"Could someone on this list help me understand the difference between the two methods used on identical samples?"

HPLC stands for high pressure liquid chromotography.  LC-IRMS stands for liquid chromatography isotope ratio mass spectroscopy.  All modern liquid chromotography used for analytical chemistry is run at high pressure to the HP does not really add any meaning above plain old LC.  The isotope ratio part simply allows you to look at isotope abundance of carbon 12 versus carbon 13 and determine if the sugar source was from beets or nectar or was it from sugar cane.   If from sugar cane that means it was not nectar and was bee keeper added.

AOAC stands for Association of Official  Analytical Chemists.  AOAC publishes standard methods that they feel have been proven accurate if followed in all details.  The idea is if everybody follows the same method everybody ought to get the same answers.  There should have also been some numbers with that AOAC method to specify exactly which AOAC method was followed as there are hundreds of such methods covering everything from how to conduct a corrosion study to how to determine quantitatively how explosive some substance is to how to analyze for pesticides to on and on and on.

The between lab comparisons of the numbers found for glucose, fructose and sucrose absolutely stink.  This does not surprise me in the slightest.  I have seen such results many, many times when you compare results from two different labs, even when both claim to be running exactly the same procedure.  I have no idea at all which lab is correct or if either lab is even close to correct.  There is a very good chance neither is correct based on such results that I have seen.  I have no reason at all to think a commercial lab would give more accurate results than a government lab.  Nor do I have any reason at all to think the inverse.  I have seen both types of labs produce garbage data many times.

The USDA lab did do isotope ratios and said based on that the honey is contaminated with sugar from cane.  This is data that is really hard to screw up regardless if the rest of the analysis was done properly or very improperly.  It comes right out of the computer that runs the mass spec and surely they cross confirmed it by looking at the isotope ratios in glucose, fructose and sucrose I would think.  It is no more human work to do all  three than it is to do just one as the puter and mass spec do all the work while the human may be off drinking coffee or home sleeping because surely that instrument is equipped with an auto sampler.

If I were you I would tell both labs I had results from another lab that were in drastic disagreement with the lab you are talking to and want to know what they are going to do to convince you that they did it right and the other lab blew it.  I would suggest they consider rerunning the sample at no charge as a minimum.  Both will likely refuse to rerun the sample which would tell me neither one has the slightest confidence in the results they produced.  If someone called me with such a problem back when I ran a commercial lab I would have asked them to submit several samples blinded by having only a sequential sample number on the label.  I would suggest that at least two of the samples should be identical and not next to each other in the numerical sequence.  At least one of the samples should have added beet sugar and another added cane sugar.  I would want at least six or eight or ten total samples.  I would run all of them at no charge and give the submitter the results on all samples.  At that point the submitter could decide what, if anything we needed to do in addition.  I have never known of any other commercial or government lab that had a policy like that.  The lab I ran was the high priced lab in the business and the only way we could justify that high price was to produce high quality results every single time.  My customers knew they were coming to the highest price in the business.  They were not stupid.  They still came.

Dick

HL Mencken said: "The whole aim of practical politics is to keep the populace alarmed — and hence clamorous to be led to safety — by menacing it with an endless series of hobgoblins, all of them imaginary. "

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