Congratulations, you broke my brain..
After the 5th or 6th time reading it, I think I’m on your wavelength. Your question seems to be a variation of my question posted in models. You were generic and used chemical A, I just said water. Let me try to restate it and find out if we are tuned in.
There is an object (Chemical A, H20, sugar) that you want to find the concentration of the object in whatever you scan. Can I take that object’s spectrum and use it as a reference to find that object in any random sample. (how it relates to my ???) I think this kind of analysis would require the comparison of more than 1 spectrum sample to the reference (sugar, water) sample of what your looking to find. Right NOW, thats where your algorithms come in.
Currently we set some attributes (sugar, h20, etc..) and tell the CP cloud machine what the quantity of your attributes will be in the sample your about to scan. These attribute levels along with the scan are recorded. When a unknown sample is scanned, CP’s proprietary software compares all the data and finds the scan most similar to the unknown scan then estimates the attribute of the unknown buy the known scans of that kind. To find an attribute in an unknown sample would require some math be done on the reference sample and the unknown sample to eliminate the “noise”.
Thought experiment:
Ingredients
Salt
Sugar
Black microfiber glass cleaning cloth
The 2 attributes are salt content and sugar content.
Procedure:
Under New Sample
pour salt on to cloth and scan. This creates the profile of pure salt. 100% – 0%
pour sugar on the cloth and scan. Same for sugar. 0% – 100%
Under test sample
Pour a 50/50 mixture of salt and sugar then scan
I do not currently believe this will give a 50%/50% readout.
For that to happen you would need to add as a sample the 50/50 mixture.
CP – Am I on the right path or lost in the woods?? 
BTW: Sak… You made me break my brain again….