How is the reference spectrum generated in the Compound Information window in Quantitative Analysis?

Question

Hi, 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. Thanks!! A) incorect ref spec 
 B) correct ref spec

howard_sanford · Answer

Hello DanDurie , 
 The Library Match Score is designed to work with a reference library. This library should have only one entry per compound and the name or CAS number must match with the target name or CAS number in the method. It is not an actual library search but gives a match score by comparing the single reference spectrum in the library to the extracted target compound spectrum. 
 If you are using a library method, the first library will be used and treated as the reference library. Any additional libraries will be utilized for the Alternate Target Hit feature, if the method is set up for that. Using anything other than a properly set up reference library for the first library has not been tested and is not recommended. 
 Be aware that if using a library method, quant will cache the libraries that are specified. If you make changes to the libraries then you will need to save, close, reopen, and then reanalyze the batch to see the changes applied.