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, unless the axes were customized within 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 version 3 MQD
• In Identification Rule, delete the existing text and enter StartsWith("<$CYT>","MACSQuant",False) AND RegExMatch("<$CYT>",",3") AND <$BEGINDATA><<$BEGINSTEXT>

• 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 version 3 MQD) so that it is listed above the standard MACSQuant setting.
  • This can be done by selecting MACSQuant version 3 MQD 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) 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 > Reload
  • 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.

Please follow the steps below to load the FCS 3.1 files with the appropriate Instrument Specific Settings. Afterward, the plots in FCS Express should appear the same as they appeared in the MACSQuant software unless the axes were customized 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

• Under Scatter Parameters and under Range Options, select Manual
  • In the top field, enter 0
  • In the lower field, enter 1000

• 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

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