Scaffold

Scaffold is a comprehensive analysis suite developed in order to assist biologists and chemists with quantitative proteomics analyses. The resource allows users to view highly accurate statistics, complete with multiple types of graphs, including bar and pie charts.

Since this tool is highly specialized, it requires similarly trained users. Professional chemists and biologists constitute the most likely users, however anyone with an interest (and solid background knowledge) in proteins can find it very handy.

The software features multiple interface objects that can, at times distract the user's attention. There are multiple menu items from which to choose from and several buttons to the top and the left side of the main frame allow for quick-links to most of the program's core functions.

In essence, the program assists users with the first two steps in conducting a scientific analysis: loading and processing the source data. Besides the considerable processing power that the software offers to users, one must say that at each step there are numerous secondary functions that significantly improve the output product.

For example, spectrum models and fragmentation tables are generated based on the source proteins. Informative quantitative bar charts and Venn diagrams are also automatically created. Students and professors will also appreciate the peptide ROC plots and protein probability calculation plots that the software generates.

One of the really nice features, which scientists will especially like, is the “Publish” option. This generates stand-alone comprehensive Excel reports, based on the analysis conducted.

In conclusion, Scaffold is a detailed and powerful protein samples analyzer that can generate numerous statistics and charts based on the quantitative data.