Electron Transfer Dissociation Ion

Application Note Protein phosphorylation, a type of post-translational modification, plays an important role in the regulation of many cellular functions. The precise determination of phosphorylation sites within a protein is crucial to the understanding of cell regulation mechanisms. MS methods using collision-induced dissociation (CID) are often unsuitable to determine phosphorylation sites because phosphate groups easily dissociate from peptides under CID. The electron transfer dissociation (ETD) technique is an ion-molecule collision process that is much gentler than CID. The phosphate group remains attached to the amino acid during the ETD process, allowing the specific location of the phosphate to be determined. This note compares the difference between CID and ETD and demonstrates the capability of analyzing samples using both CID and ETD in the same LC/MS run. Examples of the identification of site-specific phosphorylation using an Agilent HPLC-Chip system interfaced to an Agilent 6340 Ion Trap mass spectrometer equipped with ETD technology are shown. The acquired CID and ETD spectra of phosphate-containing peptides show not only the ability of ETD to identify and map phosphorylated amino acids, but also the complementary nature of CID and ETD. ETD provides additional information that can increase the confidence in protein identification. The results of this study demonstrate that a comprehensive CID and ETD approach using the HPLC-Chip/6340 Trap MS system is a powerful method for identifying low-level PTMs