I would like to identify proteins from an organism where the genome has just been sequenced. How many proteins are available in the database you use, and from what organisms?
For Protein Identification we use the public database from UniProtKB. It collects information on all known protein sequences. It consists of the Reviewed, manually annotated sequences from Swiss-Prot as well as the unreviewed computationally analyzed sequences from TrEMBL.The database is constantly updated with new sequences. Therefore, we download it to our in-house Mascot server on a regular basis. Currently, the database contains more than 70 million protein sequences.
More information here: https://www.uniprot.org/help/about