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

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, singlephase 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: paulo@pcarvalho.com. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org.