What’s new in Mnova 15.1

• Affinity Screen Ligands Table: A new "Affinity Screen Overall Ligands Table" is available in the Mgears viewer, showing results for all ligands across samples, sorted by "Score" (highest to lowest).
• Ligand Search Tool: We’ve added a search tool to find ligands within the loaded batch of results for review.

• Grouping of FBDD-Related Products: The FBDD-related tools, including Screen, Screen 2D, and Mix Design, have been reorganized and are now conveniently grouped together under the Binding tab in the Mnova ribbon, streamlining access and improving workflow efficiency.

• New Peak Purity Assessment Model (MCR): The Advanced Chemometrics and BioHOS plugins now integrate the Multivariate Curve Resolution – Alternating Least Squares (MCR-ALS) algorithm, providing a new tool for peak purity assessment in LCMS data. This model enables more detailed and accurate peak purity analysis, significantly enhancing decision-making in chromatographic workflows. Visit our Top Features web post for more information.
• Customizable Confidence Ellipses in PCA/PLS: Confidence ellipses in PCA and PLS scores charts are now dynamically rescaled for better visibility and can be customized to fit user preferences.
• PCA Scores Class Labels: Class labels in PCA and PLS scores charts are now displayed as a movable and customizable legend, which can also be hidden for a cleaner view.
• Data Tables Access via Plot Menu button: The corresponding data table for any plot can now be accessed directly from the plot’s menu, providing quicker and easier navigation between visualizations and data.
• CCSD Relative Peak Heights: A new option enables users to display relative peak intensities in CCSD spectra, with results available for copying and exporting.
• CCSD Similarity Metrics for Δδ (H): A new similarity metric feature has been added alongside relative peak heights, allowing for more detailed spectral comparisons.
• PLS Layout Templates: PLS results now fully support layout templates, ensuring consistent formatting and reporting of both graphs and tables.
• RMSEC and RMSECV in PLS Models: RMSEC (Root Mean Square Error of Calibration) and RMSECV (Root Mean Square Error of Cross Validation) are now calculated and displayed in PLS models, providing deeper insight into model accuracy.
• New PCA Settings for Components and Cross-Validation: New options for setting the number of components and cross-validation have been added to PCA data preparation, giving users greater control over their analyses.
• Improved PLS Model Check and Test Tables: The color coding in both Model Check and Test Tables has been optimized. Users can now sort tables by the Spectrum column, and Dmodx outliers are clearly displayed for easier identification of outliers.
• Context Menu in P Loadings Table for PLS: Right-clicking in the P Loadings Table now opens a context menu with options such as Copy, Show in Chart, Show in Spectrum, Edit Color, Auto Color Component, and Reset Region, enhancing the flexibility of data manipulation.
• Access to Original Bucket Table in PLS: A new table containing the original X-data has been added to the Tables Menu under Input > X Input (Original), allowing users to reference raw data for comparison.
• VIP Regions Display in NMR Spectra: VIP regions from PLS analyses can now be visualized in both 1D and 2D NMR spectra, improving insight into important spectral regions.

• Bug fixes: Two minor bugs have been resolved.

• Enhanced Output Configuration: The output configuration has been significantly enhanced for a better user experience, including the ability to fully automate the setup of the output CSV configuration with a single click.
• New Reaction Optimization Viewer Tab: A new tab has been added to the Chrom Reaction Optimization Viewer, displaying a sortable table with all the samples and customizable columns for results and metadata.
• Improved Molecular Input Capabilities: Improved capabilities for molecular input definition, including the ability to use molecular weights (MW), specify polarity for MZ values with "+" or "-" signs, and support a comma-separated list of MZ values.
• Consistent Numbering of “unknowns”: Consistent numbering and an overview of “unknowns” across the full dataset have been implemented to facilitate comparisons.
• Unknowns Tab in Optimization Viewer: The Chrom Reaction Optimization Viewer now features a new "Unknowns" tab that displays overall unknowns along with their mean RT, MZ, and the samples in which they appear.
• Custom Chart Configuration: Users can now add and configure custom charts, specifying the chart type (Pie/Bar), variables, and colors, in addition to the default charts.
• Base Peak Chromatogram Selection: Users can now select the Base Peak Chromatogram (BPC) as the trace for extraction and quantitation.
• Metadata Tooltip for Well Plates: For newly generated results, the metadata now appears in the tooltip of each well plate, providing an additional, convenient way to view metadata.
• Easy Import of Reaction Components: Reaction components can now be easily imported into the settings window from CSV, .data, .mgrs, or JSON files, eliminating the need for manual input data like SMILES, MWs, and RTs, streamlining the process.
• Comments in Results Section: Comments can now be added to the results section for each sample in the Mgears viewer and saved to the CSV output.
• Assignments Tab for Reaction Components: An "Assignments" tab has been added to the viewer results, providing clarity on the target masses or RTs alongside the matched and assigned values, especially when both masses and RTs are used together to define reaction components.

