Differentiation of 'isobaric' peptides and human milk oligosaccharides by exact mass measurements using electrospray ionization orthogonal time-of-flight analysis.

Exact mass determination is performed by electrospray ionization orthogonal time-of-flight mass analysis. For peptides in the mass range of 1200-1500 Da a mass error of < 5 ppm is achieved with internal calibration within a single mass measurement provided peak intensities are high. Peptides containing isobaric amino acids like glutamine and lysine can thus be easily differentiated by their mass. In cases where more than one of these isobaric amino acids are present, the position of the amino acid can be revealed by exactly determining the mass differences between adjacent Yi" fragment ions in the collision-induced dissociation spectrum. Mass determination accuracy can be enhanced to 0.5-2 ppm by averaging over 8-10 mass measurements. Thereby compositional analysis of human milk oligosaccharides in a mixture can be performed in the mass range up to 3000 Da, even for low-intensity molecule-ion signals and for isobaric compounds with a mass difference of only 0.025 Da.