maxquant-proteomics SKILL.md skillA
maxquant-proteomics 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/maxquant-proteomics@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/maxquant-proteomics/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- Feb 18, 2026
- Size
- 29,058 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with FDR; volcano plot; GO/pathway enrichment. Use Proteome Discoverer for Thermo-native processing; FragPipe/MSFragger for GPU-accelerated DB search.
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
# MaxQuant + Perseus — Proteomics Analysis Pipeline ## Overview MaxQuant is the community-standard software for label-free quantification (LFQ) and SILAC proteomics. It performs database search, protein grouping, and intensity-based quantification from raw LC-MS/MS files, producing `proteinGroups.txt` as the primary output. Downstream statistical analysis — filtering, normalization, imputation, differential abundance testing, and visualization — is performed in Python using pandas, scipy, and matplotlib/seaborn, mirroring the Perseus workflow in a reproducible scripting environment. ## When to Use - Performing label-free quantification (LFQ) of proteins across multiple biological conditions — MaxQuant's MaxLFQ algorithm is the community benchmark - Running SILAC (stable isotope labeling) experiments with light/heavy or triple-label designs - Processing iTRAQ or TMT isobaric labeling experiments via MaxQuant's reporter ion quantification - Identifying and quantifying proteins when you need the widely-cited MaxQuant output format (`proteinGroups.txt`) for comparison with published datasets …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/maxquant-proteomics@sha256:68ba2b945d6fdcefThe 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_o2d2uqegtac3bbky)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Feb 18, 2026 and Sep 29, 2026, about one every 56 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 29,058 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 29,107 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 26,452 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 28,241 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 28,362 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 (29058 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_o2d2uqegtac3bbky GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/maxquant-proteomics GET https://markdownregistry.com/api/v1/blob/68ba2b945d6fdcefdbf3b364ab846c3c92bb288e5497d3b4a3845c3cb4f02dc5
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.