Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides

Salvatore Cappadona, Javier Muñoz, Wim P.E. Spee, Low Teck Yew, Shabaz Mohammed, Bas Van Breukelen, Albert J.R. Heck

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

High-resolution mass spectrometry and the use of stable isotopes have greatly improved our ability to quantify proteomes. Typically, the relative abundance of peptides is estimated by identifying the isotopic clusters and by comparing the peak intensities of peptide pairs. However, when the mass shift between the labeled peptides is small, there can be the possibility for overlap of the isotopic clusters which will hamper quantification accuracy with a typical upwards bias for the heavier peptide. Here, we investigated the impact of the overlapping peak issue with respect to dimethyl based quantification and we confirmed there can be need for correction. In addition, we present a tool that can correct overlapping issues when they arise which is based on modeling isotopic distributions. We demonstrate that our approach leads to improved accuracy and precision of protein quantification.

Original languageEnglish
Pages (from-to)2204-2209
Number of pages6
JournalJournal of Proteomics
Volume74
Issue number10
DOIs
Publication statusPublished - 6 Sep 2011
Externally publishedYes

Fingerprint

Deconvolution
Isotopes
Peptides
Proteome
Mass spectrometry
Mass Spectrometry
Proteins

Keywords

  • Bioinformatics
  • Dimethyl labeling
  • Mass spectrometry
  • Overlap of isotopic clusters
  • Proteomics
  • Quantification
  • Stable isotope labeling

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry

Cite this

Cappadona, S., Muñoz, J., Spee, W. P. E., Teck Yew, L., Mohammed, S., Van Breukelen, B., & Heck, A. J. R. (2011). Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. Journal of Proteomics, 74(10), 2204-2209. https://doi.org/10.1016/j.jprot.2011.04.022

Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. / Cappadona, Salvatore; Muñoz, Javier; Spee, Wim P.E.; Teck Yew, Low; Mohammed, Shabaz; Van Breukelen, Bas; Heck, Albert J.R.

In: Journal of Proteomics, Vol. 74, No. 10, 06.09.2011, p. 2204-2209.

Research output: Contribution to journalArticle

Cappadona, S, Muñoz, J, Spee, WPE, Teck Yew, L, Mohammed, S, Van Breukelen, B & Heck, AJR 2011, 'Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides', Journal of Proteomics, vol. 74, no. 10, pp. 2204-2209. https://doi.org/10.1016/j.jprot.2011.04.022
Cappadona, Salvatore ; Muñoz, Javier ; Spee, Wim P.E. ; Teck Yew, Low ; Mohammed, Shabaz ; Van Breukelen, Bas ; Heck, Albert J.R. / Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. In: Journal of Proteomics. 2011 ; Vol. 74, No. 10. pp. 2204-2209.
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