ProjectsLab software

Ionomos

Ionomos turns a proteomics search result into a statistical report a bench scientist can read and a reviewer can check, in one offline HTML page.

Open source · GPL-3.0PythonWindows app

Ionomos
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A report from Ionomos's built-in demo, on simulated data. The source, releases, and docs are on GitHub, which opens in a new tab: GitHub doesn't allow being shown inside other pages.

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01What it does

  • Reads every major search engine. FragPipe, DIA-NN, MaxQuant, Sage, Spectronaut, AlphaDIA, MSstats-format, and Proteome Discoverer tables.
  • Runs the statistics. Filtering, normalization, imputation, limma, QC, and enrichment. Each method is a Python port of a published R tool, tested against that tool's own output.
  • Writes one report. A single offline HTML page that a bench scientist can read and a reviewer can check.
  • Runs the search, too. On the instrument PC, lab members drop a folder into an inbox, and Ionomos files it, runs FragPipe headlessly with the lab's checked workflows, and writes the report.

02Built with

Python 3.11+, a Tk desktop app packaged with PyInstaller, and CI on Windows and Linux.

03Status

In beta and in daily use in the lab. Released on GitHub under GPL-3.0, with a citation file.