Proteome Software

What Proteome Software does

Proteome Software, Inc. is a privately held, founder-led scientific software company headquartered in Portland, Oregon, founded in 2004 by Mark Turner, Brian Searle, and Ashley McCormack. The company develops the Scaffold Software suite, a portfolio of mass spectrometry data analysis applications for proteomics, metabolomics, and small-molecule research. Its products — including Scaffold DDA, Scaffold DIA, Scaffold 5, Scaffold Q+S, Scaffold Elements, Scaffold PTM, and Scaffold Variants — provide statistical validation, false discovery rate control, and unified visualization across results from multiple search engines (Mascot, Sequest, X!Tandem, OMSSA, MSFragger, DIA-NN, Spectronaut, PEAKS, Comet) and across raw data from all major instrument vendors via the ProteoWizard integration. The technology is differentiated by vendor-neutral raw file ingestion and proprietary algorithms for combining and statistically validating heterogeneous search engine outputs.

The company's commercial model is built on tiered perpetual software licenses priced between $2,995 and $15,995 per product, with academic pricing approximately 20-23% below commercial pricing, plus optional annual support and upgrade contracts at 20% of list price. Short-term 3-month licenses are available at approximately 30% of list. Distribution combines a direct North American enterprise sales team with five authorized regional resellers covering Japan, France, South Korea, Taiwan, and China. Customers span hundreds of academic, government (including the FDA), pharmaceutical, and commercial research laboratories worldwide, including Stanford, Harvard Medical School, Utrecht University, MRC Toxicology Unit, Children's Hospital of Philadelphia, Princeton, Duke, and Scripps. The company operates with approximately 10-12 employees and has not raised institutional funding, making it a profitable, bootstrapped niche vendor in the mass spectrometry informatics market.

Name

Proteome Software

Legal name

Proteome Software, Inc.

Website

https://proteomesoftware.com

Company type

Private

Founded year

2004

Operating status

Operating

Headcount range

1–10 employees

Ownership category

akta.pro rank

Product category

Proteomics / Mass Spectrometry Software

NAICS

Software Publishers (513210), Scientific Research and Development Services (5417)

SIC

Services-Prepackaged Software (7372)

akta.pro primary industry

Clinical Trial Informatics (EDC/CTMS/eCOA/eTMF) (HLAGAJAM)

akta.pro secondary industries

Proteomics & Mass Spectrometry Services (HLAGANAB), Proteomics & Biomarker Analytical Testing (HLAGADAG), Mass Spectrometry & Spectroscopy Instruments (HLAGAIAB)

Keywords

• Mass spectrometry software
• Proteomics data analysis
• Metabolomics analysis
• Quantitative proteomics
• Protein identification

Headquarters

HQ city

Portland

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

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

Revenue model

1. Perpetual Software Licenses: One-time purchase model for software licenses. Customers pay upfront for perpetual use of the software. Prices vary by product tier (DDA, Q+S, 5, PTM, Elements) and customer type (academic vs. commercial).
2. Annual Support and Upgrade Contracts: Optional annual contracts providing software upgrades and technical support. Charged at 20% of the undiscounted list price per year. Short-term licenses available in 3-month increments at approximately 30% of list price.

Pricing tiers

Go-to-market motion3 records

Distribution channels6 records

Marketing channels5 records

Core offering

Proteome Software develops and sells the Scaffold Software suite of mass spectrometry data analysis applications used by proteomics and metabolomics researchers worldwide. The portfolio includes Scaffold DDA, Scaffold DIA, Scaffold 5, Scaffold Q+S, Scaffold Elements, Scaffold PTM, and Scaffold Variants, along with a free cross-platform Scaffold Viewer, sold primarily as perpetual licenses with optional annual support and upgrade contracts.

Product overview

Proteome Software offers the Scaffold Software suite, a comprehensive portfolio of mass spectrometry analytics products for proteomics, metabolomics, and small molecule analysis. The portfolio includes two primary quantitative platforms: Scaffold DDA (for data-dependent acquisition) and Scaffold DIA (for data-independent acquisition), along with Scaffold 5 (industry-standard DDA tool), Scaffold Q+S (labeled and precursor intensity quantitation), Scaffold Elements (small molecule LC-MS analysis), and specialized add-on modules for PTM analysis (Scaffold PTM) and proteogenomics (Scaffold Variants). A free cross-platform Viewer enables collaboration and data sharing. All products share the Scaffold interface and support large-scale, data-rich biological identification and quantitative experiments.

Differentiator

Problem solved

Functional benefit

Brands

• Scaffold Software: Core product line of proteomics and metabolomics software solutions including Scaffold DDA, Scaffold DIA, Scaffold 5, Scaffold Q+S, Scaffold Elements, Scaffold PTM, and Scaffold Variants.
• Scaffold DDA
• Scaffold DIA
• Scaffold 5
• Scaffold Q+S
• Scaffold Elements
• Scaffold PTM
• Scaffold Variants

