XDIA: improving on the label-free data-independent analysis

Abstract

Abstract Summary: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (∼250%) and unique peptides (∼30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing identified spectra and peptides improves quantitation statistics confidence and protein coverage, respectively. Availability: The software and data produced in this work are freely available for academic use at http://fields.scripps.edu/XDIA Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.