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

Authors:

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!

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Resource PURL: https://gxy.io/GTN:F00289

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