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

bio-proteomics-dia-analysis

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

Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.

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

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

2 min

核心说明

CLI：diann ，用于 end-to-end DIA analysis ，支持 neural network scoring。
CLI：EncyclopeDIA ，用于 chromatogram 库-based quantification。
分析 my DIA proteomics data" → Process data-independent acquisition MS data to identify 、 quantify proteins ，使用库-free 或库-based workflows. CLI：diann ，用于 end-to-end DIA analysis ，支持 neural network scoring CLI：EncyclopeDIA ，用于 chromatogram 库-based quantification。
diann \ --f sample1.mzML \ --f sample2.mzML \ --lib "" \ --threads 8 \ --verbose 1 \ --out report.tsv \ --qvalue 0.01 \ --matrices \ --out-lib generated_lib.tsv \ --gen-spec-lib \ --predictor \ --fasta uniprot_human.fasta \ --fasta-search \ --min-fr-mz 200 \ --max-fr-mz 1800 \ --met-excision \ --cut K，R \ --missed-cleavages 1 \ --min-pep-len 7 \ --max-pep-len 30 \ --min-pr-mz 300 \ --max-pr-mz 1800 \ --min-pr-charge 1 \ --max-pr-charge 4 \ --unimod4 \ --var-mods 1 \ --var-mod UniMod：35，15.994915，M \ --reanalyse \ --smart-profiling。

原始文档

SKILL.md 摘录

DIA-NN Library-Free Analysis

Goal: Run DIA proteomics analysis without a pre-built spectral library, generating one from the data itself.

Approach: Use DIA-NN in library-free mode with FASTA-based in silico digestion and deep learning prediction.


## DIA-NN with Spectral Library

**Goal:** Analyze DIA data using a pre-built or predicted spectral library for targeted extraction.

**Approach:** Supply an existing spectral library to DIA-NN for guided peptide detection and quantification.

```bash

## Use pre-built or predicted library

diann \
    --f sample1.mzML \
    --f sample2.mzML \
    --lib spectral_library.tsv \
    --threads 8 \
    --verbose 1 \
    --out report.tsv \
    --qvalue 0.01 \
    --matrices \
    --reanalyse \
    --smart-profiling

适用场景

适合在analyzing DIA mass spectrometry data ，支持库-free 或库-based workflows ，用于 deep proteome profiling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 raw MS data
spectral-libraries - Build and use spectral libraries
quantification - Normalization methods
differential-abundance - Statistical testing

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