Which databases & organisms are used in mass spec protein ID service?

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Alphalyse
Nov 16. 2009

Question:

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?

Answer:

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

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