Ion traps in the mass spectrometry

There are several different ion-trapping techniques used in mass spectrometry.   The 3D ion traps were developed for earlier GC-MS and LC-MS instruments and were withdrawn from the market later by more effective linear ion traps. The GC-MS Polaris Q was the last 3D instrument we used in TSABAM (now discontinued) and 3D ion traps are probably not available commercially anymore.

In the quadrupole, or linear, ion trap ions are confined radially by a two-dimensional radio frequency field and axially by potentials of end electrodes. In our lab, the linear ion trap was available in Orbitrap Discovery (now discontinued) and QTRAP 6500.

In the Penning trap, ions are stored in a strong homogenous magnetic field in combination with a quadrupole electric field.  This technology is applied in ion cyclotron resonance (ICR), - ultra-high-resolution mass spectrometers. 

In the Orbitrap ions are trapped in a strong electrical field. The Orbitrap is a high-performance, accurate mass high-resolution mass analyzer widely used in modern advanced LC-MS instruments.  In TSABAM, the Orbitrap was available on Orbitrap Discovery (now discontinued) and Q-Exactive hybrid instruments.

There exist other ion-trapping techniques but not all found applications in mass spectrometry. 

Operation principles of two ion traps namely, the linear ion trap and Orbitrap, will be explained on an example of LTQ Orbitrap mass spectrometer.

LTQ Orbitrap is a hybrid system that combines the Finnigan LTQ linear ion trap mass spectrometer and the Orbitrap mass analyzer. In the hybrid system, the LTQ ion trap may be used as an independent mass analyzer utilizing all benefits of a linear ion trap, like MS and MSn scan modes, if ion detection is performed using conversion dynodes. This option however is rarely used in the LTQ Orbitrap Discovery. The ions are analyzed by Orbitrap mass analyzer for high resolution and accurate mass determination. The sequence of events in this hybrid system is following:

    a) ions generated in the API ion source are trapped in the LTQ ion trap;

    b) the ions trapped in the LTQ linear ion trap are analyzed using MS or MSn scan modes and axially ejected and collected in a C-trap (ion trap);

    c) from the C-trap the ions are ejected into the Orbitrap;

    d) the ions transferred from the C-trap are captured by rapidly increasing voltage on the center electrode of the Orbitrap;

    e) the trapped ions assume circular trajectories around the center electrode and their axial oscillations, along the center electrode, are detected.

   The principle scheme of the LTQ Orbitrap hybrid mass spectrometer and the sequence of events describing ion transfer from the LTQ linear ion trap to the Orbitrap mass analyzer is shown below.

Ions from the ion transfer capillary should pass a number of lenses and two RF multipoles until they reach the LTQ ion trap. All these lenses and RF multipoles are called ion transfer optics and are necessary to deliver ions from the API source to the mass analyzer. The parameters of ion transfer optics are adjusted automatically during tuning of the mass spectrometer. There are however some parameters to which attention should be paid. The final desolvation of ions occurs in the skimmer region. The skimmer acts as a vacuum baffle between the higher-pressure ion source interface region (~ 1 Torr) and the lower-pressure RF lens region (~50 Torr). Therefore voltages at the capillary, skimmer, and tube lens affect ion desolvation, adduct formation, skimmer-induced fragmentation, and sensitivity.

The mass analyzer is the site of mass analysis, that is, ion storage, ion isolation, collision-induced dissociation, and scanning of m/z. The mass analyzer consists of a front lens, linear ion trap, and back lens. The linear ion trap is a square array of hyperbolic rods. Each rod is cut into three sections. Two of the center section rods have a slot through which the ions are ejected during scan out.

Dividing the quadrupole into three sections, each with a discreet DC level, allow containment of the ions along the axis in the central section of the trap, avoiding any possible fringe field distortions to the trapping and resonance excitation fields. In each quadrupole rod section, rods opposite each other in the array are connected electrically (like in a quadrupole mass filter). RF voltages are applied to the rods, and these voltages are ramped during the scan. Voltages applied to the different rod pairs are equal in amplitude but opposite in sign. The RF voltage applied to the quadrupole rods is of constant frequency but of variable amplitude. When the amplitude of the RF voltage is low, all ions are trapped. During the ion scan out, the RF voltage is ramped at a constant rate. As the RF voltage increases, ions of increasing m/z become successively unstable in the radial direction and are ejected from the mass analyzer. Ejected ions are detected by the ion detection system.

Applying certain voltages on the exit rods ions of a particular m/z may be isolated and activated. During CID dissociation the resonance excitation ac voltage is applied to the exit rods. The resonance excitation ac voltage enhances ion motion in the radial direction and ions gain kinetic energy. After many collisions with helium-damping gas the ions gain enough internal energy to cause them to dissociate into product ions.

The mass analyzer contains helium (~10-3 Torr) that is used as both, a damping and a collision activation gas. The collisions of the ions entering the mass analyzer with the helium slow the ions so that they can be trapped by the RF field. These collisions reduce the kinetic energy of the ions, thus damping the amplitude of their oscillations. As a result, the ions are focused to the axis of the cavity rather than being allowed to spread through the cavity.

 The Orbitrap

For high-resolution accurate mass determination ions are transferred from the LTQ linear ion trap to the Orbitrap. On their way from the linear trap to the Orbitrap, ions move through the gas-free RF octapole into the gas-filled (~10-3 Torr nitrogen) curved rf-only quadrupole whose central axis follows a C-shaped arc (the C-trap). The C-trap was chosen to be filled with nitrogen due to better than helium collisional damping and lower carryover toward the Orbitrap. The C-trap serves as an intermediate station for ions between LTQ linear ion trap and the Orbitrap. The ions are cooled in the C-trap and they are extracted into the Orbitrap in a fast and uniform manner.

On their way from the C-trap to the Orbitrap ions are accelerated to high kinetic energies, and converged into a tight cloud which is injected at a position offset from the equator of the Orbitrap. The Orbitrap mass analyzer consists of a spindle-shaped central electrode surrounded by a pair of bell-shaped outer electrodes.

Ions are captured in the Orbitrap by rapidly increasing the electrical field and gradually spread into rotating thin rings oscillating axially along the inner electrode. As a result, the average trajectory radius shrinks by a few percent by the time the ions reach the opposite side of the Orbitrap. Finally, ions form almost circular trajectories and stay trapped in the Orbitrap. The frequency ω of harmonic oscillations along the z-axis of the Orbitrap depends only on the ion mass-to-charge ratio m/q and the instrumental constant k.

After the mass range of interest has entered the Orbitrap, the voltage on the center electrode is stabilized and the image current detection may be performed. Image current is detected on the split halves of the outer electrode of the Orbitrap. By Fourier Transformation of the image current the frequencies of the axial oscillations are obtained, and as a result, m/z of ions is determined.