What Protein Metrics does

Protein Metrics is a vendor-neutral mass spectrometry software company specializing in biotherapeutic protein characterization, founded in 2011 and based in Cupertino, California. The company provides a platform-plus-modules architecture consisting of three core products: Byonic (a high-sensitivity MS/MS search engine for peptide and protein identification validated in independent benchmarks), Byos (desktop software for protein characterization supporting intact mass, peptide, oligonucleotide, HDX, de novo sequencing, reconstruction, and chromatogram workflows), and Byosphere (cloud-based enterprise platform for data management, analysis, templated reporting, dashboards, and team-wide collaboration). The software processes data from all major mass spectrometry instrument vendors and is differentiated by proprietary algorithms including the Parsimonious Deconvolution Algorithm and an automated de novo antibody sequencing algorithm.

The company serves biopharmaceutical companies, contract development and manufacturing organizations (CDMOs), and academic research institutions globally. Named enterprise customers include Roche, Sanofi, Genentech, Pfizer, Novartis, Janssen, Bristol-Myers Squibb, Amgen, Regeneron, GSK, AstraZeneca, Lonza, Boehringer Ingelheim, and Fujifilm Diosynth Biotechnologies, alongside academic institutions such as Stanford, Oxford, and University of Tokyo. Revenue is generated through enterprise software licensing (subscription/recurring) with a direct field sales motion; the company offers free trials for Byos and Byonic while enterprise Byosphere engagements are routed through Contact Sales. Distribution is augmented by an integration with Thermo Fisher Scientific's Proteome Discoverer platform. Protein Metrics operates as a subsidiary of Dotmatics, a diversified scientific R&D software platform, and holds ISO 27001 certification with GxP-ready compliance features.

The business is small (11-50 employees) and private, with the only disclosed funding being a $950K seed round in 2014, implying capital-efficient operation and likely funding through the Dotmatics parent or operating cash flow. The product cadence — nine sequential releases between March 2024 and April 2026 — indicates active R&D investment, while the integration into the Dotmatics portfolio positions the company as the proteomics layer within a broader enterprise R&D software stack.

Name

Protein Metrics

Legal name

Protein Metrics

Website

https://proteinmetrics.com

Company type

Private

Founded year

2011

Operating status

Operating

Headcount range

11–50 employees

Short description

Protein Metrics provides vendor-neutral mass spectrometry software for biotherapeutic protein characterization, serving biopharmaceutical companies, CDMOs, and academic research institutions with its Byos, Byonic, and Byosphere platforms as a subsidiary of Dotmatics.

Ownership category

akta.pro rank

Product category

Proteomics / Mass Spectrometry Software

NAICS

Analytical Laboratory Instrument Manufacturing (334516), Computing Infrastructure Providers, Data Processing, Web Hosting, and Related Services (518210)

SIC

Laboratory Analytical Instruments (3826)

akta.pro primary industry

Proteomics & Mass Spectrometry Services (HLAGANAB)

akta.pro secondary industry

Proteomics & Biomarker Analytical Testing (HLAGADAG)

Keywords

• Mass spectrometry software
• Biotherapeutic protein analysis
• Proteomics data analysis
• Protein characterization software
• Biopharmaceutical analytics

Headquarters

HQ city

Cupertino

HQ country

United States

HQ region

North America

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Marketing or Sales, Infrastructure, Operations

Revenue model

1. Software Licenses: Protein Metrics generates revenue through software licensing of Byos (desktop), Byonic (MS/MS search engine), and Byosphere (cloud enterprise platform). The company offers free trials for initial customer acquisition, with enterprise sales motion suggesting subscription or perpetual licensing models for pharmaceutical and biotech customers.

Pricing tiers

Go-to-market motion1 record

Distribution channels3 records

Marketing channels6 records

Core offering

Protein Metrics provides vendor-neutral mass spectrometry data analysis software for biotherapeutic protein characterization and quantification. Its portfolio includes Byos (desktop analysis software), Byonic (MS/MS search engine), and Byosphere (cloud enterprise platform), sold to pharmaceutical, biotechnology, CDMO, and academic customers.

