Tooluniverse Proteomics Analysis

Handles the full mass spec proteomics workflow from MaxQuant/Spectronaut/DIA-NN output through differential expression, PTM analysis, and pathway enrichment. It's opinionated about minimums (3+ biological replicates, 2+ unique peptides, Benjamini-Hochberg correction) and includes a solid interpretation framework that walks through LFQ vs TMT tradeoffs and PTM localization scoring. The "check for pre-computed results first" rule at the top is smart since re-running raw proteomics can change numbers and burn turns. Integrates with other ToolUniverse skills for enrichment and PPI networks. If you're doing tumor vs normal protein expression or correlating proteomics with RNA-seq, this gives you the statistical testing and visualization pipeline without reinventing it.

Install to Claude Code

npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-proteomics-analysis --agent claude-code