Scaffold Q+S

Scaffold Q+S, developed by Proteome Software, is a comprehensive quantitative proteomics platform designed to support both labeled and precursor intensity-based quantitation workflows. It is suited for researchers and core facility managers who need robust tools for protein quantification and cross-sample comparison without sacrificing ease of use.

The platform enables scientists to quantify proteins using a range of popular labeling strategies as well as label-free approaches, and to visualize and interpret protein-level changes across complex experimental designs. Note that Proteome Software is phasing out Scaffold Q+S in favor of Scaffold DDA, their new and improved quantitative platform.

Quantitation Methods Supported

• iTRAQ-based labeled quantitation
• TMT-based labeled quantitation
• SILAC-based quantitation
• Precursor intensity-based (label-free) quantitation

Visualization and Analysis Capabilities

• Visualize protein-level changes across samples using fold changes, intensity values, or quantitative ratios
• Compare independent groups, repeated measures, or time-course experiments

Deployment and Availability

• Available for Windows 64-bit, macOS 64-bit, and Linux 64-bit platforms
• Current version: 5.3.4

Who It Is For

• Core facility and shared resource department managers seeking to fill gaps in their software pipeline or share results with customers
• Researchers looking for an elegant, easy-to-use solution for data processing and proteomics pipeline setup

Scaffold Q+S is supported by a range of resources including a user guide, brochure, demo data, and tutorial videos via Proteome Software's YouTube channel. Users are encouraged to explore Scaffold DDA as the next-generation replacement for this platform.