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

About Mascot

Mascot Server is the reference standard for protein identification by mass spectrometry since 1998. The product has been battle hardened under real-life use over 25 years. The search engine is very fast, scalable to any number of processors, provides transparent results and every new version increases its capabilities.

Mascot Distiller augments Mascot Server functionality with high-quality peak picking, raw data processing and quantitation, including all isotopic, isobaric, metabolic and label-free methods in common use. Mascot Daemon augments Mascot Server functionality by automating all aspects of processing, from raw data to quantified proteins. Mascot Parser provides an Application Programming Interface (API) to Mascot search results, configuration files and Distiller project files. Many vendor instrument systems and third-party products provide integration with Mascot.

Mascot is trusted by thousands of people. Our software is used for: routine research by individual scientists; high-throughput processing by core labs; industrial and pharmaceutical research; quality control; developing new proteomics methods; teaching proteomics; and as ground truth for training new machine learning models. Mascot software products fully support data from mass spectrometry instruments made by Agilent, Bruker, Sciex, Shimadzu, Thermo Scientific and Waters.

About Matrix Science

Matrix Science Ltd is an independent provider of bioinformatics tools to proteomics researchers and scientists, enabling the rapid, confident identification and quantitation of proteins. The company was founded in 1998 and is based in London, United Kingdom.

Timeline 1998-2007

John Cottrell and David Creasy founded Matrix Science Ltd in 1998. Mascot began as a fully automated, high-troughput version of MOWSE licensed from the Imperial Cancer Research Fund. The free Mascot Server launched at in November 1998, and the first product release was Mascot Server 1.0 in 1999. Mascot Daemon, our automation client, launched the following year. Our North American subsidiary Matrix Science Inc. was founded shortly after in 2001. Naoki Tanaka and Itaru Usami founded our Japanese subsidiary Matrix Science KK in 2003. By the end of 2003, Matrix Science Ltd employed several software developers and we had also released the first versions of Mascot Parser, our software toolkit, and Mascot Distiller, a Windows application for processing a wide range of native (binary) mass spectrometry data files.

By the end of the company’s first decade, software distribution agreements were in place with Bruker, AB Sciex (later Sciex), Kratos (later Shimadzu), Thermo Scientific and Waters, as well as a regional distributor Mass Solutions Technology (Taiwan). The number of Mascot Server licences sold continued to increase. There were eight major releases of Mascot Server, with version 2.2 released in 2007, and several more patch and maintenance releases. Mascot Distiller had three major releases, with version 2.1 released in 2006. And, the 10 millionth free Mascot search was submitted on this website in 2007.

Timeline 2008-2017

The company’s second decade saw four major releases of Mascot Server, Mascot Parser and Mascot Daemon (2.3 to 2.6), as well as five major releases of Mascot Distiller (2.2 to 2.6). Every product receives regular maintenance releases between major versions as needed. Two other software products, Mascot Integra and Mascot Insight, were discontinued by 2015. Integra was a proteomics data and sample management system based around a LIMS package from LabVantage. Insight, a successor to Integra, was a system for data reporting and visualisation. Much of the reporting and visualisation functionality has since then been added to Mascot Distiller.

In 2009, Cloud Scientific became the official distributor in mainland China, and a few years later SMAnalytical the official distributor in South Korea. We also launched a free, online Mascot training course, and started a monthly blog and a monthly newsletter featuring regular Mascot news and tips.

Timeline 2018-

The story of Matrix Science continues. After two successful decades, John and David have gradually stepped back from day-to-day management. Today, Matrix Science Ltd is run by Patrick Emery and Ville Koskinen. Patrick started as bioinformatics software developer at Matrix Science in 2002 and has been the primary developer on several products, most recently Mascot Distiller and Mascot Daemon. Ville joined as bioinformatics software developer in 2008 working on Mascot Server and Mascot Parser, as well as backend systems like product licensing. Matrix Science Inc. is headed by Richard Jacob, our North America country manager since 2005, and Matrix Science KK by Hirotomo Takaesu, who has been with MSKK for well over 15 years.

The 25 millionth free Mascot search was submitted at in 2019, in addition to countless more that have been run with in-house Mascot licences. We continue to improve the functionality of Mascot Server, Mascot Distiller, Mascot Daemon and Mascot Parser. Have a look at our News page for recent news, and subscribe to the newsletter for regular Mascot news and tips. We are also on Mastodon (, Twitter (@Matrix_Science) and LinkedIn (Matrix Science)