Comparison and validation of iTRAQ, emPAI and intensity-based, label-free quantification for expression proteomics using an ultrahigh-resolution QqTOF

摘要

Application of distribution-independent thresholds to volcano plots provides higher performance than using arbitrary, fixed significance thresholds for all three quantification methodologies. An in-house iTRAQ data analysis workflow is shown to outperform the standard Mascot output. Ion intensity-based label-free can deliver detection of very low fold difference with high accuracy. emPAI can be used as a reliable quantification technique for larger fold changes (>1.3 fold). iTRAQ did not perform as well as the other two methods with the low abundance proteins.