Proteome Software is a scientist-run small business based in Portland, Oregon, USA. Scaffold is its software suite for MS/MS mass spectrometry analysis. The product line covers DDA and DIA proteomics, metabolomics, small-molecule LC-MS, and post-translational modification analysis, mainly addressing processing, statistics, visualization, and results delivery for large, data-intensive biological identification and quantification experiments.
Scaffold DDA is designed for experiment-driven labeled and label-free quantification. It can analyze iTRAQ, TMT, and SILAC data, supports Sage and MSFragger, and uses Percolator to generate peptide and protein probabilities for FDR thresholding. Scaffold DIA supports DIA-NN, Spectronaut, PaSER, and PEAKS, and can search raw DIA data using DDA libraries, Prosit predictions, or DIA-only custom libraries. It includes built-in heatmaps, PCA, and statistical analysis. Scaffold Elements focuses on small-molecule MS1/MS2 identification and quantification, using spectral libraries such as NIST, HMDB, and LIPID MAPS. Scaffold PTM uses Ascore and derived probabilities to assess confidence in modification-site localization.
The products are available in 64-bit versions for Windows, macOS, and Linux, though some workflows that process vendor-format raw files require Windows. Ecosystem compatibility is a strong point: the materials list support for Thermo, Sciex, and Agilent instruments, as well as toolchains such as Mascot, Proteome Discoverer, MaxQuant, FragPipe, MS Fragger, and PEAKS. All Scaffold tools can be used as a Free Viewer without a license, making it easier for core facilities to share results with clients. Documentation is fairly complete, including user guides, brochures, demo data, release notes, and YouTube tutorials.
Scaffold uses commercial licensing. The academic versions of DDA and DIA are both priced at $9995, while the commercial versions are $12995; Q+S commercial pricing reaches $15995. Elements and PTM are relatively less expensive. A new license includes one year of upgrades and technical support, after which renewal costs 20% of the undiscounted list price. Three-month short-term licenses are available for DDA/DIA at about 30% of list price, and the cost can be credited toward a full purchase within 12 months.
The main advantages are broad coverage of mass-spectrometry use cases, rich ecosystem compatibility, a practical Viewer-based sharing model, and complete documentation and tutorials. The drawbacks are the high entry price, noticeable renewal costs, limited support for some legacy products, and the planned phase-out of Scaffold 5/Q+S. It is best suited to university platforms, core facilities, shared resource departments, and labs with steady mass spectrometry data output. For teams with limited budgets or those seeking a fully open-source workflow, MaxQuant, FragPipe, DIA-NN, and similar tools may be alternatives.
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