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

Marlon D.M. Santos, Diogo B. Lima, André R.F. Silva, Louise U. Kurt, Milan A. Clasen, Antônio F.M. Pinto, James J. Moresco, John R. Yates, Priscila Aquino, Valmir C. Barbosa, Juliana S.G. Fischer, Paulo C. Carvalho

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article number103371
JournalJournal of Proteomics
Volume202
DOIs
StatePublished - Jun 30 2019
Externally publishedYes

Keywords

  • Bioinformatics
  • Differential proteomics
  • Dimethyl
  • PatternLab

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry

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    Santos, M. D. M., Lima, D. B., Silva, A. R. F., Kurt, L. U., Clasen, M. A., Pinto, A. F. M., Moresco, J. J., Yates, J. R., Aquino, P., Barbosa, V. C., Fischer, J. S. G., & Carvalho, P. C. (2019). A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics. Journal of Proteomics, 202, [103371]. https://doi.org/10.1016/j.jprot.2019.04.021