适用场景
- 适合在analyzing phosphoproteomic data 或 other modification-enriched samples时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- peptide-identification - Identify modified peptides
- quantification - Quantify PTM sites
- pathway-analysis/go-enrichment - Enrichment of modified proteins
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