ProteinPilot is used to process qualitative and quantitative proteomics data collected on the facility’s AB Sciex 4800 MALDI TOF-TOF mass spectrometer. The software uses the Paragon database search algorithm for peptide identification and Pro Group algorithm for protein grouping, and quantitative workflows can process iTRAQ and SILAC data. All data processing is performed by the facility, but results can be viewed in either Microsoft Excel outputs or the Protein Pilot viewer.
The viewer can be downloaded at http://discoverabsciex.com/lp=739 (currently ProteinPilot 4.5 beta). The software will be loaded as a fully functional trial version (capable of database searching and viewing results) and then convert to a viewer after 30 days.
Web Locations: free download available