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: 5.0.0)*MS Fragger license required; free for academic labs
- 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
Managing a core facility or shared resource department? Need help with gaps in your software pipeline? Want to try new methods like DIA proteomics? Do you need a free and easy way to share results with your customers?
Need an elegant yet easy to use solution for data processing? Not sure where to begin when starting up a new lab. Let us help take the pressure off setting up a software pipeline so you can focus on the science.
Tutorials & Videos
Check out our YouTube channel for Scaffold tutorials, from getting started to advanced use. We have videos for all our Scaffold products, as well as videos from previous conferences and special events.