Mass Spectrometry Platform—A Brief Introduction to The Mass Spectrometer

Sample molecules are ionized and fragmented in the ion source to form ions of various mass-to-charge ratios (m/z). Ions with different m/z are subjected to forces in the electric and magnetic fields resulting in different directions of motions before separated by their m/z. Mass spectrometry is the analytical method used to collect, detect, and analyze these ions.

Mass spectrometry can: 1. Determine the molecular weight of the substance; 2. Perform structural analysis of the compound according to the characteristics of the fragment; 3. Obtain information on the composition of the compound element for high-resolution mass spectrometry; 4. Combine with another system such as GC or HPLC to qualitatively and quantitatively analyze complex samples.

The mass spectrometer consists of four parts: injection system, ion source, mass analyzer, and detector.

  • Injection system

Samples such as blood or urine will first need to be introduced into the machine for subsequent analysis. In general, direct injection and pre-separation injection are the two main methods to inject the samples. Direct injection is primarily used to analyze “pure” compounds. Most samples are very complex and require prior separation. Common separation methods are gas chromatography, liquid chromatography, and capillary electrophoresis.

  • Ion source

An ion source is a device that ionizes neutral molecules into ions. The organic compound molecules are ionized and converted to ions in the ion source. The common ion sources are shown in Table 1.

Table 1 The common ion sources

Electron Ionization (EI)Chemical Ionization (CI)
Fast Atom Bombardment (FAB)Atmospheric Pressure Chemical Ionization (APCI)
Matrix-Assisted Laser Ddesorption/Ionization (MALDI)Electrospray Ionization (ESI)

High ionization energy, chemical bond cracking, and complex spectra are characteristics of the hard ionization such as EI, which can be used to obtain information such as molecular functional groups. Soft ionization, such as APCI, ESI and MALDI, has low ionization energy, less debris, and simple spectra. It shoes molecular weight by displayed molecular ion peak.

  • Mass Analyzer

The mass analyzer is the core of the mass spectrometer. Its function is to separate the ions obtained in the ion source according to the m/z and send them to the detector for detection. The type of mass spectrometer is divided by the mass analyzer. Common types of mass analyzers are shown in table 2.

Table 2 The types of mass analyzers

Magnetic sector mass analyzer Ion trap
Time of flight (TOF) Quadrupole
Fourier-transform ion cyclotron resonance (FTICR)

The most commonly used mass spectrometers can be divided into two categories: single-stage mass spectrometers and tandem mass spectrometry systems.

Single-stage mass spectrometers, most notably the MALDI-TOF instrument, have been used for large-scale protein identification in many projects. This approach has been particularly successful in identifying proteins in species with small genomes and complete sequencing.

Tandem mass spectrometry is the sequential connection of multiple mass analyzers. In theory, it is possible to recognize series connection of n=2~9 stages. In practical applications, it is mostly 2~3 series, especially the two-stage tandem mass spectrometry (MS/MS).

Tandem MS instruments, such as triple quadrupole and mixed quadrupole time of flight (Q-TOF), are commonly used in LC-MS/MS or electrospray ionization (ESI) nanospray experiments. They are suitable for peptide fragment ion spectra for protein identification by searching sequence databases.

  • Ion detector

Ion detectors usually consists of an ion collector, an amplifier, and a recorder. Commonly used ion detectors are shown in table 3.

Table 3 Types of ion detectors

Electron Multiplier Microchannel Plate Detector
Daly DetectorFocal Plane Detectors

The most commonly used detector in mass spectrometry is the microchannel plate detector. The ion will produce a small number of electrons after hitting the detector surface. These electrons will collide and produce more electrons. The generated current can be recorded and converted into a signal.

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