A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics.

Autor: Santos MDM; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil. Electronic address: marlondms@gmail.com., Lima DB; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil; Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur, Paris, France., Silva ARF; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil., Kurt LU; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil., Clasen MA; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil., Pinto AFM; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA., Moresco JJ; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA., Yates JR 3rd; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA., Aquino P; Leônidas and Maria Deane Institute, Fiocruz, Amazonas, Brazil., Barbosa VC; Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil., Fischer JSG; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil., Carvalho PC; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil. Electronic address: paulo@pcarvalho.com.
Jazyk: angličtina
Zdroj: Journal of proteomics [J Proteomics] 2019 Jun 30; Vol. 202, pp. 103371. Date of Electronic Publication: 2019 Apr 26.
DOI: 10.1016/j.jprot.2019.04.021
Abstrakt: We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.
(Copyright © 2019. Published by Elsevier B.V.)
Databáze: MEDLINE
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