Matrix Science

Matrix Science is a software company specializing in mass spectrometry-based proteomics solutions. Their flagship product, Mascot, has served as the trusted reference standard for protein identification by mass spectrometry for over 25 years, continuing to be cited in more than 2,000 scientific publications every year. Matrix Science serves a broad range of customers including academic researchers, core laboratories, industry users, and educators.

Mascot integrates directly with a wide range of third-party platforms, including Thermo Proteome Discoverer™, Bruker BioPharma Compass, Progenesis QI, Waters PLGS, Genedata Expressionist, and Proteome Software Scaffold, making it a flexible and interoperable choice for proteomics workflows.

Core Products

• Mascot Server – The central platform for protein identification by mass spectrometry. Designed for high-throughput environments with no limits on the number of users, search size, or sequence database size. Includes native support for TMT/iTRAQ quantitation.
• Mascot Distiller – A vendor-independent Windows workstation application that provides additional tools for protein identification and quantitation, including manual and automatic de novo sequencing. Supports MS1 quantitation methods such as SILAC, 18O, metabolic labelling, and label-free quantitation (LFQ). Compatible with raw files from Agilent, Bruker, SCIEX, Shimadzu, Thermo, and Waters instruments.
• Mascot Daemon – A batch automation utility bundled with Mascot Server. When used in combination with Mascot Distiller, it enables full automation of every step in a quantitation experiment.
• Mascot Parser – An API (Application Programmer Interface) that provides programmatic access to Mascot Server result files and Mascot Distiller project files, enabling custom system integrations and pipeline development.

Key Capabilities

• Protein Identification – High-throughput identification of proteins from mass spectrometry data, with no restrictions on search scale or database size, supported by 25 years of development and widespread citation in the scientific literature.
• Protein Quantitation – Comprehensive quantitation support including TMT/iTRAQ (natively in Mascot Server) and a full range of MS1 methods via Mascot Distiller, covering label-based and label-free approaches.
• Batch Automation – End-to-end automation of proteomics workflows through Mascot Daemon and Mascot Distiller, reducing manual intervention in large-scale experiments.
• API and Integration – Mascot Parser enables developers to build custom integrations and pipelines on top of Mascot result and project files.

Support, Training, and Resources

• Matrix Science provides dedicated support resources for each product, including Mascot Server, Mascot Distiller, Mascot Daemon, and Mascot Parser.
• Training materials are available including modules, exercises, and a classic training course archive.
• The company hosts ASMS User Meetings and publishes a monthly Mascot Newsletter distributed by email.
• Additional resources include a blog covering topics such as HLA class I peptide ligand identification, news updates, and system administration help.

Matrix Science continues to advance proteomics software with regular product updates, including the latest Mascot Server 3.1 and Mascot Distiller 2.8.5.1, maintaining its position as a foundational tool in both research and applied mass spectrometry environments worldwide.