title: YADA: a tool for taking the most out of high-resolution spectra.
abstract: YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). We describe how YADA enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.
  
  
  BACKGROUND
  http://fields.scripps.edu/yada
authors.affiliation: Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro-RJ, Brazil. paulo@pcarvalho.com
authors.forename: Paulo C
authors.initials: PC
authors.lastname: Carvalho
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.forename: Xuemei
authors.initials: X
authors.lastname: Han
authors.forename: Daniel
authors.initials: D
authors.lastname: Cociorva
authors.forename: Valmir C
authors.initials: VC
authors.lastname: Barbosa
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D010455:Peptides
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