Software

The resulting tandem mass spectra from a sample are matched to peptide sequences generated from a database of protein sequences. We are currently using SEQUEST via Thermo Proteome Discoverer 1.4  as our primary search tool and MASCOT 2.7 as a complimentary search tool for comparative proteomics and peptide identifications. Results from these searches are then imported into Scaffold where the peptide IDs are assigned to their best fit protein isoforms and various quantification parameters can be applied.  from all samples are presented in an excel spreadsheet format. For those inclined a free Scafold viewer can be readily downloaded.

• Download the FREE Scaffold Viewer and brief instructions for Scaffold 3.0
• Proteome Software (Scaffold) Resource Library

This page is actively under construction  (6-12-2020). Please check back next month and in the future for more information regarding Scaffview and PEAKS Studio X+, FAQs and other items.