Evaluation of two separation techniques, SCX and OFFGEL and of two fragmentation methods, CAD and PQD, to asses iTRAQ quantitation efficiency

摘要

Number of mass spectra which can be used for quantitation is higher from the QStar instrument (*) implying that the order of magnitude increased sensitivity of the LTQ-FT relative to the quad-TOF is lost to the inefficiency of the PQD (** NOTE: sample lost due to LC caused volume injected in Q-Star only to be 1/5th of that injected into LTQ-FT). Reproducibility of technical replicates from PQD is lower than that obtained with via CAD.