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Peptide3D processing hang and ProteinLynx Global Server (PLGS) 3.0.3 stuck - WKB13412

Article number: 13412

This article is part of a troubleshooting path. If the symptoms below do not precisely match your issue, or if the solution has not fixed the issue, consider starting at the beginning of the path using this link


  • Processing MSe hangs, often during the peak matching step
  • In some cases the Job Viewer in PLGS shows processing is stuck at the "calibrate Z1 drift raw" step
  • Windows Task Manager shows RAM usage increases to 100% during spectrum processing, no matter how much RAM is installed in the PC
  • Windows Task Manager shows a process called peptide3D.exe consuming the majority of the available RAM
  • Apex3D threshold optimization does not help, or is not appropriate for the samples (e.g., PLGS Threshold Inspector is not appropriate for HCP analyses)


  • ProteinLynx Global Server (PLGS) 3.0.3
  • Other versions of PLGS are not affected by this issue


Too many peaks are being passed to the Peptide3D executable during MSe processing. This results in petide3D trying to load too much data into RAM when matching the low and high energy peaks, and using up all the RAM. This problem typically occurs when the customer tries to process their data using the default MSe processing method instead of deriving the correct parameters for their particular dataset. The situation is worse if the Apex3D low energy and elevated energy thresholds in the processing method are inappropriately low for the data being processed.


  1. Close PLGS and stop all PLGS processes (e.g., Apex3D, Peptide3D, iadbs) in the Windows Task Manager.
  2. Right-click on this link and select "save as" to download the command file Peptide3D.exe_params.txt.
  3. Save the Peptide3D.exe_params.txt  command file to C:\PLGS3.0.3\lib\apex3d\.
  4. Restart PLGS 3.0.3.
  5. Reprocess the problem data.

Where appropriate for the sample type (i.e. anything other than fractionated samples or host cell protein analyses), optimising the Apex3D thresholds may reduce the occurrence of this issue. A combination of the above fix and optimised Apex3D thresholds will give the best results.


  • The attached peptide3D_params.txt 'command' file contains commands that restrict the retention time window used by peptide3D when matching low energy (parent) peaks to associated high energy (fragment) peaks. As a result ,Peptide3D must load less data into RAM, which prevents the system RAM from being overloaded by the peptide3D process.
  • For samples that were successfully processed without this command file in place, reprocessing after the command file is applied may alter the number of proteins identified. This can be an increase or decrease in the number of identifications.


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