Open AccessZoomQuant: An application for the quantitation of stable isotope labeled peptides
Author(s) -
Brian D. Halligan,
Ronit Y. Slyper,
Simon Twigger,
Wayne A. Hicks,
Michael Olivier,
Andrew S. Greene
Publication year - 2005
Publication title -
journal of the american society for mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.961
H-Index - 127
eISSN - 1879-1123
pISSN - 1044-0305
DOI - 10.1016/j.jasms.2004.11.014
Subject(s) - chemistry , mass spectrometry , peptide , isobaric labeling , quantitative proteomics , isotope , isotopic labeling , analytical chemistry (journal) , chromatography , ion trap , abundance (ecology) , resolution (logic) , mass spectrum , natural abundance , tandem mass spectrometry , proteomics , biological system , protein mass spectrometry , biochemistry , artificial intelligence , computer science , physics , organic chemistry , quantum mechanics , fishery , biology , gene
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 (18)O exchange is a simple method to differentially label peptides, but the lack of robust software tools to analyze the data from mass spectra of (18)O 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 (18)O 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.