Advanced pre-university organic chemistry: 15.1.2 mass spectrometry - application to organic compounds

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15.1.2 Mass spectrometry of organic molecules - fragmentation patterns and equations of ion formation

[Author © Dr Phil Brown PhD: Doc Brown's advanced level organic chemistry exam revision notes on mass spectrometry suitable for students of UK based A level and IB chemistry courses & US K12 grade 11, grade 12 and AP honors chemistry courses [updated Mar 6th 2026 *]

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15.1.0 An introduction to mass spectrometry and its applications

(written before the extra sections and links below, so, some overlap!)

15.1.1 Index of mass spectra of organic compounds

15.1.2 Mass spectrometry applied to organic molecules - interpreting spectra - fragmentation patterns  (THIS PAGE)

15.1.3 More on the uses and applications of mass spectrometry, mainly in organic chemistry

15.1.4 Database of accurate m/z values and possible identity of ions formed in mass spectrometry

Sub-index for this page on fragmentation patterns

Before writing this spectrometry section, I had already written an extensive introduction to mass spectrometry, therefore I refer to this page via links, but adding some extra details on this page if needed.

(a) Sections already written on mass spectrometry

Extra notes for advanced level organic chemistry students

(b) More on fragmentation patterns and mass spectra

(c) More on the nature of fragments formed in a mass spectrometer

(d) Equations describing the possible formation of positive ion fragments

(a) Sections I'd already written on mass spectrometry before a big expansion

(in this case an introduction on a separate page with 11 sub-sections)

Each section opens up in a new window for convenience (close after use)

1. INTRODUCTION to mass spectrometry

2. How a magnetic field deflection mass spectrometer works and m/z values

3. Explaining a mass spectrum - the basics

4. The mass spectrum of chlorine - peak ratios and relative atomic mass

5. The mass spectrum of strontium - peak ratios and relative atomic mass

6. Calculating the relative atomic mass of potassium from mass spectra data

7. Analysing the mass spectrum of bromine

8. Introduction to the mass spectra of organic compounds and the molecular ion peak and fragmentation - use in identification of organic molecules

9. Isotopic masses and accurate molecular ion peaks to identify molecules and molecular formulae

10. Calculation of % isotopic composition given the relative atomic mass of an element

11. How a time of flight (TOF) mass spectrometer works

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(b) More on fragmentation patterns and mass spectra

In a mass spectrometer, of whatever design, the basic initial mechanism of forming a positive ion is the removal of one electron from the parent molecule to form the molecular ion.

This is achieved in two ways:

(i) With a laser beam:  M + h  ===>  [M•]+  +  e-

(ii) Electron bombardment: M + e-  ===>  [M•]+  +  2e-

The molecular ion is subsequently broken down into smaller fragments, which themselves can be further broken down into even small fragments.

The higher the energy of the laser beam or bombarding electrons, the greater the fragmentation, and the more complex the fragmentation pattern.

Also, the bigger more complex molecules will give more complex fragmentation patterns e.g. you can readily see this with the two hydrocarbon molecules ethane and hexane whose mass spectra are shown below.

mass spectrum of ethane C2H6 CH3CH3 fragmentation pattern of m/z m/e ions for analysis and identification of ethane image diagram doc brown's advanced organic chemistry revision notes

Both mass spectra are unique for each molecule, but comparisons should only be made under the same experimental conditions.

Note it is convention to call the ion of greatest intensity, the base peak ion, and usually given the arbitrary value of 100.

This is the tallest peak for the most stable and most abundant ion,

in this case for ethane, the m/z 28 ion, structure [C2H4]+

This is also an important feature of comparing spectra obtained under the same experimental conditions.

mass spectrum of hexane fragmentation pattern of m/z m/e ions for analysis and identification of hexane image diagram doc brown's advanced organic chemistry revision notes

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(c) More on the nature of fragments formed in a mass spectrometer

See also 15.1.4 Database of accurate m/z values and possible ions formed in mass spectrometry

At pre-university level, only the structure of certain fragments is expected e.g. expressed as simple molecular formula.

e.g. [CxHyOz]+ where x, y and z express the number of atoms of each element in the fragment ion.

