{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_gmkapk9z4eb4","handle":"proteomics-mcp","url":"https://wellknown.network/agents/proteomics-mcp","links":{"self":"https://wellknown.network/agents/proteomics-mcp/record.json","html":"https://wellknown.network/agents/proteomics-mcp","markdown":"https://wellknown.network/agents/proteomics-mcp/record.md","api":"https://wellknown.network/api/v1/agents/proteomics-mcp","status":"https://wellknown.network/api/v1/agents/proteomics-mcp/status","claim":"https://wellknown.network/agents/proteomics-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/proteomics-mcp/claim.json","badge":"https://wellknown.network/agents/proteomics-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/proteomics-mcp/history","tools":"https://wellknown.network/api/v1/agents/proteomics-mcp/tools"},"ard":{"identifier":"urn:air::server:proteomics-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"proteomics-mcp","summary":"Spectrum-level proteomics scoring tools exposed through CLI and MCP","description":"# proteomics-mcp\n\n[![tests](https://github.com/UadKLab/proteomics-mcp/actions/workflows/tests.yml/badge.svg)](https://github.com/UadKLab/proteomics-mcp/actions/workflows/tests.yml)\n[![Python](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/downloads/)\n[![License: MIT](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/UadKLab/proteomics-mcp/blob/main/LICENSE)\n[![MCP](https://img.shields.io/badge/MCP-compatible-purple.svg)](https://modelcontextprotocol.io/)\n\n<p align=\"center\">\n  <img src=\"https://raw.githubusercontent.com/UadKLab/proteomics-mcp/main/icon.svg\" alt=\"Proteomics MCP\" width=\"540\">\n</p>\n\n`proteomics-mcp` is a local-first MCP server and Python package for inspecting proteomics identification results and interrogating selected MS2 spectra.\n\nIt turns heterogeneous de novo and search-engine outputs into one usable workflow: inspect IDs and peptides, retrieve the relevant spectrum, predict fragments, score the candidate, annotate the observed signal, and render an interactive report. Interactive HTML reports load Plotly from a CDN when opened; see the [privacy policy](https://github.com/UadKLab/proteomics-mcp/blob/main/PRIVACY.md).\n\n## What It Supports\n\n- Input adapters for InstaNovo, Casanovo, MaxQuant, FragPipe, Proteome Discoverer, and user-mapped tables.\n- Modified peptidoforms normalized to inline UNIMOD notation, such as `C[UNIMOD:4]` and `M[UNIMOD:35]`.\n- Local IPC/Feather spectra, mzML, MGF, Bruker `.d`, and USI retrieval.\n- Local MS2PIP and remote Koina/Prosit fragment prediction.\n- On-demand spectrum scoring, observed-spectrum annotation, three interactive HTML views, and publication-ready static SVG/PDF/PNG spectrum figures.\n- PSM/peptide tables, structured dataset summaries, dashboards, SDRF context, and resumable batch prediction/scoring artifacts.\n\nThe package does not run local InstaNovo inference, perform FDR/q-value analysis, or carry out protein inference.\n\n## Quick Start\n\nInstall from [PyPI]…","publisher":{"name":"Simon Nándor Sugár, Jeroen van Goey, Alexey Nesterovich, Isaac H.J. Houngue, Marco Reverenna, Chiara Francavilla, Konstantinos Kalogeropoulos","url":null},"homepage":"https://uadklab.github.io/proteomics-mcp/","repository":"https://github.com/UadKLab/proteomics-mcp/blob/main/CHANGELOG.md","version":"0.1.10","license":null,"protocols":["mcp"],"tags":["proteomics","mass","spectrometry","mcp","ms2","peptide-spectrum","matches"],"pricing":null,"endpoints":[{"url":"pypi:proteomics-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi","publisherName":"pypi"}},"derived":{"capabilities":[{"slug":"analytics.reporting","name":"Reporting & Dashboards","confidence":0.814,"provenance":"derived"},{"slug":"dev.package-management","name":"Packages & Dependencies","confidence":0.768,"provenance":"derived"}],"categories":["analytics","dev"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"proteomics-mcp","registry":"pypi","observedAt":"2026-10-28T20:23:02.570Z","publishedAt":"2026-10-15T13:01:37.477099Z","latestVersion":"0.1.10"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"proteomics-mcp","url":"https://pypi.org/project/proteomics-mcp/","firstSeenAt":"2026-10-16T17:23:20.410Z","fetchedAt":"2026-10-28T20:21:28.981Z","normalizedAt":"2026-10-28T20:21:28.981Z"}]},"firstSeenAt":"2026-10-16T17:23:20.410Z","updatedAt":"2026-10-28T20:23:02.570Z"}