Annotated Protein List from MS Stats with set thresholds... in progress

Yesterday and today I got some more 2015 DIA paper-related tasks done, including making a table that includes the proteins detected above a log2FC of 3.00 and below -3.00, and one that was annotated…

Tasks completed

  1. Uploaded the skyline daily .zip file to the Roberts Lab PanoramaWeb in a new folder entitled “2015-DIA-Cgigas-seed”.
  2. Updated links in the GitHub paper-pacific.oyster-larvae/protocols

Threshold protein lists

R script

Yesterday I made one without annotation. 20190403-2015Cgseed-protcomp.csv 26 proteins.
proteins_comp.csv

Today I made one with Steven’s annotated protein list. 20 proteins.
proteins_comp_annot.csv

We cross-referenced the 20190403-2015Cgseed-protcomp.csv with Steven’s pivot table created from 0403-DIA-Cgseed.csv and determined that if the log2FC number is negative, it’s 23C, and if the log2FC is positive, it’s 29C.

Weekend and next week tasks

  1. Keep working on paper (intro, methods, discussion)
  2. Get results for the paper figured out- do I include the phenotype data even though the 29C data is pooled from 7 silos…?
  3. Get repository to the point where it only has the important information. I still think I have too much stuff in there. But once everything is finished, it’ll be easier to ID what needs to stay and what needs to go.
Written on April 5, 2019