• Record details of each Chromatography command in the Audit Trail: The Audit Trail now records details for each Chromatography command, including Set Overlay Vertical Offset, Stack Chromatograms, Shift Stacked Chromatograms, Set Chromatogram Properties, Normalize Stacked Chromatograms, Set Stacked Mode, and Edit Parameter Templates.
• Refined Peak Splitting Functionality: A new peak splitting feature has been added, allowing users to split chromatographic peaks by clicking and dragging to the desired retention time, offering more control and precision in peak adjustments.
• Support for Blind Regions: The Chromatography tool now supports Blind Regions, like the functionality in the MSChrom plugin. This allows users to avoid specific regions during peak picking, enhancing the accuracy of peak detection.
• New Integration Shortcuts for Peak Detection: Keyboard shortcuts have been introduced to streamline peak detection tasks, including:
  • Add Peak: Press K
  • Delete Peaks: Press Shift+K
  • Clear Peaks: Press Ctrl+Shift+K

• Adjust Stacked Items in Spectral View: A new tool in the Spectral Viewer allows users to adjust the scaling of the active spectrum within a stacked NMR. This provides greater flexibility when viewing and comparing spectra in Mnova DB, improving data analysis and visualization.
• Compare Spectra: A new button has been added to the Spectral View, allowing users to load spectra from Mnova and compare them with spectra stored in the database, streamlining the comparison process.
• Customizable Decimal Places in DB Browser Widgets: Users can now customize the number of decimal places displayed in the DB Browser Widgets. By default, the system uses 4 decimal places, but this can be adjusted to meet specific needs.
• CSV Export Functionality for Table Views: A new button has been added to various widgets (Scores, Item List, Item View, Table View, and Table Column View) that allows users to export table contents to a CSV file, enabling easy sharing and data management.

• IUPAC Naming for Relative and Racemic Stereochemistry: The IUPAC naming engine now supports molecules with relative and racemic stereochemistry, allowing for more accurate and comprehensive naming of stereochemical configurations.
• Support for Enhanced Stereo Marks: Mnova has implemented the ability to read enhanced stereo marks from CDXML and Molfile V3000 files, broadening compatibility with these formats.
• Improved Nomenclature for Metal-Organic Compounds: Mnova now supports naming metal-organic molecules, including those containing salts and molecules with two metals. This enhancement enables the generation of names for such molecules using multiplicative naming conventions.

• Dataset Status Monitoring Table: A new dashboard now provides a clear, at-a-glance view of dataset status during a run, eliminating the need to search through log lines. Visit our Top Features web post for more information.
• Gearbox for Automated Batch Jobs: We’ve introduced “Gearbox,” an application that allows users to automatically run multiple Mgears jobs across different batches, removing the need for manual UI submissions. Visit our Top Features web post for more information.
• Enhanced CSV Output Configuration: We’ve enhanced the "CSV Output Configuration" dialog to improve usability, streamline workflows, and provide greater control over data processing.
• PDF Output for All Samples: It is now possible to create a PDF output containing results from all the samples in a run.
• In-Viewer Log Visibility: Log information is now visible within the Mgears viewer, making it easier to review logs after recalculation.
• Software Version Tracking: The version of the software and plugin versions used to generate a dataset are now included and can be checked from the Mgears viewer.
• Improved LC/GC-MS Data Processing Speed: The speed of processing LC/GC-MS data from an online server has been improved by creating a temporary local copy of the dataset for analysis.
• Trace Browser Button: A new browser button in the Chromatogram Parameters dialog allows users to select the desired trace from a list, rather than manually typing it.
• Drag and Drop Feature: A new feature allows users to drag and drop a Mgears results folder or settings file directly into the Mgears Viewer, automatically loading the corresponding results and configurations.
• "Analyze Again" Script Option: A new option in the Mgears Viewer settings allows users to apply the processing script when the "Analyze Again" button is clicked.

