Scaffold Elements

Scaffold Elements is a small molecule LC-MS analysis tool developed by Proteome Software, designed to bring the power and familiarity of the Scaffold software ecosystem to the identification and quantification of small molecules. It is suited for both core facility managers and individual researchers who need a streamlined, easy-to-use solution for processing small molecule mass spectrometry data without the complexity of building a software pipeline from scratch.

Whether you are running a shared resource department, managing gaps in an existing software workflow, or setting up a new laboratory, Scaffold Elements provides an accessible yet capable platform for small molecule analysis using MS1 or MS/MS data.

Key Capabilities

• Identify and quantify small molecules using either MS1 or MS/MS data, enabling flexible analysis approaches depending on your experimental design.
• Load raw data directly from major vendor instruments, including Thermo, Sciex, and Agilent. Note that Windows is required to process vendor-formatted raw files.
• Search multiple spectral libraries including well-established databases such as NIST, HMDB, and LIPID MAPS, enabling broad coverage for compound identification.
• Create personal spectral libraries using spectra acquired from your own instrument, allowing you to build and maintain custom reference collections tailored to your research needs.

Who It Is For

• Core facilities and shared resource departments looking to fill gaps in their software pipeline, explore new analytical methods, and share results easily with their customers.
• Researchers and new labs seeking an elegant yet straightforward data processing solution that reduces the burden of software setup so they can focus on the science.

Platform Availability

• Scaffold Elements is available for download in the current version (3.0.5) across multiple operating systems: Windows 64-bit, macOS 64-bit, and Linux 64-bit.
• Processing of vendor-formatted raw files requires a Windows environment.

Proteome Software provides supporting resources including a dedicated brochure, a comprehensive user guide, MS/MS spectrum library references, and release notes. Tutorial videos covering everything from getting started to advanced use are also available via the Scaffold YouTube channel, alongside content from previous conferences and special events.