Unknowns Analysis - Exporting Results and Remembering the Best Hits


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 am new to this Unknowns Analysis software and although its working great I have a question. The unknowns 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. However I am dealing with complex chromatograms and don't have references for all compounds. So sometimes I run into a situation where the NIST library is making an obvious mistake. Lets say I am inspecting a component with a hit from the NIST library but I suspect the first hit is wrong. When I look at the other hits I may come across one that I think is more likely the right compound (or similar or just something I want to remember). So I select that hit at the best hit. When analyzing subsequent samples I would like to have the software automatically select my 'best hit' and not the NIST's original best hit. Obviously I can write it down somewhere else. But I am wondering what strategies I can take with the software to avoid always having to correct these situations.

Should I use the spectra from the sample to create a library of tentative hits like the ones I described? Or is there a way to export the unknowns analysis results and create a method that prioritizes the compounds described in the method? Thanks for any pointers. 

  • Hello  ,

    As you suggested, you could assign the chosen hit to a component and then export it to a custom library. If you include your RT data, then it should help prioritize that hit. To update other samples in the same analysis you would have to re-analyze, but it would then be there for future analyses. 

    Another option, which might not be practical with dozens of complex files, would be to select multiple files, sort the components by RT or compound name, and disable the option to show only the Best Hit. You would need to set your Max hit count to something high enough to see the desired alternative, but once you have the component table set up this way you can then chose multiple components, either by shift or ctrl left click, and assign them as Best Hit all at once. 

    For example, if I know that the compound around 6.5 minutes is really 2-ethenyl-Naphthalene and not Biphenyl, I can select the component in the first file, then ctrl-left click the component in the second file, then right click on one of them and choose Set Best Hits from the context menu. You could also sort by Compound Name and then they would be grouped together. 

  • Thanks Howard. Having both these options to work with should help. I didn't realize I could highlight multiple data files and get a results list that shows everything from all samples. That's actually really helpful for kind of work I am doing. 

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