# Proteome Software > Official Proteome Software business agent. Proteome Software develops the Scaffold family of mass spectrometry data analysis tools for proteomics… ## Ask it a question Proteome Software answers for itself at https://api.hailera.com/mcp/proteomesoftware. A client that speaks MCP can connect to that address; the tool is ask_proteomesoftware and the protocol is 2026-07-28. Where this file and the agent disagree, the agent is current. ## About Proteome Software Proteome Software is a scientist-operated software company based in Portland, Oregon, USA. We develop intuitive MS/MS data analysis tools for proteomics, metabolomics, and small molecule mass spectrometry. Who we are - Founded by Mark Turner, Brian Searle, and Ashley McCormack. - Team of developers, scientists, and technical operations specialists. - Focus on high-quality software, clear documentation, and responsive, scientifically informed support. What we do - Build the Scaffold family of mass spectrometry data analysis tools. - Support discovery and quantitative workflows in proteomics and small molecule analysis. - Serve core facilities, shared resource labs, and individual research groups worldwide. Source: https://www.proteomesoftware.com ## Where Proteome Software works Lists Enterprise and Portland as a location. Names Oregon as a service area. Areas beyond these are not published. ## Prices Proteome Software offers licensing for Scaffold products to both academic and commercial organizations. Standard list prices DDA and DIA tools - Scaffold DDA - Academic: $9,995 - Commercial: $12,995 - Scaffold 5 - Academic: $7,995 - Commercial: $9,995 - Scaffold Q+S - Academic: $11,995 - Commercial: $15,995 (Prices are in US dollars and subject to change. For the most current pricing, please contact the Sales Team.) Legacy products - Scaffold Elements - Academic: $4,995 - Commercial: $6,495 - Optional NIST23 MS/MS spectrum library add-on: +$300 - Scaffold PTM - Academic: $2,995 - Commercial: $3,995 - Requires loading mzIdentML and spectrum files (MZID/MGF). Legacy products include: - Minimal technical support via email only. - Documentation and license requests are still provided. Volume and enterprise licensing - In-lab licensing and discounts are available when purchasing additional licenses. - Enterprise, bulk, or site licenses are available; contact the Sales Team to discuss options and obtain a quote. Source: https://www.proteomesoftware.com ## Scaffold 5 and Scaffold Q+S (legacy DDA tools) Scaffold 5 and Scaffold Q+S are established DDA proteomics tools in the Scaffold product family. Scaffold 5 - Industry-standard DDA MS/MS proteomics application. - Searches raw data directly via MSFragger integration (MSFragger license required; free for academic labs). - Loads precursor-intensity data from multiple tools, including FragPipe and others. - Provides visualization of differential expression and statistical significance using spectrum counting or precursor intensity. - Supports collaboration via: - Cross-platform free Scaffold Viewer. - Excel reports. - mzIdentML exports. Proteome Software plans to phase out Scaffold 5/Q+S over time in favor of the newer Scaffold DDA quantitative platform. Scaffold Q+S - Full suite for labeled and precursor-intensity quantitation. - Supports iTRAQ, TMT, SILAC, and precursor-intensity based workflows. - Designed for users who require advanced quantitative options on top of Scaffold 5. For new quantitative workflows, Proteome Software recommends evaluating Scaffold DDA as the primary platform. Source: https://www.proteomesoftware.com ## Scaffold DDA overview Scaffold DDA is Proteome Software's quantitative platform for data-dependent acquisition (DDA) proteomics experiments. Key capabilities - Experiment-driven labeled and label-free quantitative analysis. - Supports iTRAQ, TMT, SILAC, and label-free workflows. - Accepts mzIdentML and related outputs from multiple search engines and pipelines. - Quantifies differential expression and tests for statistical significance. - Normalizes, rolls up, and interprets biological differences at peptide and protein levels. - Uses tools such as Sage or MSFragger for raw data searching (MSFragger license required; free for academic labs). Typical use cases - Comparing protein abundance across biological conditions. - Large-scale quantitative proteomics experiments. - Core facility pipelines needing flexible quantitation and reporting. Platforms and downloads - Installers are available for Windows, macOS, and Linux. - Current versions, installers, brochures, user guides, demo data, and release notes are provided on the Scaffold DDA product page. Source: https://www.proteomesoftware.com ## Scaffold DIA overview Scaffold DIA extends the Scaffold environment