YADA: a tool for taking the most out of high-resolution spectra.
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
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-RJ, Brazil. paulo@pcarvalho.com
Xu
Tao
T
Han
Xuemei
X
Cociorva
Daniel
D
Barbosa
Valmir C
VC
Yates
John R
JR
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
D010455:Peptides
Anal Chem. 2009 Mar 1;81(5):1996-2003
19203245
J Proteome Res. 2009 Jan;8(1):374-9
19053528
BMC Bioinformatics. 2008 Jul 21;9:316
18644148
Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2193-8
17287358
Bioinformatics. 2008 Apr 1;24(7):1021-3
18304935
Proteomics. 2001 Aug;1(8):927-33
11683509
Curr Protoc Bioinformatics. 2007 Jan;Chapter 13:Unit 13.4
18428785
J Am Soc Mass Spectrom. 2008 Jan;19(1):46-54
18293485
Rapid Commun Mass Spectrom. 2004;18(18):2162-8
15317041
J Am Soc Mass Spectrom. 2000 Apr;11(4):320-32
10757168
Anal Chem. 2000 Mar 15;72(6):1156-62
10740853
Electrophoresis. 1999 Dec;20(18):3551-67
10612281
J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
24226387