Expert Mass Spectrometry Software | ACD/MS Workbook Suite
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Mass Spectrometry Software for Advanced Spectral Interpretation and Structure Verification

The Ultimate Package for Detecting, Identifying, and Characterizing LC/MS & GC/MS Components

ACD/MS Workbook Suite provides mass spectrometrists with expert tools for identifying and characterizing compounds using LC/UV/MS & GC/MS data.

  • Import files from most major instrument vendors, including Agilent, Bruker, LECO, PerkinElmer, SCIEX, Shimadzu, Thermo Fisher Scientific, Waters, and more.
  • Facilitate knowledge sharing by enabling efficient generation of spectral, chromatographic, and structure libraries, as well as customizable reports.
  • Extract chromatograms and screen the list of components to identify known and 'known unknown' compounds
    Extract chromatograms and screen the list of components to identify known and "known unknown" compounds
  • Assign chemical structures to chromatographic peaks to automatically annotate component mass spectra
    Assign chemical structures to chromatographic peaks to automatically annotate component mass spectra
  • Evaluate assignments by comparing predicted fragment ions of candidate structures to experimental MS spectra
    Evaluate assignments by comparing predicted fragment ions of candidate structures to experimental MS spectra

Expert Mass Spectrometry Data Processing, Analysis, and Interpretation Features

An example extracted ion chromatogram (XIC) following IntelliXtract processing
An example extracted ion chromatogram (XIC) following IntelliXtract processing

Component Extraction

Employ the powerful IntelliXtract algorithm to ensure extraction of all relevant chromatographic components via our proprietary ion thread technology

  • Automatically associate imported mass spectra with matching components to increase non-targeted screening and dereplication efficiency
  • Detect components present at trace concentrations and distinguish co-eluting peaks
  • Readily add peak tags to spectral features critical for reliable interpretation, such as isotopes, adducts, multimers, fragment ions, and more

Identification

Utilize the exclusive IntelliTarget algorithm for targeted screening of known compounds, to identify expected components, regardless of concentration or sample complexity.

Rapidly identify "known unknown" components using the Intelligent Component Recognition workflow to screen experimental MS data against internal or commercial spectral libraries (ex., Wiley and NIST).

Webinar: Applications in MS: Meeting Modern Deformulation Challenges

Watch on Demand: See our Intelligent Compound Recognition workflow in action!

Component formula, structure, and MS Match value displayed in the Table of Components following characterization
Component formula, structure, and MS Match value displayed in the Table of Components following characterization

Characterization

Characterize components using built-in tools that generate molecular formulae and predict mass fragmentation, in order to verify experimental data fit with structure candidate hits.

  • Indicate a parent compound and assign predicted fragments to experimental data automatically, plus easily transfer assignments between spectra
  • Add a structure, molecular formula, or mass number manually to the 'Table of Components' to automatically scan the total ion chromatogram for a match
  • Color-coded 'MS Match' categories (Excellent, Good, Poor) indicate the consistency of monoisotopic and isotopic peaks with experimental data

