数据与复现蛋白质组与代谢组FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-proteomics-quantification

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches. Use when extracting protein abundances from MS data for differential analysis.

OpenClawNanoClaw分析处理复现实验bio-proteomics-quantification🧬 bioinformatics (gptomics bio-* suite)bioinformatics — proteomics & metabolomicsprotein

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-proteomics-quantification

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

2 min

核心说明

R：MSstats：：dataProcess() ，用于 feature-to-protein summarization。
Python：pandas ，用于 MaxLFQ-style normalization 、 ratio calculation。
R：MSnbase ，用于 isobaric tag reporter ion extraction。
Quantify proteins ，面向 my mass spec data" → Extract protein abundances ，面向 MS data ，使用 label-free (LFQ，spectral counting)，isobaric labeling (TMT，iTRAQ)，或 metabolic labeling (SILAC) approaches. R：MSstats：：dataProcess() ，用于 feature-to-protein summarization Python：pandas ，用于 MaxLFQ-style normalization 、 ratio calculation R：MSnbase ，用于 isobaric tag reporter ion extraction。
tmt_data <- readMSnSet('tmt_data.txt')。

原始文档

SKILL.md 摘录

Normalize with reference channel

tmt_normalized <- normalize(tmt_data, method = 'center.median')

Summarize to protein level

protein_data <- combineFeatures(tmt_normalized, groupBy = fData(tmt_data)$protein, fun = 'median')


## SILAC Quantification

```python
def calculate_silac_ratio(heavy_intensity, light_intensity):
    '''Calculate SILAC H/L ratio'''
    if light_intensity > 0 and heavy_intensity > 0:
        return np.log2(heavy_intensity / light_intensity)
    return np.nan

适用场景

适合在extracting protein abundances ，面向 MS data ，用于 differential analysis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

data-import - Load MS data before quantification
differential-abundance - Statistical testing after quantification
expression-matrix/counts-ingest - Similar matrix handling

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