NCBInr is dead, long live NCBIprot
NCBI recently dropped gi number identifiers, as explained in this blog article. This change breaks the old database definition, NCBInr, so we have created a new definition for accession.version identifiers, NCBIprot; now available on this site. If you search nr on your in-house Mascot Server, you’ll want to review the NCBI nr database setup page.
The strengths of nr are that it is comprehensive and frequently updated. The downside is that it is a huge database. As of September 2016, the 54 GB Fasta file contained 94 million entries. Even with a tight taxonomy filter, the size of the search space means that it is harder to get a significant match than in a database like SwissProt. If you have an in-house Mascot Server, there will usually be a better choice of database, such as a Uniprot complete proteome for your organism of interest.