You must be aware that different ions can have the same m/z value see m/z 28 or m/z 43 below - but these can readily be distinguished with a high resolution mass spectrometer.

Examples of mass spectrum ions with their m/z values (assume atomic masses C = 12, H = 1 and O = 16)

m/z 1 [H]+  m/z 13 [CH]+   m/z 14 [CH2]+  m/z 15 [CH3]+    m/z 17 [OH]+    m/z 18 [H2O]+   m/z 25 [C2H]+   

m/z 26 [C2H2]+  m/z 27 [C2H3]+  m/z 28 [C2H4]+could be  [CH2=CH2]+  or  [CH3CH]+  and also  [CO]+

m/z 29 [CH3CH2]+    m/z 29   or [HC=O]+   [CH2NH2]+  m/z 28 [CO]+  m/z 30 [H2C=O]+ or [C2H6]+  m/z 31 [CH2OH]+ 

m/z 31 [H3CO]+  m/z 32 [O2]+   m/z 39 [C3H3]+   m/z 40 [CCO]+  [C2H3N]+   m/z 41 [C3H5]+   m/z 41 [CHCO]+  

m/z 42 [C3H6]+   m/z 42 [CH2CO]+   m/z 43 [C2H3O]+ structure [CH3C=O]+ , also m/z 43 [C3H7]+ could be  [(CH3)2CH]+ 

m/z 43 [CH3CH2CH2]+  m/z 44 [C3H8]+   m/z 44 [CH2=CH-OH]+  m/z 44 [O=C-NH2]+  m/z 44 [CO2]+   

m/z 45 [COOH]+  m/z 45 [CH3CH2O]+  m/z 45 [CH2CH2OH]+  or  [CH3CHOH]+   m/z 45 [CH2CH2=OH]+  m/z 45 [C2H5O]+

m/z 50 [C4H2]+     m/z 51 [C4H3]+   m/z 55 [C4H7]+  m/z 55 [C3H3O]+   m/z 56 [C4H8]+  m/z 57 [CH2CH2CHO]+  

m/z 57 [CH3CH2C=O]+  m/z 57 [C4H9]+   m/z 58 [C3H8N]+   m/z 59 [C3H7O]+   m/z 59 [CH3CH2OCH2]+   

m/z 59  [CH3CH2CH2O]+  m/z 59 [CH3CH2CHOH]+   m/z 63 [C5H3]+    m/z 65 [C5H5]+   

m/z 73 [C3H5O2]+  possible structure  [C2H5O-C=O]+     m/z 77 [C6H5]+  m/z 91 [C7H7]+ 

Many of these ions do not normally occur in 'test-tube' chemistry!

You are dealing with highly energised particles that can take many forms prior to, and after, fragmentation.

See also 15.1.4 Database of accurate m/z values and possible ions formed in mass spectrometry

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(d) Equations describing the possible formation of positive ion fragments

When the parent molecular ion fragments, there are two possible outcomes, and either fragment might carry the positive charge, but only one of two possibilities can be the positive ion.  e.g.

[M•]+  ===>  [A]+  +  [B•]   or   [M•]+  ===>  [A•]  +  [B]+

The most stable and most energetically favoured A or B structure will predominate, often one much more than the other.

For all the mass spectra pages I've outlined possible fragmentation equations e.g.

In the mass spectrum of propanone (shown below) there are two possibilities of bond scission of the parent molecular ion:

Formation of m/z 43 ion: [CH3COCH3]+  ===>  [CH3CO]+  +  CH3

Formation of m/z 15 ion: [CH3COCH3]+  ===>  [CH3]+  +  CH3CO

mass spectrum of propanone fragmentation pattern of m/z m/e ions for analysis and identification of acetone image diagram doc brown's advanced organic chemistry revision notes

It is pretty obvious that the m/z 43 ion predominates more than the m/z 15 after the C-C bond scission of the parent molecular ion [CH3COCH3]+.

