Proteome Software Installation Guide

All Proteome Software programs are distributed via our website as free downloads, and the viewer and the full version of each program can be installed using the same installer.

Links to download the full range of products can be found here. Programs are broken down into three categories: DDA proteomics, DIA proteomics, and small molecule/metabolomics.

Windows and MacOS

  1. Download the appropriate product from the link above making sure to select the proper operating system.
  2. Once the installer finishes downloading double click to run
  3. When running any of our installers, you will be asked whether you would like to overwrite an existing installation or install into a different directory. If you have a previous version installed on your computer choose the first option. This will overwrite the existing installation.
  4.  Follow the wizard to complete the installation and allow the software to open. In most cases the installation defaults are sufficient.
  5. Scaffold DIA and Scaffold Elements require installing ProteoWizard in order to process vendor-formatted raw data. Click on the download ProteoWizard button when prompted to do so. Work your way through the ProteoWizard installer making sure to install for all users on your computer. Then return to the Proteome Software installer to complete installation.
  6. If installing Scaffold PTM, Scaffold Quant, Scaffold DIA or Scaffold Elements allocate roughly 80% of your systems total RAM in GB to the program when prompted by the installer.
  7. The software will prompt you for a license key. Enter your evaluation key, permanent license key or run as a free viewer. Your software is now installed and ready for use. Click here for documentation specific to working with license keys.
  8. After installing Scaffold adjust the amount of RAM allocated to improve performance using the Edit > Preferences > Memory menuEnter the amount of memory in MB that you want Scaffold to have access to, we recommend allocating 80% of your systems total RAM. Make sure to restart Scaffold so the new memory allocation is used.


  1. Download the appropriate product from the link above making sure to select the proper operating system
  2. Unzip the file to get the installer shell script
  3. Run one of the following commands: ./ or bash (the dot syntax requires first running chmod u+x to change file permissions for script execution)
  4. Once the installer has started, follow the steps outlined above to finish installation.

For more information and to contact support with any questions or comments see our Technical Support page.



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