Scaffold Software System Requirements


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, Scaffold Q+, Scaffold Q+S, and Scaffold PTM are available for both 32- and 64-bit operating systems and can be run with as little as 2GB of RAM. Scaffold DIA, Scaffold perSPECtives, and Scaffold Elements are only available for 64-bit systems, and require at minimum 4 GB RAM. Scaffold DIA and Scaffold Elements require installation on Windows to process vendor-formatted raw files. Note, 32-bit installers have a memory limit of 1400MB and this is started in the Memory allocation tab in Scaffold. There is no such limit for 64-bit versions, users should allocate roughly 80% of their systems RAM in that case.

Recommended Requirements

Scaffold, Scaffold Q+, Scaffold Q+S, Scaffold PTM, and Scaffold perSPECtives

  • Solid-state drive (SSD)
  • Hard drive for data storage and GOA databases (1 TB or more)
  • 64-bit Windows 10, Mac OS X Latest, or Ubuntu (16.04 LTS or above)
  • 16+ GB Usable RAM
  • Modern multi-core CPU with faster CPUs leading to increased performance

Scaffold DIA* and Scaffold Elements

  • Solid-state drive (SSD)
  • Hard drive for data storage (1 TB or more)
  • 64-bit Windows 10
  • 32+ GB Usable RAM
  • Modern multi-core CPU with faster CPUs leads to increased performance

Important Notes

  • 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
  • Updated bundled JRE to Java 1.8.0_102 for all operating systems for Scaffold as of 4.7
  • Our software is compatible with Mac OS (and OS X) 10.9 and above, but only tested on the current version (macOS 10.15.4 as of this writing, August 7, 2020)
  • Our software is primarily tested on Windows 10. Windows 7 and Windows 8 are also supported though Microsoft no longer supports Windows 7:
  • Windows Server versions are likely supported as they are similar to the desktop versions though we do not test on Windows Server
  • Linux distributions supported: Ubuntu 12.x, 13.x, 14.x, 16.x, 18.x, 20.x, RHEL/CentOS 5.6 and higher
  • 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 perSPECtives are compatible with the "All Proteomes" GOA file available from UniProt. This file when unzipped is over 120GB. 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.  

*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 a trivial thing to determine. 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. Searching large datasets against a FASTA file is discouraged as the search space tends to grow unwieldy quickly. Searching against a FASTA should really only be used to build a chromatogram library or to search just a few small raw files. For processing large datasets in general, the more RAM you can provide, the better Scaffold DIA will likely perform.

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