How to interpret a Stringdb interaction network of a mouse-proteomics dataset when it is detected only in Homo sapiens organism?

Question

[Farah]

Hello,

From an Immunoprecipitation/MS (pull down) analysis from mouse cells, I have a list of Accession IDs (such as P10809, P63261, Q09666, ...). I need to discover protein-protein interactions among all of these identified proteins and also specifically interactions with my bait protein (protein X).

So, I used String database to retrieve protein interactions. However, in String db, when I choose "Mus musculus" Organism, It does NOT find any proteins and produces this report "Sorry, the identifiers you provided did not match to any protein in your selected organism (Mus musculus)". However, when I select "Homo sapiens" organism, it can find protein interactions.

My question is that, in this case, from the String db interaction analysis of my identified proteins, in my publication, can I report this Stringdb-retrieved interaction for my proteins when they are detected by Homo sapiens organism and not Mus musculus?

Also, in this case, after retrieving the interaction, should I do further analysis or steps to also verify them in a Mus musculus organism or no need to do that?

I get confused about this issue. I will be so grateful if you can give me your advice in this regard. Best wishes

Answer 1

[andrew.j.skelton73]

Your protein identifiers are human. Take P10809 as an example

• Uniprot Entry - P10809 (CH60_HUMAN), 60 kDa heat shock protein, mitochondrial, HSPD1, Homo sapiens (Human)
• Mouse Uniprot Entry - P63038 (CH60_MOUSE), 60 kDa heat shock protein, mitochondrial, Hspd1, Mus musculus (Mouse)
• STRINGdb Entry for P63038

The solution is to use the Mouse Protein IDs, or gene symbols with the specified mouse organism.

[Farah]

That is great. Thanks a lot for your guide.