Biopolymer sequencing using a triple quadrupole mass spectrometer in the ESI nozzle-skimmer/precursor ion MS/MS mode

A variety of model biopolymers, including oligonucleotides, oligosaccharide s and a synthetic pharmaceutical agent were sequenced using a triple quadru pole mass spectrometer equipped with an electrospray source and operated in a scan mode referred to as pseudo-MS3. This scan mode consists of three st eps: (1) in-source collision-induced dissociation (CID) in the nozzle-skimm er (NS) region, (2) scanning of the fragment ions into the collision cell f or further CID, and (3) passing of the secondary fragment ions through the final mass filter at a preselected mass, generally corresponding to the mas s of a terminal sequence ion for the biopolymer. The mass spectra are recor ded. in the precursor ion MS/MS mode where ion selection and detection occu r at the third stage of the triple quadrupole but the scan function is dete rmined by the first stage. The advantages and Limitations in using this pse udo-MS3 NS/precursor ion MS/MS scan mode for biopolymer sequencing are disc ussed. (C) 2001 American Society for Mass Spectrometry.