FLASH App
Web-based analysis and visualization of top-down proteomics data
View appOpen-source · Free forever
Open science. Clear results for mass spectrometry.
An expert-crafted ecosystem of computational mass spectrometry tools — run vetted apps,build on open algorithms, and join the community.
Ready-to-use apps Modular workflows Built by the community
Adopted by labs and institutions worldwide.
Community tools
Featured Apps
Apps are scientifically validated end-to-end solutions for common proteomics and metabolomics analysis. Test online, then download and deploy locally.
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OpenDIAKiosk
Interactive DIA proteomics data analysis
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umetaflow
Web-based access to the umetaflow pipeline
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OpenDDA
Web-based workflow for DDA proteomics
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naseweis
Web-based access to the nucleic acid search engine (NASE)
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NuXL
Web-based analysis pipeline for XL-MS data
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MHCquant
Web-based analysis pipeline for immunopeptidomics
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20+
Years active
Over two decades of open-source development for mass spectrometry workflows.
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10,000+
Citations
Peer-reviewed research citing OpenMS tools and algorithms worldwide.
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180+
Contributors
Developers, researchers, and community members advancing OpenMS worldwide.
What is OpenMS?
The open-source LC-MS library
A C++ core with Python bindings for LC/MS data management, analysis, and visualization—built for rapid development of mass spectrometry software.
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BSD licensed
Open source
Core library and tools you can extend, share, and ship under a three-clause BSD license.
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C++ · Python
C++ & Python
High-performance algorithms with pyOpenMS for scripting and workflows.
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Windows · macOS · Linux
Cross-platform
Build and run on all major platforms with the same toolchain.
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200+ tools
TOPP pipeline
Ready-made command-line utilities for proteomics and metabolomics analysis.
Developer tools
Ecosystem
Build your own pipelines using our ecosystem
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OpenMS-lib
Reusable C++ algorithms and data structures for mass spectrometry software. Ships with The OpenMS Pipeline (TOPP) command line tools for mass spectrometry analysis.
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pyOpenMS
Python bindings to OpenMS-lib. Write custom analysis scripts and integrate OpenMS into Python workflows.
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OpenMS-Web apps
Web interface template for OpenMS pipelines. Deploy custom analysis tools as interactive web apps without frontend development.
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pyopenms_viz
Visualization library for mass spectrometry data. Create interactive and static plots directly from Python dataframes.
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Community
Everyone is welcome
OpenMS is built by a diverse group of contributors around the world. Whether you are new to mass spectrometry or a seasoned developer, there is a place for you in our community.
We are committed to being open, inclusive, and welcoming — read the Code of Conduct for how we work together.
Latest news
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MS Analysis with OpenMS: Free Workshop at The National University of Singapore
We are teaching a two-day workshop on MS analysis with OpenMS at the National University of Singapore on September 26–27, 2026. Click the header above for more …
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Workshop at University of Helsinki on April 30th 2026.
We are teaching a one-day workshop on MS analysis with OpenMS and OpenDIAKiosk at the University of Helsinki on April 30th 2026. Click the header above for more …
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2026 Recipient Announced: Rising Star in Computational Mass Spectrometry
OpenMS announces Maria Llambrich Rodriguez as the 2026 Rising Star in Computational Mass Spectrometry recipient.
Upcoming events
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MS Analysis with OpenMS: Free Worshop
9:00 AM – 5:00 PM CEST
National University of Singapore
Join us before HUPO for a workshop on MS Analysis.
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Google Summer of Code Ends
All day
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Contact
Take control of your mass spec workflows today
Tell us about your pipeline, integrations, or tooling goals — we will point you to the fastest next step.