Understanding and exploiting Peptide fragment ion intensities using experimental and informatic approaches.

Tandem mass spectrometry is a widely used tool in proteomics. This section will address the properties that describe how protonated peptides fragment when activated by collisions in a mass spectrometer and how that information can be used to identify proteins. A review of the mobile proton model is presented, along with a summary of commonly observed peptide cleavage enhancements, including the proline effect. The methods used to elucidate peptide dissociation chemistry by using both small groups of model peptides and large datasets are also discussed. Finally, the role of peak intensity in commercially available and developmental peptide identification algorithms is examined.