ACD/MS Fragmenter

Predict mass fragments from chemical structure

ACD/MS Fragmenter automates the rule-based task of determining the possible fragmentation of organic molecules, and displays the results for review in a convenient interface.

Simply draw or import the chemical structure, and select the fragmentation-rule parameters to mimic different ionization techniques. The fragmentation results are then presented in an organized fashion through a genealogical tree that establishes the precursor-product relationship of all fragment ions. It is easy to browse through the predicted fragments or to see the pathways through which they were created. As a result, the task of fragment prediction, that can be time consuming and which would normally require expert knowledge, is reduced from hours to seconds. ACD/MS Fragmenter also lets you easily create fragmentation reports.

MS Fragmenter Window for the Electron Ionization (EI) Fragmentation of Benzoyl Chloride Click image to magnify

A summary of the main features found in ACD/MS Fragmenter follows:

Analysis

• Predict fragmentation according to different polarity and ionization techniques
• For positive ions:
  • Apply distinctive fragmentation rules for electron ionization (EI)
  • Apply distinctive fragmentation rules for two classes of protonation techniques:
    • Atmospheric Pressure Ionization (APCI, ESI)
    • Other Protonation Techniques (e.g., CI, FAB)
• For negative ions:
  • Apply distinctive fragmentation rules for electron capture
  • Apply distinctive fragmentation rules for deprotonation techniques
  • Apply distinctive fragmentation rules for hydride attachment
• Specify fragmentation rules that are applied manually
• Control the degree of fragmentation through the number of fragmentation steps
• Navigate complex fragmentation pathways with ease

See the fragmentation options here.

Display

• Review generated fragments in a dedicated window:
  • See the mass and molecular formula at a glance
• Use a Compact View for the fragmentation scheme display, where compounds with the same formula are only represented once

Take a closer look at the display windows here.

Reporting

• Create reports for a single fragment, fragmentation branch, or fragmentation pathway
• Customize the fragment display view:
  • Display nominal, monoisotopic, or average mass
  • Hide or show formulae and labels
  • Select the number of fragments displayed at once

See examples of fragmentation reports generated with MS Fragmenter here.

Input/Output

• Draw the parent structure in ACD/ChemSketch (included with MS Fragmenter), or import structures from other drawing packages to ChemSketch
• Save the fragmentation scheme, with the structure and mass values, as an *.mfr file
• Generate a bar code mass spectrum (spectrum where all the peaks have the same intensity), and export it to JCAMP or an ASCII *.txt file
• Copy a single fragment structure to the Clipboard, and paste it to another application, such as Microsoft Word or PowerPoint

Related Products

Would you like to assign predicted mass fragments to experimental spectra? The autoassignment function in ACD/MS Manager automatically assigns mass fragments to an experimental mass spectrum, which allows you to verify possible chemical structures. ACD/MS Fragmenter and the autoassign function in ACD/MS Manager are driven by the same fragmentation rules.

ACD/MS Fragmenter includes ACD/ChemSketch.