New Features and Updates in V2025

Version 2025 of MS Workbook Suite™ improves several features including the fragmentation and labelling of cyclic peptides and more. Read below for details, andcontact us for help upgrading your software.

Highlighted Features  |  Improved Features  | Data Import & Export  |  Other Techniques

Highlighted Features

Improved Peptide Fragmentation

You can now more easily interpret your spectra for complex linear and cyclic peptides.

• Fragment and label complex linear peptides as a, b, c, x, y, and z ions
• Generate fragment ions for cyclic peptides based on the Roepstorff-Fohlman-Biemann nomenclature
  • Cyclic fragments are labelled using the anJK format where:
    • a = type of peptide ion (e.g., a, b, x, or y)
    • n = number of amino acid residues within the fragment
    • J = residue at the N-terminus end of the cycle break
    • K = residue at the opposite side of the cycle break

Mass spectrum and fragmentation table showing fragmentation of cyclic peptide and anJK peptide ion type.

Improved Features

Data Analysis & Processing

Simplified User Input and Analysis  

Improvements simplifying user input and analysis in quantitation have been made:

• Calculate and display the mean and %RSD for retention time and area in the calibration table for replicates
• You can now transfer the standard compound name to Table of Peaks

Better Efficiency in Intelligent Component Recognition Workflow (IXCR) 

• You can use a dynamic mass range to reduce the spectral search criteria to 0.5 Da above the molecular ion which will also change your HQI score accordingly
• Automatically populate desired indices into the Table of Components when they exist in a searched database to more easily compare retention characteristics

Enhanced Data Analysis and Interpretation

Several improvements have been made to the IX, IXCR, and ITA algorithms, including:

• You can now control the conversion of spectra from a profile to centroid spectra (IX 2.0, IXCR)
• You can now interrogate your data further with automatic creation and display of MS3 Component spectra following processing (manual assignment, IX 2.0, IXCR, and ITA)

Simplified Chromatogram Peak Detection

• You can now filter your picked peaks by setting a minimum area threshold (as a percentage of the total) and automatically integrate all peaks above this limit

Improved Visualization of Chromatogram Structures 

• You can now adjust the size of structures displayed on chromatographic peaks to better visualize those of interest

Reporting

Display Intensity Values on MS Peaks

• You can now view detector and relative intensity values directly over mass spectral peaks for easier analysis

Improved Visualization of Structures on Chromatograms

• You now have the ability to display chemical structures more clearly on chromatographic peaks in your reports

Updated Default MS Reports

• You now have more control over MS reports with the ability to generate improved default mass spectra reports

Expanded Component Reporting Options

• You can now report component mass spectra by collision energy, and include component UV spectra, giving you a more complete view of your data

Databasing

Audit Trail & Record History Improvements

• You can now add a column in the audit trail table to display the signature status of a record for quick identification of signed/unsigned entries
• You can now see the full history of record signing/un-signing in theRecords History dialog box

Ease of Use

• You can automatically revert back after showing all tabs of open data with the newFit to Tab Namesbutton
• You can now remove any unnamed components from the Table of Components with a single click
• You can now more easily set modifications to your mass spectra analysis with an improvedComponent Interpretation Options dialog box
• You can now display intensity values (detector or relative) over mass spectral peaks to more easily analyze your data

Data Import & Export

New Formats for MS & Chromatography Data Import

• You can now import data from the following formats:
  • TetraScience for Empower (*.json) DAD (LC-UV)
  • Waters Micromass Fraction Lynx (*.fpt)

Improved Import Filters for MS & Chromatography Data

• You can expect improved import filters for easier data analysis:
  • Shimadzu IO module
  • Waters Micromass OpenLynx RPT data to include labels of ELSD traces
  • Agilent Chemstation (*.D) folders containing multiple *.ch files will be imported together

Expanded and Improved Export of Data from Database Records 

• You can now export all record components as *.csv and *.txt files
• Options for exporting structure data to SD files have been expanded to include the MOL file version, extensions, and labels

Import Analyzed NMR Spectra from Multispectra JCAMP Files

• You can now import processed and assigned 1D and 2D NMR spectra from multispectra JCAMP files produced by third-party software as multiple separate spectra

Features for Other Techniques

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

Processing NMR Data with MS Workbook Suite

Data Analysis & Processing

Allow for Small Variations in the Integral Range of Peaks in External Standard qNMR

• You can now do external standard qNMR calculations using peaks whose integral ranges are not identical between replicates, which often occurs when working with manually defined integrals

New Parameters to Support Broader Workflows in External Standard qNMR

• You can now perform external standard qNMR calculations using replicate samples with different masses but constant volume with the help of:
  • New parameters added to Concentration Calculation Tool and default report template
    • Average w/w% (averaged across different replicates)
    • w/w% RSD%
    • Maximum Peak-to-Peak RSD% (intrasample)
  • Mass and volume information included in the table of theUsed Replicates popup menu

Customize the Position of Integral Curves

• You can now set a custom position for integral curves in the processing interface and reports by defining the desired vertical span of the highest curve in the displayed spectral region (as % relative to height of spectrum window, regardless of the vertical scale factor value)

Apply Unique Baseline Correction Parameters in Each Dimension of a 2D NMR Spectrum

• You can now apply baseline correction in each dimension of a 2D spectrum independently, allowing you to apply different parameters in each

Automatically Analyze Multiplets in¹⁹F NMR Spectra

• You can now automatically analyze¹⁹F spectra of structures with multiple fluorine atoms with an improved algorithm for better detection of first-order multiplet patterns

Improved Identification of Peaks Near Water in¹H NMR Spectra in DMSO

• You can now more accurately identify spectral peaks that appear at a similar position as the water peak in¹H spectra in deuterated DMSO (e.g., N-Me, O-Me, etc.) with an improved automatic analysis algorithm

User-Added Solvents/References Available to Macro Commands for NMR

• You can now utilize user-added solvents or references in macro commands by first invoking the newLoadSolventsTable macro command

Reporting

Optimize the Display of NMR Spectra in Reports

• You can now easily remove whitespace at the outer edges of frequency axes in 1D and 2D NMR spectra in reports. The newAuto Fit option in theReport Page Setup dialog box automatically selects a display region within ±0.5 ppm (¹H) or ±5 ppm (other nuclei) of the outermost peaks.

Summarize w/w% Values in qNMR Reports

• You can now include w/w% values for each replicate in theSample Datatable of a qNMR report

Ease of Use

• You can now quickly select/unselect all NMR integrals except for that of the solvent in external standard qNMR with new a context menu

Want to learn more?

Read more about the full features of MS Workbook Suite, or contact us for help upgrading your software.

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