XDIA: improving on the label-free data-independent analysis.
CONCLUSIONS
XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (approximately 250%) and unique peptides (approximately 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.


BACKGROUND
The software and data produced in this work are freely available for academic use at http://fields.scripps.edu/XDIA CONTACT: paulo@pcarvalho.com


BACKGROUND
Supplementary data are available at Bioinformatics online.
Carvalho
Paulo C
PC
Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro, Brazil. paulo@pcarvalho.com
Han
Xuemei
X
Xu
Tao
T
Cociorva
Daniel
D
Carvalho
Maria da Gloria
Mda G
Barbosa
Valmir C
VC
Yates
John R
JR
D000465:Algorithms; D016208:Databases, Factual; D040901:Proteomics / Q000379:methods*; D012984:Software