Exporting from Unknowns Analysis To Quantitative Analysis


I am using MassHunter Version 10. I would like to transfer results from the Unknowns Analysis software into a Quantitative Analysis Method. The goal is to generate a 'semi-quantitation' method with internal standards with samples that typically have approximately a hundred components plus or minus 50 components. I've found some good instructions in a document called: 

Webinar_2_MassHunter_Advanced_Unknowns_Analysis (see slide below). 

I have a couple questions about the best way to go about doing this. 

Basically I have 3 types of components: 

1- Components that have been fully identified using a reference standard and a custom library built from those standards

2- Components that are tentatively identified based on mass spectra or other clues (Retention index, literature etc)

3- Components that are unknown but that I still would like to keep track of in quant method

I would like to add components from category 1 to the quant method by using the compound data from the same files I used to build the library and not the samples themselves (not all references are observed in all samples etc). Can I export directly from the library into quant? I guess alternatively I can open the data files where I ran the reference standards in unknowns analysis and export them over 1 at a time but this seems cumbersome. 

Regarding compounds in category 2. How do I go about exporting compounds from multiple data files (samples) into the same quant method without having a bunch of duplicate (or triplicate compounds). Can I clean this up later? I'm just not sure exactly how this would work. 

Regarding compounds in category 3. I would like to keep track of them by calling them unknowns and using the retention time as described in the slide below. However how do I take a component and make it a non-hit component? 

Thanks for any help or advice. I am willing to look over any documentation that might be helpful. 

  • Hello  ,

    I apologize for the delayed response.

    Regarding your first case where you have a composite library and want to make a quant method, newer versions of quant (at least 10.0 and higher) have the option to create a new method from library. This should do what you want.

    If your version doesn't have this option then probably the best option would be to open the different files in UA, process them with your custom library, and then select all of the samples in the sample table. This will show all components found for all selected samples in the component table and you can export to a quant method from there. 

    For case 2 I'm not able to find a good option for avoiding or removing duplicates. You would either need to sort the compounds in UA by name and then use ctrl-left click to manually select only one copy of each or delete the duplicates in quant's method editor.

    For case 3 I'm not able to find a way to remove an assigned hit or manually rename a component in UA. You would either need to change your match criteria so that the component is not a hit or export it and then rename it in the quant method. 

    One option you may want to consider for cases 2 and 3 is to use Qual instead of UA. While Qual is missing some of the deconvolution options of UA, it does offer manual compound identification/renaming and the ability to remove duplicates when initiating quant. 

  • I figured another way around this issue. If I export results from UA to a library editor file I can then import the library into Quant. 

Reply Children
  • Well done! How do you deal with duplicates then? Can you remove them in UA or quant?

  • I ended up sending spectra one by one from my sample and standard samples. So I guess its nor really a shortcut. 

    Either way if you have a target list of compounds that you can put into a quant method you would be able to generate a data table where those compounds are aligned in a row. If you have unknowns or non-targets and are just trying to export a table of all peak areas I've never been able to figure out how to get that to align in MassHunter or Chemstation. I don't think you can without additional software add-ons. You can always export data and write programs. Or you can do it manually in excel for example. 

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