analyses
contains figures and tables from MS Stats, DAVID, Revigo, etc. used both in the paper, and as supplementary materials
data
contains data files that are results from analyses, as well as the C. gigas proteome used as the background
RAW spectral data is not included in this repository, but can be found published: here
images
contatins screenshots of EncyclopeDIA and SkylineDaily, used in creating their respective protocols
notebooks
contains jupyter notebooks used for annotating BLASTp results and MS Stats results
protocols
contains three protocols used to process and analyze the raw DIA spectral data
scripts
contains R scripts for using MS Stats R package as well as modifying data tables