Scaffold

Scaffold complements Sorcerer. High throughput confident protein identification is a two step process. First Sorcerer runs Sequest to match mass spectra to proteins. Then Scaffold validates these protein identifications. Scaffold first automatically validates Sequest results with the "prophet" statistical algorithms and by optionally cross checking Sequest with X! Tandem. Sage-N Research has bundled this part of Scaffold into their Sorcerer Integrated Data Appliance (IDA).

The automatically validated results can be distributed to collaborators who can do further validation manually with the free Scaffold Viewer. Scaffold Viewer provides a variety of ways of focusing the manual validation effort where it is most needed. The validation tactics available include visually checking for repeatability of the proteins across samples, peptides across samples, and the spectral fragmentation peaks across peptides. A more detailed tactic is to verify that the peptide is consistent with the fragmentation peaks in the spectra.

Scaffold complements Sorcerer by validating, organizing, visualizing, and publishing Sorcerer's data. Together Sorcerer and Scaffold provide a complete solution to MS/MS data analysis. Sage-N Research distributes Scaffold as an integrated part of Sorcerer 2.