Products and services

• Scaffold DDA Quantitative proteomics platform for experiment-driven labeled (iTRAQ/TMT) and label-free quantitative analysis of data-dependent acquisition (DDA) mass spectrometry data, combining results from multiple search engines (Mascot, MSFragger, Sage) with statistical validation. Used by proteomics researchers and core facilities performing quantitative DDA experiments.
• Scaffold DIA Data-independent acquisition (DIA) proteomics software that searches raw DIA data against DDA library formats, Prosit predictions, or custom DIA-only libraries. Supports multiple search engines (DIA-NN, Spectronaut, PaSER, PEAKS) for high-throughput quantitative DIA workflows.
• Scaffold 5 Industry-standard DDA MS/MS proteomics analysis tool supporting direct raw data searching via MSFragger and quantitative analysis. Loads quant data from Proteome Discoverer, MaxQuant, and FragPipe for flexible workflow integration.
• Scaffold Q+S Proteomics quantification suite providing labeled (iTRAQ, TMT, SILAC) and precursor intensity quantitation with statistical analysis and visualization for proteomics experiments.
• Scaffold Elements Small molecule LC-MS analysis software for identification and quantification of metabolites using MS1 or MS/MS data, supporting multiple spectral library searches including NIST, HMDB, LIPID MAPS, DrugBank, MoNA, YMDB, and T3DB.
• Scaffold PTM Specialized tool for analyzing protein post-translational modifications (PTMs), using Ascore for site assignment confidence and providing motif annotation for PTM characterization.
• Scaffold Variants Proteogenomics tool that generates sample-specific search databases from genomic variant call data (VCF format), integrates Comet search engine and Percolator for FDR re-scoring, and incorporates dbSNP/ClinVar variant annotations for variant-aware protein identification.
• Scaffold Free Viewer Cross-platform free viewer that enables researchers and customers to view, share, and analyze Scaffold results for collaboration. Without a paid license, all Scaffold tools function as a free viewer.

Quantifiable outcome

• Hundreds of research laboratories worldwide rely on Scaffold software for proteomics data analysis

Named customers16 records

Segments3 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration21 records

Feature7 records

Partnerships

Six partnerships are on record, tiered core.

• Matrix Science K.K.coreChannel Partner/ Reseller/ DistributorMatrix Science K.K. serves as the authorized reseller for Proteome Software products in Japan. The partnership enables local sales, distribution, and support services for Japanese customers using Scaffold software for proteomics data analysis.
• ProteigenecoreChannel Partner/ Reseller/ DistributorProteigene (formerly Proteomic Solutions) resells Scaffold Software in France, providing local distribution and customer support services for the French proteomics research community.
• ScincocoreChannel Partner/ Reseller/ DistributorScinco serves as an authorized reseller of Scaffold products in South Korea, enabling local sales and support for Korean research institutions and laboratories.
• Mass Solutions TechnologycoreChannel Partner/ Reseller/ DistributorMass Solutions Technology sells and supports Scaffold Software in Taiwan, providing local market access and customer service for Taiwanese proteomics researchers.
• CloudScientific TechnologycoreChannel Partner/ Reseller/ DistributorCloudScientific Technology sells and supports both Scaffold and Mascot products in China, providing comprehensive proteomics software solutions for the Chinese market.
• ProteoWizardcoreTechnology or IntegrationProteoWizard provides the open-source toolkit that enables Scaffold software to read raw mass spectrometry files from all major instrument vendors (Agilent, Bruker, Sciex, Shimadzu, Thermo, Waters). This ongoing collaboration ensures universal compatibility with mass spectrometry instrumentation.

Scale indicators2 records

Recent moves6 records

Expansion highlights5 records

Direct peers

• Matrix Science: Developer of Mascot, the most widely used commercial protein identification search engine. Mascot is tightly integrated with Scaffold and is one of the key search engines Scaffold aggregates, making Matrix Science the most direct commercial peer in proteomics informatics.
• Bioinformatics Solutions Inc (PEAKS Studio): Vendor of PEAKS Studio, a commercial proteomics software suite covering de novo sequencing, database search, and PTM analysis. Competes head-to-head with Scaffold in the academic and pharma proteomics market and is also integrated as a search engine option within Scaffold DIA.
• Biognosys (Spectronaut): Provider of Spectronaut, a leading DIA proteomics analysis platform and a direct competitor to Scaffold DIA in DIA-based quantitative workflows. Both target pharma/biotech customers needing high-throughput, reproducible proteomics.
• MaxQuant (Max Planck Institute of Biochemistry): Free, widely used academic proteomics software package from the Max Planck Institute. MaxQuant is integrated with Scaffold 5 for quantitative analysis, but also competes directly with it for label-free quantitation workflows in academic labs.
• OpenMS: Open-source C++/Python framework for LC-MS data management and analysis, widely used in academic proteomics and metabolomics. Competes with Scaffold in core facility and academic settings as a free alternative for spectral processing and quantification.

Broad incumbents

• Thermo Fisher Scientific (Proteome Discoverer): Developer of Proteome Discoverer, an instrument-vendor proteomics software platform tightly coupled to Thermo mass spectrometers. Represents the broad-incumbent threat of an instrument OEM bundling its own software stack against vendor-agnostic players like Scaffold.
• Bruker (Proteomics Software Portfolio): Mass spectrometry instrument vendor whose software stack (including timsControl and Metaboscape) competes with Scaffold in metabolomics and proteomics. Represents the broad-incumbent model of bundling software with proprietary instruments.

Emerging players

• FragPipe (University of Michigan, Nesvizhskii Lab): Open-source computational pipeline built around the MSFragger search engine, integrated into Scaffold 5/Scaffold DDA but increasingly used as a stand-alone alternative. Represents a fast-moving open-source threat with academic momentum.
• DIA-NN (Vadim Demichev lab): High-performance open-source DIA proteomics search engine integrated with Scaffold DIA. Has rapidly become a leading DIA tool and competes with Scaffold DIA's underlying search layer for high-throughput DIA workflows.
• Sage (Broad Institute): Open-source, fast database search engine now integrated into Scaffold DDA. As an emerging open-source player, it represents both an integration opportunity and a competitive alternative for new proteomics labs building their pipelines.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/proteome_sw
• YouTubeyoutube.com/proteomesoftware
• LinkedInus.linkedin.com/company/proteome-software

Revenue estimate

Valuation estimate

Number of profiles

Profiles6 records

Funding overview

Funding rounds

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 Proteome Software