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

Mascot for researchers

The Mascot software suite consists of four products:

Get a quote for the full stack or individual products.

Why licence Mascot?

Many free solutions exist for protein identification by database searching and protein quantitation. Some are open source; others are closed source but are distributed as freeware. Why pay money for Mascot?

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. Define project-specific crosslinking methods with custom reagents and in-house protein sequences.

Set up automated processing with Mascot Daemon batch mode and real-time monitoring. Search raw files as they come out of the instrument; automatically generate a quantitation summary report; and more.

Scale up

Mascot Server can search 1 spectrum or 100 million. The database can be a single protein or 1 billion sequences. Identify proteins from single cells to metaproteomics. Use a MALDI-TOF or high-throughput LC-MS. Install on a workstation or in the cloud.

Mascot Distiller processes raw files in parallel on all available processing cores. Multiple Mascot Daemon and Distiller instances can feed in to the same Mascot Server.

Discover the unexpected

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

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.

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.

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. Develop new quantitation methods without having to develop new software.

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

Analyse intact proteins with Mascot Top Down. Mascot ships with two dozen definitions for enzymes or enzyme mixtures – or add your own for middle-down or bottom-up analysis.

Publication ready

Mascot is mature software and has been ‘battle hardened’ under real-life use over 25 years. Mascot continues to be cited by over 2000 publications every year.

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, without invalidating past findings.

Robust PSM, peptide and protein FDR using target-decoy searching. Enable Percolator rescoring for an additional boost.

Create a list of confidently identified proteins with Report Builder. Export search results 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.

Documentation and support

Mascot Server includes 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.