MassHunter Quant Library Match Score low compared to manual search - why?

Question

Hi, 
 I'm trying to understand how the Library Match Score in Quant works. 
 I set a minimum threshold of 70%. In Batch Table, there are matches that are low, whereas when I right click on the spectra in Compound Information and Search Library, the match scores are much higher, as are the values obtained by a manual lib search. 
 Why is that? The manual search does not use deconvolution, whereas the method does, so all the target/qualifier parameters come into play? I've tested different settings for Non reference window, Correlation Window, RT Window, etc. and have not been able to increase those match scores. 
 Any insight would be appreciated, thanks!

howard_sanford · Answer

Hello DanDurie , 
 The Library Match Score is obtained by comparing the target's spectrum to the target's reference spectrum. Usually, a reference spectrum library is used for this. This library will have one spectrum for each target compound. It is not searched in the traditional way. The target spectrum is compared directly to the reference spectrum for that target by matching the target name and/or CAS number to the library entry. Reference spectrum libraries can be set up in quant from the method editor and can be created using spectrum from a standard or from another library. 
 If you are not using a reference library and just using NIST or some other large library, then I suspect that it is finding the first spectrum in the library with the target name and displaying the score for that comparison. Then when you do the search, other entries are found that are a better match. 
 I would suggest creating a reference library and then specifying that in the method Globals Setup without specifying a library method. This is the simplest way to enable the Library Match Score. Note that the latest versions of quant require that a Library Match Score Minimum be set in the outliers before this will be calculated. 
 Once you have a good reference library, then you can add that as the first library in your Library Method and start using that instead of just the Reference Library. This will give you quick access to the Library Search function if needed.