Ion trap scan function

The step in the ion trap scan function before the analytical scan. During the pre-scan the variable ionization time or ion collection time is adjusted to fill the trap to its optimum capacity with ions. 

The 2D- and 3D-Quadrupo e Field ion Trap Scan Functions and Timing Diagrams... 

Ion Trap Scan Functions Prescan and Analytical Scan... 

Figure 2.28 Ion trap scan function. The sequence of events used to generate a mass spectrum in a typical Paul trap is shown. This sequence is typically repeated many times with the individual spectra summed or averaged to produce the final spectrum. The generic parts of the scan function shown include (1) ion injection and trapping, (2) ion relaxation/cooling, (3) auxiliary excitation for selective ejection/storage of desired ions and (4) mass-selective instability scan. The timing of the resonant excitation function is also indicated two sine waves shown indicate a first pulse for selective excitation and a second pulse for enhancing the mass selective instability scan...

Many variations on ion trap scan functions are known and utilized for all manner of ion manipulation and detection coUisionally induced dissociation (CID), selective ejection or trapping, high mass resolution, ion reaction, chemically selective excitation of motion via the mass shift , etc. The interested reader is referred to the significant ion trap literature already cited. 

A third type of MS/MS instruments is a hybrid of tandem-in-space and tandem-in-time devices, including the Q-trap (QQ-2D-linear trap) [45] and the ion trap-FT-ICR (2D-linear ion trap-FT-ICR) [46]. The Q-trap takes the configuration of triple quadrupole, with the third quadrupole replaced by a 2D-linear ion trap. The uniqueness of this design is that the 2D-linear ion trap component can be used to perform either (a) a normal quadrupole scan function in the RF/DC mode or (b) a trap scan function by applying the RF potential to the quadrupole. It is well-suited for both qualitative and quantitative studies. In the case of ion Trap-FT-ICR, it combines ion accumulation and MS" features of a 2D-linear ion trap with excellent mass analysis capability (mass resolution, mass accuracy, and sensitivity) of FT-ICR. 

Figure 2.220 Scan function of the ion trap analyser within an ion trap scan, several j-scans (three p-scans shown here) are carried out and their spectra added before storage to disk. P = pre-scan, A = analytical scan, v = variable ionization time (AGC, automatic...

Fig. 11.10. Diagram illustrating the inner surfaces of the primary components of a Paul (3D) quadrupole ion trap. Ions generated by an external source are injected into the trap through an aperture in one of the end caps. Scan functions for isolating ions in the trap, exciting the mass selected ions to induce unimolecular dissociation, and ejecting ions from the trap (for detection) are implemented through the application of DC and RF voltages to the ring electrode.

An ion trap mass analyzer has a variety of differing physical arrangements of its electrodes, but the primary objective remains the same to allow the ions to enter and then to trap them in space between the electrodes. Unlike the fly-through mass analysis scheme of a quadrupole, the ion trap mass analyzer stores the ions. They are then ejected to the detector as a function of the mass-to-charge ratio, typically by scanning the rf voltage. 

The commercially available stand-alone LITs, marketed under the name LTQ, are made of four hyperbolic cross-sectional rods (Fig. 1.25). Since ions are trapped in an axial mode as opposed to central trapping on 3D ion traps, LTQs have been successfully coupled with Orbitrap and FTICR for achieving high-resolution capabilities (Peterman et al., 2005 Sanders et al., 2006) (Chapter 5). Functional improvements in 2D traps over 3D traps include 15 times increase in ion storage capacity, 3 times faster scanning, and over 50% improvement in detection efficiency and trapping efficiency. 

Figure 3.13. MS/MS spectra of tamoxifen (m/z 372) obtained using the ion trap mode in a QTRAP with (bottom panel) and without (top panel) the TDF scan function. 

The tandem-in-time instruments are mostly ion-trapping devices, including ion trap and FT-ICR. They operate in a time sequence in the scan function to yield MS/MS data, mostly product ion spectra. No additional mass analyzer is required. In the case of an ion trap, the scan function begins with the isolation of ions of interest with ejection of all other ions from the ion trap, followed by (a) translational excitation of ions by applying a supplementary RF voltage to the trap and (b) mass analysis of the product ions using resonant ejection. 

The rapid structure identification of metabolites is a powerful complement to previously described quantitative approaches. The utility of an automated metabolite identification approach, using LC/MS/MS with an ion trap mass spectrometer has been demon-strated.f In this study, MS" analysis is automated to provide maximum structural information in combination with predictive strategies for biotransformation. Automated data-dependent scan functions are used to generate full scan, MS/MS, and MS" mass spectra of... 

Data-dependent acqnisition (DDA) is a mode of operation, where the MS experiment performed in a particular scan is based on the data acqnired in a previons scan. In a simple form, a DDA experiment switches the instrument from full-scan MS acquisition to full-scan product-ion MS-MS when the total-ion intensity or a selected-ion intensity exceeds a preset threshold. This avoids the need to perform two consecutive injections for the identification of unknowns in a mixture first to obtain the m/z values for the intact protonated molecules of the unknowns, and second to acquire the product-ion MS-MS spectra of these unknowns in a time-scheduled procedure, switching between various preselected precursor ions as a function of the chromatographic retention time. The DDA was promoted by Thermo Finnigan upon the introduction of the API-ion trap combinations [44-46]. Similar procedures are available for other commercial ion-trap systems, as well as for triple-quadrupoles, e.g.. Information Dependent Acquisition (IDA) from Applied Biosystems MDS Sciex, Data-directed Analysis (DDA) from Waters, and Smart Select from Bruker. 

A relatively new and powerful tool in metabolite identification is the (J-LIT instrument. In this triple-quadrapole instmment, the third quadrupole can be apphed as a scanning quadmpole, but also as a linear ion trap (Ch. 2.4.2). Potential and additional features of a Q-LIT in metabolite identification have been discussed by various groups [44-45]. The advantages of triple-quadrupole MS-MS spectra at ion-trap sensitivity as well as the enhanced sensitivity and speed in DDA experiments with the (J-LIT was demonstrated for the collagenase inhibitor trocade [44]. Various enhanced scan functions of the Q-LlT were applied in the identification of 6-aminobutylphthalide metabolites in rat brains, using microdialysis and LC-MS-MS [45]. Simultaneous quantification of a parent compound and screening for its... 

In a quadrupole mass analyzer, only a single mass-to-charge ratio m/z) value is transmitted to the detector for any given combination of radio frequency (RF) and direct current (DC) potentials. Typically, the RF/DC ratio is held constant and scanned to provide a mass spectrum. If, for example, a quadrupole is scanned from m/z 1 to 1000 in 1 second, then any particular m/z is transmitted to the detector for only 1 millisecond, representing a duty cycle of 0.1 %. Thus, a quadrupole mass analyzer has a low transmission duty cycle in the full-scan mode, which results in limited full-scan sensitivity. In contrast, ion-trap and TOF mass analyzers have the theoretical potential to transmit all ions that enter the mass analyzer and yield far better sensitivity across the entire mass spectrum. In reality, the pulse sequences associated with these analyzers devote significant time to functions such as ionization and detection. The actual duty cycles are generally between 10 and 25%, still far better than a scanning quadrupole mass spectrometer. 

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