Discovery- and target-based protein quantification using iTRAQ and pulsed Q collision induced dissociation (PQD).

ABSTRACT: Pulsed Q collision-induced dissociation (PQD) was developed in part to facilitate detection of low-mass reporter ions using labeling reagents (e.g. iTRAQ) on LTQ platforms. It has generally been recognized that the scan speed and sensitivity of an LTQ are superior than those of an Orbitrap using the higher-energy collisional dissociation (HCD). However, the use of PQD in quantitative proteomics is limited, primarily due to the meager reproducibility of reporter ion ratios. Optimizations of PQD for iTRAQ quantification using LTQ have been reported, but a universally applicable strategy for quantifying the less abundant proteins has not been fully established. Adjustments of the AGC target, μscan, or scan speed offer only incremental improvements in reproducibility. From our experience, howe

SUBMITTER: Wu WW 

PROVIDER: S-EPMC3321122 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature