Scaffold does not support custom quantitative methods from Proteome Discoverer. Please use of the built-in quantitative methods when you plan on loading data into Scaffold.
Scaffold also does not support loading one study that was searched using multiple instances of the same search engine node. For example, searching with two Sequest nodes is not supported while searching with one Sequest and one Mascot node is supported.
Note, we also support versions 2.3 and 2.4. These versions function in a similar way to version 2.2 so instructions for loading data into 2.2 should be applicable. If you encounter any issues with any version of Proteome Discoverer please contact us.