MS-based metabolomics

In our course, we will use metaboigniter for data processing, which uses pyOpenMS to process raw data.

A manual workflow written in Python (pyOpenMS) is presented in 1_pyOpenMS_metabonaut_pipeline.ipynb for demonstration purposes.

Data-dependent acquisition (DDA)

Two videos from the NNF Center for Protein Research (CPR) on DDA timing:

• MS1 and MS2 scans

• Timing of acquisition