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.


After using Scaffold for several months now, I have to say that I have been very impressed with its ease of use, robust features, and stability. Since I am doing several replicate experiments using LC/MS/MS, I generate a substantial amount of spectra, and I especially appreciate Scaffold's ability to easily compare proteins/peptides across multiple samples. Also, since I prefer to inspect and evaluate as many MS/MS spectra as possible, Scaffold's "Spectrum" view makes it easy to quickly evaluate the quality of the spectra, while at the same time providing detailed peak labeling if more careful inspection is required.

Todd Greco, Princeton University