Scaffold 4 is available now !

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Introducing our New Reseller in France: Proteomics Solutions!

Founded in 2001, Proteomic Solutions is a specialized protein lab located between Paris and Rouen. Proteomics Solutions offers services for proteomics analysis projects, including recombinant protein technology. They also have experience in the field of bioinformatics.

Check out our other Resellers in the UK, Japan, China and Taiwan


Scaffold 4 introduces many new features!

Powerful FDR Analysis Capabilities

The new Local FDR scoring algorithm identifies significantly more proteins, particularly in high mass accuracy data.

Cluster Similar Proteins with Shared Peptide Evidence

The new shared peptide grouping algorithm retains more isoforms and related proteins, and protein clustering allows comparison of similar proteins at either the isoform or cluster level.

mzIdentML Allows New Search Engines

Scaffold reads and interprets mzIdentML files from any search engine, including PEAKS, MyriMatch, SQID and MS-GF+.

FDR Filtering Options

Browse the FDR Landscape 'heat map' to find the optimal threshold settings for your experiment.

New Quantitation Options

Scaffold now supports MaxQuant Label Free.

Based on your feedback, more quantitation options have been added: Weighted Spectra, emPAI, Weighted NSAF, and Fold Change by Category.

Improved Gene Ontology Annotation Support

Additional GOA Databases can easily be applied along with NCBI. Also, GO terms can be compared between sample categories.

Easier Interaction with Your Data

Users can now classify data with multicolored stars, quickly change preferred proteins in protein groups, save advanced filtering options as well as display settings, hide or show decoys with a click, inspect selected analytical options through 'dashboard lights' and more!

Improved Reporting and Exports

Export mzIdent ML 1.1.0 in a PRIDE compatible format or load into Skyline to create spectral libraries. Export all chart information and data, export subset databases, capture TIC, retention time and precursor intensity in the Peptides report, and more!

Also includes:

For a more complete description of these features, see the Scaffold 4 Brochure here.


Your Scaffold 4 keys...

Over the next several weeks, we will be sending out new Scaffold 4.0 keys to all our customers who have an active support agreement.

Please be patient as we complete this process.


Try Scaffold 4 Now!


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Proteome Software, Inc
1340 SW Bertha Blvd, Suite 10
Portland, OR 97219
Toll-Free (800) 944-6027