Transitioning from Scaffold LFQ to Scaffold DDA Label-free Quant

Proteome Software has released Scaffold DDA Quant, Labeled and Label-free licenses. Scaffold DDA Label-free Quant directly replaces Scaffold LFQ, which has officially be deprecated and will not be receiving any more updates. In the future, Scaffold DDA Quant (Labeled and Label-free licenses) will be the default platform for all DDA quantitative proteomics. The following procedure will guide users in transitioning their installation from one program to the other.


  1. Contact Proteome Software and let us know you would like to migrate from Scaffold LFQ to Scaffold DDA Quant Label-free. Make sure to have a record of your Scaffold LFQ License ID and Password, as you will use this license to activate Scaffold DDA Quant Label-free
  2. Deactivate your license using the Help > About menu in Scaffold LFQ. If you receive an error regarding your license not having any deactivations, please let us know
  3. Uninstall Scaffold LFQ from your system. You can reference this guide to completely remove a program
  4. Download the Scaffold DDA Quant installer
  5. Install Scaffold DDA Quant on your system. The defaults work in most cases but do make sure to set your RAM allocation to roughly 80% of your systems available memory
  6. Enter your existing Scaffold LFQ License ID and Password after we confirm that the license has be converted to support Scaffold DDA Label-free Qaunt
  7. Scaffold LFQ and Scaffold DDA Quant Label-free work in very similar ways so the transition should not be too difficult. See the Scaffold User Guide and the Scaffold DDA Quant User Guide for more information and contact us with any questions
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