# 12.2: Interpretation of mass spectra (2023)

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##### Goals

After completing this section you should be able to

1. Suggest possible molecular formulas for a given compoundm/zValue for the molecular ion or a mass spectrum from which this value can be determined.
2. Predict the relative heights of peaks M+·, (M + 1)+·, etc. in the mass spectrum of a compound, given the natural abundance of isotopes of carbon and other elements present in the compound.
3. Interpret the mass spectral fragmentation pattern of a relatively simple known compound (eg, hexane).
4. Use the fragmentation pattern in a given mass spectrum to identify a relatively simple unknown compound (for example, an unknown alkane).
##### study notes

When interpreting fragmentation patterns, it can be helpful to know that the weakest carbon-carbon bonds are the most likely to be broken. You can consult the tablebond dissociation energiesfor problems related to the interpretation of mass spectra.

This page examines how fragmentation patterns are formed when organic molecules are fed into a mass spectrometer and how information can be extracted from the mass spectrum.

## The Origin of Fragmentation Patterns

When the vaporized organic sample enters the ionization chamber of a mass spectrometer, it is bombarded by a stream of electrons. These electrons have a high enough energy to repel an electron from an organic molecule and form a positive ion. This ion is calledMolecular ion - or sometimes the parent ionand is usually provided with the M symbol+von . The dot in this second version represents the fact that there is a single unpaired electron somewhere in the ion. That's half of what was originally an electron pair - the other half is the electron that was removed during the ionization process.

Molecular ions are energetically unstable and some break down into smaller pieces. The simplest case is that a molecular ion splits into two parts - one is another positive ion and the other is an uncharged free radical.  Uncharged free radicals will do thisnoproduce a line in the mass spectrum. Only charged particles are accelerated, deflected and detected by the mass spectrometer. These uncharged particles are simply lost in the machine - eventually they are removed by the vacuum pump.

The ion, X+, runs through the mass spectrometer like any other positive ion - and creates a line on the bar graph. All kinds of fragmentations of the original molecular ion are possible - and that means you get a bunch of lines in the mass spectrum. For example, the mass spectrum of pentane looks like this: ##### annotation

The line pattern in a mass spectrumorganic connectionsays something completely different than the line pattern in the mass spectrum of aElement. For an element, each line represents a different isotope of that element. In the compound, each line represents a different fragment resulting from the decomposition of the molecular ion.

(Video) Mass Spectrometry

In the bar graph showing the mass spectrum of pentane, the line produced by the heaviest ion passing through the machine (at m/z = 72) is due tomolecular pure. The longest line on the bar graph (in this case at m/z = 43) is denoted asbasic dome. Typically this is given as an arbitrary height of 100 and the height of all other elements is measured relative to it. The base peak is the tallest peak because it represents the most frequently formed fragment ion - either because there are several ways to generate it during fragmentation of the parent ion or because it is a particularly stable ion.

## Using Fragmentation Patterns

This section ignores the information you might get from the molecular ion (or molecular ions). This is covered on three other pages accessed from the mass spectrometry menu. There is a link at the bottom of the page.

##### Example 12.2.1: Pentane

Let's look again at the mass spectrum of pentane: What causes the line at m/z = 57?

How many carbon atoms does this ion contain? It can't be 5 because 5 x 12 = 60. What about 4? 4 x 12 = 48. That leaves 9, for a total of 57. What about C?4H9+E?

C4H9+would [ch3CH2CH2CH2]+, and this would be produced by the following fragmentation: The generated methyl radical is simply lost in the machine.

The line at m/z = 43 can be found in the same way. If you play around with the numbers, you'll find that this equals a fraction that produces a 3-carbon ion:

(Video) Mass Spectrometry MS The line at m/z = 29 is typical for an ethyl ion, [CH3CH2]+: The other lines in the mass spectrum are more difficult to explain. For example, lines with m/z values ​​of 1 or 2 less than one of the single lines usually result from the loss of one or more hydrogen atoms during the fragmentation process.

##### Example 12.2.2: Pentan-3-one

This time, the base peak (the highest peak - and therefore the most abundant fragment ion) is at m/z = 57. However, it is not generated by the same ion as the peak with the same m/z value at pentane. If you recall, the peak m/z = 57 in pentane was obtained from [CH3CH2CH2CH2]+. Looking at the structure of pentan-3-one, it is impossible to extract this particular fragment.

Work the molecule, mentally cutting pieces until you find something that makes 57. Eventually, with a little patience, you will [CH3CH2CO]+- what results from this fragmentation: You would get exactly the same products on both sides of the CO group where you split the molecular ion. The m/z = 29 peak is generated by the ethyl ion - which can be newly formed by molecular ion cleavage on either side of the CO group. ## maximum height and stability

The more stable an ion, the more likely it will form. The more ions of a given species formed, the greater the peak height. We'll look at two common examples of this.

