An open-source framework for mass spectrometry and TOPP – The OpenMS Proteomics Pipeline

Workflow integration

Creating workflows

OpenMS TOPPtools are integrated into different workflow engines:

In addition to these workflow system, OpenMS also provides TOPPAS, a simple and fast workflow engine with reduced feature set.

We are currently focusing our development efforts on the integration of OpenMS into KNIME.

Download our Introduction to OpenMS in KNIME containing hands-on training material.

Creating workflows with KNIME

Knime is a well established data analysis framework which supports the generation of workflows for data analysis. Using the CTD and a node generator program, all TOPP tools can be made available to run in KNIME. The below screenshot shows the above TOPPAS workflow in KNIME.

Installing OpenMS in KNIME

Installation of OpenMS in KNIME is very easy. Download the latest KNIME release from the KNIME website. In KNIME click on Help -> Install new Software.

In the opening dialog choose “Add…”.

Add a new Software Update Site to KNIME.

In the opening dialog fill in the following Information.
Name: KNIME Nightly Community (HEAD)

Creating workflows with TOPPAS

The TOPP Pipeline Assistant (TOPPAS), is a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction thus reduces to simple drag-and-drop of analysis tools and adding connections in between. As building blocks, you can use all TOPP tools and UTILS shipped with OpenMS. Additionally we provide wrappers for external tools. To add your own external tool, all you need to do is to write a little script. More information and example workflows for TOPPAS can be foundhere. Below you see an example of a TOPPAS workflow for differential protein quantitation.

Installation instructions for all supported platforms can be found here.

In addition you can find a TOPPAS tutorial at the site.

After pressing OK KNIME will show you all the contents of the added Update Site, containing also the OpenMS nodes.

Select the OpenMS nodes and click Next. Follow the instructions. After a restart of KNIME the OpenMS nodes will be available under “Community Nodes”.