chapter  6
22 Pages

Mass Spectrometry for Post-Translational Modifications

Post-translational modification of proteins is important for the regulation of cellular processes, including the cellular localization of protein, the regulation of protein function, and protein complex formation. Post-translational modification of proteins is part of what makes proteomics so much more challenging than genomics. Not only does the proteomic “alphabet” contain more letters than the genome (21 common amino acids as opposed to four nucleotides), but these amino acids can also be modified by literally hundreds of modifications that change their molecular weights, the fundamental physical property measured by mass spectrometry. Of these modifications, the most common and naturally occurring are cleavage, acetylation, formylation, methionine oxidation, phosphorylation, ubiquitination, and glycosylation (which is a whole set of modifications rather than a single modification). A more

6.1 Introduction ....................................................................................................93 6.2 General Considerations ...................................................................................94 6.3 Database Search Considerations .....................................................................94 6.4 MS/MS-Based Modification Site Determination ...........................................95 6.5 Acetylation and Formylation ..........................................................................95 6.6 Phosphorylation ..............................................................................................96 6.7 Tyrosine Sulfation ......................................................................................... 100 6.8 Biotinylation.................................................................................................. 103 6.9 Nitrosylation ................................................................................................. 103 6.10 Ubiquitination ............................................................................................... 104 6.11 Collisional-Induced Dissociation-Cleavable Modifications ........................ 105 6.12 Glycosylation ................................................................................................ 105 6.13 Conclusion .................................................................................................... 110 Acknowledgments .................................................................................................. 111 References .............................................................................................................. 111

comprehensive list of protein modifications can be found elsewhere (1). In addition, other non-post-translational modifications, such as crosslinking, fluorescent labels, and spin labels, can be used to probe protein structure and function.