Getting Started with Scaffold

The following article contains a list of frequently asked question relating to getting started using Scaffold. For specific questions not covered in our documentation we are available by telephone Monday through Friday from 8 AM to 5 PM PST. Our toll free number is 1-800-944-6027. Additionally support can be contacted via email at

Downloading Scaffold 

What is the best way to get started using Scaffold?
Proteome Software offers free 14-day evaluations of Scaffold. To receive an evaluation, click here and follow the instructions on the page. A key will be e-mailed to you shortly.

You can download the latest version of Scaffold here. Install it onto your computer and use the key from the step above to activate your license.

How can I learn about Scaffold?
There are eight demo SF3 files loaded into the program for your convenience - four Tutorial files for analysis in Scaffold, two labelled quantitation files (one iTRAQ and one SILAC) for analysis in Scaffold Q+ and Q+S as well as a label free quantitation and a Waters IdentityE file. You can load any of these files and simply start playing around with the program if you wish.

For an tutorial introduction, read the Scaffold User's Guide. You can access the User's Guide from the Scaffold Help menu. The User Guide walks through some demo data sets which you can find here.

Installing Scaffold

What are the hardware requirements for running Scaffold?
Typically, a standard PC with a 2 GHz processor with one core will work fine, but multi-core is better. For best results on a 32-bit system, 2 GB of RAM is needed. For a 64-bit system, 4+ GB of RAM is sufficient however users will see an appreciable performance increase with more RAM. We recommend allocating roughly 80% of your systems total RAM to Scaffold. For today's large data sets hard drive space should be a consideration as well. With the increase in the size of raw files, Scaffold files and GOA database files Proteome Software recommends having access to at least 1 TB (preferably a Solid State Drive) of file storage space. Please see our system requirements for more detailed information.

Can Scaffold run on a 64-bit processor?
Scaffold can be run on a 64-bit processor. However, this requires a 64-bit computer and a 64-bit operating system. The main advantage a 64-bit processor has over a 32-bit processor is that a 64-bit processor can manage more random access memory (RAM) than a 32-bit processor. The current limiter on Scaffold's performance is RAM not processor speed. It is possible to increase Scaffold's performance by using a 64-bit processor because a 64-bit processor can manage more RAM.

Thus you would not notice much improvement in Scaffold's performance between 32-bit and 64-bit processors on a computer with 2GB of RAM. You would notice a significant increase in Scaffold's performance on a 64-bit machine with 4GB of RAM versus a 32-bit machine with 2GB of RAM. This increased performance would not be due to the processors themselves, but rather the increased RAM available to Scaffold.

Therefore, if you are in position to purchase or make recommendations for a computer to run Scaffold at your institution it recommended to use a 64-bit computer.  

Is Scaffold multi-threaded?
Scaffold is currently not multi-threaded, and does not make use of multi-processor computers. Users will not see performance gains if they install Scaffold on a multi-processor computer. Although Scaffold is not multi-threaded, the bundled version of X! Tandem that comes with Scaffold is multi-threaded. If you use X! Tandem on a multi-processor computer you will see performance gains in terms of increased speed of analysis.

Overall, Scaffold's performance is not decreased when installed on a multi-processor computer. If the user intends on using Scaffold's bundled version of X! Tandem frequently it would be useful to install Scaffold on a multi-threaded computer.

How do I install and run multiple versions of Scaffold on one computer?
There are a couple of ways to upgrade Scaffold. If you go through the wizard and keep the defaults set, you will overwrite the existing Scaffold directory and install the newer version. However, you can also choose to build a hierarchical structure of installations. To do so, first create a main "Scaffold" directory inside Program Files if you are on Windows. Inside that, create a directory called, for instance, scaffold_4.7.5, etc. Then, for each installation, you would give its installation directory a name corresponding to its version. Although possible to do this, please be mindful of our End User License Agreement (EULA) so that you use the licenses correctly.

You can have both Scaffold Desktop (GUI) and ScaffoldBatch running simultaneously on the same computer, but only one instance of Scaffold Desktop running at once. Any additional instances will be opened in the Scaffold viewer. Only one full license copy of Scaffold can be installed per MAC address.

Can Scaffold Desktop be installed on a server?
While Scaffold Desktop can technically be installed on a server, only one instance of the Desktop version can run from a server at any given time. However, with certain third party programs that allow multiple-user remote access, multiple users can potentially access the same instance of Scaffold by installing Scaffold Desktop on a server. See our EULA for more information.

How do I reset my license key?
In Scaffold, click Help in the menu toolbar and select Edit>About Scaffold. Click the Reset button next to your license key in the window that appears. This will open a browser and automatically fill your license key information in the web form located here. Alternatively, you may use that link and enter your information into the form manually.

Connecting Scaffold to External Servers

Can Scaffold connect to the Mascot Server?
Yes, Scaffold can connect to a Mascot server to queue DAT files for loading. This can be done by opening Scaffold and going to Edit>Preferences>Mascot Server. Enter your Mascot URL with http:// included and click Test Connection. This should provide details if the server is reachable from your location.

Queuing files from the Mascot Server in Scaffold is straight forward. Open a new experiment and follow the wizard as you normally would. When you get to the Queue Files for Loading step, choose Queue Files From Mascot Server. Next, highlight the files you see in the list, and click the Add button to add them to the queue. Click OK once the transfer is complete.

What databases can Scaffold query for data?
Scaffold can add GO terms from the NCBI database using a built in query function. These can be added using the Experiment>Add NCBI Annotations function, the NCBI has to be selected as the GO term source in the Edit>Edit Go Term Options dialog. GO annotation files available from UniProt can be loaded into Scaffold as well. See this article for more information on GO terms from UniProt. 

What ports does Scaffold use when connecting to remote resources?
Scaffold connects to external resources a variety of ways. It uses basic ports for doing these operations, such as HTTP (port 80), and FTP (port 21).

Can Scaffold upload files to a data repository such as PRIDE?
Scaffold has the ability to export files for uploading to the PRIDE archive in the mzIdentML format.


How can I get Scaffold to load faster?
Accessing the data over a network connection can slow Scaffold down. Its best if all your MS data and FASTA databases are located on the same computer as Scaffold.

Running X! Tandem without the "Search subset database" box checked will enable X! Tandem to search the entire database. This can take a very long time.

Scaffold could load data slowly when installed on a machine with less than 1 GB of RAM. Scaffold will run on computers with less than 1 GB of RAM but ideally, for a 32-bit system, at least 2 GB RAM is recommended. For 64-bit systems the more RAM the better (some users have systems with at least 100 GB of RAM for processing very large data sets). 

How do I find log files for Scaffold troubleshooting?
Scaffold's output and error logs are often helpful when contacting Proteome Software support and attaching these to correspondence with support will often expedite the process. The easiest way (available in newer versions of Scaffold) is to go to the Help menu and click Show Log Files. This will open the directory where these files are stored.

Alternatively, you can find these manually by looking in these locations:

C:\Users\<user_name>\AppData\Roaming\Proteome Software\Scaffold\logs

Mac OSX:
Macintosh HD\users\<user_name>\library\Application Support\Scaffold\logs


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