Leading edge analytics for mass spectrometry

Welcome to the Scaffold Software community

We offer DDA and DIA proteomics and small molecule mass spectrometry software solutions for handling large-scale, data-rich, biological identification and quantitative experiments.


Scaffold has proven invaluable in helping explain experimental results to our clients from large proteomics experiments. The visualization tools make it easy for our clients to understand complex MS/MS comparative analyses. Additionally, because Scaffold is so easy to use, it has greatly decreased the amount of time that it takes our lab to prepare experiment reports. Scaffold has quickly become our standard method to visualize, validate, and share MS/MS proteomics data with our clients.

Dave Allen, Proteomic Research Services