Additional Processing & Analysis Features

  • Import files in most major instrument vendor formats
  • 
    Vendor Data Format Import Export Extension Comments
    ACD/Labs ACD/Labs *.spectrus, *.esp
    AB Sciex Analyst (data-dependent acquisition MS2) *.wiff (single sample)
    Agilent Technologies 1100 Series LC/MSD Quad and Ion Trap Systems *.ms, *.yep DAD data and single chromatogram curve are imported also. Splitter available
    ChemStation *.ms Splitter available
    LC TOF *.wiff  
    MassHunter (6000 series) *.bin Entire *.D folder structure should be used. Agilent component requires Microsoft .NET version 2. DAD can be imported (V12) and MS/MS split controlled in newer versions
    Open Lab C v.1.04 *.D UV, LC-UV and LC-MS
    Entire *.D folder should be used
    *.ms, *.ch, *.uv
    Open Lab Rev. C.01.07 *.D UV, LC-UV and LC-MS
    Entire *.D folder should be used
    *.ms, *.ch, *.uv
    AB SCIEX Analyst *.wiff Single mass spectra, LC-MS and most LC-MSn imported. Splitter available. UV data not currently imported
    See above LightSight—Spectra are 'pushed' via ACD/Labs (NetCDF)
    Analyst QS *.wiff Single mass spectra, LC-MS and most LC-MSn imported. Splitter available
    Analyst TF *.wiff
    Applied Biosystems Mariner Data Explorer ASCII LC/MS *.txt LC-MS data only
    Bruker Daltonics and Agilent Technologies Agilent or Bruker LC/MS Ion Trap *.yep LC-MS and DAD data
    Bruker Compass (accurate mass data) *.d Entire *.D folder structure should be used. Bruker component requires Microsoft .NET version 3.5. Possible issue noted for MaXis Impact data.
    Hitachi LIT-TOF *.dat Import no longer supported in ACD/Spectrus products
    M-8000 and D-7000 *.msd; *.dad LC-MS and DAD data
    JEOL (Japan) JEOL-DX *.jsp, *.jpf, *.jmc Single mass spectra and chromatogram curves
    JEOL K9 *.spe LC(GC)-MS data
    LECO Corporation ChromaTOF-HRT™ for Citius™ (LC) and Pegasus® (GC) HRTs *.smp GC/MS or LC/MS data; LC/MS with in-source CID provides separate precursor and fragment ion (isCID) channels; LECO GC-TOF MS data is supported
    MasCom MASPEC II32 Data System MASPEC *.ms2 Single mass spectra and LC(GC)-MS data
    Matlab/Eigenvector Research DSO format *.mat Single mass spectra and LC(GC)-MS data
    National Institute of Standards and Technology NIST MS Software *.msp Uses Lib2NIST to convert .msp to supported format (.hpj or .sdf)
    NIST SDF Library *.sdf Splitter available
    Shimadzu Corporation LCMS-IT-TOF
    LabSolutions
    *.lcd LC-MS and LC-MSn data only
    For LabSolutions QTOF data import using 'Shimadzu IOmodule'
    GCMSsolution *.qgd GC-MS data (v11)
    LCMSsolution *.qld DAD data and single chromatogram curve are also imported
    Thermo Scientific Xcalibur *.raw Data splitting by Scan Filter parameters is available; format is supported only for Windows NT 4.0, Windows 2000, Windows XP, and Windows 7. Splitter available, to v2.2
    Finnigan ICIS II *.dat Splitter available
    Galactic *.spc Export is available for single MS only
    Unidata netCDF *.cdf, *.nc Splitter available
    Varian, Inc. 1200 *.dat Splitter available
    XMS *.xms, *.sms Splitter available
    Saturn 2000 *.sms Splitter available
    Waters Corporation MassLynx *.raw All files in the folder containing the _functns.inf file are necessary for data import. Splitter available
    Micromass OpenLynx *.rpt Splitter available
    Millennium32 (2D and 3D PDA data) "Connect to" ability available
    Empower (2D and 3D PDA data) and Empower 2 (2D and 3D PDA data) "Connect to" ability available
    Empower (3D MS data) LC-MS data only
    Open Source ASCII *.txt Single MS only
    JCAMP *.dx, *.jdx Splitter available
    mzML
    netCDF *.cdf, *.nc Single MS and LC(GC)-MS data
  • Process, view, and interpret all analytical data in the same software interface—MS and chromatography, plus UV/IR, NMR, Raman, and more
  • Detect chromatographic peaks automatically upon data import
  • Use powerful algorithms to seamlessly extract all relevant components, including co-eluting peaks
    • Or, extract chromatograms manually and adjust peak detection and integration
  • Generate mass spectra manually, or by automatic average subtraction
  • Produce molecular formulae for target masses
  • Simulate mass spectra for target molecular formulae
  • Assign structures to experimental data
    • Check the consistency of a structure candidate’s isotope peaks with experimental spectra using MS Match
  • Edit structures and dynamically extract their chromatograms
Complete list of supported file formats 1D & 2D NMR, LC, UV, MS, and structure data integrated in one project
1D & 2D NMR, LC, UV, MS, and structure data integrated in one project
An example MS fragmentation tree
An example MS fragmentation tree

Key Features of MS Fragmenter

(included with MS Workbook Suite)

  • Automatically predict mass fragmentation and assign fragment ions
  • Prune fragmentation trees
  • Separate fragments by chemical formulae
  • Assign fragments to corresponding spectral data
  • Easily transfer fragment assignments from one spectra to another

Efficient MS Automation and Scripting Options

Streamline MS workflows by automating routine data processing, file migration, and population of structure databases with predicted physicochemical properties.

