Proteome Software Company Profile


Proteome Software is committed to setting the industry standard in MS/MS proteome analysis with our Scaffold Software Suite. Our team of developers and technical support specialists work together to bring you the most intuitive, highest-quality products possible. From diligent programming and internal problem-solving to specific, clear customer support and product documentation, our dedicated group of employees strives to create a satisfying user experience.

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You may wonder where the name 'Scaffold' came from. In construction, scaffolding can be a temporary structure for holding workers and materials during the erection, repair, or decoration of a building. In education, teachers use the concept of scaffolding to move students beyond their current developmental stage or skill set and into progressively more difficult tasks.

In the context of proteomics, Scaffold was envisioned to compose a structure around the data so researchers have a flexible framework that would simplify their analyses. The goal was software that is intuitive and easy to use, built with powerful data manipulation that uses robust, computationally-demanding statistics and automatic data recalculation based on confidence thresholds. Scaffold was one of the first products to offer a free viewer. This capability enables researchers to share their results with colleagues. Empowering researchers and helping to further scientific advances brings us all a huge source of pride and satisfaction.

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Proteome Software is a veteran-owned, scientist-operated small business located in Portland, Oregon, USA. Here, we provide the proteomics community with the Scaffold Software Suite, an intuitive group of tools that have been built to use robust statistics for confident protein identification, verification, and quantitation. We work with researchers and other bioinformatics developers continuously to revise our algorithms in order to support new workflows.

Our customers drive us forward with their passion for doing proteomics right. In return, we strive to make pursuing those passions easier. Our software analyzes complex data with sound techniques that would be computationally difficult by other means. We have resellers around the world in order to reach the most diverse group of laboratories in the commercial and academic communities. We also distribute several other excellent products for your bioinformatics needs.

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In the spring of 2004, scientists Mark Turner, Brian Searle, and Ashley McCormick came together with an idea.

They each knew the informatics problems that faced the proteomics community that included: miles of Excel spreadsheets full of data, multiple search engines with no way of combining results, repetitive and exhausting analytical practices. At the NIH/NIST Peptide Fragmentation Workshop in 2004, Brian and Mark heard all these problems mapped out during a presentation by David Tabb. That night, they sat in their hotel room and brainstormed solutions, motivated to improve the field of proteomics.

They brought their discussions back to their colleague and several months later, the three of them developed what would soon become Proteome Software’s flagship product, called Scaffold.

Proteome Software debuted Scaffold at the 2005 ASMS conference. Members of the proteomics community were intrigued by Scaffold’s capability to combine multiple search engines’ results into a single analysis, inclusion of Peptide and Protein Prophet algorithms and Tabb's user-selectable filter concept (DTA select).

Since then, researchers and core labs around the world have learned to rely on Scaffold for their proteomics analyses. Today at Proteome Software, we continue to push our Scaffold Software Suite into – and through – the boundaries of protein examination.