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Bioinformatics Advance Access originally published online on August 14, 2009
Bioinformatics 2009 25(20):2734-2736; doi:10.1093/bioinformatics/btp489
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

YADA: a tool for taking the most out of high-resolution spectra

Paulo C. Carvalho 1,2,*, Tao Xu 2, Xuemei Han 2, Daniel Cociorva 2, Valmir C. Barbosa 1 and John R. Yates, III 2

1 Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro - RJ, Brazil and 2 Department of Chemical Physiology, The Scripps Research Institute, N Torrey Pines 10550, La Jolla, CA 92037, USA

* To whom correspondence should be addressed.


  Abstract

Summary: 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.

Availability: http://fields.scripps.edu/yada

Contact: paulo{at}pcarvalho.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on June 26, 2009; revised on August 9, 2009; accepted on August 11, 2009

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