Precursor ion isolation

Collision induced Detection of dissociation daughter ions 

FIGURE 5.20 Sequence of MS/MS with an ion trap mass spectrometer. 

---

The three steps of an MS/MS experiment are performed by DIT using an approach substantially different from that employed in 3D IT or linear ITs (Ding, 2004). In those cases, the precursor ion isolation is performed by applying one or more dipole excitation waveforms, with a maximum isolation resolution of -1300 (expressed as the isolation mass divided by the baseline width of the isolation window). In the case of DIT, ion isolation is performed by sequential forward and reverse scans, so as to eject all ions with m/z values lower and higher than that of interest, respectively. This method can provide precursor ion isolation with a resolution >3500. 

C/min to 210 °C held for 15 min El (70 eV), ion source temperature 200 °C Precursor ions isolation window 3amu, scan time at... 

Figure 9.5 Isotopic distributions of intact Ub ions (charge state +10) before (a) and after (b, c, and d) precursor ion isolation (under exchange-out conditions). Panel (a) shows the extent of H retention on partially exchanged Ub (Ub ) by overlaying its spectrum with spectra of unlabeled (Ub), completely exchanged Ub (endpoint) and fully deuterated (Ub ) protein ions on a zoom-out scale. Panel (b) shows broadband isolation of Ub ions, and panels (c) and (d) illustrate Isolation of Ub ions representing con-formers C-l and C-2, respectively (the isolation windows are shown In panel (a)). Reproduced with permission from [25]...

How is a precursor ion isolated in a quadrupole-ion-trap mass analyzer ... 

To identify the origin of a specific fragmentation product, QMF I can be scanned while fixing QMF II so that it only transmits a fragmentation product of interest. In this mode, signal is available only when the precursor ions isolated by QMF I can produce the selected fragment product in the course of fragmentation in the collision cell. 

FTMS/MS data are acquired at a resolving power of 60,000 ( m/z 400). Both collision-induced dissociation (CID) and higher energy collisional dissociation (HCD) are performed for structural identification of analyte molecules. For the latter, the collision cell placed in elongation to the curved linear ion trap is used see 6). Precursor ion isolation is achieved in the linear ion trap for both kinds of fragmentation techniques. As for the molecular (MS mode) ions, also the fragment (MS/MS mode) ions are analyzed in the Orbitrap detector in these experiments. 

The orbitrap analyzer itself does not provide for a mode of tandem MS operation. Instead, the steps of precursor ion isolation and dissociation are performed in a dedicated LIT as MSI (Chap. 4.8.4) prior to high-resolution and accurate mass analysis of the fragments by the orbitrap. Multiple-collision CID (Chap. 9.3) in the LIT of the LTQ-orbitrap instrument is sometimes not hard enough to achieve fragmentation of comparatively stable precursor ions, e.g., it can be insufficient to generate immonium ion fragments from protonated peptides. 

The first step is isolation of the precursor ion. Isolation is undergone at a certain value of V (amplitude of the radiofrequency applied to the ring electrode). This value corresponds to the m/z ratio below in which the ions are not trapped (m/z 50 in Figure 5.20). After ionization is finished, the value of V is increased in order to... 

A feature of MS-MS using the ion-trap is that having generated product ions from a selected precursor ion, any one of these product ions may be isolated, dissociated and a further product-ion spectrum obtained. This is termed MS-MS-MS or MS. This process can then be repeated to obtain further stages of MS-MS or MS" [13]. 

Multiple mass analyzers exist that can perform tandem mass spectrometry. Some use a tandem-in-space configuration, such as the triple quadrupole mass analyzers illustrated (Fig.3.9). Others use a tandem-in-time configuration and include instruments such as ion-traps (ITMS) and Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS or FTMS). A triple quadrupole mass spectrometer can only perform the tandem process once for an isolated precursor ion (e.g., MS/MS), but trapping or tandem-in-time instruments can perform repetitive tandem mass spectrometry (MS ), thus adding n 1 degrees of structural characterization and elucidation. When an ion-trap is combined with HPLC and photodiode array detection, the net result is a profiling tool that is a powerful tool for both metabolite profiling and metabolite identification. 

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... 

For confirmation of low concentrations of NPEO homologues in complex samples from the Elbe river, APCI—LC—MS—MS(+) was applied to record the substance-characteristic ion mass trace of m/z 291. The SPE isolates contained complex mixtures of different surfactants. The presence of NPEOs in these complex samples was confirmed by generating the precursor ion mass spectrum of m/z 291 applying MS— MS in the FIA-APCI(+) mode. This spectrum, showed in Fig. 2.6.5, presents the characteristic series of ions of NPEOs at m/z 458, 502,...,678, all equally spaced with A m/z 44 u. Besides the NPEOs, small amounts of impurities could be observed because of the very low concentrations of NPEOs in the water sample [25]. In the foam sample, the identity of NPEOs could be easily confirmed by APCI-FIA-MS-MS(+) because of their high concentrations in this matrix. The LC-... 

Tandem mass spectrometry (MS-MS) is a term which covers a number of techniques in which one stage of mass spectrometry, not necessarily the first, is used to isolate an ion of interest and a second stage is then used to probe the relationship of this ion with others from which it may have been generated or which it may generate on decomposition. The two stages of mass spectrometry are related in specific ways in order to provide the desired analytical information. There are a large number of different MS-MS experiments that can be carried out [9, 10] but the four most widely used are (i) the product-ion scan, (ii) the precursor-ion scan, (iii) the constant-neutral-loss scan, and (iv) selected decomposition monitoring. 

Note One of the advantages of MS/MS techniques is that they do not require the full isolation of all compounds of interest, because the precursor ion selection of MSI excludes accompanying ions from contributing to the CID spectrum of the actually selected precursor ion as acquired by MS2 (Chaps. 4.2.7, 4.3.6, 4.4.5 and 12.3). 

In tandem MS mode, because the product ions are recorded with the same TOF mass analyzers as in full scan mode, the same high resolution and mass accuracy is obtained. Isolation of the precursor ion can be performed either at unit mass resolution or at 2-3 m/z units for multiply charged ions. Accurate mass measurements of the elemental composition of product ions greatly facilitate spectra interpretation and the main applications are peptide analysis and metabolite identification using electrospray iomzation [68]. In TOF mass analyzers accurate mass determination can be affected by various parameters such as (i) ion intensities, (ii) room temperature or (iii) detector dead time. Interestingly, the mass spectrum can be recalibrated post-acquisition using the mass of a known ion (lock mass). The lock mass can be a cluster ion in full scan mode or the residual precursor ion in the product ion mode. For LC-MS analysis a dual spray (LockSpray) source has been described, which allows the continuous introduction of a reference analyte into the mass spectrometer for improved accurate mass measurements [69]. The versatile precursor ion scan, another specific feature of the triple quadrupole, is maintained in the QqTOF instrument. However, in pre-... 

---