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.


Compiling individual data sets to build a proteome database and add statistical analysis to compiled data sets required months of tedium using current free-ware and add-on utilities. We recently duplicated these efforts using Scaffold and were able to compile our database with statistical analysis within hours. Further, the data loading structure of Scaffold is dynamic, thus as we gain information on expression profiles we can update our proteome database. File export functions then allow us to rapidly annotate this proteome database with descriptors (such as structural and functional annotations) of the proteins in the database. In summary, Scaffold has become a significant asset to our research and reagent discovery program.

Karen Dobos, Colorado State University