The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

ABSTRACT: Recently, mass spectrometry has been employed in many studies to provide unbiased, reproducible, and quantitative protein abundance information on a proteome-wide scale. However, how instruments' limited dynamic ranges impact the accuracy of such measurements has remained largely unexplored, especially in the context of complex mixtures. Here, we examined the distribution of peptide signal versus background noise (S/N) and its correlation with quantitative accuracy. With the use of metabolically labeled Jurkat cell lysate, over half of all confidently identified peptides had S/N ratios less than 10 when examined using both hybrid linear ion trap-Fourier transform ion cyclotron resonance and Orbitrap mass spectrometers. Quantification accuracy was also highly correlated with S/N. We develop

SUBMITTER: Bakalarski CE 

PROVIDER: S-EPMC2746028 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature