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J Proteome Res. 2014 Mar 7;13(3):1494-501. doi: 10.1021/pr401035z. Epub 2014 Feb 11.

Interference-free proteome quantification with MS/MS-based isobaric isotopologue detection.

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Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, California 92037, United States.


Chemical labeling of peptides prior to shotgun proteomics allows relative quantification of proteins in biological samples independent of sample origin. Current strategies utilize isobaric labels that fragment into reporter ions. However, quantification of reporter ions results in distorted ratio measurements due to contaminating peptides that are co-selected in the same precursor isolation window. Here, we show that quantitation of isobaric peptide fragment isotopologues in tandem mass spectra reduces precursor interference. The method is based on the relative quantitation of isobaric isotopologues of dimethylated peptide fragments in tandem mass spectra following higher energy collisional dissociation (HCD). The approach enables precise quantification of a proteome down to single spectra per protein and quantifies >90% of proteins in a MudPIT experiment and accurately measures proteins in a model cell line for cystic fibrosis.

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