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.

Currently, MSI has only one ProteinPilot license. We ask that all users use the calendaring program to sign up for time on ProteinPilot. Please specify your name on the calendar. Prior to using the calendar for the first time please email to request access to the ProteinPilot calendar. Please limit your ProteinPilot reservation to less than 24 hours at a time. If you need additional time after your 24 hour session has ended and the license is not reserved you may reserve another 24 hour session.  If you are not able to reserve time on the calendar please email

You can use the following links to see the ProteinPilot calendar and reserve the license: ProteinPilot Calendar

Follow the instructions at to add a reservation to the calendar.

ProteinPilot™ Software v. 5.0 is available in the "Node-Locked Software" virtual desktop at Instructions for connecting to are available here. There are many new features and performance improvements in this version. Please read the Release Notes carefully to make sure you are aware of the changes.

Restore Files
If you modify the Data Dictionary and Parameter Translation files on the Xen ProteinPilot 4.5 version you must restore these files to the Original Modification Parameters after you complete your search so that the next user can ensure that the Standard, Unmodified Parameters were in use for their own search. We urge everyone to adhere to this policy.

Modifications to these files can drastically affect results outcome, in some cases, depending on exactly what modifications were made.

Clean Up Your Files
The C: drive on Xen (with node-locked licenses for ProteinPilot 4.5 version and Scaffold) has been getting full with input MGF files, search databases and output search results. We request that users back up and copy their .group, .sf3, MGF and other files once the searches are complete. Users can back up data to U: drive or any other location. Once you have backed up your files, remove the files from the C: drive so that there is enough space available for any new searches.


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 on all other MSI Windows systems. 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 the "Node-Locked Software" virtual desktop, 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.

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