Proteome Software Installation Guide

Proteome Software products for Proteomics including Scaffold, Q+, Q+S, perSPECtives and PTM, and Elements are available as free downloads from the web. Users can easily download software for evaluation or full use. Scaffold, Q+, Q+S, and PTM can also be run in viewer mode without the requirement of a license key. perSPECtives and Elements require a separate viewer installer. The following gives instructions on how to download and install our software.

Links to download the full range of products can be found here by selecting Proteomics or Metabolomics and clicking on the icon for the product of choice:

Click here to download all products

Downloads of perSPECtives and Elements viewers:

Click here to download perSPECtives and Elements viewers

Note we recommend downloading and installing as an administrator (e.g. on Linux with the sudo command). This will ensure that all users of a computer have access. 

Windows and Mac OS X 

  1. Download the appropriate product from the link above making sure to select the proper operating system. Note for Windows make sure to download the proper file for you system architecture (32-bit or 64-bit)
  2. Once the installer finishes downloading open to run. Follow the wizard to complete installation and allow Scaffold to open. In most cases the installation defaults will be sufficient
  3. 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
  4. After installing Scaffold adjust the amount of RAM allocated to improve performance. To change click: Edit > Preferences > Memory. Enter 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 (the dot syntax requires first running chmod u+x to change file permissions for script execution):



For more information and to contact support with any questions or comments see out Support page:

Proteome Software Technical Support



Have more questions? Submit a request


Please sign in to leave a comment.