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bio-metabolomics-lipidomics
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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-proteomics-dia-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-proteomics-dia-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: diann for end-to-end DIA analysis with neural network scoring.
- CLI: EncyclopeDIA for chromatogram library-based quantification.
- Analyze my DIA proteomics data" → Process data-independent acquisition MS data to identify and quantify proteins using library-free or library-based workflows. CLI: diann for end-to-end DIA analysis with neural network scoring CLI: EncyclopeDIA for chromatogram library-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.
Source Doc
Excerpt From SKILL.md
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
Use cases
- Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- data-import - Load raw MS data
- spectral-libraries - Build and use spectral libraries
- quantification - Normalization methods
- differential-abundance - Statistical testing
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