Mascot Server

Mascot Server, developed by Matrix Science, is a powerful search engine that uses mass spectrometry data to identify, characterise, and quantify proteins from DNA, RNA, and protein sequence databases as well as spectral libraries. Established as the trusted benchmark in the field for over 25 years, Mascot is unique in integrating all proven methods of database searching — peptide mass fingerprinting, sequence query, and MS/MS ions search — into a single platform. It is designed for researchers, core laboratories, industry scientists, and educators who require reliable, scalable, and high-throughput protein identification.

Mascot Server supports peptide and protein identification from both MS and MS/MS scans, with optional but highly beneficial separation via liquid chromatography or ion mobility. It is compatible with data from instruments manufactured by AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters, making it a versatile single solution for multi-vendor laboratory environments.

Supported Acquisition Modes

• MALDI – MS and MS/MS
• Data Dependent Acquisition (DDA) – MS/MS, LC-MS/MS, ddaPASEF
• Data Independent Acquisition (DIA) – coming soon

Core Capabilities

• 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
• Machine learning integration for result refinement (MS2Rescore, DeepLC, MS2PIP, Percolator)
• Identification of unsuspected modifications, amino acid substitutions, and semi-specific cleavage
• Top-down protein identification
• Quantitation using isobaric labeling (e.g. iTRAQ, TMT, TMTpro)
• Creation and searching of spectral libraries
• Identification of intact crosslinks

In-House Licence Benefits

• Full control: All aspects of hardware and software are fully under the user's control
• Unlimited: Search data sets or databases that exceed the capabilities of competing products
• Privacy: No usage tracking and no "call home" feature
• Confidentiality: Data is never uploaded to a public cloud when Mascot is installed locally
• Convenience: A single solution for data from instruments from different vendors
• Remote working: All Mascot functionality is accessible through a web browser
• Multi-user: Multiple users can run searches concurrently without restrictions
• Throughput: Multiple instruments and software packages can submit searches to the same server 24/7

Licensing Tiers

Mascot Server is available in three tiers based on the number of processor cores used for database searching. There is no limit to the number of users or the size of peak lists and sequence databases. Licences can be upgraded at any time.

• Small: Up to 8 processor cores (16 threads)
• Medium: Up to 16 processor cores (32 threads)
• Large: Up to 128 processor cores (256 threads)

Premium Support

• Priority access to expert technical support from Mascot developers and experts based in the UK and USA
• No charge to swap between Windows and Linux versions
• Remote problem diagnosis if deemed necessary
• Ability to run a Small test server in addition to a production server (Large licence only)
• Free updates to all new releases of Mascot

Top-Down Licence

• The standard Mascot Server has a 16 kDa limit for precursor masses, making it unsuitable for most top-down experiments
• An optional Mascot Top Down version is available with a limit of 110 kDa
• Existing licence holders can request a free 30-day trial of Mascot Top Down

Recommended Companion Products

• Mascot Daemon: Bundled with Mascot Server; automates every aspect of data processing from peak picking and search submission to protein quantitation
• Mascot Distiller: Integrates with Mascot Server to provide peak picking, de novo sequencing, and isotopic and label-free quantitation
• Mascot Parser: Provides an API to Mascot Server result files and Mascot Distiller project files, enabling programmatic access to search results from C++, C#, Java, Python, or Perl

Mascot Server is available for Windows and Linux on Intel and AMD processors and can be deployed on server-grade hardware, workstations, virtualised infrastructure, or in the cloud. The licence is perpetual rather than subscription-based and includes one year of Premium Support covering technical support and all updates. A free trial is available via the Matrix Science website, with a selection of popular sequence databases including SwissProt, UniProt proteomes, and the EST divisions of EMBL.