Mass Analyzer Technology Overview

Understanding mass spectrometry technology

Following ionization, analytes are accelerated into the vacuum chamber of the mass spectrometer. Here, the mass analyzer filters and (optionally) fragments the charged ions. The filtered ions hit detectors, their signals are amplified by detection multipliers, and the final outputs are analyzed by computer software systems. Alternately, they may be fragmented and filtered a second or even third time prior to analysis. Ions may pass through several mass analyses following multiple rounds of fragmentation, which is often abbreviated as MS/MS or MSⁿ.

Mass analyzer overview

What is a quadrupole mass analyzer?

A quadrupole system uses four cylindrical magnets that are set parallel to each other and function to filter ions based on their mass-to-charge ratio (m/z). The analyzer consists of two pairs of like charged magnets that oppose each other and keep the ions within the ion path of the quadrupole under vacuum. Ions are filtered based on their masses as they traverse the linear ion path.

When a linear series of three quadrupoles is used, the resulting triple stage quadrupole analyzer is able to both filter and fragment the ion stream. In most cases, the first (Q1) and third (Q3) quadrupoles act as mass filters, while the second (Q2) quadrupole dissociates ions by having them collide with argon, helium or nitrogen gas.

Quadrupole-based mass analyzers excel at tracking single ions or reactions for extended periods of time. This is why they are preferentially used in the targeted analysis of compounds, especially known compounds such as drugs and pollutants. This is also why quadrupole mass analyzers are often used in the fields of food safety, environmental analysis, clinical and forensic toxicology studies.

The triple quadrupole (QQQ) mass spectrometer (MS) consists of a series of three quadrupoles and selects ions of specific mass-to-charge ratios (m/z) when a specific DC/RF voltage combination is applied. The first and third quadrupoles (Q1) act as mass filters, while the Q2 acts as a collision cell.

The benefits of triple quadrupole technology

Triple quadrupole MS systems can be operated in a tandem MS/MS assay called Selected Reaction Monitoring (SRM) (sometimes also called Multiple Reaction Monitoring (MRM)) mode. SRM is a highly selective mode whereby a fixed set of DC and RF voltages is applied to the quadrupole, permitting only one precursor ion, which is measured by its m/z, to pass. After the Q1 filters that specific precursor ion, the Q2 produces product ions via collision of the precursor ion with a neutral gas (e.g., nitrogen) in a process called collision-induced dissociation (CID). Product ions progress to the Q3, where only a specific m/z is permitted to pass. By breaking the ion apart into its component fragments, a given molecular species can be identified not only by its mass but by product identity. In this way, SRM reduces noise and increases selectivity.

What is an ion trap system?

Most ion traps used in mass spectrometry are based on the model invented by Wolgang Paul (who shared in the 1989 Nobel Prize). The Paul-based ion trap uses a combination of direct current (DC) and radio frequency (rf) electrical fields to trap charged ions for analysis. Through the application of direct and alternating electrical currents, the ions inside of the static and oscillating electrical fields become “trapped.”

Ion traps create a three-dimensional analogue of the quadrupole mass analyzer by virtue of their construction. Here, three electrodes with hyperbolic surfaces function to trap charged ions: two endcap electrodes and a central ring electrode. Because ions are subjected to electrical fields from three directions, not two, they do not move.

Such stability offers the advantages of high sensitivity and high resolution; it also enables the selection and study of individual ion/molecule reactions through MSⁿ. As a result, ion traps are preferably used for the discovery and targeted analysis of molecules and molecular reactions in fields such as metabolomics and lipidomics, as well as post-translational modification analysis.

What is an Orbitrap system?

The Orbitrap is a modified Kingdon ion trap that consists of two endcap electrodes and a central “spindle” electrode. A DC current applied to the Orbitrap spindle electrode results in a high static voltage between the endcap electrodes. Ions entering the Orbitrap are trapped by their attraction to the spindle electrode, which is contrasted by their inertia, and begin to orbit around the spindle electrode.

The Orbitrap mass analyzer

As the ions orbit, they oscillate between the two outer electrodes at different frequencies. Eventually, the ions separate into discrete bands that are determined by their different masses. These different oscillation frequencies enable mass-to-charge measurement and mass spectra reporting using fast Fourier transforms (FFTs).

The Orbitrap’s ability to trap and separate small amounts of ions enables its high-resolution and accurate-mass detection characteristics. Orbitrap-based mass spectrometers are preferentially used for non-targeted analysis of unknown compounds in areas of biomarker discovery, proteomics and metabolism.

What is a TOF analyzer?

Ions of different masses can be separated based on their flight times because lighter ions travel faster than heavier ones. A time-of-flight (TOF) analyzer accelerates samples through the mass analyzer and measures their flight time once they reach the detector. Based on flight time differences, which depend on ion velocities and kinetic energies as well as when the ions started their acceleration and ended their journey at the detector, the ion masses are then calculated.

How do hybrid mass analyzers work?

To achieve different separation, resolution and detection goals, several mass analyzers are often combined in one mass spectrometer. For example, to better select precursor ions prior to their injection into and detection by an Orbitrap mass analyzer, Thermo Scientific Q Exactive Plus and Exploris 480 mass spectrometers contain a hyperbolic quadrupole mass filter. The Orbitrap, meanwhile, enables the resolution of spectral peaks having almost the same m/z values and contains an HCD collision cell to effectively fragment larger ions and molecules for effective detection and confirmation of molecular identities.

To increase the possible applications, it is also possible to combine three difference mass analyzers into one mass spectrometer. For example, the Thermo Scientific Orbitrap Ascend Tribrid mass spectrometer combines a hyberbolic quadrupole for mass filtering, Orbitrap mass analyzer, and duel linear ion traps. All three mass analyzers can be used simultaneously for high acquisition speeds and increased parallelization. The duel linear ion traps also allow for multiple fragmentation techniques in addition to the standard HCD including CID, ETD, and UVPD. They also can provide subsequent analysis of product ions in MSn scans.

HCD cell inside the Q Exactive Focus

There are many other hybrid mass spectrometers that combine different mass analyzers, including the following:

Q-TOF: quadrupole + time of flight (TOF)
Q-Trap: quadrupole + ion trap
LTQ-Orbitrap: linear ion trap + Orbitrap
Q Exactive: quadrupole + Orbitrap

These hybrid mass spectrometers combine the best features of each mass analyzer, providing additional precision, resolution, robustness, etc. For example, the Q Exactive™ Hybrid Quadrupole-Orbitrap™ Mass Spectrometer couples high resolution and accurate mass measurement with precursor selection and compound fragmentation.

Mass Spectrometry Resource Library

Learn more about how dissociations elucidate molecular information at our library of applications notes, scientific posters, webinars and more.