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

Mascot for core labs

Full stack solution

The Mascot software suite provides a full stack solution for core labs:

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. All sequence databases, user data and results are under your control.

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Single software, multiple instruments

Mascot Distiller supports the raw file formats of every major instrument vendor in proteomics. Once you have set up the software workflow, you can use it with any and every instrument in your lab.

Mascot Server takes peak lists as input, and it is instrument agnostic. The software ships with a dozen configurable instrument definitions, which define the expected ion series and neutral losses for your instrument.

Automate the routine

Mascot ships with two dozen predefined definitions for publicly available protein sequence databases and spectral libraries. Activate and keep databases up to date with a few mouse clicks. All standard quantitation methods are included out of the box, such as iTRAQ, TMT, SILAC, 18O, 15N metabolic labeling and label-free quantitation.

Set up automated processing with Mascot Daemon batch mode and real-time monitoring. Search raw files as they come out of the instrument; run searches on behalf of another user; share the task database between multiple Daemon instances; automatically generate a quantitation summary report; and more.

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.

Multiple Distiller and Daemon instances can feed in to the same Mascot Server. Mascot Distiller is licensed by workstation and will use all available processor cores. If you need more throughput for peak picking or protein quantitation, simply add more computers and licence more copies of Mascot Distiller.

Our Premium Support contract gives peace of mind. Your questions are answered directly by Mascot developers and experts based in the UK and USA.

Sharing results reports

Mascot Security can be used for sharing search results within your organisation. The results can be exported in a number of standard formats.

Mascot Distiller ships with a dozen quantitation reports, including ANOVA, box plots, hierarchical and K-means clustering, volcano plots and tabular reports. Export the results as XML file or CSV spreadsheet for further statistical processing.

Mascot Distiller can also be used for sharing the full quantitation project. Ask your client to install Mascot Distiller for free, without licensing it, and the product operates in view-only mode. Send them the raw file and the Distiller project file for interactive viewing of identification and quantitation results.

Boutique projects

Set up any number of in-house protein sequence databases. All aspects of quantitation are configurable, including bespoke reagents, peptide and protein quality thresholds, outlier handling, statistical parameters and (for MS1 quantitation) XIC integration parameters. Define project-specific crosslinking methods with custom reagents and in-house protein sequences.

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. Discover unsuspected variable modifications and splice variants with Mascot Error Tolerant Search. Use Mascot Distiller de novo sequencing to identify novel peptides.