Frequently asked questions

1 Troubleshooting

1.1 unable to read/write config file

This error appears if ISOQuant can not access file system with both read and write permissions. Please ensure that you have consistent read and write permissions on the folder containing ISOQuant or execute ISOQuant with elevated administrative privileges.

1.2 low performance

  1. Low performance may be a result of wrong configuration settings - carefully check your ISOQuant configuration.
  2. The performance of ISOQuant scales with used hardware and operating system. The overall performance may suffer from:

    • hardware
      - slow CPU
      • low RAM
      • slow hard drive
        • used for PLGS root
        • used for MySQL server
    • network latency
      In case you feed ISOQuant by PLGS data from a network drive or use a remote MySQL database server.
    • operating system barriers
      MySQL has a technical problem when running on MacOSX systems and is slower than on Windows or Linux.

1.3 Out of Memory error

  • while importing project data:
    you probably have really big xml files produced by PLGS as a result of very complex samples or wrong parameters for processing raw files.
  • while clustering process:
    see hanging during clustering procedure.

You can try to provide more RAM to java virtual machine for executing ISOQuant, e.g. by setting large Xmx parameter while launching ISOQuant from command line:

java -Xms256m -Xmx4096m -jar ISOQuant.jar

It is not possible to use more memory than 4096m (4GB) for a 32bit Java Virtual Machine! Try the 64bit version.

1.4 hanging during clustering procedure

If ISOQuant needs more than 10 minutes for clustering EMRTs then try to adjust its configuration by reducing preclustering parameters and increasing minimum signal mass and intensity to be included in EMRT table.

1.5 overclustered peptides

If you think ISOQuant overclusters EMRTs then try to increase clustering distance units

1.6 how can I stop ISOQuant

Use shutdown button on the right top corner of ISOQuant to close the application after current process is done. By clicking shutdown button again, you can immediately stop all processing and close ISOQuant. Stopping ISOQuant may cause an inconsistent state for the project that is being processed at that moment. You will have to reprocess it.

1.7 unable to write configuration file

On some Windows Vista or Window 7 machines ISOQuant can not write its configuration file. In this case you have to execute ISOQuant with administrative privileges (right click on ISOQuant icon and choose Run as administrator) or correct file system permissions for ISOQuant installation folder (please contact your computer administrator if you have trouble fixing file system permissions on ISOQuant installation folder). This is not an ISOQuant issue, sometimes Windows messes up file system permissions by using different and inconsistent user privileges at different time points.

Typically, folder permissions on a Windows machine are corrected as follows:

  • navigate in Windows Explorer to the ISOQuant installation folder e.g. C:Program FilesISOQuant
  • mark the installation folder and right click on it
  • select Take ownership
  • right click again
  • select Properties
  • uncheck Read only from panel General
  • click Apply
  • switch to panel Security
  • make sure that your user have all permissions checked
  • click Apply and if asked apply changes to this folder, subfolders and files!