All subjects · Chemistry · WCH12 (Unit 2)

Mass spectra of organic compounds

Mass spectrometry gives the relative molecular mass of an organic compound, and the fragment peaks give clues to its structure.

The molecular ion

When an organic molecule is ionised it forms the molecular ion, M+: M -> M+ + e-. The M+ peak is the peak with the highest m/z (ignoring the small M+1 peak caused by carbon-13). Its m/z value equals the Mr.

Fragmentation

Molecular ions break into a positive ion and a radical. Only the positive ions are detected:

M+ -> X+ + Y•

Common fragment ions: CH3+ (15), C2H5+ (29), CHO+ (29), C3H7+ (43), CH3CO+ (43), OH lost (M - 17), CH3 lost (M - 15).

Using spectra

Find M+ to get Mr. Look for peaks that match likely fragments. Isomers have the same M+ but different fragmentation patterns: propanal (CH3CH2CHO) gives a strong peak at 29, while propanone (CH3COCH3) gives a strong peak at 43 (CH3CO+). The tallest peak is the base peak; it is the most stable or most common fragment.

Worked example

An alcohol C3H8O has its molecular ion at m/z 60 and its tallest peak at m/z 31. Is it propan-1-ol or propan-2-ol?

  1. M+ = 60 matches C3H8O.
  2. m/z 31 is CH2OH+, which forms easily when the C-C bond next to a -CH2OH group breaks: CH3CH2CH2OH+ -> CH2OH+ + C2H5•.
  3. Propan-2-ol has no -CH2OH group; losing CH3 from it gives CH3CHOH+ at m/z 45 instead.

Answer: The strong peak at 31 (CH2OH+) points to propan-1-ol.

Key idea: M+ (highest m/z, ignoring M+1) gives Mr. Fragments: 15 CH3+, 29 C2H5+ or CHO+, 43 C3H7+ or CH3CO+. Isomers differ in fragmentation.

Check yourself

  1. The molecular ion peak of an alkane is at m/z 72. How many carbon atoms does it contain? (C = 12.0, H = 1.0)
    Show answer

    5. CnH2n+2: 14n + 2 = 72, so n = 5 (pentane).

  2. Which fragment ion causes a peak at m/z 29?
    • CH3+
    • C2H5+
    • C3H7+
    • OH+
    Show answer

    C2H5+. 2(12) + 5(1) = 29. (CHO+ also has m/z 29.)

  3. Propanone, CH3COCH3, has a strong peak at m/z 43. Which ion causes it?
    • C2H5+
    • COOH+
    • CH3+
    • CH3CO+
    Show answer

    CH3CO+. CH3CO+ = 15 + 28 = 43.

  4. Which particles from fragmentation are detected?
    • Only the positive ions
    • Only the radicals
    • Both the ions and the radicals
    • Only neutral molecules
    Show answer

    Only the positive ions. The spectrometer deflects and detects charged particles; radicals are uncharged.

  5. How can mass spectra distinguish butane from 2-methylpropane?
    • Their M+ peaks are different
    • Only one has an M+ peak
    • Their fragmentation patterns are different
    • Their M+1 peaks are at different m/z
    Show answer

    Their fragmentation patterns are different. Both have Mr 58; the fragments depend on structure.

  6. Ethanol has M+ at m/z 46. At what m/z is the peak for loss of CH3?
    Show answer

    31. 46 - 15 = 31, which is CH2OH+.

  7. What causes a small peak one unit above M+?
    • A 2+ ion
    • Loss of a hydrogen atom
    • Molecules containing a carbon-13 atom
    • An impurity of water
    Show answer

    Molecules containing a carbon-13 atom. About 1.1% of carbon is 13C, giving an M+1 peak.

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Last updated 7 November 2026. Spotted a mistake? Tell us.