Scaffold DDA

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Experiment-driven Labeled and Label-free Quantitative Analysis

Scaffold DDA is Proteome Software's new Quantitative Platform

Analyze iTRAQ/TMT/SILAC data from multiple search engines and Scaffold

Search raw data using MSFragger

Quantify differential expression and test for statistical significance

Normalize, roll-up, and interpret biological differences and find sources of technical variation at multiple levels

Derive peptide and protein probabilities with Percolator and use these for FDR thresholding