Ion structural information can be obtained from the fragmentation of a polyatomic ion following an energetic collision. Usually triple quadrupole mass spectrometers are used to generate such ion structural information through MS/MS techniques. The basic instrumentation required to obtain such information consists of two quadrupole mass spectrometers separated by a collision cell (commonly referred to as a triple quadrupole since the collision cell also includes a set of quadrupole rods). The first mass spectrometer selects the first precursor ion of interest, which ion is then directed with a specified energy into the pressurized collision cell. In the collision cell, collision induced dissociation (CID) occurs, producing a number of product ions. The mass to charge ratios of the product ions, as well as that of the residual precursor ion, are measured with the second resolving mass spectrometer.
RF-only quadrupoles have been used for some time as efficient containment devices for product ions formed by CID of activated precursor ions. Typically ion activation is accomplished by operating the RF-only quadrupole at pressures of up to 10 milliTorr, and introducing the precursor ions at laboratory reference frame energies of tens to hundreds of electron volts. Activation in this way is efficient (since the collision energies are sufficient readily to fragment the precursor ions) and, coupled with the high containment characteristics of the RF-only collision cell, can provide high CID product yields.
Triple quadrupole mass spectrometers perform MS/MS scans on a continuous ion beam in spatially separated segments of the instrument. This contrasts with ion trap mass spectrometers, where a pulse of ions is introduced into the containment volume of the mass spectrometer; a precursor ion mass-to-charge ratio is selected and isolated in the volume, collisional activation is induced (usually by using a supplementary RF voltage), and then product ion analysis is performed, all within the same volume but in time sequence. Of course, in the product ion analysis, the product ions are sequentially scanned out of the device and are detected using conventional means. The ion trap also allows for additional stages of fragmentation and product ion identification, and thus allows for MS.sup.n experiments, which are not currently possible employing conventional rod type triple quadrupole mass spectrometers. As mentioned, in contrast to the spatially separated segments of a triple quadrupole mass spectrometer, the steps leading to the generation of a product ion spectrum in an ion trap are separated in time rather than in space.
Collisional activation in an ion trap mass spectrometer is different from that in a triple quadrupole mass spectrometer. In the latter, the precursor ion is accelerated from a relatively low pressure region of the instrument into a much higher pressure region, where the first few collisions (which are energetic) cause fragmentation. Collisional cooling reduces the energy of later collisions so that they do not normally cause fragmentation. In contrast, in an ion trap mass spectrometer the selected precursor ion is usually activated by means of a resonance process (resonance excitation) resulting in numerous low energy collisions. In this case the activation process is step-wise, since the presence of the buffer gas (usually helium) prevents the precursor ions from attaining high kinetic energies between collisions. Thus, numerous low energy collisions (with energy added between the collisions by the resonance excitation) are required to reach the threshold energy of fragmentation.
An alternative to resonance excitation for collisional activation in an ion trap is to properly choose the "a" and "q" value of the precursor ion such that the working point is brought near a boundary of the a-q stability diagram. At this point, the amplitude of the ion oscillations in the ion trap increases, and higher energy collisions of the ion with the background gas are effected. This technique, referred to as "boundary activated dissociation", has been found to deposit sufficient energy into the precursor ion to promote efficient fragmentation. It is thought that boundary activated dissociation, like dissociation caused by resonance excitation, also occurs via a step-wise mechanism.