LC-MS for identification of post-translational modifications

The discussion in this chapter concentrates on liquid chromatography-mass spectrometry (LC-MS) related technologies to detect and identify protein phosphorylation and glycosylation. The focus is on general concepts and technologies rather than on apphcatiotrs. 

In order to characterize the modified protein, both the position(s) and the nature of the modification must be elucidated. While the nature of a PTM can be very simple, e.g., with phosphorylation or acetylation, it may also be very complex, e.g, with glycosylation. For an isolated modified protein, the strategy may involve  

Shotgun and top-down procedures can be considered complementary, especially when dealing with PTM, where the shotgun approach provides information on the amino-acid sequence and the top-down approach on nature and position of the PTM. 

Within proteomics, PTM must be studied within a complete proteome, i.e., a complex mixture of both modified and unmodified proteins. In that case, either liquid-phase or MS tools must be applied for the selective isolation of modified proteins or the enzymatic peptides derived from these. 

Identification of the PTM is just one step. In terms of functional proteomics, elucidation of the dynamics of modification and the role in the physiological process is important. This involves comparative quantitative proteomics along the lines discussed for protein-expression profiling (Ch. 18.4). 

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