Mass spectra - fragmentation pattern (2023)


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

The formation of molecular ions

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 pure- or sometimes itolder ion.

Annotation:If you're not sure how a mass spectrum is generated, it might be worth taking a quick look at the page describing a mass spectrometer works.

The molecular ion is usually given the symbolM+vonMass spectra - fragmentation pattern (1)- 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.

Mass spectra - fragmentation pattern (2)Mass spectra - fragmentation pattern (3)

Annotation:A free radical is an atom or group of atoms that contains a single unpaired electron.

More complicated fractions are beyond the scope of A Level programs.

Uncharged free radicals do not produce 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:

Mass spectra - fragmentation pattern (4)

Annotation:All mass spectra on this page are compiled with data from the Spectral Data Base System for Organic Compounds (SDBS) from the National Institute of Materials and Chemical Research of Japan.

They are simplified by omitting all minor lines with peak heights 2% or less of the base peak (the highest peak).

It is important to realize that the line pattern in the mass spectrum of an organic compound says something very different from the line pattern in the mass spectrum of an element. For an element, each line represents a differentIsotopethis part. In a connection, each line represents anotherFragmentformed when the molecular ion decays.

Annotation:If you are interestedMass spectra of elements, you can follow this link.

Molecular ion peak and base peak

In the bar graph showing the mass spectrum of pentane, the line generated by the heaviest ion passing through the machine (at m/z = 72) is due to the molecular ion.

Annotation:You have to be a little careful with this because in some cases the molecular ion is so unstable that every ion splits and none make it through the machine to be recorded in the mass spectrum. It is very unlikely that you will encounter this case in high school.

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.

Find out which ion produces which line

This is usually the easiest question you can ask.

The Mass Spectrum of Pentane

Let's look again at the mass spectrum of pentane:

Mass spectra - fragmentation pattern (5)

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:

Mass spectra - fragmentation pattern (6)Mass spectra - fragmentation pattern (7)

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:

Mass spectra - fragmentation pattern (8)Mass spectra - fragmentation pattern (9)

The line at m/z = 29 is typical for an ethyl ion, [CH3CH2]+:

Mass spectra - fragmentation pattern (10)Mass spectra - fragmentation pattern (11)

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. It is very unlikely that you will have to explain only the most obvious cases on an A-level exam.

The mass spectrum of Pentan-3-one

Mass spectra - fragmentation pattern (12)

This time the base peak (the highest peak - and therefore the most abundant fragment ion) is at m/z = 57. However, this is not generated by the same ion as the same m/z value peak 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:

Mass spectra - fragmentation pattern (13)Mass spectra - fragmentation pattern (14)

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.

Mass spectra - fragmentation pattern (15)Mass spectra - fragmentation pattern (16)

Peak heights and ion 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.

Examples of carbocations (carbon ions)

Important!If you don't know what aCarbokação (von Carboniumion)is, or because the different types vary in stability, it isessentialthat you follow this link before proceeding.

Use your browser's BACK button to quickly return to this page.

To summarize the page's main takeaway on carbocations:

Order of stability of carbocations

primary < secondary < tertiary

Annotation:The "<" symbol means "is less than". This means that primary ions are less stable than secondary ions, which in turn are less stable than tertiary ions.

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.

Mass spectra - fragmentation pattern (17)

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:

Mass spectra - fragmentation pattern (18)Mass spectra - fragmentation pattern (19)

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:

Mass spectra - fragmentation pattern (20)Mass spectra - fragmentation pattern (21)

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.

Examples with acyl ions, [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.

Mass spectra - fragmentation pattern (22)

The base peak at m/z=57 is due to [CH3CH2CO]+Ion. We've already talked about the fragmentation this causes.

Annotation:There are many other examples of positive ions that are particularly stable and are therefore produced in large numbers in a mass spectrometer. Without making this article even longer than it already is, it is impossible to cover every possible case.

Review past exams to see if you need to learn more about your options. If you don't have documents, follow the link onresumespage to find out how to get them.

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-oneMass spectra - fragmentation pattern (23)CH3ROOD2CH2CH3
pentan-3-oneMass spectra - fragmentation pattern (24)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 types of ions:

  • [CH3CH2CO]+

In that case, you get a strong line at 57.

