An introduction to Mascot Server


Mascot has become firmly established as the standard for protein identification using mass spectrometry data. It will give excellent results with peak lists from instruments manufactured by:

  • AB Sciex
  • Agilent
  • Bruker
  • Jeol
  • Shimadzu
  • Thermo Scientific
  • Waters

Although Mascot can be accessed for free on our website, there are several reasons why you might choose to license Mascot for in-house use:

  • To search data sets that exceed the size limit on this free server
  • Confidentiality issues prohibit transmission of sensitive data to a third party
  • To search your preferred collection of sequence databases (any Fasta file)
  • For automated, high throughput work
  • So that search results can be imported into a relational database
  • To add and edit modifications, enzymes, quantitation methods, etc.

The Mascot search engine is very fast and the code is threaded for execution on multi-processor systems and clusters. Whatever throughput is required, it can be achieved by running Mascot on a sufficient number of processors.

This doesn’t have to mean a heavy investment upfront. Start with just the number of processors you need today and add additional processors to the licence as and when required. Note that there is no limit to the number of users that can submit searches to a Mascot server, even if it is just a single processor licence. The licence cost is based purely on the number of processors actually used by Mascot, which can be less than the total number of processors in the system. Each licensed processor is good for up to 4 cores.

A Mascot licence includes a one year warranty, providing:

  • Access to expert technical support
  • Free updates to all new releases of Mascot
  • No charge to swap to another supported platform

You can continue receiving these benefits in subsequent years by purchasing an annual support contract.