Increasing proteomic diversity
The majority of proteins undergo some level of posttranslational modification (PTM) of their amino acid residues. These PTMs regulate interactions between proteins, nucleic acids, lipids, and cofactors. PTMs can occur at any moment of the "life cycle" of a protein, influencing its biological function in processes such as catalysis, protein–protein interaction, and degradation.
Because the proteome is complex and dynamic, PTMs are constantly influenced by a myriad of external stimuli and so are used to control cellular activity. Glycosylation and phosphorylation are of particular interest to researchers because they are critical pathways for signaling and activation; therefore, the analysis of these PTMs by mass spectrometry (MS) and other technologies offers insight into disease states.
Frequently studied PTMs
Glycosylation plays a vital role in a variety of biochemical processes ranging from cell–cell recognition and interaction to regulation of protein activation. Many glycans undergo disease-related expression level changes, and the detection and quantification of these changes offer critical diagnostic information. MS has emerged as one of the most powerful tools for glycosylation detection due to its sensitivity and ability to analyze complex mixtures derived from a variety of organisms and cell lines.
Standard glycoproteomics workflows involve sample enrichment to minimize complexity followed by MS analysis. Multiple fragmentation methods are often used to localize glycosylation sites, elucidate peptide sequences, and determine glycan composition.
Phosphorylation occurs on serine, threonine, and tyrosine residues and is one of the most important and well-studied of all PTMs. Phosphorylation plays a central role in regulating many cellular processes including cell growth and apoptosis. It is also a key player in numerous signal transduction pathways. Given the importance that phosphorylation has in biological processes, there is a huge emphasis on understanding this chemical state in the context of human disease.
The study of protein phosphorylation is referred to as phosphoproteomics. Typical phosphoproteomics workflows involve sample enrichment followed by MS analysis using complementary fragmentation techniques such as CID, HCD, EThcD, and ETD.