bio-proteomics-peptide-identification
Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-proteomics-peptide-identification --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.
## Version Compatibility Reference examples tested with: MSnbase 2.28+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Peptide Identification **"Identify peptides from my MS/MS spectra"** → Match tandem mass spectra against a protein database to identify peptide sequences, then control false discovery rate using target-decoy competition. - Python: `pyopenms` for in-memory database search and PSM handling - CLI: `comet`, `MSFragger`, `X!Tandem` for high-throughput database searching - R: `MSnbase::readMSData()` for importing search results ## Database Search with pyOpenMS **Goal:** Identify peptide sequences from tandem mass spectra by matching against a protein database. **Approach:** Load a FASTA database, perform in-silico tryptic digestion to generate theoretical peptides, then match experimental spectra against theoretical fragment ion
- Version Compatibility
- Database Search with pyOpenMS
- Working with Search Results (idXML)
- FDR Estimation (Target-Decoy)
- R: Search Result Processing
- Spectral Library Search
- Related Skills
What does the bio-proteomics-peptide-identification skill do?
Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-proteomics-peptide-identification --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.