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

• DOI: 10.1093/bioinformatics/btq031
• Publication Date: 2010-01-28T01:13:21Z
• Authors: Paulo C. Carvalho; Xuemei Han; Tao Xu; Daniel Cociorva; Maria da Gloria C...; Valmir C. Barbosa; John R. Yates
• Keywords: Proteomics; 0301 basic medicine; 03 medical and health sciences; Databases, Factual; Algorithms; Software

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.