Proteomics is the large scale study of proteins, particularly their structures and functions. Mass spectroscopy provides a means of getting information relevant to the primary structure of a polypeptide or a protein, especially when fragmentation is induced using in-source collision induced dissociation (CID) or in the reaction cell of a triple quadrupole mass spectrometer (usually termed MS/MS). Protein and peptide sequencing by MS is not simple because various covalent bonds may be broken during fragmentation, resulting in a situation in which we must rebuild the intact protein structure which is typically done using powerful data analysis software. The purpose of this module is to introduce the ways in which mass spectrometry is used in proteomics research.

Topics include:

• Amino acids, proteins and peptides
• Properties of amino acids
• Structure of proteins
• MS structure determination
• ESI considerations
• ESI applications
• MALDI ionization techniques in proteomics
• MALDI practical considerations
• Molecular weight - singly charged ions
• Molecular weight - multiply charged ions
• Multiply charged peptides
• Peptide proton migration
• Peptide and protein digestion