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

Mascot Server.

Mascot is the benchmark for identification, characterisation and quantitation of proteins using mass spectrometry data. It is the trusted reference standard for over 25 years and continues to be cited by over 2000 publications every year.

Learn more about the tools developed by Matrix Science to get the best out of your data, whatever your chosen instrument. Mascot is a great choice for researchers, core labs, industry and educators.


June 11, 2024

The ASMS 2024 conference was held in Anaheim, California, on 2-6 June 2024. It was great to see many of [...]


March 26, 2024

We are pleased to announce a new distributor for Matrix Science products! Customers in Europe can now buy Mascot through [...]

Mascot Server

Mascot Server is a powerful search engine for identifying proteins and peptides from primary sequence databases using mass spectrometry data. Fast, parallel execution is combined with probabilistic scoring, chemical and post-translational modifications, iTRAQ/TMT quantitation, robust FDR estimation, top-down protein identification, Percolator rescoring, spectral libraries, intact crosslinking, and more.

The free service running on this website is ideal for evaluation and searching smaller data sets, as well as training courses. For large scale and routine work, you'll want to license Mascot Server to run in-house.

Mascot Daemon

Mascot Daemon is a batch automation utility, bundled with Mascot Server. In combination with Mascot Distiller, every step of a quantitation experiment can be fully automated.

Mascot Distiller

Mascot Distiller offers a single, graphical user interface to native (binary) data files from Agilent, AB Sciex, Bruker, Shimadzu, Thermo and Waters. Process raw data into high quality, de-isotoped peak lists. Identify proteins with Mascot database search and de novo sequencing, and quantify proteins using isobaric, isotopic and label-free methods. Automate all steps using Mascot Daemon. Distiller can be used for free in read-only mode as a project viewer, ideal for distributing search and quantitation results to colleagues.

Mascot Parser

Mascot Parser provides an API (Application Programmer Interface) 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. Free for non-commercial use.

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