Scaffold does not support custom quantitative methods from Proteome Discoverer. Please use the built-in quantitative methods when you plan on loading data into Scaffold.
Due to how Byonic currently interfaces with Proteome Discoverer, Scaffold can only load data from Byonic run in PD versions 2.0 and 2.1. We have reached out to Byonic and are awaiting a resolution.
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.