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Current Software Versions

What’s New in MS Structure ID Suite Version 2022

Version 2022 of MS Structure ID Suite adds new features, including quantitation of LC/UV/MS data and remote database search. We have also improved existing functions. Read below for details, and contact us for help upgrading your software.

Quantitation of LC/UV/MS Data

You are now able to quantify your LC/UV/MS data with an integrated quantitative workflow within the software. Samples can be quantified based on TIC (mass of compound), DAD (auto-extracted wavelength), or flat chromatogram (specific wavelength) to achieve accurate and reproducible quantitative data.  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
MS Workbook Suite v2022
Calibration table showing unknown, blank, and standard samples, plotted on calibration curve with a line of best fit and error bars. Summary and ANOVA table populated with equation and statistics.

Data Processing

Inclusion of NIST MS Search
  • You can now use the NIST MS Search in spectral searching (also available as part of the IXCR workflow)

    Spectrus Processor v2022
    Obtain component name, MF (match factor), RMF (relative match factor) and probability of spectral match directly from NIST.
Visualize Unique Structures in IXCR 2.0 Workflow Results
  • You can now choose to see unique structures from spectral search in the IXCR 2.0 workflow
Search Remote Databases
  • Search structures by mass value in remote databases (previously you could only use local databases)
Improved Hit Refinement for GC/MS Data with Component Deconvolution Workflows
  • The software now supports radical cation (+.) structures. You can now automatically identify radical cations in data interpretation.


Review Hit Quality of Spectral Search Results in the Database
  • The hit quality index is now available in the database following spectral search using the IXCR 2.0 workflow
Choose How to Store Component MSn Data
  • You can now store component spectra as well as scans for MS and MSn data in database records
Update Database Records Based on Collision Energy of Interest
  • When you apply a filter for collision energy during componentization and spectral search through the IXCR dereplication and compound recognition workflow, the software will now update database records based on that collision energy
  • We improved data import from:
    • Waters UNIFI and Waters Connect with ACD/Labs “Connect to” tool. You can now import processed results and import and view each file within a project. Import RDa data too.
    • OpenLab CDS Add-On—we have increased the peak fields and custom parameters we import
    • Xcalibur—you can view the UV wavelength on import and in the data processing interface
    • Shimadzu LabSolutions CDS Add-On—we have increased the metadata and peak fields we import
    • Bruker CompassXtract—we have accelerated the translation process allowing you quicker access to your data

Data Processing

Improved Hit Refinement with IXCR 2.0
  • Refine returned hits by using MS1 or MS2 spectra to query and search against MS1 and/or MS2 spectra in commercially available or in-house reference databases
    MS Workbook Suite v2022
Choose to See Area % Values for Adducts
  • For samples that contain adducts you can now select to display area or area percent values for both adduct and non-adduct species (available in IX 2.0, IXCR 2.0 and for manual assignment)
Greater flexibility when working with series of flat chromatograms in hyphenated data sets (LC/UV/MS, GC/MS)
  • Flat chromatograms and hyphenated data can be combined as series and saved as separate *.spectrus files. Table of Components, structures and biotransformation maps can be saved for each trace.

    MS Workbook Suite v2022
    xC/UV/MS files can be collected as a series, saved as separate *.spectrus files and contain tables linked to each trace.
Choose How to Handle Overloaded Samples Data
  • In IX 2.0 and IXCR 2.0, scans for overloaded samples have been excluded from component spectra calculation if option and threshold is selected
Transfer Peaks to the Table of Components
  • You can now choose to merge or overwrite when transferring named peaks to the Table of Components
Filter Spectral Search Results by Spectrum Polarity
  • You can now choose to filter spectral search results by spectrum polarity to ensure hits are relevant to your data

Processing Multiply Charged Ions

Improved Verification of Multiply Charged Ions
  • Now you can include multiply charged ions in the MS match verification of your molecular formula or structure
Find Target Ions
  • You can now find target ions when any charge state (+/- 6) is present.


Report MSn Spectra
  • You can choose to report multiple spectra by collision energy range and/or a specified value(s).
Increased Flexibility in Reporting LC/MS Data
  • You can report peaks and components, one-per-page

Ease of Use Improvements

  • Choose for traces to be selected by default
  • Choose to see the most abundant isotope mass even when it is not the lightest isotope in the cluster
  • When you are looking for specific target(s) with the IntelliTarget workflow, all results for both polarities can now be stored in the same file
  • Set the number of decimal places for mass values rounding before calculating of Mass Error
  • Set the number of decimal places to be displayed for peak retention time and area values
  • Isotope clusters can now be highlighted in the spectrum for formulae generated by Formula Generator and placed in the Table of Formulae.
  • There is now a new keyboard shortcut for horizontal zooming in spectra and chromatograms

UI and Visualization

  • Improvements have been made for data visualized in plate view:
    • You can now color objects in the Record Tree according to the color in plate view
    • Well position number is now displayed below the well icon
  • Points on graphical plots are now highlighted when you navigate within a record with multiple 1H NMR spectra

Ease of Use Improvement

  • You can now copy and paste all the text from data input into a “Multi-line Edit Box” (a text box in a database record that allows data to be displayed over several lines). Previously, data could only be copy/pasted from single line boxes

As always, you can process data from other analytical techniques in MS Structure ID Suite. We’ve improved features for these techniques as well:

New Features for NMR Data Processing

Process NUS Data with New Fast Algorithm
  • You can now reconstruct 2D raw data acquired in Non-Uniform-Sampling (NUS) mode with a new, faster algorithm
Reference X Nuclei Spectra by Absolute Frequency
  • You can now perform absolute referencing of the X nucleus (e.g., 15N, 19F, 31P, etc.) axis of 1D and 2D spectra based on a starting 1H or 13C spectrum
    • For Bruker/TopSpin spectra of the same sample recorded consecutively, you use the observed absolute frequency of the reference signal from the 1H or 13C 1D spectra to reference the X spectra
Identify Overlayed 2D Spectra from New Color Legend
  • You can now see which color corresponds to which spectrum in a legend when overlaying 2D spectra

    Spectrus Processor v2022
    Legend shows which spectrum is assigned to each color when working with multiple overlayed 2D spectra.
Use *.spectrus Files in Group Macros
  • You can now execute group macros on multiple *.spectrus files

Improved Features for NMR Data Processing

Better Handling of Multiplets on the Side of Broad Water Peaks
  • You can now get a more accurate integration of multiplets found on the edges of broad water peaks by enabling the Ignore Broad Water Peak option in your multiplet analysis

    Spectrus Processor v2022
    Perform more accurate integrations of multiplets on the sides of a broad water peak.
New Fields in the Table of User Data
  • You can now see the reference and signal that were used in the Table of User Data
  • You can now see the sum of all relative integrals for 1H spectra in the Table of User Data
See When Fourier Transform is Active in Preprocessing
  • You can now see when Fourier transform is active in the Preprocessing Options to prevent disruptions to subsequent tasks
Apply 1D and 2D Preferences to all Open 1D and 2D Spectra
  • You can now apply a set of preferences to all open 1D or 2D spectra with a single mouse-click, instead of having to repeat for each spectrum
Set Filters for Auto-Peak Picking
  • You can now set a minimum USP signal to noise ratio to filter out peaks selected in the automatic peak-picking algorithm