Due to the dynamism of protein expression, a genome can give rise to different proteomes, but could we say that a proteome comes from different genomes?
Yes, different genomes can produce the same proteome.
Imagine a genome that only has a single protein-coding sequence (without splicing isoforms), the rest of the genome is simply regulatory sequences. Whatever those regulatory sequences may be, as long as that single protein is expressed, it'll be the same proteome.
If you consider a single nucleotide difference enough to say two genomes are different, then there are probably quite a lot of different genomes on earth that produce proteomes identical with at least one other genome.
No, if you want to have a generally valid statement. You can not say: "that a proteome comes form different genomes".
The official (MeSH) definition of the term "proteome" is:
The protein complement of an organism coded for by its genome.
Taking the first two answers into context, you cannot say given two proteomes that they came from different genomes, but as stated above in the first answer, if you consider a single base change to constitute what is a different genome then yes you probably have a lot of different genomes producing the same proteome.
There are a few fallacies here.
Firstly you cannot say based on a single base change that they are different genomes, Consider this, if your body is constituted by 10^13 cells, then from the time you were a zygote, with each turn in replication the replisome constituted by the DNA polymerase, introduced a few mutations in the genome.
Why you ask?
Because the fidelity of polymerase delta is 10^6 meaning that every one million bases it will introduce a mutation (link explaining differences between different types of mutation). But hold on, there are a few repair machanisms involved, this raises the aggregated fidelity to 10^9. Which means that every 1 billion bases you can expect to find a mutation in the sequence.
Are these all different genomes? No, of course not.
These are somatic mutations which are aggregated over the course of a lifetime. This is why we age, why we get cancer, and why we ultimately die.
Now consider this, your body is constituted by cells which are somehow different from each other based on their DNA sequence, they are also differently specialised to perform different tasks. These specialised subsets among those 10^13 cells produce different subsets of the entire proteome which as a cumulative whole represents the entire proteome of the organism.
Are they producing different proteomes? No, they are producing a subset of a larger whole superset, but the proteins produced are at different levels by all these cells. If you are interested, you can take a look at single cell sequencing
So I hope you understand that the question you asked has few underlying considerations which must be accounted for.
Next coming to the question at hand? Can we start from two proteomes which are the same and say they came from two different genomes even if you ignore the second answer above? Nope.
This is because of how proteins are translated. You can check out the reference translation here. Translation, the process which converts RNA to protein exhibits codon degeneracy a feature where amino acids are coded by two or more three letter combinations called codons, making the process of translation very robust to DNA mutations.
So finally, to make a very long answer short. Can we start from a proteome and say they came from different genomes? No