Scaffold 5

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The Industry Standard DDA MS/MS Proteomics Tool

Search raw data directly with MS Fragger* integration and load precursor intensity data from FragPipe

Load data from Mascot, Proteome Discoverer, MaxQuant, and more

Visualize differential expression and statistical significance using spectrum counting or precursor intensity

Core facilities: collaborate using the cross-platform free Scaffold Viewer, Excel reports, and mzIdentML exports

Download (current version: 5.0.1)

*MS Fragger license required; free for academic labs

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Release Notes

  • Implemented a new license key system
  • Implemented custom peptide thresholds for MSFragger scores
  • Bundled Percolator into the Scaffold installer
  • Created a new set of demo files
  • Scaffold 5 release notes