ITRAQ as a method for optimization: enhancing peptide recovery after gel fractionation.

ABSTRACT: At the dawn of a new era in label-free quantitation on high-resolution MS instruments, classical methods such as iTRAQ continue to provide very useful insights in comparative proteomics. The potential to multiplex samples makes this reporter-based labeling technique highly suited for method optimization as demonstrated here by a set of standard series. Instead of studying ratios of annotated proteins, we propose an alternative method, based on the analysis of the average reporter ratios of all the spectra from a sample or a large distinct subset herein. This strategy circumvents the bias, associated with the annotation and iTRAQ quantitation, leading to increased adequacy in measuring yield differences between workflows. As gel electrophoresis prior to MS analysis is highly beneficial, for

SUBMITTER: Glibert P 

PROVIDER: S-EPMC4413792 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature