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OpenMS is a versatile open-source library for mass spectrometry data analysis. Based on this library, we offer a collection of command-line tools ready to be used by end users.

OpenMS: The name of our library, which contains the algorithms. You cannot use this directly, unless you are a programmer.

TOPPView: View and explore LC-MS data, alignments, groups, peptide identifications and more!

TOPPAS: A graphical workflow design tool, which allows to create pipelines from all TOPP tools (and UTILS).

TOPP tools: A set of command line tools, each of which is a building block of an analysis pipeline. These tools chained together in a way that fits the requirements of the user. Accessible from a command prompt/shell or via TOPPAS. See also: TOPP tutorial and TOPP documentation

UTILS: Similar to TOPP tools, but with more supporting character, which you'd rarely use in a productive pipeline - but rather during pipeline construction or parameter optimization. See also: [UTILS documentation UTILS documentation]




Load modul

module add openms-2.2

Graphic tools

jenicek$ ssh

skirit$ qsub -I -l select=1:ncpus=2:mem=4gb:scratch_local=1gb -l walltime=1:00:00 

took11$ module add gui

took11$ gui start

In remote desktop

 TOPPView file1.mzML

Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.

Singularity docker image

Docker image

Tutorial for singularity is here


Supported platforms

Linux (in MetaCentrum), Windows, iOS

Program administrator