Mass Spectra of Some Miscellaneous Lipophilic Components

During the analysis of natural fatty acid samples, various less common lipids may be encountered. They may be present naturally in the samples or they can be formed as artefacts, or indeed by mistake if a derivatization reaction is carried out incorrectly. For example, sterols can interfere in GC traces if not removed from samples of fatty acid esters, and it can be helpful to have a spectrum of cholesterol available as a check. Of course, mass spectrometric analysis of sterols per se is an important task, but it is outwith my general research interests and I lack the expertise to discuss such spectra in detail.

The following spectra (free acids, trimethylsilyl esters, dimethyl acetals, cholesterol, amides, amines and hydrocarbons) have cropped up during our research activities. Most of these spectra are offered for comparison or record purposes, and I have added cursory descriptions only. I presume that many of the following spectra will have been published elsewhere, but I have not attempted to establish priority. You may find some further relevant information in our pages on artefacts and additives.


Free Fatty Acids

Free (unesterified) fatty acids are rarely analysed as such by gas chromatography-mass spectrometry, but they have distinctive mass spectra and the following are illustrated as examples. Brief comments only are offered on interpretation.

Mass spectra of saturated fatty acids are especially interesting and that of palmitic acid is -


The most abundant peaks are at m/z = 60, the McLafferty rearrangement ion, and 73 in the lower molecular weight range, but the molecular ion is clearly abundant, and there are ions representing fragmentations between methylene groups of the form [HOOC(CH2)n]+ from m/z = 115 to 255. An ion at m/z = 239 ([M-17]+) presumably reflects a loss of OH- from the carboxyl group.

The mass spectrum of stearic acid -

Mass spectrum of stearic acid

As might be expected the spectra of unsaturated fatty acids are rather different, with hydrocarbon ions (general formula [CnH2n-1]+]) being most abundant, and that of oleic acid is -

Mass spectrum of oleic acid

Ions in the low mass range predominate, and as expected, there is nothing that might serve to locate the double bond. In contrast to saturated fatty acids, the ion representing the loss of the elements of water from the carboxyl group ([M−18]+, m/z = 264) is more abundant than the molecular ion. The McLafferty ion at m/z = 60 is relatively small.

The spectrum of linoleic acid is also dominated by ions in the low mass range. In this instance, the molecular ion is more abundant than any representing the loss of elements of water from the carboxyl group.

Mass spectrum of linoleic acid

Spectra of many more free fatty acids are available in our Archive pages, but without interpretation.


Trimethylsilyl Esters

Trimethylsilyl (TMS) esters of fatty acids are rarely prepared as they are very unstable and liable to hydrolysis. However, they may by formed from the free acids in silylated lipid extracts from time to time. The mass spectrum of trimethylsilyl palmitate is illustrated –

Mass spectrum of trimethylsilyl palmitate

The base peak (m/z = 313) represents the loss of a methyl group from the TMS ester group, while that at m/z = 132 is the McLafferty rearrangement ion. Ions at m/z = 73 and 75 are typical of all TMS derivatives. More spectra are available on our Archive pages.


Dimethylacetals of Aliphatic Aldehydes

When the plasmalogen forms of phospholipids, common in animal tissues and in some microorganisms (but not plants), are treated with acidic transesterification reagents when preparing methyl esters, the vinyl ether bond is broken and aldehydes are generated, which are immediately converted to dimethyl acetals. These are almost exclusively saturated and monounsaturated (C16 and C18 in chain length), and they tend to elute just before 16:0 and 18:0 methyl esters on most GC phases. The mass spectra of the three common isomers follow.

First the dimethyl acetal of hexadecan-1-al -
Generation of an dimethyl acetal from a plasmalogen

Mass spectrum of the dimethyl acetal of hexadecan-1-al

The spectrum is not at all exciting. The base peak is the McLafferty rearrangement ion at m/z = 75, but the molecular ion can only be seen if this region of the spectrum is greatly magnified. The first significant ion in the high mass range, at m/z = 255, represents the loss of a methoxyl ion, and in practice this ion has to be used to find the molecular weight. The remaining spectra are very similar.

Mass spectrum of the dimethylacetal of octadecan-1-al -

Mass spectrum of the dimethylacetal of octadecan-1-al

Mass spectrum of the dimethylacetal of octadec-9-en-1-al -

Mass spectrum of dimethylacetal of octadec-9-en-1-al

No further comment seems necessary.


Amides and Amines

The McLafferty ion at m/z = 115 is the most abundant ion in the mass spectrum of simple amides of saturated fatty acids, such as N-butyl-octadecamide illustrated next. The mechanism for the formation of this important ion is discussed in greater detail in our web pages on mass spectra of methyl ester derivatives of saturated fatty acids.

Mass spectrum of N-butyl-octadecamide

The spectra of unsaturated acyl-amides are similar, but the molecular ion and those with higher m/z values are more abundant; for example that at m/z = 128 is relatively more abundant and that of the McLafferty ion at m/z = 115 diminishes.

The mass spectra of secondary amines, such as that of N,N-octadec-9-enylbutylamine illustrated, have simple characteristic fragmentations beta to the nitrogen atom.

Mass spectrum of N,N-octadec-9-enylbutylamine

Spectra of several more simple amides and amines are available in our Archive pages without discussion (kindly supplied by Isabel Molina (Algoma University, Sault Ste Marie, ON, Canada) and Mike Pollard and John Ohlrogge (Michigan State University, East Lansing, MI, USA).



Cholesterol is by far the most abundant sterol in animal tissues. It tends to elute from GC columns long after the methyl ester derivatives, but it does elute eventually as a broad hump in chromatograms - disrupting subsequent analyses of the latter. In practice, it is best eliminated by adsorption chromatography before methyl esters or other derivatives are analysed by GC. Of course, many lipid analysts will require to analyse mass spectra of sterols for their own sake, but I must leave detailed interpretation of the mass spectra of cholesterol and derivatives to sterol specialists. The spectra are offered here simply for record purposes. Sterols per se are best analysed separately on non-polar phases either in the free form or better as the trimethylsilyl ethers.

The mass spectrum of free cholesterol-

Mass spectrum of cholesterol

- and that of its trimethylsilyl ether derivative -

Mass spectrum of trimethylsilyl ether derivative of cholesterol

There are many more spectra of sterols from animal tissues, plants and yeasts in our Archive pages in free and silylated form, again without interpretation.


Squalene and Other Hydrocarbons

The hydrocarbon squalene tends to be a very minor component of animal tissues, where it is the biosynthetic precursor of sterols. However, it can be a major constituent of fats and oils of marine origin on occasion, for example in shark oils. Its mass spectrum follows, but no attempt is made at detailed interpretation.

Mass spectrum of squalene

Other hydrocarbons are found among the constituents of natural plant and insect waxes, and the mass spectrum of the fully saturated nonacosane from a plant wax follows as an example.

Mass spectrum of nonacosane

The molecular ion is just discernible, and as might be expected, the spectrum is dominated by ions of the form [(CH2)n+1]+.

Updated: September 6th, 2013