Integrate MS Workbook Suite with other applications, such as a laboratory information management system (LIMS), to augment laboratory informatics systems with enhanced analytical chemistry capabilities.

Automation of routine processing
Automate routine processing

Innovative Knowledge Management | Create Live Mass Spectral DBs with Chemical Context

Simple database storage and screening with Spectrus DB
Simple database storage and screening with Spectrus DB

Use MS Workbook Suite to create fully searchable, live DBs of mass spectra, chromatograms, and UV spectra together with structure assignments, annotations, and other associated data.

Effectively share knowledge across organizations by not only capturing data, but also analytical interpretations, including relationships between spectra and structures.

  • Easily store, search, and retrieve annotated & analyzed data: spectra, chromatograms, structures, text, pictures, and links to reports or spreadsheets
  • Search databases by a variety of structural, spectral, and text parameters
  • Share expert interpretations of data to improve organizational understanding
  • Avoid duplication of analyses
  • Provide a collaborative platform for scientific R&D

Powerful Enhancements for MS Workbook Suite | Expand Unknown Identification

ACD/MS Structure ID Suite

Efficiently identify unknown components by using parent accurate mass values to predict molecular formulae, then use this data to search the integrated PubChem structure database. Perform additional structural and retention time filtering of database hits, and employ Auto Assignment to evaluate the top structure candidates.

Wiley Mass Spectral Databases in ACD/Labs Format

Through direct partnership with Wiley, ACD/Labs offers multiple mass spectral databases for purchase in our native format (*.cfd). These databases include hundreds of thousands of MS spectra, covering a wide range of chemical types, that enhance ACD/MS Workbook Suite's screening, identification, and deformulation capabilities.

Search structure databases by accurate parent mass plus predicted molecular formula
MS Structure ID Suite: Search structure databases by accurate parent mass plus predicted molecular formula

Resources for MS Workbook Suite

Mass spectrometrists can benefit from informatics solutions that offer advanced GC/MS & LC/MS component characterization functionalities. Read this eBook to learn how ACD/Labs' strategies enable vendor-agnostic data import & interpretation, seamless component extraction & identification, and simple & straightforward data management.
Read more

Open and Process MS<sup>n</sup> Data

Open and work with data generated from tandem mass spectrometry techniques. 2.0min
Play

Use Auto Assignment*

This video demonstrates how to generate and assign fragments to a mass spectrum based on a structure using the Auto Assignment tool. This tool is available with MS Workbook Suite or when MS Fragmenter is installed with Spectrus Processor. 1.5min
Play

Amgen purifies approximately 5000 compounds per year in biotech/pharmaceutical discovery, with LC/MS analysis and purity reporting serving as key final steps in this process. In collaboration with ACD/Labs, they have generated automation processes which reduce time for report generation and review. In the presentation, Grace demonstrates the benefits of the LC/MS automation workflow and provides a review of report generation and data review. Automation of structure confirmation is also discussed.
Watch on Demand

Current deformulation scientists face MASSive exSPECtations they are required to detect, screen, and identify unknowns with increasing efficiency despite shrinking analytical group sizes, pressure to perform more diverse activities, increased outsourcing of work, and slow, tedious, and error-prone methods. As a result analysts are left with much less time to devote to complex deformulation projects, while being expected to streamline existing analytical procedures.
Watch on Demand

Learn how ACD/Spectrus addresses analytical data management challenges through a portfolio of interoperable products that link chemical and analytical data in a homogenous environment.
Read more

Read about a novel chromatographic deconvolution algorithm that identifies all LC/MS or GC/MS components and automatically searches spectral DBs to perform structure characterization.
Read more