Product overview

Protein Metrics offers a platform-plus-modules product architecture centered on three core software products: Byonic (full MS/MS search engine for peptide and protein identification), Byos (desktop software for comprehensive protein characterization with multiple workflow modules), and Byosphere (cloud enterprise platform for data management, analysis, and collaboration). The product portfolio includes specialized workflow modules for intact mass analysis, oligonucleotide analysis, multi-protein quantitation, peptide-level analysis, chromatogram analysis, de novo sequencing, reconstruction, and higher-order structure analysis. Additional capabilities include adaptive image compression for digital pathology and dashboard/analytics tools for data visualization and system suitability monitoring. The platform is vendor-neutral, supporting data from all major mass spectrometry platforms.

Differentiator

Problem solved

Functional benefit

Brands

• Byosphere: Cloud enterprise software platform for biotherapeutic mass spectrometry data management, analysis, and reporting.
• Byos
• Byonic

Products and services

• Byos Desktop software offering comprehensive mass spectrometry analysis workflows for robust biotherapeutic protein characterization and reporting, supporting intact, peptide, chromatogram, oligo, and multi-protein workflows with automated analysis and templated reporting.
• Byonic

Quantifiable outcome

• Deconvolution algorithm minimizes artifacts and harmonics for highly accurate mass determination
• +5 more outcomes

Named customers18 records

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration4 records

AI capability3 records

Feature6 records

Partnerships

Two partnerships are on record, tiered core.

• LonzacoreStrategic or Co-development PartnerLeading CDMO Lonza uses Byosphere to overcome bottlenecks in mass spectrometry and accelerate biologics development. Lonza shared how Byosphere enables high-throughput processing, automated workflows, and faster decision-making—empowering analysis of complex formats like bispecifics and multi-chain constructs. Heather Oakes from Lonza presented at Protein Metrics webinar on their CDMO mass spectrometry approach.
• Thermo Fisher ScientificcoreTechnology or IntegrationProtein Metrics provides Proteome Discoverer nodes that integrate Preview/Byonic into Thermo Fisher Scientific's Proteome Discoverer platform, enabling seamless workflow within the widely-used proteomics software environment.

Scale indicators1 record

Recent moves6 records

Expansion highlights6 records

Direct peers

• Genedata: Provides biopharma R&D informatics including Expressionist for MS-based protein characterization and Screener for assay data. Competes head-to-head with Byos/Byosphere in enterprise biopharma workflows with comparable per-customer contract economics.

Broad incumbents

• Thermo Fisher Scientific: Ships Proteome Discoverer and Chromeleon as native proteomics/mass spec software for its instrument installed base. Also a Protein Metrics integration partner via Preview/Byonic nodes, creating a coopetitive relationship where Thermo both distributes and competes with Protein Metrics.
• Waters Corporation: Offers MassLynx and Progenesis QI for proteomics/metabolomics, bundled with its LC-MS instruments. Direct competitor for biotherapeutic characterization software, especially in intact mass and peptide mapping workflows.
• SCIEX: Provides BioPharmaView and SCIEX OS for biologics characterization on its mass spec instruments. Comparable in targeting biopharma analytical workflows with similar intact mass and peptide mapping use cases as Protein Metrics.
• Bruker: Offers ProteinScape, BioTools, and timsControl for proteomics and biotherapeutic characterization. Competes in the same biopharma MS software category with both standalone tools and instrument-bundled offerings.
• Agilent Technologies: Ships MassHunter and Spectrum Mill for LC-MS data analysis including biotherapeutic characterization. Comparable incumbents in mass spec vendor software competing for the same enterprise pharma accounts.

Others

• Dotmatics: Parent company and adjacent platform owner of multiple scientific R&D software brands including Protein Metrics. Thematically adjacent as a scientific data management / ELN / informatics platform, but not a direct product competitor.

Emerging players

• Mestrelab Research: Specializes in analytical chemistry software including MS data interpretation (Mnova MS). An emerging specialist in molecular characterization tools that overlaps with Protein Metrics' analytical workflow footprint in pharma and academic settings.

Market position

Strengths4 records

Weaknesses4 records

Competitive moat6 records

Key risks6 records

Key highlights7 records

Customer concentration

Compliance2 records

Revenue estimate

Valuation estimate

Number of profiles

Profiles4 records

Funding overview

Funding rounds1 record

Investors

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Protein Metrics