Exporting from Unknowns Analysis To Quantitative Analysis

Question

Hello, 
 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.

howard_sanford · Accepted Answer

Hello Justin_F , 
 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.

howard_sanford · Answer

Justin_F , 
 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.

Exporting from Unknowns Analysis To Quantitative Analysis

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