I am dealing with full scan TIC data from a GC-MS Agilent 8890 with 7000D triple quadrupole mass spectrometer with MassHunter software (version 10). I have come across an issue when using Unknowns Analysis (version 10.2) software library search functions. The method is setup to search a custom library created with in house spectra and retention time data using the Library Editor software followed by NIST library. See settings for library search and compound identification in the screenshots below. I've noticed when analyzing the data if the software finds a hit in a sample from the custom library at a similar retention time it will prioritize that hit over the NIST library hit even if the NIST library hit is a much closer match.
Here's an example (I am making up compounds). Lets say in custom library I have hexane at retention time 10 minutes. Lets say in the sample there is a compound at 10 minutes but its not hexane and its not in my custom library. Lets say its cyclohexane (or whatever). The results will show hexane with a low match from my custom library as the main hit. But if I go to select best hit to look at other hits from the NIST library I would see cyclohexane with a really good match and have to change the result. I would the software to stop doing this.
I am not sure but maybe I have to change the settings under Compound Identification - Multi Library Search Type from 'Stop when Found' to 'All'? Or maybe I should set a higher match threshold for the custom library (right now its at 50 but I just picked that because that is what worked well with NIST to give a result for all components found)? Is there another setting which might fix this? Thanks for any help.