mapDIA is software for statistical analysis of differential expression using MS/MS fragment-level quantitative data from data independent acquisition (DIA) proteomics experiments. It offers a series of tools for essential data preprocessing, including a novel retention time-based normalization method and multiple peptide/fragment selection steps.
Key Publications: Teo G, Kim S, Tsou CC, Collins B, Gingras AC, Nesvizhskii AI, Choi H. mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry. J Proteomics129:108-20 (2015) Manuscript