Grace’s Notebook: Tuesday, January 9, 2018

(1) 2015 OysterSeed Data

Today I revisited the 2015 OysterSeed skyline project. I left off at Step 5b .

I am going through ~100 peptides to check that Skyline chose the correct peaks. Peaks are there when peptide or transitions were detectable, and the greater the peak, the stronger the detection was.

I am not sure what to do when the peaks are inconsistent across all oyster seed samples within a peptide. I believe that in Yaamini’s SRM protocol, I was to delete the peptide if the pattern was inconsistent between samples.

Additionally, I am supposed to determine the per-sample and per-peptide error rates. To do this, I will be following what Yaamini did in her spreadsheet: here. Unfortunately, I asked about this after already checking 26 peptides. I didn’t keep track of which ones I checked, so I’ll have to start over tomorrow. I don’t think it should take too long.

(2) Roberts Lab Onboarding

I am going to transition to using a GitHub notebook in order to keep things to do with my projects more organized.