Instrumentation ion trap

In addition to the diversity of ionisation techniques available, mass spectrometers offer a selection of mass analyser configurations. Of note are single (MS) and triple quadrupole (MS—MS) instruments, ion trap analysers (MS)n, time-of-flight (ToF) analysers, sector field analysers, and Fourier transform-ion cyclotron resonance (FTICR) instruments. 

Fig. 5.9 Design of the chip-based enzyme ESI-MS assay. MS instrument Ion-trap mass spectrometer (LCQ Deca, Thermo Electron). I Sample components/inhibitors injected by flow injection or eluting from capillary HPLC column. E Infusion pump delivering the enzyme cathepsin B. S infusion pump delivering the substrate Z-FR-AMC. Micro-chip design Vrije Universiteit Amsterdam. Micro-chip production Micronit Microfluidics BV (Enschede, The Netherlands).

Fig. 5.15 Analytical set-up for on-line label-free assay based on ESI-MS. MS instrument Ion-trap mass spectrometer (LCQ Deca, Thermo Electron). PI Carrier/HPLC pump. P2 HPLC pump delivering receptor solution. P3 HPLC pump delivering dissociation solution. PA HPLC pump for final LC-MS analysis of released ligands. 1 Mixing union. 2 Microcoil reactor. VI injection valve.

Fig. 5.17 Demonstration of MS-based bioassay functionality using a plant extract. MS instrument Ion-trap mass spectrometer (LCQ Deca, Thermo Electron), (a) MS analysis of pure extract by direct injection onto restricted-access column 2 in the absence of affinity protein, (b) Analysis of the same natural extract spiked with digoxin using the label-free MS assay method as shown in Fig. 5.15.

In contrast to triple quadrupole instruments, where MS-MS experiments can be conducted in space in separate regions of the instrument, ion traps enable MS-MS sequentially in the same physical space, and thus, occur tandem in time. After the ions have been formed an trapped, a parent ion is selected by resonance ejection of all ions except those of the selected m/z ratio. This is done by applying a resonance ejection radiofrequency voltage to the end-cap electrodes which stimulates motion of the ions in the axial direction. The next step in the MS-MS sequence is to effect collisionally... 

Reacting the peptides in each sample with an individual, mixed-label reagent adds 145 Da to each peptide. Addition of the same mass allows selection of differentially labeled peptides using a single miz in the first analyzer of a QqQ, QTOF, or TOF/TOF MS/MS instrument. Ion traps cannot be used in iTRAQ analyses because of the low masses of the reporter ions... 

Besides TOP instruments, other mass analyzers such as quadrapole-orthogonal TOP instruments, ion traps, Pourier transform (PT) ion cyclotron resonance mass spectrometers and, most recently, orbital trapping mass spectrometers were employed for MALDI imaging in microprobe mode, as described later in this chapter (see also Chapter 2). 

Ion Trap Instruments Ion trap mass spectrometers with internal ionization can be used for Cl without hardware conversion. Because of their mode of operation as storage mass spectrometers, only a very low reagent gas pressure is necessary for instruments with internal ionization. The pressure is adjusted by means of a special needle valve which is operated at low leak rates and maintains a partial pressure of only about 10 Torr in the analyser. The overall pressure of the ion trap analyser of about 10 -10 Torr remains unaffected by it. Cl conditions thus set up give rise to the term low pressure CL Compared to the conventional ion source used in high pressure Cl, in protonation reactions, for example, a clear dependence of the Cl reaction on the proton affinities of the reaction partners is observed. Collision stabilization of the products formed does not occur with low pressure Cl. This explains why high pressure Cl-typical adduct ions are not formed here, which would confirm the identification of the (quasi)molecular ion (e.g., with methane besides (M + H), also M + 29 and M +41 are expected). The determination of ECD-active substances by electron capture (NCI) is not possible with low pressure Cl (Yost, 1988). 

Other types of mass spectrometer may use point, array, or both types of collector. The time-of-flight (TOF) instrument uses a special multichannel plate collector an ion trap can record ion arrivals either sequentially in time or all at once a Fourier-transform ion cyclotron resonance (FTICR) instrument can record ion arrivals in either time or frequency domains which are interconvertible (by the Fourier-transform technique). 

