Mass Spectrometry & Mass Spectrometers

mass spectrometry instrument machine

What is mass spectrometry?

Mass spectrometry (also known as mass spec) is an analytical technique that can be used to identify unknown substances, quantify known substances, and determine the structure of molecules. The basic idea of the spectrometer is to ionize the molecules and then direct them to a detector using electric and magnetic fields. Where or when the molecules hit the detector will depend on the mass-to-charge ratio (m/z).

The output of a mass spectrometry instrument is a mass spectrum. The spectra plot the relative abundance of each m/z value. The mass depends on the fragmentation of the molecule.

The highest m/z value will usually be the molecular ion. That is the unfragmented original molecule that has been ionized. Due to heavier isotopes of certain atoms within the molecule, there may be a few higher m/z values. But these will have significantly lower abundance. More details are in the ‘Reading a Mass Spectrum’ section.  

Mass spec instrument or mass spectrometer machine
Image of a mass spectrometer (Credit: Wikipedia Commons)

Important Vocabulary for Mass Spectrometry

Mass-to-charge ratio (m/z): Ratio of the mass of an ion to the charge of the ion. Commonly used unit in mass spectrometry.

Ion: A molecule with an electric charge. The charge can be positive (cation) or negative (anion).

Amu: atomic mass unit. One atomic mass unit is equal to 1/12th of the mass of a carbon-12 atom. It is also about 1.66 x 10-27 kg.

Spectrometers: Instruments that separate particles (molecules, atoms, ions) by one of their physical characteristics. Common characteristics include mass, optical properties, and energy.

How Do Mass Spectrometers Work?

A mass spectrometer operates in a vacuum due to ion lifetimes being very short. Operating in a vacuum extends the ion lifetime.

There are three main parts to a mass spectrometer. Each different part can have many variations.

1. Ionization source:

The ionization source turns the molecule of interest into a gaseous ion. The ions can be either positively or negatively charged. The specific technique used will often depend on the sample type.

The most common technique for ionization is electron bombardment. A high-energy electron hits the molecule, causing it to ionize. Electrospray ionization (ESI) is often used for biological samples. For solid samples, matrix-assisted laser desorption ionization (MALDI) is more commonly used. Other common techniques include thermal ionization, direct-current arc, photonionization, desorption electrospray ionization(DESI), and field ionization.

2. Mass analyzer:

The mass analyzer sorts and separates ions based on their m/z ratio. So both the mass of the ion and the charge of the ion influence the separation. Ions move through the mass analyzer to reach the ion detection system.

One of the most common techniques is time of flight (ToF). Time-of-flight relies on the concept that ions of different masses will have different travel speeds. The ions with the largest m/z will arrive at the detector last due to moving at a lower velocity. The smaller m/z ions will arrive first. The analysis is then based on arrival time at the detector. 

There are multiple other techniques for achieving mass separation: ion cyclotron resonance, quadrupole ion, magnetic sector mass analyzers, and many others.

3. Ion detection system

The ion detection part of the instrument measures the already separated ions. The detected ions are then displayed on a mass spectrum based on their m/z and relative abundance.

Techniques for detecting the ions are as varied as the previous parts of the instrument. Often the detector needed depends on the type of mass separation technique used. The separation can be measured either spatially, temporally, or both.

Some of the detection systems used are electron multipliers, faraday cups, array detectors, and various dynodes.  

The output after these three steps is a mass spectrum.

Reading a Mass Spectrum

Mass spectrum of acetone
Mass Spectrum of Acetone from the NIST Chemistry WebBook

The output of a mass spec is a mass spectrum. The x-axis of the plot is the m/z value. The y-axis is the relative abundance. The higher the relative abundance, the more particles of that m/z ratio were detected.

The base fragment is the tallest peak in the spectrum and therefore also the most common fragment. This m/z value is assigned a relative abundance of 100 and the rest of the abundances are based off this. The base fragment may or may not be the largest m/z fragment.

In many ionization techniques, the molecules are also fragmented in addition to being ionized. This means that if CO2 is the sample, there will also be peaks for CO and O. These peaks will be at m/z values of 28 and 16 respectively. Fragments are a great tool for helping determine the structure of a molecule.

Additionally, mass specs are sensitive enough to also detect different isotopes of atoms in a sample. For example, you may have a small cluster of peaks around a certain m/z. The tallest peak will be the most common isotope of an atom in the ion. Examining the m/z around that peak, the smaller peaks could be the same ion fragment just with a different isotope. The weight difference of that isotope gives the fragment a different mass. Looking at the ratio of these peaks you can determine the occurrence of the different isotopes in the sample.

Any uncharged particles will not show up in the mass spectrum.

Common Applications of Mass Spec:

With the rise in the ease of performing mass spectrometry, the number of uses for the technique has also rose. Below are some common uses of mass spectrometry. There are many more applications of mass spectrometry that are not listed below.

  • Protein Analysis and Proteomics
  • Identifying Unknown Materials
  • Quantifying Known Materials
  • Drug Testing
  • Pesticide Identification and Analysis
  • Isotope Ratio Determination
  • Carbon Dating

Additionally, mass spectrometry combined with other analytical techniques provides even more information. A common pairing in gas chromatography with mass spectrometry.

History of Mass Spectrometry

J.J. Thomson and his assistant E. Everett built the first mass spectrometer while working on discovering the electron in the early 1900s. The first mass spectrometers primarily examined isotopes of different atoms. These isotopes were important during the mid-1900s due to the Manhattan Project.

In the 1940s mass spectrometers became commercially available, and the various applications began to rapidly expand.

For an excellent history of the mass spectrometer, see this article by Jennifer Griffiths.

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