General

• Restore Column Names Button: A new button, "Restore Column Names," has been added to all configuration tables dialogs, including Customize Table - Assignments, Customize Table - Integrals, Customize Table - Multiplets, Customize Table - Peaks, and Customize Table - Stacked Items, allowing users to quickly revert column names to their default settings.
• Customizable Data Browser Columns: A new tab in the Data Browser settings dialog allows users to select and customize the columns displayed in the Data Browser window, offering more flexibility in data management.
• Spanish Translation of Table Column Titles: Spanish translations have been added to table column titles across Mnova, improving accessibility for Spanish-speaking users.

Molecule Sketcher

• JSON Molecule Converter: A new converter has been added, allowing users to export and import molecule items in JSON format. Visit our Top Features web post for more information.
• Improved Export Formats (SDF, JSON, JCAMP-DX, CDXML): Significant improvements have been made to exporting molecules in various formats, including SDF, JSON, JCAMP-DX, and CDXML, along with better labeling and chemical bond overlays.
• Peptide Export Enhancements: Improvements have been made to the export of peptide molecules to SDF file format, resolving previous issues with improper export.
• Enhanced Stereochemistry Marks: New support for enhanced stereochemistry marks has been added, including three new stereo descriptors (Or, And, and Absolute) for representing relative, racemic, and absolute stereochemistry. These descriptors are exportable to CDXML and Molfile V3000 formats (Note: Molfile V2000 does not support these enhancements).
• Read Molecule Fragment in CDXML: When exporting CDXML files, molecules that contain lone atoms with non-expandable labels will now display the molecular fragment instead of a text label.
• Grouping Molecules in CDXML Exports: Multiple molecules can now be grouped into a single entity during CDXML export, using tags. When loaded into Mnova, these grouped molecules are displayed as a merged entity.
• Support for CDXML/CDX Format: ChemDraw XML (.cdxml) has been added to Mnova’s list of export formats, allowing users to save molecules and reactions in this format.
• Save Molecules in Molfile V3000 Format: Mnova now supports saving molecules in Molfile V3000 format, adding to the list of compatible export formats.
• Expanded Labels for Peptides: A new “Expand Labels” command has been added to the molecule right-click context menu, enabling label expansion for peptides and other structures, including amino acids.
• Create Bio sequences from Clipboard: Users can now create bio sequences by pasting biopolymer strings (using 3-letter or 1-letter amino acid short names) directly from the clipboard.
• Draw Cis/Trans Double Bonds: Two new commands have been added to the toolbar and ribbon: “Undefined Double Stereo Bond” and “Double/Undefined”. These commands allow users to draw cis or trans double bonds where stereo procedures do not generate E/Z descriptors.
• Drawing Modified Peptides: Mnova now allows users to add protecting groups (PG) to the amino acid side chain, as well as to the N-terminus and C-terminus of peptides, enabling more detailed peptide modifications.
• Superscript Numbers in Molecule Labels: Users can now add superscript numbers in molecule atom labels via the "Edit Atom" dialog, using the syntax ^{NNN} to display the number as a superscript.

