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

Sequence database setup: TrEMBL

Overview

UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization. About 85 % of the protein sequences in UniProtKB are derived from the translation of coding sequences (CDS) from the EMBL-Bank/GenBank/DDBJ public nucleic acid databases.

In 2026, TrEMBL underwent a major reorganisation. Since the 2026_02 release, the unreviewed section is solely composed of proteins from reference proteomes, and an additional limited number of biologically interesting proteins.

UniProtKB is a collaboration between the European Bioinformatics Institute, the Swiss Institute of Bioinformatics and the Protein Information Resource.

Using the database in Mascot 2.5 and later

TrEMBL is a predefined database, meaning up-to-date configuration information can be downloaded automatically by Database Manager. In Database Manager, choose TrEBML under predefined definitions. Database Manager will download the up-to-date configuration information and the sequence database files.

Using the database in Mascot 2.4

Mascot Server 2.4 does not support HTTPS file downloads. We recommend updating to a later version of Mascot Server.

Using the database in Mascot 2.3 and earlier

Please refer to the local copy of this help page shipped with your version of Mascot Server.

Download URLs

The URLs are provided here for reference. If you are using Database Manager, you do not need to manually download these files.

UniProt: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/
EBI: https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase

The EBI site mirrors the UniProt site. The relevant files are:

  • Version info: reldate.txt
  • TrEMBL Fasta file: uniprot_trembl.fasta.gz
  • TrEMBL Dat file: uniprot_trembl.dat.gz

Parse Rules

A typical Trembl Fasta title line is:

>tr|A0AQI4|A0AQI4_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1

You can use either the ID (A0AQI4_9ARCH) or the AC (A0AQI4) as the identifier.

ID from Fasta title: ">..|[^|]*|\([^ ]*\)"
AC from Fasta title: ">..|\([^|]*\)"
Description from Fasta title: ">[^ ]* \(.*\)"

The corresponding lines in the Dat file are:

ID   A0AQI4_9ARCH              Unreviewed;         206 AA.
AC   A0AQI4;

ID from Ref file: "^ID   \([^ ]*\)"
AC from Ref file: "^AC   \([-A-Z0-9_]*\)"