Tandem mass spectrometric methods for the analysis of iTRAQ labeled peptides in a quadrupole ion trap

Alternative ion activation methods in a quadrupole ion trap mass spectrometer (QITMS) have been studied to determine their utility for iTRAQ. The collisional activation methods, thermally assisted CID (TA-CID) and high amplitude short time excitation (HASTE) CID, allow the low-mass cut-off (LMCO) to be reduced to similar to 10% of the parent ion mass-to-charge ratio allowing the iTRAQ reporter ions to be trapped and detected. An alternative to CID for ion activation/dissociation in a QITMS is infrared multiphoton photodissociation (IRMPD), which can be performed at LMCOs of <10% of the parent ion mass-to-charge ratio. Reported here are experiments comparing the efficiency of these methods for relative quantification using iTRAQ. All methods generated the reporter ions but there were differences in overall MS/MS efficiency and the conversion efficiency to the iTRAQ reporter ions. (C) 2011 Elsevier B.V. All rights reserved.