Don't worry about the other lines in the spectrum - lines 43, 57 and 71 provide enough of a 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.

Annotation:Do not confuse the line at m/z = 58 in the pentane-2-ene spectrum. This is due to a complicated reorganization that was not foreseeable at the Abitur level.

The two spectra look like this:

Mass spectra - fragmentation pattern (25)

Mass spectra - fragmentation pattern (26)

Computer comparison of mass spectra

As you've seen, even the mass spectrum of very similar organic compounds will be very different due to the different fragmentations 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.

Questions to test your understanding

If these are the first questions you asked, read themintroductory pagebefore you begin You must use your browser's BACK BUTTON to come back here later.

Questions about fragmentation patterns


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© Jim Clark 2000 (reviewed February 2014)


What is fragmentation pattern in mass spectrometry? ›

In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules mass spectrum. These reactions are well documented over the decades and fragmentation pattern is useful to determine the molar weight and structural information of the unknown molecule.

How do you predict fragmentation patterns? ›

A molecule's structure can give you an idea of what peaks will be seen in the mass spectrum. By simply looking for the pieces that are most likely break to produce stable cations, you can easily identify the molecular fragmentation patterns that will eventually be observed in the spectrum.

How will fragmentation affect the mass spectrum? ›

Fragmentation separates unstable molecular ions from the subject by passing molecules through the mass spectrum. It's a chemical dissociation in which the electron removal from the molecule results in ionization.

What causes fragmentation in mass spectrometry? ›

The Origin of Fragmentation Patterns

The molecular ions are energetically unstable, and some of them will break up into smaller pieces. The simplest case is that a molecular ion breaks into two parts - one of which is another positive ion, and the other is an uncharged free radical.

What are the 4 types of fragmentation? ›

  • 2.1 Internal fragmentation.
  • 2.2 External fragmentation.
  • 2.3 Data fragmentation.
  • 2.4 Comparison.

How is fragmentation measured? ›

The two basic indices used to quantify fragmentation are number of patches and patch area, usually measured as mean patch area. However, they provide an incomplete picture because the fragmentation concept also encompasses the relative sizes of the pieces that result.

What does fragmentation result in? ›

Fragmentation limits wildlife mobility. Individuals struggle to move between habitat patches, which can lead to inbreeding and a loss of genetic diversity. This reduces the long-term health of a population, making it more vulnerable to disease and at greater risk of extinction.

Does fragmentation increase species richness? ›

In general, we see that response to fragmentation is not necessarily monotone: species richness may increase at small and intermediate levels of fragmentation, but decrease at high levels of fragmentation.

What does fragmentation reduce? ›

3, A and B). As predicted by theory (6, 30, 31), fragmentation strongly reduced species richness of plants and animals across experiments (Fig. 3, A and B), often changing the composition of entire communities (Fig.

What does high fragmentation mean? ›

Fragmentation happens when there is no clear leader within an industry. This means while many companies may operate in a specific industry, none of them have enough market share to influence prices, production, investment, and competition. Profitability isn't a problem when industries are fragmented.

What factors affect fragmentation? ›

  • a) Energy of the molecular ion and the fragments formed from it.
  • b) Stability of the bonds in the ions.
  • c) For rearrangements: steric factors.
  • d) Stability of the formed ions or neutral particles.
  • Stevenson's Rule:
  • Upon dissociation of AB+.
  • → A+ + B.

What is a fragmentation pattern? ›

In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a unique pattern in the mass spectrum.

How do you solve data fragmentation? ›

How to solve data fragmentation
  1. Organize your data infrastructure. Companies might have multiple programs and systems collecting, storing and analyzing their data throughout different departments. ...
  2. Delete duplicates. ...
  3. Refine cloud usage.
Jun 24, 2022

What is fragmentation and interpretation of spectra? ›

2.6 Fragmentation

The goal of interpreting mass spectra is identifying the structure of the molecular ion by examining pieces (fragments) of the original molecule. The frequency and size of the fragments is dependent on the structure and bond energy of the sample molecule.

