Configuring Proteome Discoverer

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.

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.

Configuring Proteome Discoverer 2.0-2.1 for Compatibility with Scaffold

Configuring Proteome Discoverer 2.2 and forward for Compatibility with Scaffold

 

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