Part 6. Penta- and Hexaenoic Fatty Acids

Mass Spectrometry of 3-Pyridylcarbinol Esters


The greater complexity of the mass spectra of 3-pyridylcarbinyl esters of polyenoic fatty acids can make interpretation rather difficult (more even than with trienes and tetraenes). The availability of standards for comparison purposes does make the task somewhat easier, as each isomer always has a distinctive fingerprint. The main problem is usually in locating the first double bond in the chain. The principles of locating double bonds via 3-pyridylcarbinol esters are discussed in the web page on 3-pyridylcarbinol esters of monoenoic acids and in subsequent documents, but in brief we are looking for gaps of 26 amu for each double bond or better for gaps of 40 amu for the double bond and the preceding methylene group. The main fragments here are illustrated but not discussed. The widely used term 'picolinyl ester' is inaccurate and should now be avoided. References are listed when we are aware of prior formal publication of spectra in the scientific literature, but many of the following spectra will not have been published elsewhere. The widely used term 'picolinyl ester' is inaccurate and should now be avoided (see our web page on the saturated derivatives).


Pentaenoic Fatty Acids

The spectrum of 3-pyridylcarbinyl 5,8,11,14,17-eicosapentaenoate (20:5(n-3) or 'EPA') is the first to be illustrated (Wolff et al., 1999). This is arguably the most important of the natural pentaenes, as it is an important constituent of the phospholipids in animal tissues, especially in brain, and it is the precursor of the PG3 series of prostaglandins.

Mass spectrum of 3-pyridylcarbinyl 5,8,11,14,17-eicosapentaenoate

The expected gaps of 26 amu for fragmentations at the double bond are not always easy to see, although they are indeed present, but those of 40 amu for the double bond and an associated methylene group can be distinguished.

3-Pyridylcarbinyl 3,6,9,12,15-octadecapentaenoate (18:5(n-3)) -

Mass spectrum of 3-pyridylcarbinyl 3,6,9,12,15-octadecapentaenoate

It was quite an achievement to obtain a spectrum of this acid, which is a minor component of some marine organisms, as the double bond in position 3 isomerizes very readily on attempting to prepare derivatives (Prof. M.V. Bell of Stirling University kindly provided a sample). Interpretation is as described elsewhere for tri- and tetraenoic fatty acid derivatives. Note that the usual ions at m/z = 151 and 164 are scarcely apparent. Again, the double bonds are most easily located from the gaps of 40 amu, although the expected gaps of 26 amu are also detectable for all but the first double bond. The isomerized product, 2,6,9,12,15-octadecapentaenoate, has a very different spectrum with the base peak at m/z = 177 for cleavage at the centre of the bis-methylene interrupted double bond system (author, unpublished - available in the Archive pages here...).

3-Pyridylcarbinyl 4,7,10,13,16-docosapentaenoate (22:5(n-6)). All but the first double bond are easily located from the ions marked, and the same is true for the following spectrum of the n-3 isomer.

Mass spectrum of 3-pyridylcarbinyl 4,7,10,13,16-docosapentaenoate

3-Pyridylcarbinyl 7,10,13,16,19-docosapentaenoate (22:5(n-3)) -

Mass spectrum of 3-pyridylcarbinyl 7,10,13,16,19-docosapentaenoate


Hexaenoic Fatty Acids

The mass spectrum of 3-pyridylcarbinyl 4,7,10,13,16,19-docosahexaenoate (22:6(n-3) or ‘DHA’) is illustrated (Harvey, 1984). This is a key essential fatty acid of the n-3 family, especially in the brain, and is the precursor of a family of docosanoids, including the protectins and resolvins. The molecular ion is easy to distinguish in comparison to spectra of methyl esters, for example.

Mass spectrum of 3-pyridylcarbinyl 4,7,10,13,16,19-docosahexaenoate

3-Pyridylcarbinyl 6,9,12,15,18,21-tetracosahexaenoate (24:6(n-3)), the biosynthetic precursor of the previous fatty acid -

Mass spectrum of 3-pyridylcarbinyl 6,9,12,15,18,21-tetracosahexaenoate

For both spectra, diagnostic ions are easily located for all but the first double bond.

Further relevant spectra are available in our Archive section (but without interpretation).



  • Harvey, D.J. Picolinyl derivatives for the structural determination of fatty acids by mass spectrometry. Applications to polyenoic acids, hydroxy acids, di-acids and related compounds. Biomed. Mass Spectrom., 11, 340-347 (1984) (DOI: 10.1002/bms.1200110705).
  • Wolff, R.L., Christie, W.W., Pedrono, F. and Marpeau, A.M. Arachidonic, eicosapentaenoic, and biosynthetically related fatty acids in the seed lipids from a primitive gymnosperm, Agathis robusta. Lipids, 34, 1083-1097 (1999) (DOI: 10.1007/s11745-999-0460-y).

Updated August 8, 2013