Introduction

OpenMS offers a wide range of tools you can use for your mass spectrometry analysis. Users without programming experience or those who want to quickly run common pipelines and analyses on their data can check out our webapps.

Those who want to have more control over the settings in their pipeline can pick a pre-defined workflow or create a new one themselves with one of our supported workflow systems.

If you want to develop high performance pipelines including a large amount of data, you can use our TOPP tools either in the command line or create a new Nextflow workflow.

Should you be missing something you can also add new functions or classes to the OpenMS C++ core library.

Users

Developers

WebApps

Run pre-built analysis applications in your browser.

Run FLASHTaggerViewer, NuXL or UmetaFlow directly in your browser or host them locally.

pyOpenMS

Use the pyOpenMS python library to rapidly prototype methods and scripts.

Quickly prototype new methods and scripts or interface with other prominent data science, machine learning or visualization libraries in Python.

Workflow Editor

Use a supported workflow editor to create or run predefined workflows.

Use applications such as KNIME, Nextflow, Galaxy or our tool TOPPAS, to apply predefined workflows or custom workflows you have designed on your data.

TOPP Tools

Use over 100 command-line tools to automate pre-defined tasks efficiently.

Automate tasks and create workflows that can be saved, stored and used on multiple datasets.

TOPPView

Use the OpenMS graphical user interface to inspect your results.

Visualize your mass spectrometry data in 1D, 2D and 3D with TOPPView.

OpenMS C++ core library

Develop your own efficient tools and methods with the OpenMS C++ core library.

Using the OpenMS C++ core library directly provides faster access to tools and shorter run-times.