What is an example of a fragmentation reaction? ›

The most popular example is the interconversion of the radical cations of toluene and cycloheptatriene, which interchanges C atoms within the C skeleton and which gives rise to stable tropylium ions (Scheme 13) after H loss.

What is the problem of fragmentation and how can it be solved? ›

The problem of internal fragmentation may arise due to the fixed sizes of the memory blocks. It may be solved by assigning space to the process via dynamic partitioning. Dynamic partitioning allocates only the amount of space requested by the process. As a result, there is no internal fragmentation.

What are the three 3 fragmentation strategies? ›

In essence, there are three fundamental fragmentation strategies: Horizontal Fragmentation (HF), Vertical Fragmentation (VF) and Mixed Fragmentation (MF).

What is the problem of fragmentation? ›

Fragmentation refers to an undesirable problem that occurs in operating systems where processes are unloaded and loaded from memory and free space is fragmented. The process cannot be allocated a memory block due to its small size. Therefore, memory blocks always remain unused.

How much fragmentation is acceptable? ›

As a general rule, any time your disk is more than 10 percent fragmented, you should defrag it. In Windows 10, Windows 8, and Windows 7, you can schedule defragmentation to happen as often as necessary.

How much index fragmentation is acceptable? ›

Ignore: Fragmentation levels of 10 percent or less should not pose a performance problem, so you don't need to do anything.

What is 50% rule in fragmentation? ›

Depending on the total amount of memory storage and the average process size, external fragmentation may be a minor or a major problem. blocks will be lost to fragmentation. That is, one-third of memory may be unusable! This property is known as the 50-percent rule.

Why is fragmentation important? ›

The process of fragmentation is very vital in biology for asexual reproduction. As described earlier, this is the form of reproduction in which small organs or parts of the body of the parent individual get separated and finally grows into a completely mature organism.

What is the purpose of fragmentation? ›

Fragmentation enables you to define groups of rows or index keys within a table according to some algorithm or scheme . You can store each group or fragment (also referred to as a partition ) in a separate dbspace associated with a specific physical disk.

How does fragmentation work? ›

1. Fragmentation is a type of asexual reproduction in which an organism simply breaks into individual pieces at maturity. 2. These individual small pieces then grow to form a new organism e.g., Spirogyra.

Which is most likely an effect of fragmentation on an ecosystem? ›

Fragmentation can create detrimental edge effects along the boundaries of habitat patches, precipitate population decline, restrict animal movement and gene flow, and sever landscape connectivity (5).

What is the cause of fragmentation? ›

Fragmentation can be caused by natural processes such as fires, floods, and volcanic activity, but is more commonly caused by human impacts. It often starts with what are seen as small and harmless impacts. As human activity increases, however, the influence of fragmentation becomes greater.

How does fragmentation affect populations? ›

Anthropogenic habitat fragmentation leads to small and isolated remnant plant and animal populations. The combination of increased random genetic drift, inbreeding, and reduced gene flow may substantially reduce genetic variation of remnant populations.

What is the disadvantage of fragmentation? ›

Disadvantages Fragmentation

Asexual reproduction could limit the genetic diversity of their descendants because only one parent can pass on their traits and characteristics. This results in the organism's population being exactly the same.

Is 0% fragmentation good? ›

If everything is running smoothly, your HDD should read OK (0% fragmented) under Current Status. For those with an SSD, the current status will just say "OK" with a note about when the TRIM command was last run.

Is 20 fragmentation bad? ›

15% or less fragmentation – excellent sperm DNA integrity. 15-to 25% DFI – good to fair. 25 – 50% DFI – fair to poor.

Is a highly fragmented market good or bad? ›

Fragmentation might sound like a bad thing, but these markets come with some unique advantages. Chiefly, the lack of a clear leader means that new entrants can find a quick path to profitability. This can be good news for investors and traders too, as smaller, cheaper stocks have a better chance of succeeding.

What are the four consequences of fragmentation? ›

At least four effects form the basis of most quantitative measures of habitat fragmentation (Fahrig, 2003): (a) reduction in habitat amount, (b) increase in the number of fragments, (c) decrease in fragment size and (d) increase in fragment isolation.

