How is the reference spectrum in Quant generated / where does it come from?
I know it's supposed to come from the spectrum in the library provided in the method. In my case, it's an in-house library (so it has multiple entries per compound, in most cases).
In the image A) below, the match for hexanoylglycine was high, but the reference spectrum IS NOT the spectrum from the library.
I then realized that the CAS numbers and compound names in the method MUST be the same as those in the chosen library (I knew this about reference libaries, but didn't realize this was also the case for any library used in Quant). Some compounds had CAS numbers of 0-00-0 in the method. Some compounds have multiple CAS numbers in the library. I solved this by deleting the CAS numbers in the method and was able to get the correct reference spectrum as in image B) below.
However, this doesn't explain WHERE the reference spectrum comes from, if it's not the spec from the library. What's going on behind the scenes. Is it just a bug?
We just want to know what exactly a sample is matching TO.
A) incorect ref spec
B) correct ref spec