While Proteome Software programs will technically run with minimal requirements on a broad range of operating systems we suggest users follow the recommended requirements to ensure the best experience.
Scaffold 4/5, Scaffold Q+S, and Scaffold PTM can run with as little as 2GB of RAM. Scaffold DIA, Scaffold DDA, and Scaffold Elements are only available for 64-bit systems, require at minimum 4 GB RAM, and require installation on Windows to process vendor-formatted raw files.
Starting with Scaffold DIA 6.0, cross-platform support was added for vendor formats like Thermo raw and Bruker timsTOF dia-PASEF data (Windows, Linux, and Mac).
Scaffold, Scaffold Q+S, Scaffold PTM
- Solid-state drive (SSD) for processing directory
- Hard drive for data storage (1 TB or more)
- 64-bit Windows 10
- 16+ GB Usable RAM
- Modern multi-core, faster CPUs enable OSes to handle more complex jobs
Scaffold DIA* and Scaffold Elements, Scaffold DDA
- Solid-state drive (SSD) for processing directory
- Hard drive for data storage (1 TB or more)
- Windows 11 (64-bit)
- 32+ GB Usable RAM
- Modern multi-core, faster CPUs enable OSes to handle more complex jobs
- A rule of thumb is to have as much memory as you do input data, eg, if you load or search 50 GB of data, you should allocate at least that much RAM in the Scaffold software you are using
- Swap space is important to memory management on operating systems. Make sure to have a large enough swapfile to handle your system's overhead: https://en.wikipedia.org/wiki/Memory_paging
- Storing data on the same computer as your Scaffold installation will lead to increased processing speed. It is not recommended to load data into Scaffold across a network connection
- Our software is compatible with Mac OS (and OS X) 10.9 and above, but only tested on more recent versions (most recent tested is 15.3.2). Starting with Scaffold DIA 6.0, macOS is supported only on Apple Silicon Macs using ARM64 architecture, including systems with M1, M2, M3, M4, or later Apple chips; Intel-based Macs are not supported
- Our software is primarily tested on Windows 10 and Windows 11. Windows 7 and Windows 8 are also unofficially supported, though Microsoft no longer supports Windows 7, 8, and 10: https://www.microsoft.com/en-us/windows/end-of-support
- Scaffold will likely run on Windows Server and Enterprise versions, as they are similar to the desktop versions, though they are not officially supported
- We do not support running our software with remote access software (VNC, RDP, etc); eg, we do not actively test remote software to discover and resolve potential issues. However, we have found that it does work in these environments in most cases across OS platforms
- Linux distributions supported: Ubuntu 16.04 and higher (routinely tested on 24.04+)
- It is advisable to adjust your automatic updates and power settings to disable sleep or hibernate, as these might interfere with processing data
- Scaffold and Scaffold DDA are compatible with the "All Proteomes" GOA file available from UniProt. This file when unzipped is over 100GB. We discourage the use of this file and suggest using individual taxonomy files instead. If you would like to use the "All Proteomes" file we suggest having at least 250GB available for storing GOA files and other data
- Scaffold software requires the drive on which the program is installed to have adequate storage space for temporary files. On windows, the temp space is located on the C drive by default:
C:\Users\<username>\AppData\Local\Temp\<ScaffoldXXX_<username>
*A note on Scaffold DIA resources. Processing DIA is quite intensive from a computing standpoint. Determining exactly how much processing power one needs for a data set is not trivial. Both the size of the files and the complexity of the data play a role in determining the amount of resources required. The more data you wish to process at once, the more resources you will need. This is particularly true for RAM.