Frequently Asked Questions

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, 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.