Tandem Mass Spectrometry – MS/MS – for Peptide Sequencing

Tandem Mass Spectrometry, MS/MS, is a technique used to sequence peptides and identify their primary structure. MS/MS involves multiple stages of mass analysis, where the first mass spectrometer selects the precursor ion, which is then fragmented, and the second mass spectrometer analyzes the resulting fragment ions. This approach provides detailed information about peptide sequences and post-translational modifications.

Fragmentation Techniques

In MS/MS, peptides are fragmented to generate b-ions and y-ions, which correspond to fragments from the N-terminus and C-terminus, respectively. The fragmentation pattern is unique to each peptide and can be analyzed to deduce the amino acid sequence. Common fragmentation techniques include collision-induced dissociation, CID, where peptides are fragmented by collisions with inert gas molecules, and electron transfer dissociation, ETD, which preserves post-translational modifications while cleaving peptide bonds.¹

Applications in Proteomics

MS/MS is a cornerstone of proteomics research, enabling the identification of peptides and proteins from complex mixtures. In shotgun proteomics, peptides are first separated by liquid chromatography, LC-MS/MS, followed by MS/MS analysis to identify thousands of peptides in a single run. MS/MS is also essential for characterizing post-translational modifications, PTMs, such as phosphorylation and glycosylation, which play critical roles in regulating protein function.²

Conclusion

Tandem mass spectrometry is a powerful tool for peptide sequencing and proteomics, providing detailed insights into peptide structure and function. The ability to resolve peptide sequences and detect modifications makes MS/MS invaluable in the study of complex biological systems.

Citations and Links

1. Domon, Bruno, and Ruedi Aebersold. “Mass Spectrometry and Protein Analysis.” Science, vol. 312, no. 5771, 2006, pp. 212–217. doi:10.1126/science.1124619.

2. Olsen, Jesper V., et al. “Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks.” Cell, vol. 127, no. 3, 2006, pp. 635–648. doi:10.1016/j.cell.2006.09.026.