Proteome Software Installation Guide

All Proteome Software programs are distributed via our website as free downloads. With the exception of Scaffold Elements, 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. To download an Elements viewer, click here. Note, downloads of all of our programs are available on that same page.

Windows and MacOS

  1. Download the appropriate product from the link above making sure to select the proper operating system and system architecture (32-bit or 64-bit). Scaffold Elements, Scaffold DIA and installers for MacOS are only available for 64-bit systems
  2. Once the installer finishes downloading open 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 currently have Scaffold installed on this computer choose the first option. This will overwrite the existing installation
  4.  Follow the wizard to complete installation and allow the software to open. In most cases the installation defaults will be sufficient
  5. If installing Scaffold PTM, Scaffold perSPECtives, Scaffold DIA or Scaffold Elements allocate roughly 80% of your systems total RAM to the program when prompted by the installer
  6. 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
  7. 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


  1. Download the appropriate product from the link above making sure to select the proper operating system and architecture (32-bit or 64-bit)
  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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