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Slow processing with ProteinLynx Global Server (PLGS): A troubleshooting strategy - WKB2580

Article number: 2580


Troublshooting slow PLGS MSe processing
A basic troubleshooting path for PLGS slow MSe processing issues
Pages: 8


  • PLGS takes a very long time to process MSe, HD-MSe, or SONAR spectra
  • PLGS takes a very long time to run searches from MSe, HD-MSe, or SONAR acquisitions.


  • PLGS 3.0.3
  • PLGS 3.0.2
  • PLGS 3.0.1
  • PLGS 3.0


There are several possible causes of slow MSe processing in PLGS 3.0. It's possible that more than one of these will occur at the same time, with additive or synergistic effects that further slow PLGS 3.0.

Details and solutions to individual issues can be found in other KCS articles linked in the troubleshooting path at the top of this article.


The troubleshooting path at the top of this document contains links to KCS articles that offer known solutions to things that cause PLGS MSe, HD-MSe, or SONAR data processing to be slow. This is article #1. The order of the other articles creates a troubleshooting strategy to rule out PC and software configuration issues, and then fix any issues with the individual MSe spectrum processing and sequence databank search steps as shown below.

 A basic troubleshooting strategy for slow MSe processing (this article)

First things to check

  1. Tesla GPU configuration
  2. Queued samples
  3. Multiple hung Apex3D or Peptide3D processes in task manager after canceling a job
  4. Too many files in database/project
  5. Database Purge required

Once you have done the above checks, start sample processing, open the Windows Task Manager, and watch whether Apex3D, peptide3D, or iadbs.exe is taking a long time. Alternatively, look in PLGS log files to determine which step is slow.

If Apex3D.exe is slow

  1. Apex3D thresholds and the Tesla GPU
  2. Optimizing MSe spectrum processing parameters using PLGS Threshold Inspector

If Peptide3D.exe is slow

8. PLGS3.0.3 Peptide3D hang due to wrong Apex3D thresholds being used

9. PLGS3.0.3 Peptide3D MSe processing hang despite Apex3D thresholds being optimized

If Iadbs.exe is slow

10. Nonspecific sequence databank

11. Missing file

12. Hang when performing metaproteomics analyses

If you are unable to resolve the problem, seek GSS assistance

13. Information required by GSS for additional PLGS troubleshooting

14. PLGS 3.0.2 processing slow: CUDA peak mask error in logs


The above articles are not in any order of likelihood, and there may be other reasons why processing is slow.


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