### The carbocation (carbonium ion)

To summarize the page's main takeaway on carbocations:

Order of stability of carbocations

primary < secondary < tertiary

Applying this logic to fragmentation patterns means that a cleavage that produces a secondary carbocation is more successful than one that produces a primary carbocation. A cleavage that produces a tertiary carbocation will be even more successful. Let's look at the mass spectrum of 2-methylbutane. 2-Methylbutane is an isomer of pentane - isomers are molecules with the same molecular formula but different spatial arrangements of atoms. First notice the very strong peak at m/z = 43. It is caused by a different ion than the corresponding peak in the pentane mass spectrum. This spike in 2-methylbutane is caused by:  The ion formed is a secondary carbocation - it has two alkyl groups attached to the positively charged carbon. So it's relatively stable. The peak at m/z = 57 is much larger than the corresponding line in pentane. Again, a secondary carbocation is formed - this time by:  Of course you would get the same ion as the left CH3When we drew them, one group split off instead of the last one. In these two spectra, this is probably the most dramatic example of the additional stability of a secondary carbocation.

### Aciliumion, [RCO]+

Ions with a positive charge on the carbon of a carbonyl group, C=O, are also relatively stable. This can be clearly seen in the mass spectra of ketones like pentan-3-one. The base peak at m/z=57 is due to [CH3CH2CO]+Ion. We've already talked about the fragmentation this causes.

##### annotation

The more stable an ion, the more likely it will form. The more of a given ion is formed, the greater the height of the peak.

(Video) MS Lecture 2 spectral features and measures
(Video) A Brief Introduction to Mass Spectrometry

## Using mass spectra to distinguish between compounds

Suppose you need to come up with a way to distinguish between pentan-2-one and pentan-3-one based on their mass spectra.

 pentan-2-one CH3ROOD2CH2CH3 pentan-3-one CH3CH2ROOD2CH3

Each of these is likely to split, creating ions with a positive charge on the CO group. In the case of Pentan-2-one, there are two different ions like this:

• [CH3CO]+
• [ROOD2CH2CH3]+

This would give strong lines at m/z=43 and 71. With pentan-3-one, we would only get one of these ions:

• [CH3CH2CO]+

In that case you would get a strong line at 57. Don't worry about the other lines in the spectrum - lines 43, 57 and 71 provide enough difference between the two. Lines 43 and 71 are missing from the pentane-3-one spectrum and line 57 is missing from the pentane-2-one spectrum.

The two mass spectra look like this:  As you've seen, even the mass spectrum of very similar organic compounds will be very different due to the different fragmentation patterns that can occur. As long as you have a computer database of mass spectra, any unknown spectrum can be analyzed by a computer and easily compared to the database.

(Video) NMR Part 2 (How to Read NMR) Heinemann 12.2

## FAQs

### How do you read mass spectroscopy results? ›

A mass spectrum will usually be presented as a vertical bar graph, in which each bar represents an ion having a specific mass-to-charge ratio (m/z) and the length of the bar indicates the relative abundance of the ion. The most intense ion is assigned an abundance of 100, and it is referred to as the base peak.

What is the rule of 13 in mass spectrometry? ›

In the Rule of Thirteen first, a base formula is generated which consists of only hydrogen and carbon atoms. This base formula is calculated by dividing the molecular mass by 13 (C + H: 12+ 1 =13).

What is the M 2 peak in mass spectrometry? ›

The larger peak, the M peak, corresponds to the compound containing the 35Cl. The smaller peak, the M+2 peak, corresponds to the compound containing 37Cl. molecular ion consists of two peaks (M and M + 2) in a 1:1 ratio, a Br atom is present.

What does mass spectrometry score mean? ›

This number reflects the combined scores of all observed mass spectra that can be matched to amino acid sequences within that protein. A higher score indicates a more confident match. A mass spectrometry experiment never produces “perfect” data.

What is the ideal concentration for mass spectrometry? ›

Signal in mass spectrometry is concentration dependent, and thus depends on the molecular weight (g/mole) of your analyte. However, as a rule of thumb, please keep your concentration around 10-20 μM. This corresponds to 0.01 mg/ml for a molecule of 500 g/mole molecular weight.

What is M +1 in mass spectrometry? ›

What is an M+1 peak? If you had a complete (rather than a simplified) mass spectrum, you will find a small line 1 m/z unit to the right of the main molecular ion peak. This small peak is called the M+1 peak.

What is the rule of 13 in multiplicity? ›

The rule of 13 states that the formula of a compound is a multiple n of 13 (the molar mass of CH ) plus a remainder r .

