Low mass cut-off

If the instrument allows for multistage fragmentation, the MS3 spectra of the most intense MS/MS fragment ions should also be acquired. There is never too much data in a de novo sequencing experiment. Even if the MS2 spectrum provides the complete sequence, data obtained from additional stages can still be used for sequence validation. In case of three-dimensional ion-traps that suffer from low mass cut-off, MS" spectra are indispensable to cover low mass fragments. For further explanation of this phenomenon, please refer to Chapter 3. 

Low Mass Region. All spectra shown in the examples were acquired using the quadmpole ion trap mass spectrometer. As noted previously, this widely used and relatively cheap mass analyzer suffers the low-mass cut-off phenomena. In addition to techniques used in the examples shown above, other mass analyzers applied for tandem mass spectrometers may cover the low mass region of the fragmentation spectmm that can be information rich. 

An appropriate RF storage voltage is applied to the ring electrode to trap and accumulate ions with an m/z above a low-mass cut-off value. The ion-injection and trapping process may be influenced, e.g., by filtering low-mass interferences in the RF-only ion guide prior to injection into the trap [40], or by the application of auxiliary RF waveforms to the end caps [41]. 

A recent innovation is the commercial availabihty of linear two-dimensional ion traps [54], The linear ion trap (LIT) is found to be less prone to space-charging effects, enabling a higher number of ions to be accumulated, which results in enhanced sensitivity. In the conunercial instrument, the linear ion trap is the third quadrapole in a triple-quadrapole arrangement, i.e., (J-q o -LlT. In that setup, it can be used to accumulate product ions generated by CID in a LINAC colhsion cell, providing enhanced sensitivity and lack of low-mass cut-off. Further stages of MS-MS can be performed in the linear ion-trap, which then has similar features as the three-dimensional ion-trap. Early reports described the application of the hnear ion trap in metabolite identification and quantitative bioanalysis [55-56],... 

Since this original description of the ETD/CID MS/MS scan type (ETcaD), it has been implemented on commercial instruments, applied toward biologically-relevant samples, and expanded upon [28,85,91,92]. For example, Han et al. [92] coupled ETD with beam-type CID on their QTRAP hybrid triple quadrupole/linear ion trap instrument (Figure 3.4). An advantage of both this implementation, and beam-type CID in general, is that the spectra do not suffer from the low mass cut-off that is... 

For both chemical and physical reasons, product ions of low mass can be problematic for MRM detection. The practical interpretation of low mass in this context varies with circumstances. Thus, the chemical disadvantage is mainly concerned with the observation (Aebi 1996) that chemical noise (background) from API sources is considerably more intense at lower m/z values. While this observation directly affects SIM rather than MRM detection, it can also apply to MRM to some extent. The physical problem with low mass product ions for MRM concerns the low mass cut off that exists for all RF-quadrupolar field devices (Section 6.4.2). This problem is extremely important for 3D ion traps, as expressed in the so-called one third rule whereby the low mass (really low m/z) cut off for product ions in MS/MS is 30%... 

In practice, for quadrupole collision cells operated with typical values of rg and Vg, the low mass cut off problem is not often a major concern. In such cells that are operated with a sufficiently high pressure of collision gas to be in the collisional focusing regime (Section 6.4.3), the loss to the quadrupole rods of ions with q > 0.908 and mjz < ijnlz) (predicted for collision free conditions) is countered to a large degree by the collisional focusing of ions on the main axis of the device. 

FIGURE 10.8 Basic principles of a low-mass cut-off collision/reaction cell. 

The first PSIT work at PNNL showed how important such reactions can be. Adventitious water in the ion trap was shown to be responsible for rapid reaction of Ar+ to form H2O+ and H30 . With the low-mass cut-off of the ion trap set to m/z 19 or more, H3O+ ions are ejected from the trap as they are formed, thereby interrupting the mechanism by which H2O+, and H3O+ chemically ionize background species. Unfortunately, H2O also reacts with a wide variety of cations that are of great analytical interest, in particular, metal atomic cations. A more selective reagent gas is needed. 

Chemical ionization by Ar+ in the ion trap (of H2O, O2, N2, pump oil, etc.) can produce background at nearly every elemental m/z. The intensity of the chemical ionization background spectrum in PNNL s early ion trap work was in the range <0.005 to 1 ppb BEC (background equivalent concentration) as shown by a comparison of the mass spectra in Figure 2.38. The background is nearly eliminated if the low mass cut-off of the ion trap is set above m/z 40 during... 

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