Ensembl protein identifiers from different assemblies In order to obtain orthologs for human genes, I am working with InParanoid version 7.0. This version of the database uses Ensembl Protein Identifiers (ENSP) from ENSEMBL version v54, which is based on NCBI 36 assembly of the human genome.

For my project, I need to have the Ensembl Gene Identifiers (ENSG) of these proteins, but in the last version of ENSEMBL, which is based on GRCh38 assembly. I need to use this version of InParanoid for consistency with previous analyzes.

Thus, my question is, could I just use biomaRt to map ENSP (from NCBI36) to ENSG (actual version) or this approach is inherently wrong?

Is it possible to "convert" ENSP identifiers from NCBI36 to GRCh38 and then do the map to ENSG?. I am aware of liftOver but I am not sure it would work here.
Those IDs are elderly! Ensembl 54 was 2009!

I would recommend using BioMart combined with the ID history converter. The ID history converter will convert old IDs to new, and BioMart will convert ENSPs to ENSGs. You can either use the ID history converter with the ENSPs first, then the current BioMart to get the ENSGs. Or you can use Ensembl 54 BioMart to convert the old ENSPs to old ENSGs, then update the ENSGs with the ID history converter. I would probably do both and compare results.