Proteome Software - Version Scaffold DDA -Quantitative Analysis Platform

Scaffold DDA is a quantitative analysis platform developed by Proteome Software to facilitate experiment-driven labeled and label-free analysis. Designed primarily for the processing of iTRAQ, TMT, and SILAC data, Scaffold DDA integrates with multiple search engines, including Sage and MSFragger, to offer versatile analytical capabilities. It supports quantification of differential expression and statistical significance testing, and provides normalization, roll-up, and interpretation of biological differences while identifying technical variation sources. The platform uses Percolator to derive peptide and protein probabilities, which are crucial for false discovery rate (FDR) thresholding. Scaffold DDA is particularly beneficial for managing core facilities or shared resource departments, as it assists in streamlining software pipelines and enhances the ease of sharing results, thus optimizing proteomics research processes.