Sequence database setup: Contaminants
Overview
If you search a single organism database, its usually a good idea to include sequences for common contaminants, such as keratins, BSA, and trypsin.
Two groups make their collections available for download. The Max Planck Institute of Biochemistry, Martinsried, maintains a file of approximately 250 proteins selected from various sources. The Global Proteome Machine Organization common Repository of Adventitious Proteins contains some 116 proteins selected from Swiss-Prot. (Numbers as of October 2026).
Using the database in Mascot 2.4 and later
Both contaminants and cRAP are a predefined databases, meaning up-to-date configuration information can be downloaded automatically by Database Manager. In Database Manager, enable contaminants or cRAP from predefined definitions. Database Manager will download the up-to-date configuration information and the sequence database files.
Using the database 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.
https://www.matrixscience.com/downloads/contaminants.zip
for contaminants by MPI, hosted by Matrix Science
ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta
for cRAP from GPM
Taxonomy
Taxonomy is not appropriate. You want to include all contaminants in every search.
Parse Rules
Fasta title lines in the MPI collection vary according to the source database.
Fasta title lines in the GPM collection contain SwissProt ID and no description.