Proteomics solutions you can trust
Matrix Science develops software solutions for mass spectrometry proteomics. Mascot is a great choice for DIA, DDA and PMF analysis.
Many third-party systems integrate directly with Mascot: Thermo Proteome Discoverer™, Bruker BioPharma Compass, Progenesis QI, Waters PLGS, Genedata Expressionist and Proteome Software Scaffold.
This server is running a pre-release candidate of Mascot Server 3.2. If you find any issues, please let us know by email.
Blog
September 23, 2026
The Cyber Resilience Act (CRA) is a European Union regulation that aims to improve the cybersecurity of all digital products sold in the EU – including proteomics tools. The regulation [...]
News
November 7, 2026
This website is now running a Mascot Server 3.2 release candidate, which is undergoing extensive beta testing. What’s new in Mascot Server 3.2 If you spot any bugs or experience [...]
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Protein identification
Mascot Server is the trusted reference standard for protein identification by mass spectrometry for 25 years. Mascot is designed for high throughput, and has no limits on the number of users, the size of the searches or the size of sequence databases. It continues to be cited by over 2000 publications every year.
Mascot Distiller is a vendor independent application for identifying and quantifying proteins using Mascot database searching. It offers a single, intuitive interface to native ("raw") mass spectrometry data files for DIA, DDA and PMF analysis.
Protein quantitation
Mascot Distiller supports a range of MS1 and MS2 quantitation methods for both DIA and DDA, such as label-free (LFQ), SILAC, 18O and metabolic labelling. Process raw files from Agilent, Bruker, SCIEX, Shimadzu, Thermo and Waters.
Mascot Server includes native support for TMT/iTRAQ quantitation.
Batch automation
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 Parser provides an API (Application Programmer Interface) to Mascot Server result files and Mascot Distiller project files, suitable for implementing your own system integrations and pipelining.