Hello,
So I have mouse brain tissue MS data from one of my predecessors and I have human serum data from the hospital that I collaborate with.
We are trying to find markers for the diagnosis of autism.
My PI told me that there is a tool in STRING that lets you see if the proteins found in tissue is secreted to serum or a tissue protein. He wants to use that tool to find proteins that are secreted into serum by the mouse brain tissue and compare that with human serum data. Here is where I have my first question/doubt:
I know that you can annotate keywords such as "Secreted" in the UniProt keyword. I also saw that you can annotate "serum" in one of the databases to see which proteins are enriched in serum... but serum proteins can also be found in tissue and tissue proteins can be found in serum... so how can we know for sure based on this fact that the protein enriched IS appropriate for comparison with human serum?
Also, I tried, as a test, of copy and paste of human serum proteins into STRING and enrich for "Secreted" and/ or "Serum", shouldn't ALL proteins be enriched? I found that only some were enriched for "secreted" or "serum"
I mean,,, would it not make sense to compare plain old tissue MS data and human serum MS data?
Thanks!!