Andrew Webb - Resources

Andrew Webb - Resources

Systems Biology Mascot Server


The Australian Proteomics Computational Facility is funded by the Australian National Health and Medical Research Council (NHMRC grant number 381413), under the Enabling Grant scheme for providing support for a high quality, world-class computational research facility that will enhance the national health and medical research effort.


Access to the Mascot Server at the institute is free to all Australian Academic users.

  • To get access to the WEHI Mascot Server, please email There is no phone support for any Mascot issue.
  • For IT issues, i.e. if you can not access the Mascot Server, please ring the IT Help desk and log a fault P +61 3 9345 2589.


Please note that 7zip or gzip are used to compress the files. You will need a compatible program to decompress them.


The MSPnr100 is a ~8.9 GByte compressed fasta file compiled from all known reference protein sequences including NCBI, Refseq, UniProt, EuPathDB and Ensembl.

The sequence database is non-redundant at the species level, taxonomy enabled with consistent fasta header lines. A suitable regex for parsing the accession number and description in Mascot is as follows: >[^|]*|\([^|]*\) and >\(.*\) and for Scaffold use >[^\|]*\|([^\|]*) and >(.*)


The MSPnr95 is a ~7.9 GByte compressed fasta file compiled from the MSPnr100 sequence database at 95% sequence homology at the species level. A suitable regex for parsing the accession number and description in Mascot is as follows: >[^|]*|\([^|]*\) and >\(.*\) and for Scaffold use >[^\|]*\|([^\|]*) and >(.*)


Mascot updates SwissProt automatically on the first of every month, the most recent version is best downloaded directly from other sites. One possible mirror site is

If you have the utility wget you can fetch it with:



A file of common contaminants is available.  Note that this is different to the default Mascot contaminants database.

Useful tools

Tired of downloading your Mascot results one at a time? Download some handy tools, including a command line submission tool and conversion tools.