Grace’s Notebook: Start new DIA analysis using Walnut, EncyclopeDIA, and Bri-line

Today I tried doing the mprophet model in Skyline Daily. It wasn’t super great and I got stuck, but Emma reminded me that a lot of people who do DIA analysis prefer a new method using Walnut, EncyclopeDIA, and Bri-line. I started this new protocol today and am currently letting Walnut make the new chromatogram library, which will take a while. I’ll move on to the next phase for this tomorrow when the library is done.


mprophet is part of the Advanced Peak Picking Tutorial. I finished the model, but didn’t go into checking the error rates because Emma reminded me that the Walnut, EncyclopeDIA, “Bri-line” method is what others have been preferring. is too large to add to OWL… but it’s on Woodpecker (FTR 209)

New method in a nutshell

  1. Convert .raw to .mzML using MSConvert (Check)
  2. Walnut –> make .elib file using the .mzML files made in Step 1. “Save Chromatogram Library” (in progress – will be done tomorrow)
  3. EncyclopeDIA –> Search wide-window data with library from Step 2.
  4. Bri-line –> ELIB browser: look at peaks; RAW file browser: look at RAW files

This method is pretty straight forward and seemingly easy to follow – will report back on that in tomorrow’s notebook post.

Goals for the week:


  1. Finish new DIA analysis method


  1. Extraction plan for Crab samples – get input from Steven and Sam
  2. Start extractions (?)

I have a million classes (3), so I won’t have time to fit in extractions, but:

  1. Work on R script for adding new Qubit data


  1. Extractions
  2. Anything from my previous goals that I couldn’t finish

from Grace’s Lab Notebook