Journal of the American Society for Mass Spectrometry

, Volume 16, Issue 3, pp 302–306

ZoomQuant: An application for the quantitation of stable isotope labeled peptides

  • Brian D. Halligan
  • Ronit Y. Slyper
  • Simon N. Twigger
  • Wayne Hicks
  • Michael Olivier
  • Andrew S. Greene
Application Note

DOI: 10.1016/j.jasms.2004.11.014

Cite this article as:
Halligan, B.D., Slyper, R.Y., Twigger, S.N. et al. J Am Soc Mass Spectrom (2005) 16: 302. doi:10.1016/j.jasms.2004.11.014

Abstract

The main goal of comparative proteomics is the quantitation of the differences in abundance of many proteins between two different biological samples in a single experiment. By differentially labeling the peptides from the two samples and combining them in a single analysis, relative ratios of protein abundance can be accurately determined. Protease catalyzed 18O exchange is a simple method to differentially label peptides, but the lack of robust software tools to analyze the data from mass spectra of 18O labeled peptides generated by common ion trap mass spectrometers has been a limitation. ZoomQuant is a stand-alone computational tool that analyzes the mass spectra of 18O labeled peptides from ion trap instruments and determines relative abundance ratios between two samples. Starting with a filtered list of candidate peptides that have been successfully identified by Sequest, ZoomQuant analyzes the isotopic forms of the peptides using high-resolution zoom scan spectrum data. The theoretical isotope distribution is determined from the peptide sequence and is used to deconvolute the peak areas associated with the unlabeled, partially labeled, and fully labeled species. The ratio between the labeled and unlabeled peptides is then calculated using several different methods. ZoomQuant’s graphical user interface allows the user to view and adjust the parameters for peak calling and quantitation and select which peptides should contribute to the overall abundance ratio calculation. Finally, ZoomQuant generates a summary report of the relative abundance of the peptides identified in the two samples.

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Copyright information

© American Society for Mass Spectrometry 2004

Authors and Affiliations

  • Brian D. Halligan
    • 1
  • Ronit Y. Slyper
    • 1
  • Simon N. Twigger
    • 1
  • Wayne Hicks
    • 2
  • Michael Olivier
    • 2
  • Andrew S. Greene
    • 2
  1. 1.Bioinformatics Research Center-HMGCMedical College of WisconsinMilwaukeeUSA
  2. 2.Biotechnology and Bioengineering CenterMedical College of WisconsinMilwaukeeUSA