Proteome Software, Inc.

Proteome Software is a scientist-operated small business founded by Mark Turner, Brian Searle, and Ashley McCormack, headquartered in Portland, Oregon, USA. The company provides the MS/MS analytics community with an intuitive suite of proteomics, metabolomics, and small molecule mass spectrometry tools designed for handling large-scale, data-rich biological identification and quantitative experiments. Their team of developers, scientists, and technical operations specialists is dedicated to delivering high-quality products with clear customer support and thorough product documentation.

Proteome Software serves two primary audiences: core facility managers and individual researchers. Core facilities benefit from tools that fill gaps in software pipelines, support newer methods such as DIA proteomics, and provide easy ways to share results with customers. Researchers gain an elegant, easy-to-use solution for data processing that reduces the burden of setting up a software pipeline, allowing scientists to focus on their work.

Key Software Solutions

• Scaffold Software™ — the flagship platform and central product of the Proteome Software community, supporting both DDA and DIA proteomics workflows as well as small molecule mass spectrometry analysis.
• Solutions for large-scale biological identification and quantitative experiments, enabling researchers to compile individual data sets into a proteome database and apply statistical analysis in a fraction of the time required by free-ware alternatives.
• Dynamic data loading structure that allows users to update proteome databases as new expression profile information becomes available.
• File export functions that enable rapid annotation of proteome databases with structural and functional descriptors of identified proteins.

Core Capabilities

• Support for both Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) proteomics methodologies.
• Small molecule and metabolomics mass spectrometry data analysis.
• Statistical analysis tools integrated directly into the data compilation workflow.
• Streamlined pipeline setup suitable for new labs and established core facilities alike.
• Tutorials and video resources available via a dedicated YouTube channel, covering beginner to advanced use across all Scaffold products, as well as recordings from conferences and special events.

Team and Background

• Brian Searle, PhD (Co-founder/Owner) — co-founded Proteome Software in 2004 following proteomics research at Oregon Health and Science University; member and former board member of the American Society for Mass Spectrometry (ASMS); co-founder of the Proteome Informatics Research Group of the Association of Biomolecular Resource Facilities (ABRF).
• Kathy Bryant (President) — joined Proteome Software in 2004 and assumed expanded business leadership responsibilities in 2015, overseeing the company's core business functions.
• Caleb Emmons, PhD (Staff Scientist, Development) — holds a PhD in Mathematics from UC San Diego and brings expertise in algorithm development, statistics, and advanced probability to the software development team.
• Nick Vincent-Maloney (Director of Operations) — has worked in proteomics since 2002, with backgrounds in biochemistry and computer information systems, supporting researchers in leveraging powerful software applications and computing platforms.

Proteome Software has earned recognition from researchers at leading institutions, including Colorado State University, where users have reported reducing months of tedious data compilation work to just hours using the Scaffold platform. The company continues to develop cutting-edge analytics tools that empower the proteomics and mass spectrometry community worldwide.