ACD/MS Fragmenter Trial: Frequently Asked Questions
Software Installation
Q: How do I install the ACD/MS Fragmenter trial?
A: Follow the steps outlined below to install the 30 Day ACD/MS Fragmenter Free Trial:
- Double-click on the ACDLabs11_MSFragmenterTrial_Install.exe file.
- The ACD/Labs Software Web Setup Wizard appears. Click Next.
- Click Install Trial Version and then click Next.
- Click I accept the terms in the License Agreement and then click Next.
- Enter your user information (name, company, and e-mail) and then click Next.
- The installer will now connect to the trial server to dispense registration information to requesting computer.
- Note: You will need an active internet connection to complete this process. An e-mail containing the activation key for the trial will have been sent to the e-mail address provided.
- Complete the rest of the installation steps by accepting the default values.
- At the end of the installation, enter the Activation key you received in your e-mail to activate the software.
- The trial period begins once the software is activated, so if you are not ready to use it, you can activate the software at a later time by following instructions contained in the trial activation e-mail.
- Enjoy the software.
Q: The company I work for has a firewall that prevents me from connecting to the trial server. What should I do?
A: E-mail fragmenter@acdlabs.com and we will send you a new registration key. Please include your full name, and company information.
Q: I have additional ACD/Labs products. Is the trial version of ACD/MS Fragmenter compatible?
A: The trial version of ACD/MS Fragmenter is NOT compatible with any commercial ACD/Labs software, or earlier versions of ACD/Labs freeware. The MS Fragmenter trial software should be installed separately, in a different folder on your computer.
Using ACD/MS Fragmenter
Q: Can you help me get started with ACD/MS Fragmenter?
A: Certainly. Please refer to the Quick Start Guide.
Q: Can I use MS Fragmenter to predict the fragmentation of proteins, carbohydrates, or other large molecules?
A: No. ACD/MS Fragmenter is restricted to small molecule fragmentation prediction. Structures containing up to 255 non-hydrogen atoms may be predicted.
Q: In the ACD/MS Fragmenter Options, how do I set the Maximum Number of Fragments Generated on Each Step, and the Number of Fragmentation Steps?
A: We recommend starting with the default settings, as shown below:

Q: A fragment ion structure that I expected to see wasn't predicted. Why?
A: You can try to increase the number of predicted fragments within the MS Fragmenter Options (see the above FAQ response), or increase the number of fragmentation steps. You might also consider switching on some of the Specific Fragmentation rules that are off by default. If you increase the number of selected rules, you should also consider increasing the Maximum Number of Fragments Generated on Each Step as well.
Finally, ACD/MS Fragmenter is a rules-based predictor, and is based on well-documented fragmentation rules reported in the literature. It is possible that the fragment isn't predicted by the MS Fragmenter rule set.
Q: Where can I find information on the fragmentation rule set used by ACD/MS Fragmenter?
A: Open ACD/MS Fragmenter. In the bottom left corner, click 4-Options. In the window that appears, in the bottom right corner, click Help. In the Help window, use the tabs and the hyperlinks in the table to review the rules.


Q: Can I assign predicted fragments to experimental spectra?
A: Yes, but it requires another software module, ACD/MS Manager or ACD/MS Processor.
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