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An important and challenging aspect of proteomics is not only to identify all proteins from complex biological samples, but also to accurately measure their relative abundances.
To address this challenge many analytical methods have been developed, including several isotope labeling techniques: ICAT, SILAC, 18O, AQUA and iTRAQ. The data presented here describes a data dependent LC-MS/MS method where fragmentation using an infrared multi-photon decomposition (IRMPD) laser in the ion cyclotron resonance cell is employed to perform simultaneous protein identification and iTRAQ quantitation. The IRMPD fragmentation technique produces spectra with rich fragmentation patterns, including fragments in the low m/z range. The resulting spectra also have high mass accuracy and resolution of the precursor and peptide fragments, including the iTRAQ reporter ions. Thus, the application of data-dependent LC-MS/MS using IRMPD fragmentation is ideally suited for confident identification and simultaneous quantitation of complex protein digests.