Isotope Peaks of Ionic Fragments in Mass Spectrometry

Theory

Mass Spectrometry is based on the formation of a beam of ionic fragments by bombardment of test molecules, usually with energetic electrons. The generated ions are then separated by application of electrostatic or magnetic fields or by a combination of both. The separation is based on the mass-to-charge ratio (m/z) of each ionic fragment. Because most ions in mass spectrometry are singly charged (z=1), the term mass-to-charge ratio is often shortened to the more convenient term mass.

The capability of a mass spectrometer to differentiate between masses is usually expressed in terms of its resolution, which is defined as R = m/D_m, where D_m is the mass difference between two adjacent peaks that are just resolved and m is the nominal mass of the first peak. For example, in order to discriminate the ionic species C₂H₄⁺ and CH₂N⁺, which have the same nominal mass (m=28), but different exact masses (28.0313 and 28.0187, respectively) an instrument with a resolution of at least R = 28/(28.0313-28.0187) ≈ 2200 is required. Less expensive low resolution mass spectrometers (R ≈ 500-1000) can readily differentiate simple ions of different nominal masses.

Isotope peaks

Ιonic fragments of the same chemical formula are usually represented by multiple adjacent peaks attributable to ions of different isotopic compositions. The number of isotope peaks and the relative intensity of each peak depend on the chemical formula of the ionic fragment and the natural isotopic composition of its constituent elements. For example, the ion CH₃⁺ consists of fragments with nominal mass ranging from 15 (for the "lighter" fragment ¹²C¹H₃⁺) up to 19 (for the "heavier" fragment ¹³C²H₃⁺). The natural isotopic abundance percentage for C is 98.90% ¹²C - 1.10% ¹³C, and for H is 99.985% ¹H - 0.015% ²H, therefore the more intense peak M=15 is attributed to the more abundant ¹²C¹H₃⁺. The next in intensity peak (much smaller than peak M) is M+1=16, which is attributed to both ¹³C¹H₃⁺ and ¹²C¹H₂²H⁺, whereas the last peak M+4=19, attributed to ¹³C²H₃⁺, has practically zero intensity because of the extremely low probability of occurrence of all heavy isotopes in the same ionic fragment.

How the relative intensities of mass peaks for the ionic fragment CH₂Cl⁺ can be exactly (without approximations) calculated, taking into consideration the isotopic abundance for C, H and Cl (75.77% ³⁵Cl - 24.23% ³⁵Cl) is shown below:

The intensity of each peak (from M to M+5) is proportional to the probability of occurence of each mass. This probability is the sum of probabilities of all combinations resulting in the same nominal mass. The most intense peak is called base peak and the relative intensities of the other peaks are commonly reported as % of base peak (blue numbers). Usually the base peak corresponds to the "lighter" ionic fragment, unless the fragment contains atoms (such as B, Fe, Se, Hg), whose more abundant isotopes are of higher mass.

The relative intensity of isotope peaks (and their overall pattern as well) provide a useful means for the identification of ionic fragments of the same nominal mass that normally cannot be further resolved due to relatively low resolution of the available mass spectrometer. For example, the relative intensities of the M+1 peak of ionic fragments N₂⁺, CO⁺, CH₂N⁺, and C₂H₄⁺ (all of them having the same nominal mass, M=28) are: 0.74%, 1.15%, 1.51% and 2.28%, respectively. Therefore, a peak at M=28 with an adjacent peak at M+1=29 with intensities ratio 100:1.51 can be safely attributed to CH₂N⁺.

Applet

With this easy to use applet you can obtain the relative intensities of isotope peaks of ionic fragments and also observe the expected pattern of peaks on the mass spectrum. Up to 18 different elements can be used, whereas the fragments can contain up to 15 atoms.

In order to obtain these data for a particular fragment, you only have to insert the empirical formula of the fragment by clicking on the corresponding elements as many times as they occur in the fragment and then click on the button "CALCULATE". Use the "CLEAR" button to delete the empirical formula before inserting a new one.

The numerical results can be either expressed in terms of % of base peak (the more common expression mode), or in terms of % abundance (or % probability of occurrence). Click on the corresponding radiobutton to select the desired expression mode.

The calculations are exact and may take some time, particularly for fragments containing atoms of elements consisting of many isotopes such as Se, Hg and Zn. The natural isotopic abundance of an element can readily be obtained by clicking a fragment consisting of a single atom of the element in question.

Natural isotopic abundance data were obtained from: J. Emsley: “The Elements”, 3rd ed., Oxford University Press, 1998.