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Mass Spectrometry - Fragmentation Patterns

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    327
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    Following are examples of compounds listed by functional group, which demonstrate patterns which can be seen in mass spectra of compounds ionized by electron impact ionization. These examples do not provide information about the fragmentation mechanisms that cause these patterns. Additional information can be found in mass spectrometry reference books.

    Alcohol

    An alcohol's molecular ion is small or non-existent. Cleavage of the C-C bond next to the oxygen usually occurs. A loss of H2O may occur as in the spectra below.

    3-Pentanol (C5H12O) with MW = 88.15

    alcohol.gif

    alcpic.gif

    Aldehyde

    Cleavage of bonds next to the carboxyl group results in the loss of hydrogen (molecular ion less 1) or the loss of CHO (molecular ion less 29).

    3-Phenyl-2-propenal (C9H8O) with MW = 132.16

    aldehyde.gif

    aldpic.gif

    Alkane

    Molecular ion peaks are present, possibly with low intensity. The fragmentation pattern contains clusters of peaks 14 mass units apart (which represent loss of (CH2)nCH3).

    Hexane (C6H14) with MW = 86.18

    alkane.gif

    alkpic.gif

    Amide

    Primary amides show a base peak due to the McLafferty rearrangement.

    3-Methylbutyramide (C5H11NO) with MW = 101.15

    amide.gif

    amidepic.gif

    Amine

    Molecular ion peak is an odd number. Alpha-cleavage dominates aliphatic amines.

    n-Butylamine (C4H11N) with MW = 73.13

    amine.gif

    aminepic.gif

    Another example is a secondary amine shown below. Again, the molecular ion peak is an odd number. The base peak is from the C-C cleavage adjacent to the C-N bond.

    n-Methylbenzylamine (C8H11N) with MW = 121.18

    amine2.gif

    amine2pic.gif

    Aromatic

    Molecular ion peaks are strong due to the stable structure.

    Naphthalene (C10H8) with MW = 128.17

    aromatic.gif

    arompic.gif

    Carboxylic Acid

    In short chain acids, peaks due to the loss of OH (molecular ion less 17) and COOH (molecular ion less 45) are prominent due to cleavage of bonds next to C=O.

    2-Butenoic acid (C4H6O2) with MW = 86.09

    carboxylic.gif

    carbopic.gif

    Ester

    Fragments appear due to bond cleavage next to C=O (alkoxy group loss, -OR) and hydrogen rearrangements.

    Ethyl acetate (C4H8O2) with MW = 88.11

    ester.gif

    esterpic.gif

    Ether

    Fragmentation tends to occur alpha to the oxygen atom (C-C bond next to the oxygen).

    Ethyl methyl ether (C3H8O) with MW = 60.10

    ether2.gif

    ether2pic.gif

    Halide

    The presence of chlorine or bromine atoms is usually recognizable from isotopic peaks.

    1-Bromopropane (C3H7Br) with MW = 123.00

    halide.gif

    halpic.gif

    Ketone

    Major fragmentation peaks result from cleavage of the C-C bonds adjacent to the carbonyl.

    4-Heptanone (C7H14O) with MW = 114.19

    ketone.gif

    ketpic.gif

    Contributors and Attributions

    Dr. Linda Breci, Associate Director Arizona Proteomics Consortium University of Arizona


    Mass Spectrometry - Fragmentation Patterns is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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