Search Software

ProteinPilot™ Software can perform protein identification and quantitation, along with prediction of hundreds of peptide modifications and non-tryptic cleavages simultaneously. The protein grouping algorithm helps in distinguishing protein isoforms and visualize peptide-protein associations and relationships. The new version can take in generic input for non-AB SCIEX instruments via .mgf format. Other features include : Automatic and Rigorous False Discovery Rate (FDR) Analysis; Improved Quantitation for iTRAQ Reagent-Based Workflows; Speed and Scalability Improvements; Extended Gel Workflow Support; Open Control of Parameter Settings; Extended Support for Instruments from Other Vendors; Improved Identification Quality; Command Line Control and Open Results.

SW Documentation: 

ProteinPilot™ Software v. 4.5 Beta (rev1656) is available via Remote Desktop to the windows application server For transferring data onto, your group might require a folder that can be used to transfer your data from project space for ProteinPilot analysis. Please send a mail to if you need project space for your group. There are many new features and performance improvements in this version, however, remember that this is a Beta version!  Please read the Release Notes carefully to make sure you are aware of the changes.  

ProteinPilot is also available on Galaxy-P ( A screencast for using ProteinPilot within Galaxy-P is available at:

A "viewer" version of the software is available via Remote Desktop to the windows application server Please note that this version of software can be used to view previously generated .group files. This version cannot be used for searching the data. For searching data, use ProteinPilot on copper or via Galaxy-P as mentioned above.

Some highlights in the new version:
  • Improved quantitation results for SILAC and other survey-level quantitation
  • Improved mass accuracy from better feature detection
  • Improved identification results
  • Support for new AB SCIEX instruments released in 2012, including the TripleTOF® 4600, TripleTOF® 5600+, QTRAP® 4500, and QTRAP® 6500 systems.
  • Peptide shared status is provided for better downstream use of ProteinPilot results with the MS/MSALL with SWATH™ Acquisition MicroApp 1.0 add-in for PeakView® Software (versions or higher)
  • New Spectrum Summary export
  • Reduction in false singleton and blank ratios


A number of tutorial materials and webinars have been created for ProteinPilot users.   You can find a complete list here.

Short Name: 
Service Level: 
SW Category: