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.
20181126-2015-Cgseed.sky.zip is too large to add to OWL… but it’s on Woodpecker (FTR 209)
New method in a nutshell
- Convert .raw to .mzML using MSConvert (Check)
- Walnut –> make .elib file using the .mzML files made in Step 1. “Save Chromatogram Library” (in progress - will be done tomorrow)
- EncyclopeDIA –> Search wide-window data with library from Step 2.
- 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:
- Finish new DIA analysis method
- Extraction plan for Crab samples - get input from Steven and Sam
- Start extractions (?)
I have a million classes (3), so I won’t have time to fit in extractions, but:
- Work on R script for adding new Qubit data
- Anything from my previous goals that I couldn’t finish