Proteome Software Company Profile


Proteome Software is committed to setting the industry standard in mass spectrometry analysis with our proteomics and metabolomics software. 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 employees work every day to create a satisfying user experience.

Scaffold Icon

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.

Elements Icon

Scaffold Elements employs parallel processing to efficiently analyze hundreds of MS samples with or without MS2 spectra. Metabolites are identified using multidimensional search and scoring algorithms.

Select a level of summarization and create filtered, interactive heat maps. Analyze complex experiments by using metadata to flexibly categorize your samples. Organize and re-organize data for fast visualization and quantitative analyses. Test for differential expression and calculate fold changes between samples and categories based on signal intensity.

Learn Icon

Proteome Software is a scientist-owned/operated small business located in Portland, Oregon, USA. We provide the mass spectrometry and proteomics community an intuitive group of proteomics and metabolomics tools. We use robust statistics to enable confident identification, verification, and quantitation, working with researchers and other bioinformatics developers to continuously revise our algorithms and support new workflows.

Our customers drive us forward with their passion for doing their analytics 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. Our resellers around the world reach a diverse group of laboratories in the commercial and academic communities. We also distribute several other excellent products to support your bioinformatics needs.

History Icon

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

They each knew the informatics problems that faced the proteomics community. There were miles of Excel spreadsheets full of data, multiple search engines with no way of combining results, and 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, 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, Proteome Software had developed several landmark products, including launching their first Metabolomics software tool, Elements, in 2015. Today, researchers and core labs around the world have learned to rely on Proteome Software for performing complex MS/MS analytics. Today, we continue to push our technologies into – and through – the boundaries of biological examination.