Quantitative Proteomics Using Isobaric Chemical Tagging and HCD

Multiplexed stable isotope reagents such as iTRAQ and Tandem Mass Tag (TMT) designed for MS/MS-based quantitation of peptides rely on accurate and robust detection of low mass fragments for peptide precursor ions. In the past, such analyses depended upon mass spectrometers capable of producing the so-called “triple-quadrupole-like” fragmentation including triple quadrupole mass spectrometers (TQMS) and quadrupole time-of-flight (Q-TOF) instruments. The “one-third rule” on an ion trap (IT) instrument precluded the use of these reagents on this widely available instrument platform until the invention of Pulsed Q Dissociation (PQD), which in itself manifests problems in generating sufficient reporter ion intensities for accurate quantitation. The introduction of high energy collisional-activated dissociation (HCD) on LTQ-Orbitrap XL and LTQ-Orbitrap Velos platforms has opened up great opportunities for accurate quantitative analysis of proteins and their post-translational modifications (PTMs) using chemical tagging by generating “triple- quadrupole-like” fragmentation mainly in the low mass range in MS/MS mode.