How can I load MACSQuantify files that were exported from MACSQuantify software version 3.0.1?

MQD files exported from version 3.0.1 of MACSQuantify software , and files exported as .FCS 3.1, are compatible with FCS Express. Utilizing the instrument specific settings below will ensure data visualizations between MACSQuantify and FCS Express are equivalent.

IMPORTANT NOTE: If exporting .FCS files from MACSQuantify version 3.0.1 (as opposed to using direct .MQD file format compatibility), please ensure that your MACSQuantify Options are set to use FCS 3.1 as the Export type. These options in MACSQuantify version 3.0.1 can be accessed via the Edit tab>Software>Export>FCS.

(Please note that "FCS 3.1 compatible" and "Custom" options in MACSQuantify version 3.0.1 should not be used as these options are intended for special use cases and may result in inaccurate results or visualizations in some third party software tools, including FCS Express).

Please follow the steps below to load the MQD files with the appropriate Instrument Specific Settings. Afterward, the plots in FCS Express should appear the same as they appeared in the MACSQuant software.

• Within FCS Express, click the File tab and select Options
• Expand Data Loading, expand FCS File Options, select Instrument Specific Settings
• Click MACSQuant in the list
• Click Duplicate

• Change the Instrument Name to MACSQuant 3.0.1
• In Identification Rule, delete the existing text and enter StartsWith("<$CYT>","MACSQuant Analyzer 16,3.0.1",False)

• Under Scatter Parameters and under Range Options, select Manual
  • In the top field, enter 0
  • In the lower field, enter 1000
• Under Scatter Parameters, under Division Factor, select Scale by factor
• Enter a value of 0.00000093132416

• Under Fluorescence Parameters and under Range Options, select Manual
  • In the top field, enter -1
  • In the lower field, enter 1000
• Under Fluorescence Parameters and under Scale Options, uncheck Automatic
  • From the dropdown menu for Scale, select Hyperlog
  • For Transition Point, enter 1
• Under Fluorescence Parameters, under Division Factor, select Scale by factor
  • Enter a value of 0.00000093132416

• Move the new setting that you created (MACSQuant 3.0.1) so that it is listed above the standard MACSQuant setting.
  • This can be done by selecting MACSQuant 3.0.1 and clicking the up arrow button several times.

• Click OK to save the new User Options.
• When you load an MQD file (that was exported from MACSQuantify software version 3.0.1) onto an FCS Express layout in the future, these unique settings will automatically be applied.
• If the MQD file has already been loaded onto the FCS Express layout, you will need to Refresh/Reload the data to apply the new instrument specific settings.
• To reload the current MQD file being displayed on the layout, click Data tab > Refresh
  • Add a checkmark to each checkbox
  • Click Reload selected files
• To reload all other MQD files within your data list, save the layout, close the layout and re-open the layout.