I figured out how to upload results in Skyline such that there are 4 tabs (because I have 4 samples) and each tab has four files associated with it. Moving foward in DIA (confusion in determining error rate, so I’m stuck); plans for tomorrow and RNA isolation.
Today I moved forward with the 2015 oysterseed DIA analysis. I followed the DIA Analysis Protocol and for Step 4f I followed the instructions from Skyline’s tutorial:
This allowed for the data to be combined in tabs per sample. There were four oysterseed samples, and four RAW files per sample.
After emailing with Emma, I will calculate the error rate with the assistance of a Skyline tutorial and then will continue with analysis. After analyses and peaks are chosen, I will go back and check peaks on the peptides we want to look at.
Tomorrow I will isolate the RNA for the crab samples and will hopefully do it correctly. If it doesn’t go well, there are plenty of extra samples to choose from. The final sampling day (yellow-cap) were done in triplicate! The first and second had one sample/crab.