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 capabilities
Mascot can identify peptides and proteins from MS scans and MS/MS scans. Separation with liquid chromatography or ion mobility is optional but very beneficial. Several acquisition modes are supported:
- MALDI – MS and MS/MS
- Data Dependent Acquisition (DDA) – MS/MS, LC-MS/MS, ddaPASEF
- Data Independent Acquisition (DIA) – coming soon!
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
- Refine results with machine learning (MS2Rescore, DeepLC, MS2PIP, Percolator)
- Identify unsuspected modifications, amino acid substitutions and semi-specific cleavage
- Top-down protein identification
- Quantitation using isobaric labeling (e.g. iTRAQ, TMT, TMTpro)
- Create and search spectral libraries
- Identify intact crosslinks
Mascot has become firmly established as the trusted benchmark 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.
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
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.
Mascot Server makes many aspects of data processing trustworthy, convenient and scalable.
- Full control: All aspects of the hardware and software are fully under your control
- Unlimited: Search data sets or databases that exceed the capabilities of competing products
- Privacy: We never track your software usage; no “call home” feature
- Confidentiality: Your data is fully under your control; if Mascot is installed on your local computer, your data is never uploaded to a public cloud
- Convenience: A single solution for data from instruments from different vendors
- Remote working: All Mascot functionality is available through a web browser
- Multi-user: Multiple people in your group can run searches concurrently, without restrictions
- Throughput: Multiple instruments and software packages can submit searches to the same server 24/7
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.
Licensing tiers
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.
Mascot Server is available in three ‘sizes’, determined by the number of processor cores used for database searching. There is no limit to the number of users that can submit searches to a Mascot server, and there is no limit to the size of peak lists or sequence databases.
Entry level is a Small licence, which uses up to 8 processor cores (16 threads) for the sequence database search. 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 a higher tier at any time. Start with just the number of cores you need today and upgrade as and when required.
| Tier | Processor cores |
|---|---|
| Small | up to 8 cores (16 threads) |
| Medium | up to 16 cores (32 threads) |
| Large | up to 128 cores (256 threads) |
If you have an existing Mascot Server licence, please contact us for a free 14-day trial of a tier upgrade.
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 Small ‘test server’ in addition to a ‘production server’, provided the licence is for Large
- 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 35% of the licence fee per year. Alternatively, you can buy a version update, which includes one year of Premium Support.
Software and version updates
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 the new version to you for free. Otherwise, the cost depends on whether your licence is for the current major version (3.x) or an earlier version (2.x).
| Your version | Support contract? | Version update cost |
|---|---|---|
| 3.x | under support | free |
| 3.x | expired | 35% of licence tier cost |
| 2.x | expired | 50% of licence tier cost |
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.
