Matrix Science
Matrix Science Limited, founded in 1998 in London, develops the Mascot software suite—a 25-year reference standard for protein identification in mass spectrometry proteomics. It serves researchers, core labs, pharmaceutical and biotech firms, and major instrument vendors via direct sales, regional distributors, and OEM partnerships.
- Company typePrivate
- Founded1998
- HeadquartersLondon, United Kingdom
- Headcount1–10
- GTM typeB2B
- OfferingSoftware
What Matrix Science does
Matrix Science Limited is a privately held UK software company founded in 1998 and headquartered in London (registered in England and Wales, company number 3533898). It develops the Mascot suite of software for mass spectrometry-based proteomics, with Mascot Server serving as the company's flagship product and a reference standard in protein identification for over 25 years. The Mascot product line comprises Mascot Server (a high-throughput search engine with no limits on users, search size, or sequence databases, supporting TMT/iTRAQ quantitation, label-free methods, error tolerant searching, and ML-based rescoring), Mascot Distiller (a vendor-independent Windows workstation for peak picking and quantitation across raw files from Agilent, Bruker, SCIEX, Shimadzu, Thermo, and Waters), Mascot Daemon (batch automation bundled with Mascot Server), Mascot Parser (an API and Python-compatible skill for system integrations and custom AI/ML adapters), and complementary tools including Mascot Cluster and Mascot Wizard.
The Mascot Server probability-based scoring algorithm is augmented with machine learning components (Percolator, MS2Rescore, MS2PIP, DeepLC) introduced in the 3.0 and 3.1 releases. The company monetizes through CPU-count software licenses (one-time and annual), recurring support and maintenance contracts, and professional services including training modules. Go-to-market combines direct enterprise sales (quotations in EUR, USD, CAD, GBP, AUD, JPY), five regional distributors (Europe, Taiwan, China, Korea, India and neighboring countries), and OEM/marketing partnerships that bundle Mascot with mass spectrometers from Bruker Daltonics, Shimadzu Biotech, AB SCIEX, Thermo Scientific, Waters, and Agilent. Customers span academic and industrial researchers, proteomics core labs, pharmaceutical and biotechnology companies, and educators, with the Mascot brand cited in over 2,000 scientific publications per year according to Google Scholar.
Matrix Science firmographics
Firmographics- Name
- Matrix Science
- Legal name
- Matrix Science Limited
- Website
- https://matrixscience.com
- Company type
- Private
- Founded year
- 1998
- Operating status
- Operating
- Headcount range
- 1–10 employees
- Short description
- Matrix Science Limited, founded in 1998 in London, develops the Mascot software suite—a 25-year reference standard for protein identification in mass spectrometry proteomics. It serves researchers, core labs, pharmaceutical and biotech firms, and major instrument vendors via direct sales, regional distributors, and OEM partnerships.
- Ownership category
- akta.pro rank
Matrix Science industry classification
Industry- Product category
- Proteomics Software
- NAICS
- Software Publishers (51321)
- akta.pro primary industry
- Proteomics & Mass Spectrometry Services (HLAGANAB)
- akta.pro secondary industry
- Proteomics & Biomarker Analytical Testing (HLAGADAG)
Keywords
Where Matrix Science is headquartered
LocationHeadquarters
- HQ city
- London
- HQ country
- United Kingdom
- HQ region
- Europe
Offices2 records
Markets served
Matrix Science business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure
Revenue model
- Software Licenses: Mascot Server and Distiller are sold as licenses. Mascot Daemon is bundled with Mascot Server license. Pricing is quote-based with quotations in major currencies (EUR, USD, CAD, GBP, AUD, JPY).
- Support and Maintenance: Annual support and updates available under warranty or support contracts. Update keys and download links provided to customers under support.
- Professional Services: Training modules and materials provided. Exercises and classic training course available.
Pricing tiers
| Model | Billing | Price |
|---|---|---|
| Subscription | Annual | Mascot Server - CPU-based licensing |
| One time/ perpetual license | Multi-year contract | Mascot Distiller - Workstation license |
| Subscription | Annual | Mascot Daemon - Bundled with Mascot Server |
Go-to-market motion3 records
Distribution channels4 records
Marketing channels6 records
Matrix Science product offering
Product offeringCore offering
Matrix Science develops and sells the Mascot software suite for mass spectrometry-based proteomics. The flagship offering, Mascot Server, is a search engine for protein identification from mass spectrometry data, supported by Mascot Distiller for quantitation, Mascot Daemon for batch automation, Mascot Parser for system integration APIs, and Mascot Cluster for parallel processing. The software is sold via licenses to research laboratories, core facilities, pharmaceutical companies, and academic institutions worldwide.
Product overview
Matrix Science develops the Mascot software suite for mass spectrometry proteomics. The core offering is Mascot Server, a search engine for protein identification that has been the trusted reference standard for 25 years. Mascot Distiller provides additional tools for protein identification including de novo sequencing and quantitation from multiple vendors' instruments. These core products are complemented by Mascot Daemon for batch automation, Mascot Parser for API access and custom integrations, Mascot Cluster for parallel processing on commodity hardware, and Mascot Wizard for guided workflows. The suite supports TMT/iTRAQ quantitation natively and integrates with machine learning tools including Percolator, MS2PIP, and DeepLC for improved identification rates.
