Location of Scaffold Software Parameter and Key Files


This article describes where to find configuration and key files, which are often required to troubleshoot technical problems related to Proteome Software programs. Most operating systems make certain files/directories invisible to the user by default. Therefore, it is often necessary to gain access to hidden folders to find these files. The following article lists steps to make hidden folders visible by OS, and the directories for these files. 

View Hidden Folders by OS

Windows 7

  1. From the Start menu select the Control Panel
  2. Click on Folder Options and select the View tab
  3. Under the Hidden Folders section click Show hidden files, folders and drives and select Apply

Windows 8.1

  1. Click on the Folders icon in the lower left corner of the screen
  2. Select the View tab in the top left of the folders dialog box
  3. Click the check box for Hidden Items

Windows 10

  1. Click on the Folders icon
  2. Select the view tab and click Options
  3. From the Options dialog box click the View tab and select the Show hidden files, folder and drive button and click OK

Mac OS X

  1. To show hidden folder in OS X you must run a terminal command. Open the terminal: Finder > Utilities > Terminal
  2. Paste the following command into the terminal: defaults write com.apple.finder AppleShowAllFiles YES and press Return
  3. Hold the Option/Alt key and right click on the Finder icon, select relaunch
  4. Finder should relaunch and hidden folders should now be visible
  5. If you would like to disable hidden folders reopen the terminal and run the following command:defaults write com.apple.finder AppleShowAllFiles NO and press Return. Once you relaunch Finder they should be invisible again


In general, for Linux/UNIX systems, hidden files and folders are prepended with a period, eg, ~/.ssh (where encryption keys are stored). You can make these visible in the GUI (on Ubuntu, for example) by going to View > Show Hidden Files or by running a command like this: ls -a

Directories for Parameters Files


Note, to follow paths hidden folders must be made visible


C:\Users\<username>\AppData\Roaming\Proteome Software\Scaffold\parameters

Mac OS X

From the Go dropdown menu: Home/Library/Application Support/Scaffold/parameters



Scaffold Elements, Scaffold PTM, Scaffold DIA, Scaffold LFQ, Scaffold perSPECtives

These programs use a similar file path, however the *_params.stp file is not contained within a parameters folder.

C:\Users\<username>\AppData\Roaming\Proteome Software\Elements\Elements_params.stp


C:\Users\<username>\AppData\Roaming\Proteome Software\ScaffoldPTM\ScaffoldPTM_params.stp

Once you have navigated to the correct directory, find the program_settings_S4.sfp or *_params.stp file. It is possible that during use this file has become corrupted and must be backed up. To do so rename to file add _back to the name of the file. This will force the program to write an new file and should allow it to boot properly. Note, when the program launches again,  you will have to reenter Network settings .

Directories for License Key Files

These are the locations of key files for Proteome Software products in if the default file option is selected. These examples are for Scaffold keys, there should be separate folders for corresponding to each product you have installed.


C:\ProgramData\Proteome Software\<program_name>\registeredKey.lkeynew

Mac OS X/ macOS

Go > Library/Application Support/<program_name>/registeredKey.lkeynew



Directories for Log Files

Navigate to these folders to find Scaffold error and output logs. 



Mac OS X/ macOS

Go > Users/<your_username>/Library/Application Support/Scaffold/logs




Scaffold DIA/ PTM / Elements / Quant


Have more questions? Submit a request


Article is closed for comments.