PNNL

Abstract

The interpretation of tandem mass spectra of peptides from collision-induced dissociation is discussed from the perspective of a multinomial data analysis problem and from the perspective of statistical mechanics. Both approaches use the same statistical likelihood function, and it is shown that this statistical likelihood is equivalent to an information theory entropy when scaled appropriately. The likelihood function provides a physically and chemically principled way to incorporate intensity information into the interpretation of tandem mass spectra and enables the use of predictive modeling and simulation to inform the peptide identification process.