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

An introduction to Mascot Server


Mascot Server is a powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries. While a number of similar programs are available, Mascot is unique in that it integrates all of the proven methods of database searching: peptide mass fingerprinting, sequence query and MS/MS ions search.

Mascot’s capabilities increase with every major version. Below is an overview of functionality, and full descriptions can be found in the online documentation.

  • Very fast, parallel execution on any number of processors
  • Probabilistic scoring universally applicable to any instrument type
  • Novel protein inference
  • Standard and custom chemical and post-translational modifications
  • Robust false discovery rate (FDR) estimation, optionally followed by semi-supervised machine learning using Percolator
  • Identify unsuspected modifications, amino acid substitutions and semi-specific cleavage
  • Top-down protein identification
  • Quantitation using isobaric labeling (e.g. iTRAQ, TMT)
  • Create and search spectral libraries
  • Identify intact crosslinks

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

Benefits of in-house licence

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) or spectral libraries
  • For automated, high throughput work using Mascot Daemon or your own pipeline
  • So that search results can be imported into a relational database
  • To add and edit modifications, enzymes, quantitation or crosslinking methods, etc.

Additionally, an in-house licence integrates with Mascot Distiller. Distiller complements Mascot Server capabilities with peak picking, de novo sequencing and isotopic and label-free quantitation.

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 CPU licence. The licence cost is based purely on the number of CPUs actually used by Mascot, which can be less than the total number of processors in the system. Each licensed CPU is good for up to 4 cores.

Premium Support

A Mascot licence includes a one year Premium Support, providing:

  • Priority access to expert technical support
  • No charge to swap to another supported platform
  • Remote problem diagnosis if deemed necessary
  • Run a 1 CPU ‘test server’ in addition to a ‘production server’, provided the licence is for 8 CPU or more
  • Free updates to all new releases of Mascot

Your questions are answered directly by Mascot developers and experts based in the UK and USA.

You can continue receiving these benefits in subsequent years by purchasing an annual support contract. Please see Licensing overview for details.