• MCR – A New Mode for Peak Purity Assessment: The Multivariate Curve Resolution – Alternating Least Squares (MCR-ALS) algorithm introduces a new mode for Peak Purity Assessment, offering enhanced accuracy and detailed analysis of peak purity in complex datasets. This mode allows for more precise identification and separation of overlapping peaks, significantly improving chromatographic data interpretation and decision-making. Visit our Top Features web post for more information.
• Improved Molecule Match Scoring with H+ Adducts: A new Purity Threshold setting has been added to the Molecule Match settings, defaulting to 30%. Matches with a mass purity below this threshold are ignored, helping users focus on more reliable results. Visit our Top Features web post for more information.
• Molecule Match Parameter for Isotope Cluster Matching: A new threshold option has been added to the Molecule Match settings for the number of lines in the isotope cluster to use in the matching stage. This setting allows users to define the threshold, and peaks below the specified value are ignored in the match. Visit our Top Features web post for more information.
• Save MS Data as JSON: MSChrom datasets can now be saved as JSON files, providing greater flexibility in data sharing and interoperability. Visit our Top Features web post for more information.
• OpenLab 2.8 Added as New Mnova CDS Converter: Expands the range of Mnova CDS converters, enabling seamless integration with more chromatography data systems.
• Updated Mnova CDS Converters: The Mnova CDS converters for Chromeleon, Empower, and OpenLab 2.7 have been updated to improve compatibility and performance.
• Independent Alignment Parameters for Each Trace: Users can now configure independent alignment parameters for each trace in a dataset using the Automatic Traces Alignment feature.
• Refactored Peak Splitting Options: The peak splitting functionality has been refined. By default, splitting now keeps the baseline unchanged. Holding the Shift key allows users to move the split point freely outside the original baseline. (Note: The Alt key option has been removed.)
• Audit Trail for Peak Detection Settings: The default peak detection settings for chromatograms are now included in the Audit Trail, improving traceability.
• Synchronization of Blind Regions by Percentage: The Synchronization button for MS blind regions has been updated with a menu that allows users to synchronize blind regions either by time (minutes) or by percentage.
• Drag and drop for Agilent MassHunter .D Folders: Users can now drag and drop the AcqData directory from an Agilent MassHunter .D folder directly into Mnova, where it will be correctly identified and opened.
• Simultaneous Movement of Adjacent Peaks' Common Point: A new feature allows users to move the common point of two adjacent peaks in the Mass Plugin by holding the Alt key and dragging. Holding Alt+Shift will place the new point where the mouse is released.
• Retention Time Delay Between UV and MS Channels: A new tool, Automatic Traces Alignment, has been added to the Analysis tab in the MSChrom ribbon, which automatically calculates the offset between UV and MS channels.
• Maintain Zoom for Mass Spectra While Scanning: A new option, Reset Zoom While Scanning, has been added to the MSChrom Preferences dialog. This option ensures that zoomed-in MS spectra remain zoomed while navigating through the chromatogram.
• Option to Open BPC Instead of TIC: A new checkbox in the Preferences dialog allows users to open the Base Peak Chromatogram (BPC) instead of the Total Ion Chromatogram (TIC) by default, providing a cleaner view of the highest peaks in the MS chromatogram.
• UV and Corona Traces in mzData Files: When importing mzData files, all available traces, including UV and Corona traces, will now be loaded.

Assignments

• Enhanced Correlation Highlighting in 2D Spectra: Hovering over a row in the Assignments Table now highlights both the correlation label in the spectrum and the corresponding correlation arrow in the molecular structure, improving visual clarity and usability.

Data Analysis

• Automated Region Creation: A new feature has been introduced for the automated creation of data analysis regions. A drop-down menu now allows users to easily import and auto-select regions, including options for Integrals, Concentration, Peaks, and Import YY' from File. This functionality is accessible from both the main Data Analysis menu and the Data Analysis Table.
• Parameter Import for X-Column in Stacked Spectra: A new feature allows users to import any parameter into the X-Column for stacked spectra. This imported parameter is displayed both in the corresponding table and the associated graph, enhancing the flexibility and control over data visualization.

Formats

• Support for RS2D/Nanalysis Formats: Mnova now supports RS2D and Nanalysis formats, including both FID and processed spectra, broadening compatibility and workflow flexibility.
• New File Saving Option for LOGS: A new file-saving option allows users to export NMR spectra as a package (.zip) containing a JSON file for each spectrum along with the associated Mnova document. This is available via the File > Save As option with the new type: “Script: LOGS Data Bundle (.zip).”

General

• Improved 3D NMR Spectrum Viewer Performance: Optimized loading times for large 3D NMR spectra, providing a smoother and faster user experience when handling extensive datasets.
• DOSY Methods in Parameters Tab: All DOSY methods (Peak Fit, Inverse Laplace, Bayesian) are now fully displayed under the Parameters tab, ensuring easy access and clearer method selection.
• Enhanced Handling of Pseudo-nD Spectra: Pseudo-2D and pseudo-3D spectra are now treated as true nD spectra, improving the accuracy of data representation and analysis.
• Extended 3D Spectrum Viewer Capabilities: Now 3D iDOSY experiments can be opened with this tool for data visualization.
• Improved 3D iDOSY Transform Performance: Significant performance improvements have been implemented for 3D iDOSY transformers using the Inverse Laplace method.
• Diffusion Unit Display in Arrayed Data Table: The Arrayed Data Table now includes diffusion units in the headers, enhancing the readability and interpretation of results.
• DOSY Scaling as an Advanced Option: The scaling option for DOSY spectra has been moved to the DOSY Spectrum tab, streamlining the advanced settings and making them easier to access.
• Improved Absolute Reference Performance: Enhanced the performance of the Absolute Reference functionality, enabling accurate referencing even when spectra are recorded at different temperatures.
• 19F Multiplet Reports: The number of fluorine atoms is now included in 19F multiplet reports, providing more detailed and accurate data output.
• Peak Ticks Checkbox in NMR Tab: A new checkbox has been added to the NMR ribbon, allowing users to easily select or deselect Peak Ticks, providing more control over the display of peak annotations in spectra.

