Mass Spectrometry

Mass Spectrometry Definition

Mass spectrometry is a laboratory technique used to analyze the molecular composition of a sample. Mass spectrometry starts by vaporizing and ionizing the sample, most often using heat and a beam of electrons. The sample is then accelerated through a magnetic field, where its path is curved. Small particles bend more along the path. Once they reach the detector, they can be analyzed according to their mass to charge ratio. The computer attached to the detector will print a graph, showing which species were most abundant, along with their mass to charge (m/z) ratio.

This method is used in many different fields to analyze unknown substances. The data received can be used to determine the formula and structure of many different substances. High resolution mass spectrometry, which contains the most advanced ionization and detection equipment, can accurately determine the formula and structure of almost any compound. Mass spectrometry is used not only in sciences such as chemistry and biology to identify substances, but also in criminal forensics, to identify almost any substance encountered.

How Mass Spectrometry Works

Ionization of the Sample

The first process of mass spectrometry is ionization. Molecules tend to be hard to work with, unless they are charged. Charged molecules can easily be manipulated using electric and magnetic fields. To create ions, the substance must first be vaporized. A mass spectrometer will contain a chamber in which the sample is placed. This chamber will be heated, until a vapor is created of the sample.

This vapor will move through an electric field, through which electrons are passing. These electrons will knock electrons off of the molecules being analyzed. Alternatively, the sample could be chemically induced to create ions. Sometimes, the removal and redistribution of electrons causes different species of the molecule to form, which are fractions of the original molecule. These will be seen on the final output from mass spectrometry, and give vital clues to the structure of a molecule. This ionic vapor is now ready to be accelerated and analyzed.

Sorting the Ions

The ions are accelerated between two negative plates. This means that only positive cations can be detected. The negative species are removed via a vacuum pump. The positive ions travel down a curved tube. To bend the path of the ions, a large electromagnet encircles the tube. The voltage to this magnet can be adjusted, which will increase or decrease its overall strength. At the end of the tube is a small slit, through which molecules can exit and be detected by a sensitive screen.

Because the magnet can be adjusted, the computer controlling the unit will cycle through different power levels. The slit is small, and the power must be exactly right to get a particle to curve just right and exit the slit. Larger molecules will tend to curve less than small molecules. The computer graphs the output at each level, which corresponds the mass to charge ratio of the molecules at each level. In other words, only molecules of a certain size and charge can get through the slit at any given level of power. As this is adjusted, the computer can sense the total amount of molecules which make it through the slit. This allows the operator to effectively sort and analyze the entirety of any sample by processing it through mass spectroscopy. However, because the molecules must be ionized, there are also fractional species produced. This can aid in identifying the structure of the molecule, but it can also make identification vastly more complicated.

Detecting the Ions

The sensitive screen on the other side of the silt is bombarded with molecules. The computer analyzing this screen tracks their relative abundance at each mass to charge ratio. It will display the results as a graph, similar to the one below of carbon dioxide.

Carbon Dioxide Mass Spectrum

Note that the most abundant species is the carbon dioxide cation, or molecular ion. This is a radical ion created by the loss of 1 electron from the original carbon dioxide. The smaller peaks represent the other fragments of the molecule which are created during the analysis. You can see the peaks for carbon monoxide, oxygen, and carbon cations. These correspond to their molecular weights, and the strength of the bonds in the original molecule determine how easily fragments are created and how abundant they will be.

How to Read Mass Spectrometry

Mass spectrometry is analyzed by studying the graph created by the mass spectrometer. The machine will produce a graph with several bars. The tallest bar will reach the top of the graph. This was the most abundant species, and everything else is compared in abundance to this main species. The mass to charge ratio of this species can roughly tell you the molecular weight of the original molecule.

The peaks can tell you a lot about the molecule. The base peak is the most abundant and also represents the most stable species formed after the sample is ionized. Take for instance, the following analysis of the mass spectrometry of hexanal. You can see the chemical structure of this molecule imposed on the graph of mass to charge ratio versus abundance below.


Notice first the base peak, at 44 m/z. This means that a species is formed when this molecule ionizes which has the mass of about 44 atomic units. The highest bar created is at 100 units. This represents the most complete version of the molecule, telling us the weight of the entire molecule. If we add all the molecules in hexanal (C6H12O), we will find it does indeed have an atomic mass of 100.

The peak at 44 represents a fraction of the molecule created by the oxygen, two carbons, and two of the hydrogens. The peak at 57 represents a larger portion of the carbons attached. The strong electronegativity of the oxygen double bonded to the carbon makes it a highly stable species, making it the most relatively abundant ion. All of these clues in the graph can lead us to the conclusion that our sample contained hexanal.


1. Why do only positive ions make it to the detector?
A. The accelerator plates are negative
B. The magnet only affects positive ions
C. The ionization process only creates positive ions

Answer to Question #1
A is correct. The negative plates used to accelerate positive ions repulse negative ions. These are usually removed via a small vacuum tube. These help repel electrons and small negative ions created. Usually the larger fractions are positively charged.

2. What is the purpose of the magnet in mass spectrometry?
A. The magnet affects the charge, bending molecule’s path according to weight
B. The magnet pulls metal fragments, purifying the sample
C. Only magnetic materials will be affected, allowing categorization

Answer to Question #2
A is correct. All charged particles will be affected by the magnet, causing them to change course. The heavier a molecule is, the less it will be affected. Thus, heavier molecules can be distinguished from smaller ones based upon their mass to charge ratio.

3. Why is mass spectrometry useful in criminal forensics?
A. Forensic scientists don’t use mass spectrometry
B. It can be used to identify almost any unknown substance
C. It can measure if bullets came from the same gun

Answer to Question #3
B is correct. When forensic scientists find an unknown substance, the fastest and most efficient way to classify it is to run it through mass spectrometry. This will produce a graph which should be able to identify the substance, or at least parts of the substance. High resolution mass spectrometry uses computer algorithms and other advanced technology to further help identify substances.


  • Bruice, P. Y. (2011). Organic Chemistry (6th ed.). Boston: Prentice Hall.
  • Moore, J. T. (2010). Chemistry Essentials for Dummies. Indianapolis: Wiley Publishing, Inc.
  • Nelson, D. L., & Cox, M. M. (2008). Principles of Biochemistry. New York: W.H. Freeman and Company.
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