Proteome Software - Version Scaffold 5 -Data-dependent Acquisition (DDA) MS/MS Proteomics Tool

Scaffold 5, developed by Proteome Software, is a prominent data-dependent acquisition (DDA) MS/MS proteomics tool that facilitates researchers in processing complex proteomic data. It integrates seamlessly with MS Fragger for direct raw data searches and supports loading precursor intensity data from FragPipe. Users can also import data from other platforms such as Mascot, Proteome Discoverer, and MaxQuant. Scaffold 5 provides tools to visualize differential expression and assess statistical significance using either spectrum counting or precursor intensity. This platform offers collaborative options via the cross-platform, free Scaffold Viewer, alongside facilities for generating Excel reports and mzIdentML exports. Although Scaffold 5/Q+S will be phased out, users are encouraged to transition to Scaffold DDA for enhanced quantitative analysis capabilities. The current version, 5.3.4, continues to support core facilities and shared resource departments in refining their software pipeline.