Hybrid FT-ICR instrument

Since 2000, the field has moved increasingly toward hybrid FT-ICR instruments in which the FT-ICR is interfaced with a front-end mass analyzer. The groups of Marshall [46,47] and Smith [48,49] introduced the quadrupole-FT-ICR. That configuration is available commercially. The hybrid linear ion trap FT-ICR [87] was introduced commercially in 2003. Hybrid instruments offer greater versatility in terms of mass-selective external accumulation with the associated increase in sensitivity and dynamic range. 

Chapter 5 provides an overview of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and its applications in the structural characterization of peptides and proteins. The principles of FT-ICR, that is, ion motion, ion excitation/ detection, and instrumental considerations, are discussed and an explanation of the features of FT-ICR that make it so suitable for peptide/protein analysis is presented. New methods for the fragmentation of peptide and protein ions in FT-ICR mass spectrometry, such as sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD), blackbody infrared radiative dissociation (BIRD), surface-induced dissociation (SID), and electron capture dissociation (BCD), are described in detail. Innovative hybrid FT-ICR instruments, which have recently become available, are reviewed. In conclusion, the chapter discusses the applications of FT-ICR in bottom-up and top-down proteomics. 

A recent implementation of ETD reactions on the third type of hybrid instrument, a hybrid LIT/FT-ICR instrument [76], presents another example of the value in bringing high mass accuracy and mass-resolving power to the measurement of ion/ion reaction products. The hybrid instrument used a hexapole LIT as the reaction vessel by the superposition of auxiliary RF signals to the end lenses to effect mutual storage ion/ion reactions, the products of which were sent directly to the adjacent FT-ICR for mass analysis. The arrangement of the positive and negative ions sources is very similar to that for the Bruker Daltonics HCTultra post-translational modification (PTM) ion trap mass spectrometer [42] described in the previous section, which introduces positive ions formed by ESI from the front end of the instrument and... 

HYBRID FOURIER TRANSFORM ION CYCLOTRON RESONANCE (FT-ICR) INSTRUMENTS... 

An alternative approach was introduced by Hunt and co-workers [87], Those researchers coupled a linear quadrupole ion trap, consisting of four rods of hyberbolic cross-section, with an FT-ICR mass spectrometer. The linear ion trap allows accumulation of larger populations of ions than does a standard three-dimensional (3D) ion trap. The hybrid linear ion trap-FT-ICR instrument enables simultaneous detection in both mass analyzers. This aspect is particularly advantageous for data-dependent MS/ MS methods used in proteomics, and is discussed further below. The commercial version of this instrument features automated gain control that accumulates a fixed number of charges before delivery to the ICR cell. Because the ideal ion density is attained in the cell, space-charge effects resulting in loss of mass resolution and mass accuracy, are eliminated. 

Note Modem LT-ICR mass spectrometers offer ultrahigh resolving power (R= 10 -10 ) [185,186] and highest mass accuracy (Am = 10" -10 u, cf. Chaps. 3.5, 3.6) [183,184], attomol detection limits (with nanoESI or MALDI sources), high mass range and MS capabilities [187], Most of the modem FT-ICR instruments actually represent some sort of hybrids with linear quadmpole or LIT front ends. 

The majority of H/D studies that have been reported employ quadrupole ion trap (QIT) instruments due to their ease of use, excellent sensitivity, ability to perform MS/MS experiments, compact size, and low cost. Other reports discuss the use of instruments with higher mass-resolving power such as the hybrid QqTOF instruments [47]. A few groups have utilized FT-ICR mass spectrometry, which offers ultra-high mass-resolving power and improved mass accuracy [48, 49]. 

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. 

Alternatively, the high resolving power of the FT-ICR-MS in the measurement of fragment ions can be exploited by performed fragmentation of the precursor ion, prior to introduction into the FT-ICR cell, e.g., via in-source CID, or a hybrid instrument consisting of a quadrupole or LIT front-end and a FT-ICR-MS back end. Both types of instruments are commercially available. 

FT-ICR-MS systems equipped with external API sources are conunercially available from Bruker Instruments, lonSpec, and Thermo Fimiigan. In order to control the number of ions in the ICR cell, hybrid systems have been developed. Bruker offers a FT-ICR-MS hybrid with a quadrapole front-end (APEX-Qh) [121], whereas the LTQ-FT instrument from Thermo Fimiigan features a linear-ion-trap (LIT, Ch. 2.4.2) front end [122]. In this way, MS-MS can be performed prior to ion introduction into the ICR-cell, avoiding problems with CID in the ICR-cell. 

