Journal Article

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

Paulo C. Carvalho, Xuemei Han, Tao Xu, Daniel Cociorva, Maria da Gloria Carvalho, Valmir C. Barbosa and John R. Yates

in Bioinformatics

Volume 26, issue 6, pages 847-848
Published in print March 2010 | ISSN: 1367-4803
Published online January 2010 | e-ISSN: 1460-2059 | DOI:
XDIA: improving on the label-free data-independent analysis

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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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1337 words. 

Subjects: Bioinformatics and Computational Biology

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