mProphet Questions

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mProphet Questions anirudhkashyap511  2024-07-16 11:31
 

I have two questions

  1. Understanding Default Peak Picking Models in Skyline: When you import data into Skyline, does it utilize an mProphet or another default peak picking model? Furthermore, is it recommended to train an mProphet model enhance peak identification accuracy in Skyline?

  2. Exporting mProphet Features via Skyline Runner: Is it possible to export all mProphet features (for all the skyline files) using Skyline Runner? While exporting a report file is straightforward, incorporating mProphet features into this report seems challenging. Are there any methods or workarounds to include these features in the export?

 
 
Nick Shulman responded:  2024-07-16 13:16
When you Import Results into a Skyline document, Skyline always uses the default peak picking model.
In order to pick peaks using your trained model you would need to use the "Refine > Reintegrate" menu item.

We do believe that a trained peak picking model will do better than the default model. The other thing that it does is give you "Detection Q-Value" and "Detection Z-Score" values that you can find in the Document Grid which will tell you how good the peaks are.

If you are using Skyline-daily, then there is a command line command "--exp-mprophet-features" that you can use to export mProphet features.
This command is not available in Skyline 23.1.

We will be releasing Skyline 24.1 in a week or two, and Skyline 24.1 will also support the "--exp-mprophet-features" command.
-- Nick
 
anirudhkashyap511 responded:  2024-07-16 13:29
Hi Nick, Thank you so much for the reply. It was helpful. However I do have one question, I'm not sure how I see the "Detection Q-Value" and "Detection Z-Score" values. Do I add it into a report file?
-Anirudh
 
Nick Shulman responded:  2024-07-16 14:28
Yes, you would need to create a custom report with the "Detection Q-value" and "Detection Z-score" columns on them.

If you would like to learn more about custom reports you should look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

When you are editing a report definition, there is a binoculars button on the toolbar at the top of the Edit Report form which will let you search for a column by name.
-- Nick