An alternative method to peptide fragmentation is a hybrid system, involving either a triple-quadrapole type of a (J-LfT-type first stage of mass analysis and an FT-ICR-MS second stage of mass analysis. This decouples fragmentation and accurate-mass determination and results in a more user-friendly instrument (Ch. 17.7.3). More elaborate use of these coimnercial instruments can be anticipated. 

The types of tandem mass spectrometers capable of performing MS/MS experiments fall into two basic categories tandem in space and tandem in time. Tandem-in-space instruments have discrete mass analyzers for each stage of mass spectrometry examples include multisector, triple-quadru-pole, and hybrid instruments (instruments having mixed types of analyzers such as a magnetic sector and a quadrupole). Tandem-in-time instruments have only one mass analyzer where each stage of mass spectrometry takes place in the same analyzer but is separated in time via a sequence of events. Examples of this type of instrument include Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers and quadrupole ion traps, described in Chapter 3. 

Fourier transform ion cyclotron mass spectrometry (FT-ICR-MS) instrumentation offers excellent sensitivity, accuracy (<1 ppm), and high mass resolution (>1,000,000) (Table 10.2). However, because of being too expensive, difficult to use, and not compatible with conventional HPLC columns and flow rates, FTMS has not been frequently used in pharmaceutical research. This changed with an introduction of a hybrid instrument consisting of a linear ion-trap mass spectrometer compatible with LC and an ion-cyclotron-resonance (ICR) detector. Such a hybrid instrument is compatible with conventional HPLC and allows for acquisition of accurate mass data-dependent MS" spectra. Sanders et al. [128] recently reviewed the utility of hybrid LTQ-FTMS for drug metabolism and metabonomics applications while Brown et al. [129] reviewed the metabolomics applications of FT-ICR-MS. 

Various hybrid tandem mass spectrometers, which combine two or more distinct types of mass analyzers, have been developed to maximize analytical performance and functionality. From the standpoint of ion/ion reactions, the incorporation of an electrodynamic ion trap into a hybrid instrument allows for the physical separation of the three basic steps involved in an ion/ion reaction experiment, that is, ionization, ion/ion reaction, and mass analysis of reaction products. The separation of these processes provides for the highest degree of flexibility and minimal compromises in the optimization of each step. To date, three major types of hybrid instrnments have been described for ion/ion reaction studies using an electrodynamic ion trap as the reaction vessel. The three major types of hybrid instruments are (i) quadrupole/TOF tandem mass spectrometer (ii) Orbitrap and (iii) LIT /FT-ICR. 

Linear Ion Trap-Orbitrap Mass Spectrometer A recent addition to the family of hybrid tandem mass spectrometers is a linear ion trap (LTQ)-orbitrap mass spectrometer [69,70]. Conceptually, this instrument is similar to the LTQ/FT-ICR tandem mass spectrometer discussed above but uses an orbitrap in place of a Penning trap, thus avoiding the complexity and cost of a superconducting magnet. The working principle of an orbitrap was described in Section 3.9 [71,72]. A schematic diagram of the LTQ/orbitrap mass spectrometer is shown in Figure 4.14. This hybrid tandem mass spectrometer consists of an... 

These ionization techniques can be combined with a variety of instruments for the sensitive determination of peptide masses. Widely used instruments include triple quadrupole, time-of-flight (TOP), hybrid quadrupole-TOF, TOF-TOF, quadrupole-ion trap, and FT-ICR mass spectrometry. 

More recently, instruments with a hnear two-dimensional ion trap (LIT), i.e., a linear quadrupole as ion trap, have become commercial available [24, 62, 63]. As a LIT is less prone to space charging effects, a higher number of ions can be accumulated, and enhanced sensitivity can be achieved. Initially, LITs were apphed in hybrid Q-LIT [24] a LIT and hybrid LIT-FT-ICR-MS [64] instruments, but later on stand-alone versions of an LIT were introduced too, thus competing the three-dimensional ion traps. A dual-pressme two-stage LIT has been reported as well the first high-pressure ion trap serves to capture, select, and fragment ions, whereas the second low-pressure ion trap is used to perform fast scamiing of product ions, eventually at enhanced resolution [65]. 

This is true for ion trap hybrids with FT-ICR-MS (see Sect. 4.4.7) and Orbi-trap (see Sect. 4.4.9) instruments, but also for the ion trap-time-of-flight hybrid system. The latter system has been pioneered by the group of Lubman [87, 88]. It has become commercial available for both MALDI and LC-MS applications [89]. All these hybrid MS system are frequently applied in combination with LC and electrospray ionization in, for instance, drag metabolite identification studies and in various proteomics-related studies. 

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