What is fragmentation in analysis? ›

Fragment analysis is a genetic analysis method comprising a series of techniques in which DNA fragments are fluorescently labeled, separated by capillary electrophoresis (CE), and sized by comparison to an internal standard.

What are the different levels of fragmentation? ›

The degree of fragmentation is most often expressed as the percentage of the total cytoplasmic volume. The relative degree of fragmentation is defined as mild (<10%, Figs 223–225), moderate (10–25%, Figs 226–235) and severe (>25%, Figs 236–242).

What is a simple example of fragmentation? ›

When an organism breaks down into several fragments is known as fragmentation. Each fragment develops into an individual and is a clone of the original organism. Plants, fungi, sea stars, and annelid worms all display fragmentation.

How do you read a mass spectrometry graph? ›

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 fragmentation pattern electron impact? ›

Fragmentation Patterns. Electron Impact sources introduce a vapor into a beam of electrons. The electron transfers energy to the vaporized molecule; this energy can often result in fragmentation of the molecule. As a result, less (and sometimes none) of the molecular ion is seen on the mass spectrum.

What is the difference between fragmentation and splitting? ›

Fragmentation is also referred to as splitting in various literature and are the synonyms of each other. The process of fragmentation is asexual, which means that only a single parent is involved. Therefore, the offspring most likely will carry the same genetic characteristics.

What is fragmentation in mass media? ›

Audience fragmentation describes the extent to which audiences are distributed across media offerings. Traditional outlets, such as broadcast networks, have long feared that technological and regulatory changes would increase competition and erode their audiences.

What are the two 2 types of fragmentation? ›

Fragmentation is of three types:
  • External Fragmentation.
  • Internal Fragmentation.
  • Data Fragmentation (which exists beside or a combination)

How much fragmentation is bad? ›

As a general rule, any time your disk is more than 10 percent fragmented, you should defrag it. In Windows 10, Windows 8, and Windows 7, you can schedule defragmentation to happen as often as necessary. Check inside the defrag desktop program to see how and when it's scheduled to run and then adjust accordingly.

Why is fragmentation a concern? ›

Greater fragmentation increases the distance between habitat patches, making it harder for individuals to move from one patch to another. Potential movement routes can also be fragmented – e.g. by a road that cuts through a strip of woodland.

What is a simple explanation of fragmentation? ›

Fragmentation most generally means the process of fragmenting—breaking into pieces or being divided into parts. It can also refer to the state or result of being broken up or having been divided.

What is 1 example of fragmentation? ›

Even in nonvascular plants, the process of fragmentation is a common phenomenon like mosses and liverworts. In the case of moss leaves or stems, they are carried by the wind, animals or even water. Once the moss fragment reaches an environment that is suitable, it would root itself to form a new plant.

Is fragmentation good or bad? ›

Habitat fragmentation is a major problem across the Earth. A decrease in the overall area of wild places is bad enough. But combined with fragmentation, it can undermine the integrity of whole ecosystems. Roads, urbanisation and agriculture are some of the main activities that break up natural areas.

What causes data fragmentation? ›

Finally, data fragmentation can occur when data is spread across both on-prem and public and private cloud locations, which causes the creation of even more copies of the same data.

What divides by fragmentation? ›

Fragmentation as a method of reproduction is seen in organisms such as filamentous cyanobacteria, molds, lichens, sponges, acoel flatworms, some annelid worms and sea stars.


1. Part 5.Alkanes' Mass Spectrum (Fragmentation pattern) for CSIR/NET GATE
2. Part 17: Mass Spectrometry - Fragmentation Pattern | Homolytic & Heterolytic Cleavage
(Dr. Puspendra Classes)
3. Solving Mass Spectroscopy Problems - Analyzing Fragmentation Patterns
4. Mass Spectra : Principle, Instrumentation, Fragmentation & Mclafferty rearrangement
(G Sai Rajesh)
5. Fragmentation McLafferty rearrangement alpha fission Mass spectrometry(Part-3) Organic Spectroscopy
(J Chemistry)
6. 11.3/S3.2.8 Analyse fragmentation patterns in mass spectra to find structure [SL IB Chemistry]
(Richard Thornley)


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