Waters | Nonlinear Dynamics

Progenesis QI for proteomics

The next generation in LC-MS proteomics data analysis software.
Discover the significantly changing proteins in your samples.

Support for Scaffold v3.0 and v4.1

Download Scaffold v3.0 and v4.1

About this plug-in

Supports the use of Scaffold from Proteome Software. Scaffold allows you to use proven statistical algorithms to calculate the probability that proteins are actually present in your biological samples and so reduce the chance of including incorrect identifications in your results.

To be able to load Scaffold search results, the search should be performed in Mascot using .mgf files created by Progenesis QI for proteomics. The search results can then be processed by Scaffold and exported as a Excel format Spectrum Report to be read back into Progenesis QI for proteomics.

Export results from Scaffold by clicking on the Export menu, then the "Spectrum Reports" sub-menu and finally the "Spectrum Report..." command

See also