Skyline Test Run

We have data!!!

Kind of. After meeting with Emma, we realized that for the purpose of the poster, we could use any oyster .blib file we had on hand. We used an oyster seed .blib for our Skyline analyses. A .blib file is a list of peptide spectra found in designated samples. Using a different .blib would change the reference spectra we would match the peptides in our samples with. While this method isn’t ideal for a paper, it’s good enough for a preliminary poster.

To use Skyline, we followed these tutorial slides, steps 2 through 6. My Jupyter Notebook can be found here.

In the end, we exported the data as a .csv and modified it. The files I’ll use going forward are below:

Maximum Area Spectra Average Area Spectra

Written on March 14, 2017