Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Posted by Web Master (January 30, 2024)

Obsolete IPI definitions and SARS-CoV-2 pre-release definition have been removed

Mascot Server ships with predefined configuration for several sequence databases, stored in databases_1.xml. The following definitions have become obsolete and have now been removed from databases_1.xml:

  • IPI_arabidopsis
  • IPI_bovine
  • IPI_chicken
  • IPI_human
  • IPI_mouse
  • IPI_rat
  • IPI_zebrafish
  • SARS-CoV-2

The International Protein Index (IPI) databases were superceded by Uniprot proteomes as long ago as September 2011. We kept the predefined definitions, because the FASTA files were still available at the EBI website. However, those files are no longer available, so there is no reason to keep these long-obsoleted definitions.

The SARS-CoV-2 predefined definition was added in March 2020, when Uniprot published a pre-release database for the virus. Since then, the sequences have been reviewed and incorporated in SwissProt, and in fact, the pre-release FASTA file disappeared from the Uniprot servers around September 2023. There is no reason to keep the SARS-CoV-2 definition – please use SwissProt instead, or set up a suitable Uniprot proteome database.

Removing the predefined definitions does not delete any databases in your local Mascot Server installation. If you had enabled any of the above, their local configuration points to the previous version of databases_1.xml and the sequence databases continue to work. The removal simply means you won’t be able to enable them on a new system or re-enable if you delete them. If you still need the databases, it’s best to make a copy in Database Manager and make sure it’s part of your backups.

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