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MS Structure ID Suite

Our Most Advanced MS Toolset for Structure Characterization

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MS Structure ID Suite Overview

Characterize Samples and Identify Unknown Components

Do you often need to identify unknown compounds from complex samples? ACD/MS Structure ID Suite offers a simple, replicable workflow for generating and narrowing down structural candidates.

  • Deconvolute complex LC/MS and GC/MS data into individual component traces
  • Search proprietary and commercial databases for spectral matches
  • Search PubChem for accurate-mass and molecular-formula matches
  • Narrow down candidate structures by retention time and fragment include/exclude lists

One Deformulation Workflow for All Your Samples

Extract traces from complex samples

  • In two clicks, separate co-eluting peaks by turning your unresolved total ion chromatogram into component extracted ion chromatograms

Identify ‘known unknown’ components

  • Search in-house and commercial databases for spectral matches
  • Evaluate match accuracy with mirror plots and hit-quality indicators

Increase number of identified compounds

  • Don’t have spectra for all the compounds in your sample? Expand the number of compound IDs by using accurate mass and molecular formula to search the PubChem database of > 100 million unique structures

Focus large candidate lists

  • Rank candidates by predicted LC or GC retention time, or by correspondence between experimental mass spectrum and predicted fragmentation pattern

Build on your knowledge

  • Increase the number of compounds you can identify quickly by building a database from in-house experimental data

Assemble database search results for a given component, and further trim this catalog via elemental composition and structure include/exclude lists.

Store your results in a searchable database so you can always find all relevant information.

Extract components from a Total Ion Chromatogram and search for candidate structures by mass.

Auto-assign predicted structure fragments to mass spectral peaks, and see the assigned fragments on your mass spectra.

How it Works

Sample Deformulation in 4 Easy Steps

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  • 1 Import your data (in any common format).
  • 2 Run the deconvolution and spectral search algorithms to separate components and identify compounds by spectra.
  • 3 Choose a component that remained unidentified after spectral search, and generate a molecular formula for it. Search its mass and molecular formula against more compound libraries.
  • 4 Report your results and upload them to the shared database.
Product Features

Features of MS Structure ID Suite

  • Deconvolute LC/MS and GC/MS total ion chromatograms
    • IntelliXtract algorithm uses unique ion-thread technology to extract components
  • Automatically associate component mass spectra with each extracted peak
  • Detect components present at trace concentrations and distinguish co-eluting peaks
  • Screen for known compounds with the IntelliTarget algorithm
    • Identify expected components even at low concentrations or in complex samples
  • Use spectra to identify “known unknowns” with the Intelligent Component Recognition workflow
    • Screen experimental MS spectra against internal or commercial libraries (e.g., Wiley, NIST)
  • Use mass and molecular formula to identify “known unknowns” using the Automated Structure ID workflow
    • Generate molecular formulae from molecular ion mass-to-charge values
    • Narrow candidate lists with fragment include/exclude lists
    • Search chemical structure databases using accurate parent mass and predicted molecular formula
    • Rank structure candidates by predicted LC/MS or GC/MS retention time, or by correspondence between spectrum and predicted fragmentation pattern
  • Search against > 100 million unique structures contained in the PubChem database
  • Color-coded match-quality indicators rate matches by consistency of theoretical isotopic pattern with experimental data
  • See the full list of sample components in the Table of Components, including each compound’s retention time, mass-to-charge, structure (if available), mass spectrum, fragment ions, hit-quality indicators, and more
  • Import files in all major instrument-vendor formats
    Review the list of supported formats
  • Detect chromatographic peaks automatically
    • Adjust integration and peak-detection options or manually detect peaks to suit your data
  • Add tags to spectral features, such as isotopes, adducts, multimers, fragments, and more
  • Subtract average spectra from a total ion chromatogram, or subtract one mass spectrum from another, to remove background signals
  • Get more structural information by analyzing data for neutral loss
    • Generate neutral loss spectra
    • Search for peak pairs with a fixed mass difference
  • Simulate mass spectra from a molecular formula, accounting for isotopic pattern
  • Automate routine processing via macros

Quantify your LC/UV/MS data samples based on TIC (mass of compound), DAD (auto-extracted wavelength), or flat chromatogram (specific wavelength).

The quantitation tools provide curve fitting via linear regression with options to:

  • Simultaneously quantify several compounds
  • Process replicate samples
    • Plot the average and standard deviation represented by error bars
  • Option to quantify additional unknowns after the calibration project has been constructed
  • Create customizable reports containing calibration curve, compound metadata, summary table, statistics table, ANOVA table, and peaks table
  • Automatically add calibration projects and individual sample files to a database
  • Confirm compound identity by matching predicted fragment structures to spectral peaks
  • Predict MS fragmentation pathways based on established literature rules
    • Estimate fragments for molecules containing up to 255 non-hydrogen atoms
  • Get results tailored to your experiment with extensive filtering options. Filter by:
    • Positive or negative ionization
    • Common fragmentation 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
  • Expand your searchable spectra by creating live databases containing spectra, chromatograms, spectral assignments, annotations, and more
  • Use these databases in your next spectral search, or search them by method, structural, and text parameters
  • Export data and analysis as customizable reports
  • Expand your analytical understanding by viewing data from different techniques side-by-side
    • Import data from NMR, IR, and more
  • Analyze data:
    • NMR: Fourier transform, calibrate, peak pick, integrate, and analyze multiplets
    • Optical techniques: Correct baselines, pick peaks, and smooth
  • Automate basic processing workflows
Deployment/Integration Options

Compatible with All Your Instruments and Techniques

We help you put all your data back together again. Your lab probably has MS instruments from many manufacturers, and that’s not counting the NMR, IR, and other analytical equipment. As the leader in vendor-agnostic chemistry software, ACD/Labs partners with dozens of vendors to support > 150 file types and thousands of instruments. So you can use the equipment you need, without worrying about having data in a dozen different formats.

More Reasons to Use MS Structure ID Suite

MS-Based Unknown Characterization

Mass spectrometry is one of the most widely used techniques for unknown characterization. It offers broad applicability, easy integration with separation techniques, and low limits of detection. But digging through the ensuing data is difficult—especially for complex samples.

First, the signals must be separated into different components. Though chromatography can separate peaks, complex samples will often have many co-eluting species, which must be teased apart based on their spectra.

Then each component must be identified, usually by spectral match, though fragmentation pattern can be used if fragmentation is relatively predictable (as for proteins). Components contained in spectral libraries will be identified in this manner. Components with no library spectra won’t produce candidate hits. MS Structure ID deals with these components using formula generation, formula-and-mass search, and filtering via retention time or fragment match.

What's New!

What's New in MS Structure ID v2023

  • Get quicker answers by filtering automated structure search results by d(MS)
  • Get results quicker with improved peak detection and integration, and component integration
  • Improved peak naming for xC/UV/MS data—import from CDS, define your own, and more
  • Consolidated visualization of mass spectral search results—query spectrum, hit spectra, metadata, and structures, together
Learn More about MS Structure ID Suite