Scaffold 5

Scaffold 5 by Proteome Software is the industry standard tool for data-dependent acquisition (DDA) MS/MS proteomics. Designed for both core facility managers and individual researchers, it provides a comprehensive platform for searching, loading, visualizing, and sharing proteomics data. Whether you are running a shared resource department or setting up a new lab, Scaffold 5 offers an accessible yet powerful solution for building and managing your proteomics software pipeline.

Note that Proteome Software is phasing out Scaffold 5 in the future, with Scaffold DDA serving as the new and improved quantitative platform for users seeking the latest capabilities.

Key Capabilities

• Direct raw data searching via integrated MSFragger support (MSFragger license required; free for academic labs), enabling streamlined database searching without additional preprocessing steps.
• Precursor intensity data loading from FragPipe, allowing label-free quantification workflows to be incorporated directly into the Scaffold environment.
• Broad data import compatibility, with support for loading results from Mascot, Proteome Discoverer, MaxQuant, and other major search engines and data processing platforms.
• Differential expression visualization using either spectrum counting or precursor intensity methods, paired with statistical significance assessment to support robust biological interpretation.

Collaboration and Sharing Features

• The cross-platform Scaffold Viewer is available free of charge, enabling core facilities to share results with customers and collaborators without requiring a full Scaffold license.
• Excel report exports provide straightforward data sharing and downstream analysis in widely used spreadsheet tools.
• mzIdentML exports support interoperability with other proteomics software and data repositories, facilitating compliance with community data standards.

Who Scaffold 5 Is For

• Core facilities and shared resource departments looking to fill gaps in their software pipeline, share results easily with customers, and explore new methods such as DIA proteomics.
• Researchers and new labs seeking an elegant, easy-to-use data processing solution that reduces the burden of software pipeline setup so scientists can focus on their research.

Platform Availability and Learning Resources

• Scaffold 5 (current version 5.3.4) is available for Windows 64-bit, macOS 64-bit, and Linux 64-bit platforms.
• A brochure, user guide, and demo data are available to help users get started quickly.
• Tutorials and videos covering everything from getting started to advanced use are available on the Proteome Software YouTube channel, including content from previous conferences and special events.