pyopenms-mass-spectrometry SKILL.md skillA
pyopenms-mass-spectrometry from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pyopenms-mass-spectrometry@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/proteomics-protein-engineering/pyopenms-mass-spectrometry/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- Feb 18, 2026
- Size
- 23,879 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
MS data processing with PyOpenMS for LC-MS/MS proteomics and metabolomics — mzML/mzXML I/O, signal processing (smoothing, peak picking, centroiding), feature detection/linking, peptide/protein ID with FDR, untargeted metabolomics. Use matchms for simple spectral matching.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# PyOpenMS — Mass Spectrometry Analysis ## Overview PyOpenMS provides Python bindings to the OpenMS C++ library for computational mass spectrometry. It supports proteomics and metabolomics data processing including file I/O for 10+ MS formats, signal processing, feature detection, peptide/protein identification, and quantitative analysis across samples. ## When to Use - Processing raw LC-MS/MS data (mzML, mzXML) for proteomics or metabolomics - Detecting chromatographic features and linking them across multiple samples - Identifying peptides and proteins from MS/MS search engine results with FDR control - Running untargeted metabolomics workflows (peak picking → feature detection → alignment → annotation) - Converting between mass spectrometry file formats (mzML, mzXML, featureXML, idXML) - Smoothing, filtering, and centroiding raw spectral data - For simple spectral library matching and metabolite identification, use **matchms** instead - For protein sequence analysis (not mass spec), use **biopython** instead ## Prerequisites ```bash uv pip install pyopenms numpy pandas matplotlib ``` - Python 3.8+; NumPy for peak array operations …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pyopenms-mass-spectrometry@sha256:7717ce9349769b6fThe line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_jrf24pfe7kg7ovpa)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Feb 18, 2026 and Sep 29, 2026, about one every 74 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 23,879 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 23,928 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 22,032 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 22,143 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (23879 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_jrf24pfe7kg7ovpa GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pyopenms-mass-spectrometry GET https://markdownregistry.com/api/v1/blob/7717ce9349769b6fd66db4fa1612b540993d86dbfd5205700b4b09441b92cf0c
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.