Scaffold PTM

Scaffold PTM, developed by Proteome Software, is a dedicated software tool for the analysis and visualization of protein post-translational modifications (PTMs). Designed for proteomics researchers and core facility teams, it provides a comprehensive environment for evaluating modification site assignment confidence, annotating known biological motifs, and performing quantitative analysis at the modification site level.

Scaffold PTM is available for Windows, macOS, and Linux (all 64-bit) and is currently at version 4.0.2, making it accessible across a wide range of laboratory computing environments.

Key Capabilities

• Modification site confidence evaluation: Scaffold PTM uses Ascore and Ascore-derived probabilities to assess the confidence of PTM site assignments, helping researchers distinguish high-confidence modifications from ambiguous ones.
• Motif annotation: The tool annotates motifs reported in the scientific literature and associates specific enzymes and kinases with identified PTM sites, providing biological context to modification data.
• Quantitative data analysis: Users can export quantitative data from Scaffold Q+S and analyze it at the modification site (modsite) level within Scaffold PTM, enabling detailed quantitative PTM workflows.
• Statistical significance testing: Scaffold PTM allows researchers to assess the significance of differences between modified and unmodified peptide intensities using built-in statistical testing, supporting robust comparative analyses.

Who It Is For

• Core facilities and shared resource departments: Scaffold PTM helps core facility managers address gaps in their software pipelines, explore new methods such as DIA proteomics, and share results easily with their customers.
• Individual researchers: The tool offers an elegant yet easy-to-use solution for data processing, helping new and established labs set up efficient software pipelines so they can focus on the science.

Learning Resources and Support

• A dedicated brochure, user guide, and demo data are available to help users get started quickly.
• Release notes are provided to keep users informed of updates and changes across versions.
• Proteome Software offers tutorials and video content via their YouTube channel, covering everything from getting started to advanced use of Scaffold PTM and other Scaffold products.