Differentiator
Problem solved
Functional benefit
Brands
- Mascot Server: Core protein identification software for mass spectrometry, the trusted reference standard for 25 years. Supports high throughput processing with no limits on users, search size, or database size.
- Mascot Distiller
- Mascot Daemon
- Mascot Parser
Products and services
- Mascot Server The trusted reference standard for protein identification by mass spectrometry for 25 years, designed for high throughput with no limits on users, search size, or sequence database size. Includes native support for TMT/iTRAQ quantitation, error tolerant searching, spectral library searching, and crosslink search, and integrates Percolator, MS2PIP, and DeepLC for machine learning rescoring. Licensed by CPU count with cluster mode available for licenses of 5 CPU or more.
- Mascot Distiller A vendor-independent Windows workstation application for quantifying proteins and peptides from Mascot database searches. Provides tools for manual and automatic de novo sequencing, peak picking for raw files from Agilent, Bruker, SCIEX, Shimadzu, Thermo, and Waters instruments, and MS1 quantitation including SILAC, 18O, metabolic labelling, and label-free methods. Sold as a perpetual workstation license with a free evaluation option.
Quantifiable outcome
- Mascot is cited in over 2000 publications every year
Companies that use Matrix Science
Customer profileNamed customers6 records
Segments4 records
Ideal customer profiles4 records
Matrix Science technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- Yes
- API docs
- API detail
Core technology
AI maturity
App detail
Integration17 records
AI capability7 records
Feature7 records
Matrix Science partnerships and signals
Strategic signalPartnerships
Eleven partnerships are on record, tiered regional distributor, marketing partner and integration partner.
- MS Wilregional distributorMS Wil distributes Matrix Science products in Europe.
- Mass Solutions Technologyregional distributorMass Solutions Technology distributes and supports Matrix Science products in Taiwan.
- CloudScientific Technology Co. Ltd.regional distributorCloudScientific distributes and supports Matrix Science products in China. Contact by phone on +86 21 54975000 or by email to [email protected].
- SMAnalyticalregional distributorSMAnalytical distributes and supports Matrix Science products in Korea. Contact by phone on +82-32-851-2220 or by email to [email protected].
- BioInnovationsregional distributorBioInnovations distributes Matrix Science products in India and neighboring countries (Bangladesh, Bhutan, Maldives, Nepal, and Sri Lanka).
- Bruker Daltonicsmarketing partnerBruker Daltonics offers Mascot as part of their instrument package to enable seamless integration between the Mascot search engine and Bruker's BioTools.
- Shimadzu Biotechmarketing partnerMascot is the search engine of choice for Axima and LCMS-IT-TOF instruments from Shimadzu Biotech (incorporating Kratos Analytical).
- AB SCIEXmarketing partnerUsers can specify Mascot for searching data from TOF/TOF, TripleTOF, QSTAR, and QTRAP systems from AB SCIEX.
- Thermo Scientificmarketing partnerMascot is widely used for searching data from Thermo Scientific instruments including LTQ-FT and Orbitrap. Deep integration with Proteome Discoverer workflow software.
- Waters Corporationmarketing partnerUsers can submit searches to Mascot direct from Waters ProteinLynx Global Server.
- Agilent Technologiesintegration partnerMascot is highlighted as a software tool by Agilent Technologies to enhance productivity on their LC/MS systems for life science applications.
Scale indicators4 records
Recent moves6 records
Expansion highlights5 records
Matrix Science competitors and assessment
Company assessmentMarket position
Competitive moat5 records
Key risks4 records
Key highlights6 records
Customer concentration
Matrix Science social profiles
Digital presenceMatrix Science financial estimates
Financial estimateRevenue estimate
Valuation estimate
Matrix Science leadership team
Management profileNumber of profiles
Matrix Science funding detail
Funding detailFunding overview
Funding rounds
Investors
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
Matrix Science M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about Matrix Science
What does Matrix Science do?
Matrix Science develops and sells the Mascot software suite for mass spectrometry-based proteomics. The flagship offering, Mascot Server, is a search engine for protein identification from mass spectrometry data, supported by Mascot Distiller for quantitation, Mascot Daemon for batch automation, Mascot Parser for system integration APIs, and Mascot Cluster for parallel processing. The software is sold via licenses to research laboratories, core facilities, pharmaceutical companies, and academic institutions worldwide.
Is Matrix Science a public or private company?
Matrix Science is a private company. It is classified as founder individual operated bootstrapped and is currently operating.
When was Matrix Science founded?
Matrix Science was founded in 1998. It employs 1 to 10 people.
Where is Matrix Science based?
Matrix Science is headquartered in London, United Kingdom, in the Europe region.
How does Matrix Science make money?
Three revenue lines are on record. Software Licenses are the primary driver. The others are support and Maintenance and professional Services.
Does Matrix Science have an API?
Yes. Mascot Parser provides an API (Application Programmer Interface) to Mascot Server result files and Mascot Distiller project files, suitable for implementing system integrations and pipelining. Mascot Server 3.0 and later also ship with MS2Rescore for predicting retention time and spectral similarity, with support for custom AI/ML adapters via a Python-based API. Developer documentation is at www.matrixscience.com/msparser.html.
What industry is Matrix Science in?
Matrix Science's product category is Proteomics Software. Its primary akta.pro industry code is HLAGANAB, Proteomics & Mass Spectrometry Services, with a secondary code of HLAGADAG, Proteomics & Biomarker Analytical Testing. Its NAICS code is 51321.