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Progenesis QI for Proteomics version 3 MSe processing hanging - WKB55784

Article number: 55784


  • MSe, HD-MSe or SONAR data processing hangs Progenesis QI for Proteomics version 3
  • All the RAM on the computer is being used and so the computer is generally slow and unsresponsive
  • If you open the Windows Task manager, go the Process tab and sort by RAM usage a process called peptide3D.exe is using almost all the available RAM


  • Progenesis QI for Proteomics version 3

NOTE - this is specific to version 3. It is corrected in version 4 and later


The default low energy to high energy peak matching settings used by the peptide3D.exe during MSe processing mean peptide3D requires a lot of RAM, particularly if the Apex3D thresholds are too low due to not having been optimised correctly. As a result even a PC with 64GB of RAM may struggle with some data sets. These settings are not configurable from within Progenesis QI for Proteomics, but they can be modified using a command file.


  1. Save the attached file peptide3D_params.txt to C:\Program Files (x86)\Nonlinear Dynamics\Progenesis QI for proteomics\Plugins\WatersRawFolderReader\Processing\
  2. Optimise the Apex3D thresholds for the data being processed (see WKB1232) and reprocess the data.




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