pyopenms
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
SkillSpector found no issues but could not fully inspect the package, usually because SKILL.md refers to a file that is not present, so it fails closed to CAUTION instead of SAFE. Read it as "not fully checked", not as a finding. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
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.
- Package
- 24 files, 112 KB
- SKILL.md
- 1421 words, 12+ sections
- Code
- Python (17)
- Allowed tools
ReadWriteEditBash- License
- 3 clause BSD license
- Compatibility
- Requires CPython 3.11+ and pyOpenMS 3.6.0; pandas and NumPy for tables, Matplotlib for plots. Wheels support macOS 15+ arm64, Linux glibc 2.34+ x86-64/arm64, and Windows x86-64. Search-engine executables are separate.
SKILL.md covers: PyOpenMS · Overview · Installation · Scripts (start here) · Inspect & convert · Feature detection & quantification · Annotation · Identification · Chemistry · Targeted & visualization · Common script recipes · Inspect a file
Findings
No findings. SAFE
What is in the package
24 files, 112 KB. Show the list.
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 12 KB |
references/data_structures.md | doc | 5.3 KB |
references/feature_detection.md | doc | 5.9 KB |
references/file_io.md | doc | 3.9 KB |
references/identification.md | doc | 5.4 KB |
references/metabolomics.md | doc | 6.0 KB |
references/signal_processing.md | doc | 5.7 KB |
scripts/_common.py | script | 1.0 KB |
scripts/accurate_mass_search.py | script | 3.7 KB |
scripts/align_link_quantify.py | script | 5.9 KB |
scripts/consensus_to_matrix.py | script | 2.7 KB |
scripts/convert_format.py | script | 3.3 KB |
scripts/detect_adducts.py | script | 3.9 KB |
scripts/detect_features_centroided.py | script | 3.3 KB |
scripts/detect_features_metabo.py | script | 4.3 KB |
scripts/digest_protein.py | script | 3.6 KB |
scripts/export_gnps_sirius.py | script | 4.2 KB |
scripts/extract_chromatograms.py | script | 3.9 KB |
scripts/inspect_ms_data.py | script | 5.8 KB |
scripts/mass_calculator.py | script | 3.5 KB |
scripts/plot_ms_data.py | script | 3.9 KB |
scripts/process_identifications.py | script | 6.4 KB |
scripts/process_spectra.py | script | 4.8 KB |
scripts/theoretical_spectrum.py | script | 3.1 KB |
External hosts referenced
github.com openms.de pyopenms.readthedocs.io arxiv.org pypi.org www.openms.org doi.org export.arxiv.org
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-pyopenms-scan.json
- Badge for your README:
- Request a re-scan