Yes, LC/MS (Liquid Chromatography/Mass Spectrometry) and GC/FID (Gas Chromatography/Flame Ionization Detection) can give different answers for fatty acid amounts in the same sample.

The main reason for this discrepancy is the difference in the principles and techniques used by these two analytical methods.

LC/MS is a technique that combines liquid chromatography with mass spectrometry to separate and identify compounds in a sample. It is particularly useful for analyzing polar and non-volatile compounds, such as fatty acids. LC/MS provides high sensitivity and specificity, allowing for accurate identification and quantification of individual fatty acids.

On the other hand, GC/FID is a technique that combines gas chromatography with flame ionization detection to separate and detect volatile compounds. It is commonly used for analyzing volatile fatty acids. GC/FID provides good separation of individual fatty acids based on their volatility but may not be as sensitive or specific as LC/MS.

The differences in separation mechanisms, detection principles, and instrument sensitivities can lead to variations in the quantification of fatty acids between LC/MS and GC/FID methods. Additionally, sample preparation techniques may also differ between these two methods, further contributing to the discrepancies.

Therefore, it is important to consider these differences when comparing results obtained from LC/MS and GC/FID analyses of fatty acids in the same sample.

Cannot compare as mentioned by Fatemeh. You can only calibrate using either method based on what you want to detect meaning the target substance that analyse. Chiose the more sensitive one for a particular peak/material based on the trsukts you have obtained.

How are you calibrating your measurements? Are you using internal standards to calibrate? Could you be more specific in your measurement techniques?

Fatemeh Gharahdaghigharahtappeh Hi Fatemeh, thank you so much for your input! It was my suspicion indeed that something analytically could contribute to this divergence between LC/MS and GC/FID. Could sample composition of the oil be a contributing factor? I.e., something present in the oil sample could lead to falsely higher readings for it?

Kuok Sum Cheong Thank you Kuok!

Ademario Junior Hi Ademario, I am using free fatty acids standards from Sigma to make calibration curves for the LC/MS. Then I am dissolving the oil in isopropanol, and targeting the fatty acids via SIR and MRM. For GC/FID, I am using a methylation process (oil mixed with 1.25 M HCl in MeOH, heating at 90 deg C, then mix with 0.9 % NaCl and hexane, transfer of upper layer to new vial and reconstitution in hexane) to convert the free fatty acids into fatty acid methyl esters. Identification is based on retention times of FAME standards I got from Sigma.

If to compare two method, I would suggest to look for application notes or standards methods (ASTM or ISO and etc), to look for the most suitable method to use (in terms of sensitivity, selectivity and accuracy).

As for your case, is the same sample preparation method used for both LCMS and GC-FID for the standard and sample you have use? I would presume that the same method of preparation for the sample and the standard as you use for GCFID.

Please check if the GC/FID method you use able to provide good resolution? meaning separation between the fatty acids and the oil. GC/FID is also a universal detector, as in principally, anything with carbon passes through it and burnt inside the detector will give you a peak. If substance co-eludes, it will give a result showing higher concentration. Please check this as the LCMS and GCFID method are totally different even though both are chromatography (difference in terms of sample preparation, injection (LCMS is direct while GCFID requires volatilization of the sample), carrier and column (mobile and non-mobile phase, as well as the polarity of the column), detector).

Theoretically, I would prefer to use the results from LCMS as there is no alteration to the sample (provided that the LC resolution is good). There is no further reaction to the sample to convert them into fatty acid methyl esters and etc. Furthermore, you can check the MS spectrum to further confirm by identify the compound (by comparing it with library or your standard material). May want to run a SCAN mode vs SIM mode for the identification.

Just my two cents worth. Hope it helps.

An internal standard that is not found in the original sample can correct any loss that you can have in the preparation processes or injection. Rather than using just the peak areas to calibrate you should use the ratio [peak analyte area / peak internal standard area]. Your standards for the calibration curve should also incorporate the internal standard and you should use the same internal standard quantity in all standards and samples in both methods - GC-FID and LC-MS. The internal standard is arguably the best method to avoid differences in chromatographic methods when the possibility of analyte loss exist since the ratio is the same with or without losses if the loss is the same for the analyte and the internal standard. Thus, try to choose or find an internal standard with similar properties in relation to your analytes.