Peptide3D MSe processing hang with ProteinLynx Global Server (PLGS) 3.0.3 - WKB3426

SYMPTOMS

• Processing MSe hangs, often during the peak matching step
• Memory consumption increases to 100%, 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

ENVIRONMENT

• PLGS 3.0.3
• MSe, HD-MSe, or UD-MSe data processing

CAUSE

The Apex3d thresholds in the MSe spectrum processing parameters may be too low for the data. This means a lot of noise peaks are being detected by the Apex3D executable. This noise is passed to the peptide3D executable, which then overloads the system RAM as it tries to process the noise, causing the hang.

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.

FIX or WORKAROUND

1. Stop all processing jobs in PLGS.
2. Stop the peptide3D executable or Apex3D executable using the Windows task manager.
3. In PLGS, create a new MSe processing method using higher Apex3D low energy and elevated energy thresholds. 
   • Ideally, users should optimize the Apex3D low energy and elevated thresholds for each dataset as this produces the maximum number of identifications. 
   • PLGS Threshold Inspector is a useful freeware tool for optimizing Apex3D thresholds semiautomatically.
4. If the optimal Apex3D parameters identified by PLGS Threshold Inspector are lower that those used when the processing hang occurred, the problem is not simply the Apex3D thresholds. Contact GSS.
5. If the optimal Apex3D thresholds identified by PLGS Threshold Inspector are higher than those used when the processing hang occurred, try reprocessing the problem data file using those thresholds.
6. If the optimized Apex3D threshold parameters can process the problem file, reprocess the entire dataset with the new MSe processing method.
7. If processing hangs again using the optimized thresholds, or if the optimized thresholds cannot process the problem file, apply the solution described in article 13412.

ADDITIONAL INFORMATION

The Apex3D thresholds used in the default MSe processing method installed with PLGS are only appropriate for passing the system suitability test with the samples specified by Waters. They are not optimal for any other data, and in many cases they may be completely inappropriate for the data.

Contact GSS if you require further information on installing and using PLGS Threshold Inspector.

Note that every time you analyze a different data set, it may be necessary to reoptimize the Apex3D thresholds, irrespective of whether the fix in article 13412 has been applied.

The same problem affects Progenesis QI Proteomics version 3. However, Progenesis QI for Proteomics v4 does not suffer from this problem.