NMR Tools

• 13C/HSQC Molecule Search Tool Integration: A new NMR tool that allows users to search 13C data in a large database using 13C and or HSQC experimental data, along with a molecular formula. This tool helps to determine if a compound is known by providing a ranked list of possible compounds, with direct links to PubChem for more detailed information about each potential match. Visit our Top Features web post for more information.

• Color Coding for Prediction Quality in Modgraph NMRPredict: The Modgraph NMRPredict now includes color coding in the Drill Down Table to indicate the quality of predictions. Predictions are categorized as Good, Questionable, or Bad, based on the “Shells” number, allowing users to easily assess the reliability of each prediction.

• Bug fixes: Minor bugs have been resolved.

Python Engine

• New Scripting Language Support: Mnova now supports Python as a scripting language, allowing users to create and run custom scripts directly within the software. This addition provides greater flexibility and control over automated tasks and workflows. Visit our Top Features web post for more information.

JavaScript Engine

• Access to Zoom Coordinates for NMR Layout Templates: The zoom coordinates of NMR Layout Template items are now accessible through the Scripting Engine, allowing users to programmatically control the layout.
• Command Line Script Directory Setting: Users can now set script directories directly from the command line, improving flexibility in scripting workflows.
• Lock Document for Faster Analysis: A new feature allows users to lock a document to increase analysis speed, optimizing performance during scripting operations.
• TreeView Wrapper Enhancements: Additional functionality has been added to the TreeView Wrapper, including the ability to access the getModel function.
• Polynomial Fitting from Eigen C++ Library: The Scripting Engine now supports parsing polynomial fitting functions from the Eigen C++ library, enabling advanced mathematical operations.
• Modify Peak Position and Width via Scripting: Users can now adjust both the position and width of peaks directly through scripting. This enhancement provides greater control over spectral data adjustments, allowing for more precise manipulation of peak parameters in an automated workflow.
• Improved Documentation for "TemporaryFile" Object: The documentation for the "TemporaryFile" object has been corrected to provide an accurate example of its usage.
• Row Manipulation in TableWidget: New functions — hideRow, isRowHidden, and showRow — have been added to the TableWidget, allowing for enhanced row visibility control through scripting.
• Frame Wrapper: A wrapper for Frame has been added, allowing for easier manipulation of this widget type within the Scripting Engine.
• Widget Adjust Size Function: The Widget::adjustSize() function is now accessible from the Scripting Engine, allowing users to programmatically adjust the size of widget elements.

• Improved Tolerances for Snapping 2D Multiplets to 1D Chemical Shift Lines: The default tolerances for snapping 2D multiplets to 1D chemical shift lines are now automatically calculated based on the digital resolution of each spectrum, providing more precise snapping functionality.
• HSQC and Molecular Connectivity Diagram Interaction: When hovering the mouse over a label (multiplet or peak label) in the HSQC spectra, the corresponding CHx group is now highlighted in the Molecular Connectivity Diagram (MCD). In addition, the chemical shifts for the peaks are displayed in red in both the horizontal and vertical traces of the spectra. The corresponding CHx group is also highlighted in the Elucidation Constraints table for easy identification.
• Restored Peak Snapping to Gridlines: The ability to snap peaks to the gridlines during peak picking in 2D spectra has been restored. In manual mode, peaks are now properly assigned to gridline positions, and when multiplets are used for assignments, they are automatically selected by hovering the mouse over the 2D spectra.

• StereoFitter 1.1.7 supports Orca 6.0.
• Alignment Tensors information in StereoFitter Results Table: When StereoFitter is executed with anisotropic data (RDC (Residual Dipolar Coupling), RCSA (Residual Chemical Shift Anisotropy), or PCS (Pseudocontact Shift)), the Alignment Tensors information is displayed at the end of the Couplings Tree, featuring two sections:
  • Alignment Tensors parameters: Alignment tensor in the molecular frame, Eigenvalues (Axx’, Ayy’, Azz’), Principal Frame, Axial Component, GDO, Asymmetry Parameter, Rhombicity Component, Rhombicity, Q, Q(error scaled). 
  • Angles: Beta, cos(Beta).
• Support of anisotropic data from different alignment media StereoFitter Results table visualizes each group of values on its corresponding tab.