title: XDIA: improving on the label-free data-independent analysis.
abstract: 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.
authors.affiliation: 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
authors.forename: Paulo C
authors.initials: PC
authors.lastname: Carvalho
authors.forename: Xuemei
authors.initials: X
authors.lastname: Han
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.forename: Daniel
authors.initials: D
authors.lastname: Cociorva
authors.forename: Maria da Gloria
authors.initials: Mda G
authors.lastname: Carvalho
authors.forename: Valmir C
authors.initials: VC
authors.lastname: Barbosa
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D000465:Algorithms; D016208:Databases, Factual; D040901:Proteomics / Q000379:methods*; D012984:Software