Proteomics Data Analysis

Protein Pilot

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.

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Proteome Discoverer

The Proteomics Facility utilizes Proteome Discoverer for processing qualitative and quantitative proteomics data collected on ThermoScientific mass spectrometers (LTQ, OrbiTrap, and OrbiTrap Elite).  The software has qualitative workflows utilizing SEQUEST and Z-core algorithms for protein database searching of CID, HCD, and ETD data and quantitative workflows supporting TMT, iTRAQ, SILAC, and dimethyl labeling.

All data processing is performed by the facility, but results can be viewed in either Microsoft Excel outputs or the Proteome Discoverer viewer, which will allow for filtering and sorting of results and downstream processing of the results by the end user.  Please contact the facility for details regarding data processing as workflows can be modified for the type of experiment being performed.

To download the viewer, go to http://portal.thermo-brims.com and create an account.  After the account has been created, go to the Proteome Discoverer tab, downloads, update existing software if needed (be sure to follow instructions on prerequisite software required to run Proteome Discoverer) and download Proteome Discoverer.  A trial version of Proteome Discoverer will be installed on your computer which is fully functional.  After 30 days the trial version will only act as a viewer of output files.

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