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MS Fragmenter

Predict MS Fragments for Your Compound

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MS Fragmenter Overview

Rules-Based Fragment Prediction for Mass Spectrometry

ACD/MS Fragmenter helps you predict mass spectral fragmentation in seconds. Have more confidence in your compound IDs, learn about fragmentation mechanisms, and publish your results easily.

It’s as simple as this:

  • Draw your compound
  • Select the ionization polarity and fragmentation options
  • View its fragmentation tree

Use MS Fragmenter To…

Predict MS fragmentation patterns

  • Draw a structure and see its complete fragmentation tree
  • Select ionization and reaction type

Confirm your compound IDs

  • Have confidence that your spectrum shows the compound you’re expecting
  • Select an experimental spectrum, and the software will compare the predicted fragments with the spectral peaks

Quickly compile fragmentation pathways for publication

  • Compile mass spectral fragmentation pathways for reports or publications with a few clicks
  • Edit the results template to suit your needs

Predict MS fragmentation from chemical structure.

Generate fragmentation trees for compounds of interest.

How it Works

Simple Prediction with MS Fragmenter

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  • 1 Enter your compound. (Use the drawing tools, select it from the Dictionary, or copy/paste.)
  • 2 Select fragmentation and ionization options
  • 3 Press “Generate Fragments.”
  • 4 Report your findings.
Product Features

Features of MS Fragmenter

  • Predict MS fragmentation pathways based on established literature rules
    • Estimate fragments for molecules up to 255-atoms large (excluding hydrogen atoms)
  • Get results tailored to your experiment with extensive filtering options. Filter by:
    • Positive or negative ionization
    • Common reactions (resonance reactions, ring formation, and hydride shift)
    • Distonic-ion formation (hydrogen shift, double-bond cleavage, triple-bond cleavage, saturated-ring cleavage)
    • Type of bond cleaved (acrylic, non-aromatic, C-het aromatic, C-het cyclic)
    • Hydrogen rearrangements, skeletal rearrangements, oxygen loss, and neutral losses
  • Review the prediction rules to learn about the mechanics behind fragmentation
  • Compare predicted fragments to peaks in an experimental spectrum
  • Assign predicted fragments to peaks in the processing interface
  • View the results as a fragmentation tree
    • Expand and collapse branches to see all pathways or simplify your view
    • Choose between viewing all isomers and rearrangements separately, or condensing radical and ionization isomers into one representative compound
  • See all fragment structures and their nominal, monoisotopic, and average masses
  • Create reports showing a specific fragment, fragmentation branch, or the entire fragmentation pathway
  • Customize the report template to suit your needs
  • Use the processing interface to process data from many analytical techniques
  • Analyze data:
    • MS: Interpret spectra, confirm molecular formulas, and screen spectral libraries for unknowns
    • Chromatography: Smooth, correct baseline, peak pick, integrate
    • NMR: Fourier transform, calibrate, peak pick, integrate, and analyze multiplets
    • Optical techniques: Correct baselines, pick peaks, and smooth
  • Automate routine processing workflows
More Reasons to Use MS Fragmenter

Why Choose Software to Predict MS Fragmentation?

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Compounds ionized by mass spectrometry fragment according to specific patterns, which have been documented in the literature (e.g., McLafferty rearrangement, double-bond cleavage). The situation is complicated by nuances for ionization polarity and for collision-induced dissociation (CID/CAD). An understanding of these rules can take the scientist from compound structure to predicted fragments.

It’s theoretically possible to do by hand—but who would want to? Gathering all the experimental evidence and systematically applying the rules is a job better suited for a computer algorithm. MS Fragmenter assists mass spectrometrists, organic chemists, and anybody else who uses mass spectrometry to understand fragmentation pathways and confirm compound identity.

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