There are a variety of possible linked scanning methods, but only those in more frequent use are discussed here. They differ from the linked scanning methods used in triple quadrupole instruments and ion traps in that two of the three fields (V, E, and B) are scanned simultaneously and automatically under computer control. The most common methods are listed in Table 34.1, which also defines the type of scanning with regard to precursor and product ions. 

Commercial mass analyzers are based almost entirely on quadrupoles, magnetic sectors (with or without an added electric sector for high-resolution work), and time-of-flight (TOE) configurations or a combination of these. There are also ion traps and ion cyclotron resonance instruments. These are discussed as single use and combined (hybrid) use. 

Almost any type of analyzer could be used to separate isotopes, so their ratios of abundances can be measured. In practice, the type of analyzer employed will depend on the resolution needed to differentiate among a range of isotopes. When the isotopes are locked into multielement ions, it becomes difficult to separate all of the possible isotopes. For example, an ion of composition CgHijOj will actually consist of many compositions if all of the isotopes ( C, C, H, H, 0, O, and 0) are considered. To resolve all of these isotopic compositions before measurement of their abundances is difficult. For low-molecular-mass ions (HjO, COj) or for atomic ions (Ca, Cl), the problems are not so severe. Therefore, most accurate isotope ratio measurements are made on low-molecular-mass species, and resolution of these even with simple analyzers is not difficult. The most widely used analyzers are based on magnets, quadrupoles, ion traps, and time-of-flight instruments. 

This focusing action gives an ion beam, in which the m/z values can be measured so accurately that the resolution of a magnetic/electric-sector instrument (separation of ions of different m/z values) is measured as a few parts per million, compared to the more modest few parts per thousand in, say, a quadmpole or ion-trap instrument. 

The result of the Back-to-Basics series is an accumulation of some 50 separate but interrelated expositions of mass spectrometric principles and apparatus. Some areas of mass spectrometry, such as ion cyclotron resonance and ion trap instruments, have not been covered except for passing references. This decision has not been due to any bias by the authors or Micromass but simply reflects the large amount of writing that had to be done and the needs of the greatest proportion of users. 

Instruments are available that can perform MS/MS type experiments using a single analyzer. These instruments trap and manipulate ions in a trapping cell, which also serves as the mass analyzer. The ion trap and fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers are examples. 

Tandem quadrupole and magnetic-sector mass spectrometers as well as FT-ICR and ion trap instruments have been employed in MS/MS experiments involving precursor/product/neutral relationships. Fragmentation can be the result of a metastable decomposition or collision-induced dissociation (CID). The purpose of this type of instrumentation is to identify, qualitatively or quantitatively, specific compounds contained in complex mixtures. This method provides high sensitivity and high specificity. The instrumentation commonly applied in GC/MS is discussed under the MS/MS Instrumentation heading, which appears earlier in this chapter. 

More recently, certain MS-MS scans have been made available on the ion-trap instrument. This type of system differs from those described previously in that the MS-MS capability is associated only with the way in which the ion-trap is operated, i.e. it is software controlled, and does not require the addition of a collision cell and a further analyser. This is because ion selection, decomposition and the subsequent analysis of the product ions are all carried out in the same part of the instrument, with these processes being separated solely in time, rather than time and space as is the case for the instruments described previously. 

As with the Q-ToF instrument, only two types of MS-MS experiment are available with the ion-trap, i.e. the product-ion scan and selected-decomposition monitoring, as described in Sections 3.4.2.1 and 3.4.2.4, respectively. 

The ion-trap and Q-ToF instruments are, because of the way that they operate, unable to carry out precursor-ion scans. Computer manipulation of data generated during product-ion scans of the Q-ToF system, however, can yield equivalent data to that produced directly by precursor-ion scans on other instruments and an evaluation of this software-based approach has been carried out [14],... 

This is not always the case, and the ability to use accurate mass measurements to confirm that certain ions do, or do not, have the same atomic composition would certainly be an advantage. As discussed earlier in Chapter 3, the instruments most widely used for MS-MS studies, i.e. the triple-quadrupole and the ion-trap, do not routinely have accurate mass capability for product ions. 

One of the features of an ion-trap is that ion selection is carried out in time rather than space. In this type of instrument, MS-MS data are generated by ionizing the analyte of interest in the normal way but then, instead of causing ions of all m/z values to become unstable and reach the detector, ions other than those being studied by MS-MS are ejected from the trap. The selected ion is then caused to fragment, in the trap, and the ions so generated are made unstable in order to generate the MS-MS spectrum. The procedure may then be... 

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