Creating a Peptide Library in Skyline with a ProteinPilot™ 5.0 Software .Group File

If a user installs ProteinPilot™ 5.0 software with Skyline, old and new group files will not be able to be opened because the converter has changed. An error message will be displayed when building peptide libraries while importing a ProteinPilot group file. If ProteinPilot 4.0 or 4.5 software is installed with Skyline, older group files, but not 5.0 group files, will be able to be opened.

For users that upgrade to ProteinPilot 5.0, they can make a copy of the file C:\Program Files\ABSCIEX\ProteinPilot\GroupFileExtractor.exe and rename the copy as group2xml.exe, and place this file in the same location. This will allow Skyline to find the converter and open the new 5.0 group file formats.

However, older group files will not be able to be opened. To handle older files, a separate installation of Skyline and Pilot 4.0 / 4.5 software would need to be in place.