Tandem Mass Spectrometry

Tandem mass spectrometry (MS/MS), originally introduced to study physicochemi-cal properties of small molecules [8], found its way into bioanalytics in combination with soft ionisation methods. MS/MS gives access to the structural characterization of analytes in mixtures by allowing the recording of compound-specific fragment ion spectra without the need for their isolation in a pure state. By mass analysis, a single analyte is isolated and fragmented by collision-induced dissociation (CID), and its fragment ions are analysed in a second stage of mass analysis. The first instrument type designed for tandem MS analysis in biochemistry was the triple quadrupole instrument [9], consisting of three quadrupole analysers. Q1 operates as the first mass analyser, Q2 is designed and operated as a collision cell, and Q3 performs the second stage of mass analysis. In the product ion scan mode, a precursor ion is selected with Q1 and fragmented in Q2, followed by fragment ion analysis in Q3. Moreover, this type of instrument can selectively detect all analytes in a mixture exhibiting a certain neutral loss (neutral loss scan) or all analytes forming a certain fragment ion (precursor ion scan mode). This mode of analysis is named 'tandem in space', since the single steps proceed in spatially separate units of the tandem MS system.

The 'tandem in time' systems are either 3D [10] or 2D (linear) [11] ion traps, schematically displayed in Figure 6.3.

In these ion trap systems, ions are trapped, selectively fragmented, and mass analysed by the use of a single device. The 3D ion trap consists of a ring electrode with electrically isolated end caps, through which the ions are introduced for trapping and ejected for mass analysis. The 2D (linear) ion trap is a compact arrangement of three electrically separated quadrupole analysers. The ions are introduced concentrically into the central quadrupole system, which performs both stages of mass analysis and the intermediate fragmentation step. The ions are ejected either axially or perpendicularly for detection. Ion traps have the unique ability to perform multistage MS/MS experiments (MS"), in which the product ions of a fragmentation process are selected as precursor ions for the next fragmentation step. In spite of their extreme specificity, MS" techniques have so far found only sporadic application in protein modification analysis. Ion traps can be operated at variable resolution (low to moderately high resolution) (see below); however, due to the low scan speed required for increased resolution, complete spectra are usually recorded at low to medium resolution.

Fig. 6.3 Tandem in time MS systems implemented as (a) 3D ion trap or (b) 2D (linear) ion trap. In the central part of these analyzers, the ions are trapped, selectively fragmented, and mass-analyzed by dynamic electromagnetic fields in the presence of a mediator/collision gas (mostly He).
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