proteomics
Mass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.
npx skills add BioTender-max/awesome-bio-agent-skills --skill proteomics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Proteomics ## Version Compatibility Reference examples assume: - `pyopenms` 3.0+ - `pandas` 2.2+ - `numpy` 1.26+ - `seaborn` 0.13+ ## Overview Use this skill when the user needs: - proteomics QC - protein table cleanup - replicate review - differential abundance analysis - publication-ready proteomics figures ## When To Use This Skill - MaxQuant, FragPipe, DIA-NN, or similar outputs exist - the task is protein-level quantification or comparative proteomics - missingness, batch effects, and replicate quality need review before interpretation ## Quick Route - DDA and DIA should not be treated identically - protein-level tables should remain distinct from peptide-level tables - QC comes before differential analysis ## Progressive Disclosure - Read [technical_reference.md](technical_reference.md) for assay branching, QC interpretation, and missingness handling. - Read [commands_and_thresholds.md](commands_and_thresholds.md) for table-loading patterns, QC thresholds, and output conventions. ## Expected Inputs - protein or peptide result table - sample metadata - assay context: DDA, DIA, PTM-enriched, or targeted ## Expected Outputs - `results/protein_abundance.tsv` - `qc/proteomics_qc
- Version Compatibility
- Overview
- When To Use This Skill
- Quick Route
- Progressive Disclosure
- Expected Inputs
- Expected Outputs
- Starter Pattern
- Workflow
- 1. Clarify assay and table level
- 2. Run QC before comparisons
- 3. Normalize and summarize consistently
- 4. Perform comparative analysis
- 5. Export interpretable artifacts
What does the proteomics skill do?
Mass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill proteomics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.