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MS Workbook Suite

Mass Spectrometry Software for Spectral Interpretation and Component Characterization

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MS Workbook Suite Overview

One MS Software for All Your Mass Spectral Data Analysis and Management

ACD/MS Workbook Suite is an all-in-one package for MS data handling.

  • Process MS, LC/MS, and GC/MS data acquired with instruments from any major vendor
  • Auto-annotate peaks and associate them with compound structures
  • Identify unknowns by deconvoluting spectra and searching databases for spectral matches
  • Create easily shareable and searchable spectral databases

Complete All Your MS Processing in One Place

Auto-annotate mass spectra

  • Automatically annotate molecular, fragment, and adduct ion peaks
  • Better understand your spectra and sample

Identify compounds in complex samples

  • Deconvolute your LC/MS and GC/MS spectra in two clicks
  • Identify known compounds, or putatively identify unknowns by searching commercial and proprietary libraries

Confirm compound identity

  • Increase confidence in your structure assignment
  • Compare predicted fragment ions to the experimental spectrum, and see the highlighted matches.

Connect mass spectra to chemistry

  • Don’t lose the context of your data. Connect peaks to structures, so you’ll immediately know what you’re looking at when you come back to your files in the future

Build your own database

  • Build a spectral database from all of your organization’s data, no matter what hardware it was collected on
  • Everyone can find and reuse prior work, and discover if new unknowns match previous hits

Generate fragmentation trees for compounds of interest.

Identify known unknowns through database searching and review results in the Table of Components.

Assign chemical structures to chromatographic peaks and automatically annotate component mass spectra.

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

Hover over a spectral peak to see the corresponding fragment.

Reduce time for component interpretation with automated extraction using the IntelliXtract algorithm.

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

How it Works

How MS Workbook Suite Can Work for You

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  • 1 Import MS, LC/MS, and GC/MS data from any major instrument vendor
  • 2 Deconvolute TICs into component XICs in two clicks
  • 3 Auto-assign spectral peaks to predicted mass fragments
  • 4 Automatically annotate mass spectra to mark molecular and adduct peaks
  • 5 Search spectral databases for any unknown component
  • 6 Report your results and upload them to a shared database
Customer Reviews
“[The software] can be applied to rapidly identify targeted molecules in complex mixtures, following a well defined and validated analytical protocol. It is well adapted to rapid and automated analyses of large series of samples, [and] improves and increases the selectivity performance of simple and low-cost LC/MS instruments.”

Patrick Arpino

“So we now have a gold-standard database of […] mass spectra, fully searchable. So [it] can be searched by [...] the Pfizer compound number, structure, and substructure, but also folks can do spectral matches, right? So they can input mass spectra and you say, 'Hey, is there is there a spectrum or compound in the database that matches closely?'”

David Foley

Product Features

Features of MS Workbook 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
  • Identify known unknowns with the Intelligent Component Recognition workflow
    • Screen experimental MS spectra against internal or commercial libraries (e.g., Wiley, NIST)
  • Color-coded match-quality indicators rate matches by consistency of theoretical isotopic pattern with experimental data
  • Generate molecular formulae from molecular ion mass-to-charge values
  • 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
  • Assign chemical structures to chromatographic peaks (including Markush structures for ambiguous assignments)
  • 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
  • Analyze 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
  • 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
  • View the results as a fragmentation tree
  • Review the prediction rules to learn about the mechanics behind fragmentation
  • Assign predicted fragment structures to peaks in an experimental spectrum
  • Create fully searchable, live databases containing spectra, chromatograms, spectral assignments, annotations, text notes, and more
    • Link associated documents (e.g, .docx, .xlsx, .pptx, .pdf, .txt)
  • Search databases by spectral, method, structural, and text parameters
    • Store your search history to rerun searches in multiple databases
  • Customize your database functions with scripting
  • Export data and analysis as customizable reports
  • Expand your analytical understanding by viewing data from different techniques side-by-side
  • Analyze data:
    • NMR: Fourier transform, calibrate, peak pick, integrate, and analyze multiplets
    • Optical techniques: Correct baselines, detect peaks, and smooth
  • Automate basic processing workflows
Deployment/Integration Options

Compatible with All Your Instruments and Techniques

Your lab probably has MS instruments from many manufacturers, and that’s not counting the NMR, IR, and other analytical equipment. We help you put all your data back together again.

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 Workbook Suite

Why Choose Third-Party Software for Your MS Processing?

MS data comes from many instruments, each with their own advantages. Some are better for targeted quantitation; some for high-resolution analysis; some for quick and cheap scans. This data will usually live in different instrument silos, but that’s not efficient.

Working with your data in our interface allows you to:

  • Apply the same processing workflow to all your data for consistency
  • Make use of the same characterization and fragment-prediction tools for all your data
  • Easily switch between files taken on different instruments without readjusting to different interfaces and options
  • Future-proof your lab so you can change instruments without retooling your analysis workflows
  • Add all your spectra to one searchable database and speed up future sample characterization
  • Database your data together in live format, so you can find and reprocess any file immediately
  • Connect MS data with all the other analytical data used to characterize the sample
What's New!

What's New in MS Workbook Suite v2023

  • Conduct more thorough searches and extract additional information using the IXCR workflow
  • Improved quantitation – nonlinear curve calibration, the addition of residual plots to the workflow, and more
  • 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 Workbook Suite