Selecting SRM Targets Part 4
Differential Expression + Protein Function = Targets?
Using the MSstats output I got from looking at pairwise comparisons with both Site and Eelgrass Condition, I looked at protein annotations to identify a short list of potential targets. In this Jupyter notebook, I first merged my pairwise comparisons with both protein annotations and accession codes.
I went through the list in search of proteins related to oxidative stress, hypoxia, heat shock, immune resistance and shell formation. To do this, I used the search command within Excel and copied the protein names into a new list. I looked for key terms in both the name of the protein and biological process GOterms. I also searched specifically for versions of the following proteins:
- Superoxide dismutase
- Glutathione peroxidase
- Cytochrome P450 (CYP1A)
- MDR proteins
Finally, I created a long list of about 100 proteins and shared it with Steven. We merged it with e-value information and he selected proteins I should start with for SRM target identification. The next step is to use Skyline!