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. 

  • Hi Howard

    I see so there is no way UA can do this automatically for us? We have 60 over samples and 100 over compounds and going through manually is time consuming. I use Thermo Tracefinder which has the capability to do this only on thermo raw file. 

    If UA can align the compounds im excel when export, with all 60 samples , at least we can run PCA or ANOVA easily. Rather than showing ethanol 60 times, it automatically shows 1.

    So imagine left column you have all compounds and the rest of columns are 60 samples. If any samples doesn't have that compound it will be zero. 

    Hope that makes sense?

  •  ,

    Yes, it can be a little confusing if you are using full scan data from a TQ, or if you are initiating quant from qual. 

    No matter what type of data is opened in qual, it will always launch the QQQ version of quant. The method setup task is called MRM Compound Setup regardless of the scan type specified, but you can set up MS scan methods. It just looks a bit odd because by default it will still use columns such as Transition, Precursor, and Product Ion.

    What I would recommend is to go ahead and save the method or batch in the QQQ version. Then open the MS version, create a new batch with all of your data files, and open and apply the method here. The method will now appear to be a standard MS scan type method. You can use the MS version of quant for scan data acquired from either a TQ or SQ.

  • Thanks, that makes sense. Will give this a try. 

  • Hi Mui, 

    Ah yes I know what your trying to do now. I have no idea how to do this in UA or if its even possible. If you move your UA method over to a quant method I would image its a bit easier to get closer to what you want. Might be a good idea to start a fresh post about this. You might get more views / responses that way. 

  •  ,

    UA does not offer this type of data review. As you mention, the best you would be able to do is export a CSV to Excel and then manipulate the data there.

    There are other MassHunter applications that can do what you describe, though you'd need to pick the right programs/workflow depending on your data and ultimate goals. It would probably be best to contact your local Agilent support team Contact Us | Agilent and they would be able to have a detailed discussion with you about what tools would work best for your needs.

  • 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. 

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