bio-metabolomics-metabolite-annotation
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-metabolite-annotation --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: pandas 2.2+, xcms 4.0+ 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 - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Metabolite Annotation ## Database Matching by m/z **Goal:** Generate putative metabolite identifications by matching observed m/z values against HMDB. **Approach:** Convert m/z to neutral mass by subtracting adduct mass, then query HMDB within a specified ppm tolerance. **"Annotate my metabolomics features with compound identities"** → Match detected features against metabolite databases by exact mass, MS/MS spectra, and retention time to assign compound identities with confidence levels. ```r library(MetaboAnalystR) # Load feature table features <- read.csv('feature_table.csv') # Search HMDB by exact mass search_hmdb <- function(mz, adduct = '[M+H]+',
- Version Compatibility
- Database Matching by m/z
- MS/MS Spectral Matching
- SIRIUS + CSI:FingerID
- MetFrag In Silico Fragmentation
- RT Prediction for Validation
- Confidence Levels (MSI)
- CAMERA Adduct Annotation
- Batch Annotation Pipeline
- Export Annotated Results
- Related Skills
Molecular formula and structure prediction sirius \ formula \ fingerid Output structure: sirius_results/ compound_1/ formula_candidates.tsv fingerid_candidates.tsv
What does the bio-metabolomics-metabolite-annotation skill do?
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-metabolite-annotation --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.