Collision-cell fragmentation

Figure Bl.7.7. Summary of the other collision based experiments possible with magnetic sector instruments (a) collision-mduced dissociation ionization (CIDI) records the CID mass spectrum of the neutral fragments accompanying imimolecular dissociation (b) charge stripping (CS) of the incident ion beam can be observed (c) charge reversal (CR) requires the ESA polarity to be opposite that of the magnet (d) neutiiralization-reionization (NR) probes the stability of transient neutrals fonned when ions are neutralized by collisions in the first collision cell. Neutrals surviving to be collisionally reionized in the second cell are recorded as recovery ions in the NR mass spectrum.

Precursor ions are selected by Ql and passed into the collision cell (Q2 orq2 of Figure 33.5). Here, collision with an inert gas (argon or helium) causes dissociation to occur, and the resulting fragment (product) ions are detected by scanning Q3 (Figure 33.6). 

A precursor ion scan. Source ions f,. . .., f, ) are all passed successively by Q1 into the collision cell, Q2, where a selected fragment (i ) is produced and detected by Q3. Only the ions (m, f,. fj) give f, fragment ions in this example. 

Typical MS/MS configuration. Ions produced from a source (e.g., dynamic FAB) are analyzed by MS(1). Molecular ions (M or [M + H]+ or [M - H]", etc.) are selected in MS(1) and passed through a collision cell (CC), where they are activated by collision with a neutral gas. The activation causes some of the molecular ions to break up, and the resulting fragment ions provide evidence of the original molecular structure. The spectrum of fragment ions is mass analyzed in the second mass spectrometer, MS(2). 

This is probably the most widely used MS-MS instrument. The hardware, as the name snggests, consists of three sets of quadrupole rods in series (Figure 3.8). The second set of rods is not used as a mass separation device but as a collision cell, where fragmentation of ions transmitted by the first set of quadrupole rods is carried out, and as a device for focussing any product ions into the third set of quadrupole rods. Both sets of rods may be controlled to allow the transmission of ions of a single mjz ratio or a range of mjz values to give the desired analytical information. 

Figure 2.3. A. Mass spectrometer consisting of an ionization source, a mass analyzer and an ion detector. The mass analyzer shown is a time-of -flight (TOF) mass spectrometer. Mass-to-charge (m/z) ratios are determined hy measuring the amount of time it takes an ion to reach the detector. B. Tandem mass spectrometer consisting of an ion source, a first mass analyzer, a collision cell, a second mass analyzer and a detector. The first mass analyzer is used to choose a particular peptide ion to send to the collision cell where the peptide is fragmented. The mass of the spectrum of fragments is determined in the second mass analyzer and is diagnostic of the amino acid sequence of the peptide. Figure adapted from Yates III (2000).

A tandem-in-space mass spectrometer consists of an ion source, a precursor ion activation device, and at least two nontrapping mass analyzers. The first mass analyzer is used to select precursor ions within a narrow m/z range. Isolated precursor ions are allowed to enter the ion activation device, for example, a gas-filled collision cell, where they dissociate. Created fragments continue on to the second mass analyzer for analysis. The second mass analyzer can either acquire a full mass fragment spectrum or be set to monitor a selected, narrow, m/z range. In principle the second mass analyzer could be followed by more ion activation devices and mass analyzers for MSn experiments. However, due to rapidly decreasing transmission and increasing experimental... 

In linear quadmpoles the CID activation time is equal to the time the accelerated precursor ion (<100 eV) takes to pass through the collision cell. The primary fragments produced will continue to undergo collisions that cause them to fragment as well, and so on, thus producing richer and more complex fragment-ion spectra. 

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