Scaffold version 1.5 Update

Scaffold has built a reputation as an efficient and accurate MS/MS proteomics analysis tool. Across the country, our customers tell us they like working with it and have confidence in Scaffold results. Our job at Proteome Software is to keep improving the software, and the user experience. Here are the latest feature additions and improvements designed to meet -- and exceed -- our customers' expectations.

One Click to Publish

The major proteomics journals are making a push toward proteomic data submission standards. Scaffold is the first tool available that automatically prepares your data for submission according to journal standards. This is a huge headache that Scaffold fixes: we generate the supplemental material and even write your methods section for you.

Improved Data Handling

The latest version of Scaffold has serious improvements in the amount of spectra that can be loaded into Scaffold, and in the graphic user interface performance. This means you can now realistically load in 1 million + spectra.

Data Security

As a scientist you want to share your findings with the community at large, but how can you do it while keeping your underlying data secure? Scaffold allows you to password protect your results at different levels so you get to choose what information is shared.

Statistics Improve Your Data

Protein identifications expressed as probabilities are a great way to easily understand MS/MS results. Our algorithms help you zero in on correct identifications and unlike other programs, our GUI lets you decide if we are doing a good job. Plus, with Scaffold you can always fallback to peptide scores instead.