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Key words and phrases:

Fragmentation of molecular ion, structure of ion fragments, equations to show possible fragmentation reactions

Website content © Dr Phil Brown 2000+. All copyrights reserved on revision notes, images, quizzes, worksheets etc. Copying of website material is NOT permitted. Exam revision summaries & references to A level chemistry course specifications are unofficial. Website content © Dr Phil Brown 2000+. All copyrights reserved on these organic chemistry exam revision notes on interpreting ion fragmentation patterns & equations for mass spectra, these A level chemistry revision notes are suitable for use of pre-university students studying AQA advanced level organic chemistry revision notes on interpreting ion fragmentation patterns & equations for mass spectra, Edexcel advanced level organic chemistry revision notes on interpreting ion fragmentation patterns & equations for mass spectra, OCR advanced level organic chemistry revision notes on interpreting ion fragmentation patterns & equations for mass spectra, IB advanced level organic chemistry revision notes on interpreting ion fragmentation patterns & equations for mass spectra, WJEC (Eduqas) advanced level organic chemistry revision notes on interpreting ion fragmentation patterns & equations for mass spectra, CIE Cambridge advanced level organic chemistry revision notes on interpreting ion fragmentation patterns & equations for mass spectra, CCEA advanced level organic chemistry revision notes on interpreting ion fragmentation patterns & equations for mass spectra, and useful for US grade 11 grade 12 AP honors organic chemistry courses involving interpreting ion fragmentation patterns & equations for mass spectra Explaining the importance of interpreting ion fragmentation patterns & equations for mass spectra in organic chemistry, What you need to know about interpreting ion fragmentation patterns & equations for mass spectra for organic chemistry, Explaining the use of interpreting ion fragmentation patterns & equations for mass spectra knowledge in organic chemistry, Examples of interpreting ion fragmentation patterns & equations for mass spectra explained when studying organic chemistry, What is the significance of interpreting ion fragmentation patterns & equations for mass spectra in organic chemistry, What is the use of interpreting ion fragmentation patterns & equations for mass spectra in organic chemistry  Describing and explaining the theory of interpreting ion fragmentation patterns & equations for mass spectra when studying organic chemistry, exam revision notes for interpreting ion fragmentation patterns & equations for mass spectra in exams, online help for interpreting ion fragmentation patterns & equations for mass spectra, revision notes for interpreting ion fragmentation patterns & equations for mass spectra, what do I need to learn for interpreting ion fragmentation patterns & equations for mass spectra in exams? revision summary for interpreting ion fragmentation patterns & equations for mass spectra, help in teaching interpreting ion fragmentation patterns & equations for mass spectra, learning notes for interpreting ion fragmentation patterns & equations for mass spectra, help to pass the interpreting ion fragmentation patterns & equations for mass spectra exam, how to prepare for examination questions on interpreting ion fragmentation patterns & equations for mass spectra?

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Website content © Dr Phil Brown 2000+. All copyrights reserved on revision notes, images, quizzes, worksheets etc. Copying of Doc Brown's pre-university advanced level chemistry website material is NOT permitted. Exam revision summaries & references to science course specifications are unofficial. These organic chemistry revision notes on spectroscopy (on interpreting mass spectra of organic compounds - molecular ion and fragmentation patterns and ion formation equations) suitable for use of pre-university students studying AQA advanced level chemistry, Edexcel advanced level chemistry, OCR advanced level chemistry, IB advanced level chemistry, WJEC (Eduqas) advanced level chemistry, CIE advanced level chemistry, CCEA advanced level chemistry, US grade 11-12 AP honors chemistry courses and they will also prove useful to 1st year undergraduate students of chemistry.

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