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:

  • 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.

Screenshot of the Mascot search form

Screenshot of the Mascot search results report

Free trial

You are welcome to use the free service running on this website. It is ideal for evaluation and searching smaller data sets. A selection of popular sequence databases are online, including SwissProt, Uniprot proteomes and the EST divisions of EMBL.

Most of Mascot Server functionality is available in the free service, but it has some restrictions. For routine or high throughput work, we recommend licensing Mascot in house.

In-house licence

There are several reasons why you might choose to license Mascot for in-house use:

  • You need a proven and high performance solution for protein identification
  • To search data sets that exceed the size limit on this free server
  • To search data sets or databases that exceed the capabilities of competing products
  • Confidentiality issues prohibit transmission of sensitive data to a third party
  • You need a single solution for data from instruments from different vendors
  • Multiple people in your group need to run searches concurrently
  • 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.
  • To be able to drill down into the data and validate the software’s decisions

Mascot Server is available for Windows and Linux on Intel and AMD processors. The software is typically installed on a server grade computer at your own premises, but you can also run it on your workstation, virtualised infrastructure and in the cloud. All aspects of the hardware and software are fully under your control, and there are no restrictions on the number of users submitting searches to the Mascot server or the size of the searches.

The licence is perpetual, not an annual fee, and includes 1 year warranty covering technical support and all updates. After the first year, if you wish to continue receiving technical support and updates, you have the option of purchasing a support contract.

Mascot Server is shipped as a digital download. Get a quote, send us the purchase order and we will send you the download link.

CPU upgrade

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.

Entry level is a single processor (1 CPU) licence. For licensing purposes, 1 CPU equals 4 cores. For example, a 1-CPU licence will use the first four cores in a system with 1 x 6-core processor or 2 x 4-core processors. If the system has more cores than are covered by the licence, the surplus cores are used for generating reports and web server/operating system overhead.

A licence can be upgraded to use additional processors at any time. 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.

If you have an existing Mascot Server licence, please contact us for a free 14-day trial of a CPU upgrade. Your licence does not need to be at the latest version.

If your licence is for 5 CPU or larger, you will get the best performance by setting up a Mascot cluster.

Premium Support

A Mascot licence includes one year of 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. After the first year, if you wish to continue receiving technical support and updates, you have the option of purchasing a support contract for 20% of the licence fee per year. Alternatively, you can buy a version update, which includes one year of Premium Support.

Version update

Your Mascot Server licence entitles you to use the licensed version or any earlier version (at your option). We regularly release new versions with major new functionality. If have an active Premium Support contract when a new version is released, we will send it to you for free.

If you are out of support, the cost is based on the version difference.

Version differenceCost
1 version25% of new licence
2 versions50% of new licence
3 versions75% of new licence
4+ versions90% of new licence

For example, if you have Mascot Server 2.5, and the latest version is 2.8, then the cost to update is 75% of the cost to buy a new licence with the same number of CPUs. When you update, you can optionally increase or decrease the number of licensed CPUs.

All version updates include one year of Premium Support. Please contact us for more information and a quote.

Top-down licence

The standard Mascot Server has a 16kDa limit for precursor masses, making it unsuitable for most top-down experiments. An optional special version of Mascot, known as Mascot Top Down, is available which has a limit of 110kDa.

If you have an existing Mascot Server licence, please contact us for a free 30-day trial of Mascot Top Down. Your licence does not need to be at the latest version.

Recommended products

Mascot Server bundles Mascot Daemon. Daemon complements Mascot Server capabilities by automating every aspect of data processing, from peak picking and search submission to protein quantitation.

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

Mascot Parser provides an Application Programming Interface (API) to Mascot Server result files and Mascot Distiller project files, making it easy to access search results from programs written in C++, C#, Java, Python or Perl.