A systematic comparison between the up-front Collision induced dissociation (CID) mass spectra and low-energy CID tandem mass spectra from twenty-one singly and/or doubly charged peptides has been made. CID spectra of the peptides were recorded at different electrode voltages in the up-front source region of a single quadrupole instrument and different collision energies in the collision cell of a tandem quadrupole instrument. It was observed that up-front CID and low-energy CID yielded comparable product ion spectra from protonated peptides, and that the instrumental settings necessary for obtaining comparable CID mass spectra from the two methods are correlated.

The design of a mass spectrometer for the determination of the structural formulae of organic compounds is discussed. The ion-optieai characteristics of electric and magnetic sectors and also of quadrupole mass adysers are considered and the additional information that can be gleaned when such components are combined in various ways is listed. The advantages of using collision cells for inducing fragmentation of selected ion speaes are listed including those that result when the collision cell is floated at an electrical potential different from that of the incident ion beam. Important performance characteristics are the resolution with which a particular ion may be selected and the resolution with which daughter ions formed from it can be separated. It is concluded, that for instruments comprising three analysing units together with the appropriate collisiin cells, the most versatile combinations and those with the highest performance are an arrangement consisting of a magnetic sector followed by an electric sector, this being followed either by a further magnetic sector or a quadnrpole. The properties of these two systems are compared in detail.