Identification of tandem mass spectra of mixtures of isomeric peptides.

Shotgun proteomics separates peptides by chromatography and precursor mass over charge, yet in almost any large data set of a complex sample, there will be some tandem mass spectra containing more than one peptide. These mixture spectra contain two coeluting peptides with close precursor mass over charge, and sometimes contain exact isomers, often the same peptide with the same modification in two different positions. Isomers present a problem when the position of the modification is of special interest, as in histone modification studies or "oxidative footprinting" studies of protein structure. Here we give algorithms for identifying isomeric mixtures, and present results on two different histones and four oxidative footprinting targets. Five of the six targets contain at least one peptide that appears in isomeric mixtures, but in none of the cases are mixtures so prevalent that they greatly impact the overall identification rate.