Can DNA sequencing of food provide quantitatively the fraction of protein from chicken vs soy?

Question

update: New York Times X, 2021: The Big Tuna Sandwich Mystery:

For about $500, his lab could conduct a PCR test — which rapidly makes millions or billions of copies of a specific DNA sample — and try to tell me whether this substance included one of five different tuna species.

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There is some news about a report from Canada's CBC about fast-food chicken items containing as much as 50% soy protein, based on DNA testing. I won't do the report the service of linking to it directly, but you can search for the news "What's in your chicken sandwich? DNA test shows Subway sandwiches could contain just 50% chicken."

Isn't quantifying ratios of various DNA sequences fairly difficult, requiring rigorous sample preparation? Could results vary dramatically by varying cooking times, and the independent processing of the animal protein and the vegetable protein? Is there an reason to expect isolated DNA ratios to be a good indicator of protein ratios?

I'm also curious, is there a better way to at least try to do this study - perhaps search for key sequences of amino acids within the proteins to at least try to distinguish animal from vegetable proteins quantitatively?

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edit: Here is a newer, more reliable, independent news item not written by the agency who paid for the testing.

The NPR news article DNA Tests Find Subway Chicken Only 50 Percent Meat, Canadian News Program Reports says:

The tests were conducted by a DNA researcher at Trent University's Wildlife Forensic DNA Laboratory, for a CBC Marketplace episode dedicated to testing fast-food chicken dishes, and have not been independently confirmed.

Later in the same article a strong statement by one of the companies refuting the results has also been provided.

Answer 1

In reference to the update in the question three years later, I'll include additional quotes from the same New York Times article.

“No amplifiable tuna DNA was present in the sample and so we obtained no amplification products from the DNA,” the email read. “Therefore, we cannot identify the species.”

The spokesman from the lab offered a bit of analysis. “There’s two conclusions,” he said. “One, it’s so heavily processed that whatever we could pull out, we couldn’t make an identification. Or we got some and there’s just nothing there that’s tuna.” (Subway declined to comment on the lab results.)

With all testing, there are major caveats to consider. Once tuna has been cooked, its DNA becomes denatured — meaning that the fish’s characteristic properties have likely been destroyed, making it difficult, if not impossible, to identify.

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While this question falls somewhat between biology, chemistry, and food science, the use of quantitative DNA analysis as a proxy for estimation of relative protein fractions from two different species (in this case plant vs mammal) is probably on-topic here considering it is biologists who have invented, use, and interpret results of DNA amplification and sequencing analysis, and can best speak to their correct use and potential problems when used outside their accepted protocols.

I am not a trained biologist myself, so I can not state with authority that starting with a food product whose plant and animal components may have started from different places on Earth, been processed differently, then combined and further processed involving major excursions in heat (cooking) and in pH deviate substantially from accepted protocols for DNA quantitative analysis, but I have a strong hunch that this is probably so.

As @BryanKrause has noted in a comment, the laboratory in question's primary expertise is in animal identification - does a carcass or piece of meat or fish come from the species claimed or not, and this is a laudable service. But using relative fractions of DNA within a single sample of prepared food as proxy for relative contribution of protein is far outside that kind of service, and as far as I know, is not an accepted practice anywhere.

Ars Technica is a popular technical news source that generally does a excellent job of summarizing scientific topics when they do cover them, in my opinion at least. In an update to the article Subway releases data after scientists weigh in on 50% chicken test [Updated] they summarize released information from two independent laboratories using an "ELISA methodology designed for food products to quantify soy in the chicken." ELISA is a quantitative method that can be used to measure the presence of various proteins directly, and does not use DNA as a proxy.

Update, March 6: Subway has released the lab reports from both of its independent tests. Both Maxxam Analytics in Ontario, Canada and Elisa Technologies, Inc. in Florida used enzyme-linked immunosorbent assays (ELISA) designed for food products to quantify soy in the chicken. ELISA's are a standard type of assay that generally detect and quantify substances based on binding by an antibody. In the assay, antibody binding kicks off a detectable chemical reaction, commonly resulting in a color change. In the case of Elisa Technologies, the lab used an antibody that binds to soy flour proteins and the lab used known concentrations of those soy proteins for comparison to determine the quantity of soy protein in Subway's chicken samples.

In all samples, Elisa detected 3 parts-per-million or less of soy proteins, which is well below one percent of the chicken. Maxxam detected 5.3 ppm of soy protein in the chicken, which is still well below one percent. (emphasis added)

Answer 2

I now read the article. They don't include/show a standard curve so take it with a grain of salt.

It's possible to do Carbon Isotope analysis to distinguish plant vs. animal carbon from an isolated protein fraction.

Besides that you could also do quantitative mass-spectrometry and look for animal vs. plant peptides.

If you want both cell number, protein abundance of known targets there's the fancy Mass Cytometry that could do this.

That being said, IMHO: DNA-sequencing is probably fine and definitely robust. If you set-up a standard curve (mix soy and chicken at known ratios and DNA sequence it) then that's probably the easiest/cheapest way to do this. Without a standard curve testing this though you can't draw a definitive conclusion.

Also from the NPR article; analysis from other fast-food sources of meat gave lower Soy DNA ratios with Subway being an outlier. That's an important distinction to make. Subway subsequently claiming that it's 100% chicken appears more misleading after previously saying there was soy as a stabilizer.