Scaffold DDA

Scaffold DDA is Proteome Software's quantitative proteomics platform designed for experiment-driven labeled and label-free quantitative analysis. It is built for both core facility managers and individual researchers who need a powerful yet accessible solution for processing and interpreting mass spectrometry data from data-dependent acquisition (DDA) experiments.

The platform supports a wide range of workflows, from managing shared resource pipelines to setting up new laboratory software environments. Scaffold DDA is available for Windows, macOS, and Linux (all 64-bit), making it accessible across common operating system environments.

Key Capabilities

• Labeled quantification: Analyze iTRAQ, TMT, and SILAC data sourced from multiple search engines as well as Scaffold itself.
• Raw data searching: Search raw data directly using Sage or MSFragger (MSFragger requires a separate license; free for academic laboratories).
• Differential expression quantification: Quantify differential expression across samples and test results for statistical significance.
• Multi-level data interpretation: Normalize, roll-up, and interpret biological differences while identifying sources of technical variation at multiple levels of analysis.
• Peptide and protein probability scoring: Derive peptide and protein probabilities using Percolator, and apply these scores for false discovery rate (FDR) thresholding to ensure high-confidence identifications.

Who It Is For

• Core facilities and shared resource departments: Scaffold DDA helps fill gaps in software pipelines, supports new methods such as DIA proteomics, and provides an easy way to share results with customers.
• Researchers: Offers an elegant and easy-to-use solution for data processing, helping new and established labs set up robust software pipelines so scientists can focus on their research.

Learning Resources

• A dedicated brochure and user guide are available for reference.
• Demo data is provided to help users get started quickly.
• Tutorials and videos covering beginner to advanced use are available on Proteome Software's YouTube channel, including content from previous conferences and special events.

Scaffold DDA is distributed as a downloadable application (current version 6.8.0) and is supported across all major operating systems. Release notes are published to keep users informed of updates and improvements.