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

Mascot for industry

The Mascot software suite is a complete solution for industrial and pharmaceutical research:

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Mascot Server, Mascot Distiller and Mascot Daemon are installed on your own hardware. They do not require an Internet connection to function, and there is no ‘call home’ feature that would send data out of the system. Install the products behind a firewall and use Mascot Security to control access. All sequence databases, user data and results are under your control.

System integrations

Mascot Server takes peak lists as input, and it is instrument agnostic. Many instrument control systems and third-party software integrate with Mascot Server, which means it ‘slots in’ to many existing workflows, such as Thermo Proteome Discoverer™, Waters ProteinLynx Global Server and Bruker Biophama Compass.

Mascot Distiller supports the raw file formats of every major instrument vendor in proteomics. It is the ideal front-end to Mascot Server for both interactive and batch use. All aspects of processing can be automated using Mascot Daemon.

If you have an in-house pipeline, use Mascot Parser to submit searches from C++, C#, Java, Python or Perl programs and read back the results for downstream processing.

Solid performance

Mascot is mature software and has been ‘battle hardened’ under real-life use over 25 years. Database searches are fully reproducible. The results files record all relevant input parameters and configuration values. And when you update the software, you can expect to get the same or better results in the new version.

With Mascot products, you can always drill down into the data and inspect the evidence for yourself. Diagnose common issues like instrument calibration, noise, missed cleavages, unsuspected variable modifications and labeling efficiency. View the quantitation profiles in Distiller to understand what is really happening in your sample.

Mascot Server is coded to be ‘embarrassingly parallel’. Whatever throughput is required for protein identification, it can be achieved by running Mascot on a sufficient number of processors, including cluster systems and the cloud. There is no limit to the number of concurrent users or searches.

Multiple Distiller and Daemon instances and instrument control systems can feed in to the same Mascot Server for efficient sharing of resources.

Configurable workflows

Set up any number of in-house FASTA files as searchable protein sequence databases. Mascot also ships with two dozen predefined definitions for publicly available protein sequence databases and spectral libraries.

Mascot takes modification definitions from the Unimod database, containing over 1,500 known chemical, artefactual and post-translational modifications, glycans, amino acid substitutions and crosslinking reagents. If these are not sufficient, add your own chemistry.

Mascot ships with two dozen quantitation methods, including iTRAQ, TMT, SILAC, 18O, 15N metabolic labeling and label-free quantitation. All aspects are configurable, including bespoke reagents, peptide and protein quality thresholds, outlier handling, statistical parameters and (for MS1 quantitation) XIC integration parameters.

Find unsuspected chemical and post-translational modifications, splice variants and unexpected cleavage with Mascot Error Tolerant Search. Identify endogenous peptides with Mascot no-enzyme search. Use Mascot Distiller de novo sequencing to identify novel peptides.

Set up crosslinking methods with standard or custom crosslinking reagents and public or in-house protein sequences tailored to your workflows.

Documentation and support

Mascot Server ships with extensive online documentation and training materials. Mascot Distiller ships with help and tutorials for common workflows.

Our Premium Support contract gives peace of mind. Receive all new versions for free as bugs are fixed and features added. Your questions are answered directly by Mascot developers and experts based in the UK and USA, who are also available for remote problem diagnosis.