What is spectra interpretation? ›

The interpretation of infrared spectra involves the correlation of absorption bands in the spectrum of an unknown compound with the known absorption frequencies for types of bonds.

What does mass spectrometry tell you a level chemistry? ›

In A-Level Chemistry, mass spectrometry is often used to reinforce concepts related to atomic structure and the behavior of ions. Students may also use mass spectrometry to study real-world examples of chemical reactions and to perform experiments to identify unknown compounds.

What is M 15 peak in mass spectrum? ›

The M-15 peak of mass spectrometry indicates a certain component of the compound that has an estimated molecular weight of 15 grams/mole. Specifically, an M-15 peak tells us that the compound has a methyl substituent.

### What are the significant peaks in mass spectrometry? ›

The two most important peaks in any mass spectrum are the base peak and the molecular ion peak. The base beak is the largest peak in the spectrum.

What do mass spectrum peaks mean? ›

The mass spectrum will contain peaks that represent fragment ions as well as the molecular ion (see Figure 1.3). Interpretation of a mass spectrum identifies, confirms, or determines the quantity of a specific compound. Figure 1.3. Mass spectrum showing a small molecular ion at m/z 137 and lower mass fragment ions.

How accurate is mass spectrometry? ›

Modern mass spectrometers generally report accurate mass measurements to four decimal places (seven significant figures for masses between 100 and 999 Da) and sometimes more.

What is considered high resolution mass spectrometry? ›

High-resolution mass spectrometry (HRMS) uses mass spectrometers capable of high resolution, as well as high mass accuracy measurements. These instruments can be used to distinguish between compounds with the same nominal mass, determine elemental compositions, and identify unknowns.

What are the 5 stages of mass spectrometry? ›

The four stages of mass spectrometry are – ionization, acceleration, deflection, and detection. The sample is vaporized before being passed into an ionization chamber where it is bombarded by a stream of electrons emitted by an electrically heated metal coil.

What are two things spectroscopy can tell us? ›

The science of spectroscopy is quite sophisticated. From spectral lines astronomers can determine not only the element, but the temperature and density of that element in the star. The spectral line also can tell us about any magnetic field of the star. The width of the line can tell us how fast the material is moving.

What four things does spectroscopy tell us? ›

A stellar spectrum can reveal many properties of stars, such as their chemical composition, temperature, density, mass, distance and luminosity. Spectroscopy can show the velocity of motion towards or away from the observer by measuring the Doppler shift.

What do you analyze with spectroscopy? ›

Spectroscopy is the field of study that measures and interprets the electromagnetic spectra that result from the interaction between electromagnetic radiation and matter as a function of the wavelength or frequency of the radiation.

What is the range of mass spectrometry scan? ›

Typically the mass spectrometer is set to scan a specific mass range. This mass scan can be wide as in the full scan analysis or can be very narrow as in selected ion monitoring. A single mass scan can take anywhere from 10 ms to 1 s depending on the type of scan.

What determines intensity in mass spectrometry? ›

Signal intensity may be dependent on many factors, especially the nature of the molecules being analyzed and how they ionize. The efficiency of ionization varies from molecule to molecule and from ion source to ion source.

### What is the range of spectrometry? ›

UV-visible spectrophotometer: uses light over the ultraviolet range (185 - 400 nm) and visible range (400 - 700 nm) of electromagnetic radiation spectrum. IR spectrophotometer: uses light over the infrared range (700 - 15000 nm) of electromagnetic radiation spectrum.

What is mass spectrometry formula? ›

m=q B2x2 8V where B is the magnetic field intensity, x is the distance to each peak, and V is the ion accelerating voltage.

What is the basic of mass spectrometry? ›

“The basic principle of mass spectrometry (MS) is to generate ions from either inorganic or organic compounds by any suitable method, to separate these ions by their mass-to-charge ratio (m/z) and to detect them qualitatively and quantitatively by their respective m/z and abundance.

What does multiplicity 1 mean? ›

This is called multiplicity. It means that x=3 is a zero of multiplicity 2, and x=1 is a zero of multiplicity 1. Multiplicity is a fascinating concept, and it is directly related to graphical behavior of the polynomial around the zero.

What is multiplicity 3? ›

The graph passes through the axis at the intercept, but flattens out a bit first. This factor is cubic (degree 3), so the behavior near the intercept is like that of a cubic—with the same S-shape near the intercept as the toolkit function f(x)=x3. We call this a triple zero, or a zero with multiplicity 3.

