MassHunter Compound Discovery - custom option


I am performing untargeted analysis using MH Qualitative Analysis 10.0 - method workflow of 'Compound Discovery' - find by molecular feature and LB/DB/MFG. Mainly, I am doing MFE, then search the known compound using lcoal DB (Metlin), then those that are not found, do generate formula based on their m/z and RT. 

Regarding this, I have a few questions:

1) I also set up the method workflow 'Custom' - then add 'Find by molecular feature' and 'Search Compound (LB, DB, MGF)'. I just want to clarify if is this the same workflow or algorithm of 'Compound Discovery? 

2) With 'Custom' workflow, I have tested doing only 'Find by molecular feature' on batch data file using DA Reprocessor first. Then I made another method (Custom work flow with only 'Search Compound (LB, DB, MGF)') and ran DA Reprocessor on those data file that were ran for MFE. Then I realized the second DA Reprocessor process overwrote (?) and when opening the datafile (with load results), nothing was there. So if I do DA Reprocessor with two different methods separately, do it keeps overwrite the data results?

The reason why I did as described in 2) is because when I ran my batch with 'Compound Discovery' workflow method, it sometimes stopped when the data processor took a long time (see my previous forum question). So I decided to make two different 'Custom' method (MFE and Search Compound), run first MFE on DA Reprocssor, then run Search Compound on DA Reprocessor.

Much appreciate for any advice. Thank you in advance!

  • Hello  ,

    You should be able to set up a custom workflow that duplicates any of the default workflows. The one limitation would be that you would not have direct access to the default workflow's reporting templates. Since the workflow determines what report template is available you would have to use the custom report template. If needed, you can change another template's type so that it shows under the custom workflow drop down. To do this you have to manually edit the report template with a text editor and change the entry in the DesignerType tag from CompoundDiscoveryReport to CustomWorkflowReport, for example.

    I have been able to confirm the behavior you are seeing in DA Reprocessor and trying to reprocess using saved data. DA Reprocessor appears to always start without loading saved results and then saves the results obtained using the current method. I'm not aware of any way to force it to run a method starting with saved results. 

  • Thank you very much Howard. So I guess if a single method as "Compound Discovery" workflow runs more than a hour in the DA Reprocessor.. I should go to MH Qual to run the workflow one-by-one.

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