Using Mass Spectrometry to Find Chemical Formulas

Instructor: Justin Wiens

Justin teaches college chemistry and has Bachelor and Doctorate degrees in chemistry.

In this lesson, we discuss how to determine the chemical formula for a molecule from its mass spectrum when we know the precise mass of its molecular ion.

Fingerprints of molecules

Mass spectrometry is a powerful tool to determine the chemical formulas of compounds, even if we have no clue what type of atoms are in the compound. The unique 'fingerprint' of a molecule is given by its unique mass spectrum, which can be compared to a database of known molecules. Even if the mass spectrum for a molecule is not in a database, the fragments formed when it is ionized in the mass spectrometer often provide good hints about the type of molecule.

How about the case when we know that several compounds have nearly the same molecular mass? For example, CO and N2 both have masses near 28 amu, so how can we distinguish them if they do not break into fragments? With high-resolution mass spectrometry, this is often possible with just a little math and chemical insight!

Review of Mass Spectrometry

Mass spectrometry measures the mass-to-charge ratio, m/z, of ions as they fly through a mass spectrometer and are deflected by magnetic and/or electric fields. Ions with larger masses and/or smaller charges have high m/z values when we look at the mass spectrum for a sample. Typically, ions have a unit charge of +1 or -1 in a mass spectrum.

For ionized CO or N2, the peaks at m/z = 28 thus directly correspond to CO+ and N2 +. These peaks are therefore called molecular ions. In cases where a molecule fragments in the mass spectrometer, it is also possible to observe fragment ions, which are not the focus of this lesson. Here, we only discuss molecular ions with unit charges.

In a high-resolution mass spectrometer, we can often measure to hundredths or even thousandths of an amu, depending on the instrument. Suppose we observe a peak at 28.016 amu in the mass spectrum. Is the peak due to CO, or perhaps N2?


Unknown Mass Spectrum


Calculation of Precise Molecular Mass

Since CO and N2 molecules are composed of atoms, we can calculate their precise molecular masses from the precise atomic masses of the elements that compose these molecules. These values are conveniently found on the Periodic Table:


Periodic Table


Let's look at CO first. It is composed of one C atom, with an average atomic mass of 12.011 amu, and one O atom, with an average atomic mass of 15.999 amu. The values from the Periodic Table are averages primarily because not all C atoms have 6 neutrons, some have 7 or 8 neutrons. Similarly, not all O atoms have 8 neutrons, some have fewer or greater than 8. For this reason, the average atomic masses are not exactly 12 amu for C, for example, unless we are talking about a specific isotope of an element. But, if we scoop up a sample of C atoms from the ground, we would find that they weigh 12.01 amu on average. In order to determine the mass of an average CO molecule, we simply add up the masses of our average C and O atoms: 12.0101 amu + 15.999 amu = 28.010 amu. We would expect to see a peak at m/z = 28.010 amu in the mass spectrum if our sample truly contains CO.

Now for N2. It simply has two N atoms, each with an average mass of 14.007 amu. The total mass of N2 is thus 2 x 14.007 = 28.014 amu.

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