Proteome Software Scaffold

The Discovery Proteomics Core has Scaffold Q+/Q+S analysis software that helps visualize and validate complex MS/MS proteomics experiments. Mascot data files are directly input into a licensed version of Scaffold by staff in the Discovery Proteomics Core. After this point, Center users may download a free viewer to process the data remotely at any PC or Mac computer. The software is highly intuitive. Scaffold offers three alternative scoring systems for judging the significance of peptide identifications – including a new LFDR method that uses a Bayesian approach to estimate Local False Discovery Rate. Scaffold provides several statistical tests including T-Test, Fisher’s Exact Test, ANOVA, and Coefficient of Variance to assess the significance of observed differences in expression. Scaffold also has other useful capabilities such as Volcano and Pie charts. If you would like assistance using Scaffold – either directly at Yale or indirectly via use of the free viewer please contact the Co-Directors, Angus Nairn and Ken Williams.

• Proteome Software Scaffold Web Site
• Proteome Software Scaffold User's Manual
  
• Proteome Software Scaffold Q+ Tutorial
  
• Download free Scaffold Software viewer from here. From the dropdown menu, choose Scaffold Q+/Q+S, then your operating system and whether your computer is 32-bit or the recommended 64-bit. After installing the software, you should be able to open the sf3 file from the Discovery Proteomics Core.
• Scaffold Processing Flow Chart for Isobaric Tag Data Sets with a Pooled Reference