Accuracy and Precision of a New Covalent Modification- and Quantitative MS-Based Proteomics Approach for Protein-Ligand Binding Analyses in Complex Mixtures

摘要

False Positive Rate (FPR) of SPROX is ～2% with the Q-ToF platform and ～0.8% with the Orbitrap platform False positives are largely the result of random error associated with the isobaric mass tag quantitation Ion purity contributes to the false positive rate in SPROX. Eliminating product ion data generated from low purity ions reduced the false positive rate in SPROX to 1.2% and 0.2% in Q-ToF and Oribtrap experiments described here. Technical replicates can be used to eliminate false positives FPR is largely dependent on the iTRAQ reporter ion intensity variability as seen by the decrease in FPR when the co-efficient of variation was decreased by 2.5 fold in the Orbitrap as compared to the Q-ToF