GC Analysis of Omega 3 Fatty Acids in Fish Oil Capsules and Farm Raised Salmon

By: Katherine K. Stenerson, Principal Scientist; Michael R. Halpenny, R&D Technician; Leonard M. Sidisky, R&D Manager; and Michael D. Buchanan, Product Manager, Reporter US Volume 31.2

The speculated health benefits from the consumption of omega 3 fatty acids are numerous1. Variants that appear to be most important in human physiology are:

  • C18:3n3, α-linolenic acid (ALA)
  • C20:5n3, eicosapentaenoic acid (EPA)
  • C22:6n3, docosahexaenoic acid (DHA)

The purpose of the work published here was to identify the omega 3 fatty acids in two different sources of fish oil. Only a single sample of each source was processed, so this work should not be considered a definitive comparison of profiles between these source types.


The samples analyzed for this work were as follows:

  • Fish oil capsule purchased locally, listed as containing EPA, DHA, and “other” Omega 3.
  • Atlantic salmon filet (farm raised), purchased frozen and vacuum packed.

The fish oil capsule was prepared for analysis using alkali hydrolysis followed by methylation as described in AOAC Method 991.392. The mixture was blanketed with nitrogen throughout the extraction process to prevent oxidation of the polyunsaturated fatty acids. The salmon sample underwent acid digestion, alkali hydrolysis, and methylation as described in AOCS Official Method Ce 1k-093. Butylated hydroxytoluene (BHT) was added to the salmon sample as an antioxidant prior to extraction. The methylation procedure used in both methods converts fatty acids to fatty acid methyl esters (FAMEs) prior to analysis. All extracts then were concentrated to 1 mL prior to gas chromatography (GC) analysis.

Two capillary GC columns of slightly different selectivities were used for analysis. Conditions were according to AOAC 991.39 and AOCS Ce 1i-07 methods2,4. This was possible as both methods share the same set of run conditions. Peak identification was done by retention time matched to standards. This data was published previously5.

Results and Discussion

Sardine and anchovy were listed as the fish sources on the fish oil capsule packaging. Based on published fatty acid compositional data for these types of fish oils, C16:0 and C20:5n3 (EPA) were expected to be the most abundant FAMEs present, followed by C16:1, C18:1, and C22:6n3 (DHA)6. The chromatogram of the fish oil capsule extract is shown in Figure 1, and matches the expected pattern. The C14:0 peak detected was from the sardine portion of the oil. This fatty acid is of much lower abundance in anchovy oil.

Fish Oil Capsule

Figure 1. Fish Oil Capsule

GC Conditions
: Omegawax®, 30 m x 0.25 mm I.D., 0.25 µm (Product No. 24136) SLB®- IL60, 30 m x 0.25 mm I.D., 0.20 µm (Product No. 29505-U); oven: 170 °C, 1 °C/min to 225 °C; inj. temp.: 250 °C; detector: FID, 260 °C; carrier gas: helium, 1.2 mL/min; injection: 1 µL, 100:1 split; liner: 4 mm I.D., split/splitless type, wool packed single taper FocusLiner™ design


Figure 2 shows the chromatogram of the farm raised Atlantic salmon. Published fatty acid composition for salmon oil indicates C22:6n3 (DHA), C18:1, and C20:5n3 (EPA) as the most abundant, followed by C16:0, C16:1, C18:0, C20:1, and C22:1 [6]. The profile obtained for this sample does not match this pattern, although all the listed fatty acids were detected. Specifically, high levels of C14:0, C18:1, and C18:2 relative to C22:6n3 (DHA) and C20:5n3 (EPA) were observed, which may be the result of the specific diet the fish were fed.

Good peak shapes were observed with both GC columns for these analytes. Because both columns have similar selectivity, elution order was comparable, but not exact. With the SLB-IL60:

  • The elution of C22:6n3 (DHA) before C22:5n3 was observed
  • The partial co-elution of C20:4n3 and C20:5n3 (EPA) occurred

These highlight the differences in analyte-stationary phase mechanisms between the columns. Lastly, an overall faster elution (31 minutes compared to 52 minutes) was obtained with the SLB-IL60.

Farm Raised Atlantic Salmon

Figure 2. Farm Raised Atlantic Salmon

GC Conditions: Peak IDs and conditions are the same as Figure 1


The data presented here provide an indication of the different omega 3 fatty acids that may be found in two different sources of fish oil. Only a single sample of each source was processed, so this work should not be considered a definitive comparison of profiles between these source types. Two GC columns of slightly different selectivity were used to generate chromatograms with subtle elution order changes, indicating these phases for analysts who wish to perform confirmatory analysis.

Legal Information

Omegawax and SLB are registered trademarks of Sigma-Aldrich Co. LLC
FocusLiner is a trademark of SGE Analytical Science Pty Ltd.




  1. P.M. Kris-Etherton, W.S. Harris, and L.J. Appel, “Fish Consumption, Fish Oil, Omega-3 Fatty Acids, and Cardiovascular Disease” Circulation: Journal of the American Heart Association, November 19, 2002, p. 2747.
  2. AOAC Official Method 991.39, “Fatty Acids in Encapsulated Fish Oils and Fish Oil Methyl and Ethyl Esters” AOAC International 2003.
  3. AOCS Official Method Ce 1k-09, “Direct Methylation of Lipids in Foods for the Determination of Total Fat, Saturated, cis-Monounsaturated, cis-Polyunsaturated and trans Fatty Acids by Gas Chromatography” AOCS Official Methods and Recommended Practices, 2011-2012 Method Additions and Revisions.
  4. AOCS Official Method Ce 1i-07, “Determination of Saturated, cis-Monounsaturated, and cis-Polyunsaturated Fatty Acids in Marine and Other Oils Containing Long Chain Polyunsaturated Fatty Acids (PUFAs) by Capillary GLC” AOCS Official Methods and Recommended Practices.
  5. K.K. Stenerson, M.R. Halpenny, L.M. Sidisky, and M.D. Buchanan, “Ionic Liquid GC Column Option for the Analysis of Omega 3 and Omega 6 Fatty Acids” Supelco Reporter 31.1 (February 2013), p. 10.
  6. D. Firestone (ed.), “Physical and Chemical Characteristics of Oils, Fats, and Waxes” AOCS Press, US FDA, Washington, D.C., 1999.


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