Skill All skills & plugins / Scientific Agent Skills (K-Dense)
pyopenms
Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.
- Type
- Skill by K-Dense Inc.
- Catalog
- Scientific Agent Skills (K-Dense)
- Source
- K-Dense-AI/scientific-agent-skills/skills/pyopenms (24 files scanned)
- Install and details
- Agent Skills Index entry
- License
- 3 clause BSD license (SKILL.md frontmatter)
- Signals
- Pre-approved shellBundled scripts
Pre-approved tools
Shell (any command). Tools listed in allowed-tools (or an agent's tools) can be used without a permission prompt while the skill is active, depending on your agent and settings.
| Kind | Tools |
|---|---|
| read/search | Read |
| write/edit files | WriteEdit |
| shell, any command | Bash |
Declared in pyopenms/SKILL.md.
Hooks
No hooks.
MCP servers and apps
None.
Bundled code
17 code files (Python):
pyopenms/scripts/detect_adducts.pypyopenms/scripts/extract_chromatograms.pypyopenms/scripts/align_link_quantify.pypyopenms/scripts/process_identifications.pypyopenms/scripts/detect_features_metabo.pypyopenms/scripts/process_spectra.pypyopenms/scripts/detect_features_centroided.pypyopenms/scripts/theoretical_spectrum.pypyopenms/scripts/digest_protein.pypyopenms/scripts/convert_format.pypyopenms/scripts/plot_ms_data.pypyopenms/scripts/inspect_ms_data.pypyopenms/scripts/mass_calculator.pypyopenms/scripts/accurate_mass_search.pypyopenms/scripts/_common.py- and 2 more
Network calls
No HTTP or socket call pattern found in the code.
Starts other programs
No subprocess, exec or eval pattern found.
Credentials referenced
No key, token or secret environment variable found in code or MCP config.
Static scan of commit 5f2bc03 on 2026-10-27. Signals are patterns found in the files, not a verdict: a network call can be the whole point of a skill. Read the linked lines before you decide. How the scan works.