Scaffold DIA

Scaffold DIA, developed by Proteome Software, is a data-independent acquisition (DIA) proteomics analysis platform that brings the familiar look and feel of the Scaffold interface to the power of DIA workflows. It is designed for both core facility managers and individual researchers who need a streamlined, easy-to-use solution for processing, analyzing, and sharing DIA proteomics data without the complexity of building a software pipeline from scratch.

Whether you are managing a shared resource department looking to adopt new DIA proteomics methods, or a researcher setting up a new lab and seeking an elegant data processing solution, Scaffold DIA is built to reduce the burden of software setup so you can focus on the science.

Data Input and Search Engine Support

• Search raw DIA data against various DDA library formats, Prosit predictions, or sample-specific DIA-only custom libraries
• Compatible with major search engines including DIA-NN, Spectronaut, PaSER, and PEAKS
• Load raw data from major vendor instruments, including Thermo, Sciex, and Agilent
• Windows is required to process vendor-formatted raw files; the application is also available for macOS and Linux

Quantitative Analysis and Visualization

• Track quantitative trends across samples using advanced statistical analysis tools
• Built-in heatmaps for visualizing expression patterns across experimental conditions
• Principal component analysis (PCA) for exploring sample relationships and data structure

Data Sharing and Export

• Share results with collaborators or customers using the free Scaffold DIA Viewer
• Export data in Excel-formatted files for downstream analysis and reporting
• Generate publication-quality images directly from the platform

Scaffold DIA is available for Windows 64-bit, macOS 64-bit, and Linux 64-bit platforms (current version 4.3.1). Proteome Software also provides a range of supporting resources including a user guide, DIA proteomics tips, a product brochure, and tutorial videos via their YouTube channel, making it accessible for users at all experience levels.