Multi-Laboratory Examination of a Set of Designed Quantitation Standard Samples to Establish Benchmark Metrics for Isobaric Label-Based Differential Expression Studies

摘要

We present the first of a multi-part study to develop high quality complex mixture quantitation standard samples to enable detailed metric and performance assessment for a variety of quantitation workflows in proteomics. The first part of this study focuses on iTRAQ~(~R) reagent labeling and includes a careful control experiment to assess the impact of labeling on identification rate - a point of recent debate in the proteomics cocommunity. Counter to a recent publication, we do not find a large decline. Initial assessment of the first generation of quantitation standards shows encouraging results, finding the majority of expected differential proteins and very few proteins that should not be detected as different. The target-decoy approach used to estimate false discovery rate of quantitation is shown to accurately detect real changes.