What are 3 types of spectra and how do they differ? ›

The first spectrum is a continuous collection of wavelengths from the radiation of a heated body. The second is a brightline emission spectrum illustrating the wavelengths a particular gas emits. The third is a darkline absorption spectrum showing the wavelengths that would be aborbed if the gas above were cooled.

What are the three types of spectra? ›

Types of Spectra: Continuous, Emission, and Absorption.

What is spectral analysis in simple terms? ›

Spectral analysis involves the calculation of waves or oscillations in a set of sequenced data. These data may be observed as a function of one or more independent variables such as the three Cartesian spatial coordinates or time.

What is 91 peak in mass spectrum? ›

Answer and Explanation: The prominent peak in the mass spectrum of ethylbenzene gives an m/z value of 91.

What is the most intense peak in mass spectrum? ›

The most intensive peak in a spectrum is called the "Base Peak", whose intensity is taken as 100 percent.

### How do you report mass spec data? ›

Reporting Data

You should report the Base Peak (BP), Molecular Ion (MI) [or quasimolecular ion(s) (M+X)+] and any other significant peaks. For EI spectra the eight major peaks are considered representative. Remember higher mass ions of low intensity can be more important that high intensity low mass ions.

Can mass spectrometry identify concentration? ›

5 Mass spectrometry detection. MS can provide both qualitative and quantitative information about specific analytes (e.g., proteins, peptides, DNA, and small molecules) and identify their elemental compositions, chemical structures, and concentrations.

What can mass spectrometry tell you about a protein? ›

Mass spectrometry (MS) analysis of proteins measures the mass-to-charge ratio of ions to identify and quantify molecules in simple and complex mixtures. MS has become invaluable across a broad range of fields and applications, including proteomics.

How are molecules identified through mass spectrometry? ›

In a mass spectrometer, molecules are converted to charged fragments called ions, which are then separated according to their masses. The chart that records the masses of the fragments together with a measure of their relative abundance is known as a mass spectrum.

What does peak at 29 mean mass spec? ›

The m/z = 29 peak is produced by the ethyl ion - which once again could be formed by splitting the molecular ion either side of the CO group. The more stable an ion is, the more likely it is to form. The more of a particular sort of ion that's formed, the higher its peak height will be.

What causes an M 2 peak? ›

The presence of a chlorine atom in a compound causes two peaks in the molecular ion region - the M+ peak and the M+2 peak depending on whether the particular molecular ion contains a chlorine-35 or chlorine-37 isotope.

What is an M 18 peak? ›

The M-18 peak is due to the formation of the fragment that is 18 mass units less than the molecular weight of the compound. This fragment is formed upon the loss of a water molecule which has a molecular weight of 18.

What does a base peak of 43 mean? ›

The tallest line in the stick diagram (in this case at m/z = 43) is called the base peak. This is usually given an arbitrary height of 100, and the height of everything else is measured relative to this.

How is mass measured in mass spectrometry? ›

A mass spectrometer determines the mass of a molecule by measuring the mass-to-charge ratio (m/z) of its ion. Ions are generated by inducing either the loss or gain of a charge from a neutral species.

What do the peaks on the mass spectrum represent? ›

The mass spectrum will contain peaks that represent fragment ions as well as the molecular ion (see Figure 1.3). Interpretation of a mass spectrum identifies, confirms, or determines the quantity of a specific compound.

### What does M 1 peak mean on mass spec? ›

What is an M+1 peak? If you had a complete (rather than a simplified) mass spectrum, you will find a small line 1 m/z unit to the right of the main molecular ion peak. This small peak is called the M+1 peak.

What is accurate mass mass spec? ›

Accurate Mass measurements are routine experiments performed by modern mass spectrometers. The accuracy of a measurement refers to the degree of conformity of a measured quantity to its actual true value. Well, the more accurate a mass spectrometer is, the more expensive it is.

What is the output of mass spectrometry? ›

The output of a mass spectrometry instrument is a mass spectrum. Because ions are sorted by mass, the spectra plot the relative abundance of each m/z value. Thus, these m/z values depends on the fragmentation of the molecule.

What is high resolution mass spec data? ›

High-resolution mass mass spectrometry is an ideal technique for identifying and determining the elemental and isotopic contents of a sample with high levels of precision. The technique generally cannot determine the difference between geometric isomers of organic compounds with the same exact masses.

How is mass measured accurately? ›

Balances and Scales

Different types of balances include digital scientific balances and beam balances, such as a triple beam balance. The standard unit of measure for mass comes from the metric system and is either grams or kilograms. At home, you typically use a modern digital or spring scale to determine mass.

What are the 4 stages of mass spectrometry? ›

Mass spectrometry is used to accurately measure the mass of the various molecules within a sample. The four stages of mass spectrometry are – ionization, acceleration, deflection, and detection.

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