If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide).

No, one is limited to the modifications which are installed in MaxQuant. The mqpar only contains more parameters / options than the GUI in galaxy. Note: one must use an mqpar from the same version like MaxQuant!

Still have questions?
Gitter Chat Support
Galaxy Help Forum
Want to embed this snippet (FAQ) in your GTN Tutorial?
{% snippet  topics/proteomics/tutorials/maxquant-msstats-dda-lfq/faqs/mqpar.md %}
Persistent URL
Resource purlPURL: https://gxy.io/GTN:F00289