Hi Andrew,

This will do what you want; https://biit.cs.ut.ee/gprofiler/orth

I predict you'll run into problems where one mouse protein will map to two, or more, human proteins. That always makes things interesting.

Just make sure you are transparent about what you are doing, mice are not human. Another way would be to search the mouse data against a human database. In this case you also need to make it very clear what you have done.

Peter G Hains ah thanks!! is this tool compatible with UniProt accession numbers?

if not, should I find a way to somehow convert the UniProt no. to some other ID or would that just complicate things?

Yes, it works with Uniprot

Peter G Hains so I have screenshotted the screen and what is this "Numeric ID treated as" section? I thought this was where you put in "Uniprot Accession" but maybe not?

I suggest you look at the online help which includes examples.

https://biit.cs.ut.ee/gprofiler/page/docs#organism

It seems likely you do not have to select anything for numeric IDs.

Peter G Hains ahh thanks!! you are a life-saver! (my PI asked me to convert mouse proteome data to human proteome data and I was getting like really stressed cuz, well... ive never done it before lol)

you mentioned one protein mapping with multiple proteins... would that be like a database issue or biological/species issue?

Isoforms most likely. You also see it when you go from protein to gene or vice versa. You also have the complication of different species.