to data-independent acquisition (DIA) proteomics experiments. Key capabilities - Provides the familiar Scaffold look and feel for DIA data analysis. - Searches raw DIA data against: - DDA-based spectral libraries. - Prosit-predicted libraries. - Sample-specific DIA-only custom libraries. - Supports visualization and interpretation of DIA-based differential expression. Typical use cases - Large-scale DIA proteomics studies. - Core facilities and shared resource labs adopting DIA workflows. - Researchers who want DIA analysis in a graphical environment consistent with other Scaffold tools. Platforms and downloads - Installers are available for Windows, macOS, and Linux. - The Scaffold DIA product page provides current download links and documentation. Source: https://www.proteomesoftware.com ## Scaffold Software solutions overview Proteome Software provides the Scaffold family of proteomics, metabolomics, and small molecule MS/MS data analysis tools for handling large-scale identification and quantitative experiments. Main products Scaffold DDA - Experiment-driven labeled and label-free quantitative analysis. - Works with iTRAQ/TMT/SILAC and label-free workflows. - Integrates results from multiple search engines and analysis pipelines. - Provides statistical testing, normalization, and roll-up from spectrum to protein level. Scaffold DIA - Uses the familiar Scaffold interface for data-independent acquisition (DIA). - Searches raw DIA data against DDA spectral libraries, Prosit-predicted libraries, or DIA-only custom libraries. Scaffold 5 - Industry-standard DDA MS/MS proteomics tool. - Supports direct raw data searching via MSFragger (separate license required; free for academic labs). - Loads precursor intensity data from tools such as FragPipe. Scaffold Q+S - Full suite for labeled and precursor-intensity quantitation. - Supports iTRAQ, TMT, SILAC, and precursor-intensity based workflows. Scaffold Elements - Small-molecule LC-MS analysis. - Identifies and quantifies small molecules using MS1 and MS/MS data. Scaffold PTM - Focused on post-translational modification (PTM) analysis. - Evaluates modification site assignment confidence using Ascore-based probabilities. Free viewer - All Scaffold tools can be run in a free viewer mode without a license. - Enables collaborators and core facility customers to view and explore results across platforms. Source: https://www.proteomesoftware.com ## Small molecule and PTM tools: Scaffold Elements and Scaffold PTM Proteome Software provides tools beyond classic proteomics, supporting small-molecule analysis and post-translational modification (PTM) studies. Scaffold Elements - Designed for small molecule LC-MS analysis. - Identifies and quantifies small molecules using MS1 and MS/MS data. - Suitable for metabolomics and other small-molecule workflows. Scaffold PTM - Focused on protein post-translational modification analysis. - Evaluates modification site assignment confidence using Ascore and Ascore-derived probabilities. - Helps researchers interpret PTM localization and confidence alongside standard identification results. Source: https://www.proteomesoftware.com ## Support, tutorials, and documentation Proteome Software provides resources to help users get started with and make the most of the Scaffold product family. Tutorials and videos - Scaffold tutorials covering: - Getting started. - Advanced analysis workflows. - Product-specific features across the Scaffold tools. - Additional videos from past conferences and special events. - Tutorials are available via Proteome Software's YouTube channel and product pages. Documentation and quick links Each major Scaffold product page includes: - Product brochures. - User guides. - Demo data sets. - Release notes. These resources provide detailed information on features, workflows, and software changes. Technical support - Standard Scaffold products include technical support and product documentation. - Legacy products (such as Scaffold Elements and Scaffold PTM) receive minimal technical support via email, with documentation and license requests still supported. - For complex workflows, such as DIA, large-scale quantitative studies, or core facility deployments, the Proteome Software team can advise on software pipeline options and best practices. Source: https://www.proteomesoftware.com ## What Proteome Software has not published yet These are things people ask Proteome Software that its published information does not yet cover. - prices - availability - delivery times - contract terms or warranties - regulatory or compliance status - clinical or diagnostic outcomes Ask anyway — the agent will say plainly that it is not published rather than guess. ## Where this comes from https://www.proteomesoftware.com