MASS SPECTROMETRY RESOURCE

In the "classical" ionisation methods for mass spectrometry, like EI and CI, spectra usually contain a good amount of fragment ions that can be used to help confirm or elucidate chemical structures. In the more modern methods of ionisation, like ESI or MALDI, spectra often only contain the ionised molecule with very little fragmentation data and consequently the spectra are of little use for structural characterisation. In these cases, induced fragmentation is required using collision induced dissociation (CID) and tandem mass spectrometry (MS/MS). One of the most commonly available tandem mass spectrometers is the triple quadrupole (QQQ) instrument. There are many other varieties and configurations of tandem instrument and although this page will describe how a triple quadrupole works - most of what is said will apply generally with little modification.

In a triple quadrupole mass spectrometer, there are several types of experiment that can be performed. The figure shows a schematic representation of three common types of MS/MS experiment. (1) Product ion scan. In this case, the precursor ion is focussed in Q1 and transferred into Q2 - the collision cell - where it interacts with a collision gas and fragments. The fragments are then measured by scanning Q3. This results in the typical MS/MS spectrum and is the method most commonly employed with ESI ionisation and/or LC-MS. (2) Precursor ion scan. In this case Q3 is held to measure the occurrence of a particular fragment ion and Q1 is scanned. This results is a spectrum of precursor ions that result in that particular product ion - this is especially useful when used with EI or CI ionisation and/or GC-MS. (3) Neutral loss scan. In this case Q1 is scanned as in (2) but this time Q3 is also scanned to produce a spectrum of precursor ions that undergo a particular neutral loss. Again this mode is especially useful for EI and CI ionisation.

In ESI-MS/MS it is often desirable to fragment more than one precursor ion of the same compound. In the example below, the two spectra show the ESI-MS/MS of the sodiated [M+Na]⁺ and the protonated [M+H]⁺ precursors respectively of the antibiotic erythromycin A. These two spectra show a very different series of fragment ions that are the result of different gas-phase chemical processes. The Na cation is able to stabilise some structures through chelation, which enables some of the fragment routes, whereas the proton is able to initiate chemistry especially with heteroatoms (like oxygen or nitrogen). In this example it is not possible to say where the cations are in the molecule, and in fact it is quite likely that each route is initiated by the cation being in a different location. This extra data obtained in this way is essential in structural elucidation studies. More information is contained in the research section of this web site.