High resolution electrospray mass spectrometry with a magnetic sector instrument: accurate mass measurement and peptide sequencing.

The accurate molecular weights for a series of 37 unknown synthetic peptides, used in research studies involving synthetic vaccines, antibacterial peptides or the de novo design of helical peptides and proteins, were determined with a magnetic sector instrument. All data were obtained with external calibration over a wide mass range during magnetic scanning. Errors between observed and theoretical monoisotopic molecular weights were typically in the 5-60 ppm range for the unknowns at sector resolutions between 2500 and 9000 (10% valley). Isotopic clusters for charge states up to 10+ were resolved through the use of high resolution. Collisionally activated dissociation (CAD) in the electrospray interface resulted in product ions that enabled either full or partial sequencing of most unknown peptides of molecular weights below 2000 Da. The complete primary sequence for one peptide was determined and the importance of high resolution was demonstrated by the differentiation of lysine from glutamine, two amino acids differing in residue mass by only 0.0364 Da. Two other peptides, with identical monoisotopic masses, but different primary sequences, were differentiated based on CAD-MS data.