- Targeted feature detection for label-free quantification
- Parallel execution of OpenMS tools in KNIME
- DNA heteroconjugate detection (Flett et al.)
- Non-targeted LC-MS-based lipidomics
- Basic Peptide Identification
- Consensus Peptide Identification
- Peptide Identification and Label-free Quantification
- Protein Inference
- SWATH Analysis
- Small Molecule Identification and Quantification
On this page we list some KNIME and TOPPAS workflows which we find useful and worth sharing. Most of them are tested and were successfully used in projects. If you run into trouble executing one of these workflows, please file an issue.
We are currently building a workflow repository for KNIME so stay tuned. Below you find some workflows we assembled for previous user meetings.
In KNIME, you can import ready-made workflows.
To import, click
File -> Import KNIME Workflow…
If you are unfamiliar with the installation process, see our Getting Started page for Workflows.
Although not actively supported anymore, we list workflows created on and for our own workflow platform TOPPAS for backwards compatibility. To download one of the workflows to your computer, just click the Download link on the subpage. You will also find these workflows if you open TOPPAS and click on
File -> Online Repository
Other sources of workflows
The workflows listed on this page comprise well-tested workflows that are actively maintained by developers. This does not mean that there are more resources out there which can be used to find a good template for your own analysis workflow.
Old TOPPAS workflows by OpenMS developers
On our GitHub wiki you can find a collection of TOPPAS workflows that were not converted to KNIME and tested on the newest OpenMS releases, yet. We are working on the conversion and their update, so stay tuned. Once they are converted and tested they will show up on this page.
MyExperiment is an online repository for all kinds of workflows, including KNIME pipelines. All workflows using OpenMS can be found through their search.
Here we list resources for workflows that were created by OpenMS users around the world. Certainly, this list is not complete. If you want your workflow resource listed here, please contact us. We can not guarantee a smooth experience with all OpenMS versions. In case you encounter problems, please contact the respective author first.