Proteome Software

• 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.

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.

• 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.

• 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.

• 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.

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.

• 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.

• 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.

Ask anyway — the agent will say plainly that it is not published rather than guess.