What’s new in Mnova 15.0.0

• Now Peak Picking information noted in Audit Trail is the same in manual as in automatic peak picking processing.

Mnova 15 includes three new chemometrics packages:

• Chemometrics: Includes Basic PCA to run experiments from Data Preparation.
• Mnova Advanced Chemometrics: The toolset includes Full PCA, SIMCA and PLS functionalities.
• Mnova BioHOS: This package incorporates all chemometrics tools available in Mnova, including the Advanced Chemometrics package and more tools such as CCSD, ECHOS, and PROFILE.

• Now, the Report Table to CSV function, within Data Analysis dialog, allows the user to save data in CSV files. This makes it possible to open the CSV file in the same format as saved in Mnova.
• A new Deleted Function button has been added to delete custom functions in Model Function dialogue.

• Now it is available to do DB queries from scripting by Text, Numeric, DateTime, Molecule Structure, Molecular Formula, Molecular Mass, Mass Retention Time, NMR Peaks, NMR Multiplet, NMR Spectrum, ElViS Spectrum, Mass, and Combined.
• Stereochemistry Search options were implemented, including relative or absolute stereochemistry, to be considered in Molecule Search.
• Two new columns to fill with SMILES (Simplified molecular Input Line Entry Specification) and InChI (IUPAC International Chemical Identifier) notation were implemented in the DB Browser.
• Now, in the DB Browser the user can add clickable links in the HTML Display Mode.
• The user can customize the order and the height of the rows in the Fields Table and save it.
• The combined search process has been improved to reduce the time to return results.
• The option to Show Password Button in the connection panel has been added to the Database settings.
• In the Search results dialogue the columns are sorted by number for the database field Types INTEGER and NUMERIC.
• The DB password is now encrypted.
• The Sequence generator allows users to manage custom IDs in database fields.
• Before Paste option has been added in the Database – Record View menu in DB Browser.
• Improvements have been made in the user management of DB. Now, users can change their password themselves in the Database toolbar, Database>Management>Change Password.
• A new button, Keep the Scale, has been implemented to keep the scale of the spectra in the Spectral View of the DB Browser.

The MnDB Server 2.1.0 has undergone significant enhancements, introducing improvements in search times, LDAP authentication, heightened security, and the integration of various functionalities in both database and user management:

Databases can now be exported and imported:

• Facilitating the distribution of databases, along with moving, copying, and managing backups and restores.
• Allowing for easy modification of database information.

Moreover, the Admin role now boasts enhanced capabilities in managing server users through the User Management tool within the Mnova DB toolbar, providing a streamlined approach to:

• Creating or deleting user accounts.
• Assigning user roles.
• Handling passwords.

LDAPS authentication support

• This allows for more secure validations in active directory environments.

• PLS based baseline correction tool (IarPLS) has been implemented with a button to automatically compute a near-optimal value of its asymmetry parameter.
• The Normalization processing action has been enhanced to offer three modes of operation: Largest peak (previously “Normalization”), Integral and Vector Length.
• The ability to create, get and set ElViS integrals by scripting has been added.
• A scripting function has been implemented to return the integral value for a specified range.

• The settings dialog has been revamped, now organized into four tabs, offering a more logical and intuitive user experience. These tabs categorize all settings into Input, Analysis, Quality Controls, and Output sections.
• The user experience has been further improved with the inclusion of warning messages and tooltips, ensuring a smoother and more informed interaction with the plugin.
• One notable improvement is the prevention of duplicate component names when defining reaction components. Users will now receive a warning message if they attempt to enter the same name twice, ensuring data accuracy.
• The automatic population of the MZ column when adding a molecular formula, molfile, or smiles has been removed.
• It is now possible to define both RT and molecular input (e.g. MZ or Molecular formula) values for the same components, to enhance peak assignment accuracy.
• Multiple assignments are now better managed by selecting the best assignment according to a set of rules based on input type and match scores or parameters.
• The plugin now offers expanded compatibility by detecting and analyzing traces in both positive and negative Total Ion Chromatograms (TICs), particularly beneficial for compounds that typically ionize negatively.
• The Peak Picking and the Mol Match settings are now available from within the plugin which enables you to streamline configuration and allows you to save distinct settings for different experiments.
• For enhanced control over the peak assignment process, two new options have been introduced within the quality control tests. Users can now detect samples where multiple peaks are detected in a specified RT range or when the match based on the MS data diverges from the specified RT input.
• Customization has been taken to the next level with the ability to create your own output values using formulas based on default outputs. This feature utilizes a predefined set of parameters, including component areas (and concentrations if calibration data is available), as well as total area and total concentration.
• Flexibility to name the CSV file based on the name of the results folder, rather than the default "results.csv" naming convention. This enhancement allows you to customize the CSV file name to match the specific results folder, making it easier to organize and identify your data.
• A new "Unknowns (Area)" field has been introduced in the CSV output, allowing assessment of the total area of unidentified peaks. To utilize this feature, you must enable the "Evaluate Unknowns" option in the settings.
• The Chrom Reaction Optimization user guide is now available from within the brick’s settings.
• The settings file (.data) is now presented in a more user-friendly format.

• The settings dialog has been restructured into three tabs: Input/Output, Analysis, and Quality Controls, facilitating easier navigation and configuration for analysis.
• An improved method has been implemented for the detection of unknown components under assigned peaks, along with a Quality Control test to flag samples with unknowns.
• The CSV inspection tool has been added to all relevant dialogs to make it easier to visualize and select the desired column for input or output.
• Enhancements have been made to the CSV inspection dialog, allowing users to manipulate the position of various CSV configuration elements within the CSV file content.
• Enhanced capability to define the chromatogram used for quantification, including the implementation of chromatogram definition (TIC, DAD, PDA, etc.), alignment, and baseline correction parameters.
• Peak detection settings are now directly accessible from within the QC Profiling settings, allowing users to modify these settings for analysis without affecting the current Mnova settings.
• It is now possible to exclude a chromatogram peak from the purity calculation.
• The "Results" section in the Mgears viewer has undergone significant improvements, now providing a breakdown of the results for general contents, groups, individual peaks in a sample, deconvolution results, and controls.
• In the "Deconvolution" tab, a button allows the direct addition of an input m/z, taking the main m/z value obtained in the deconvoluted spectrum.
• It is now possible to add and edit comments for peaks in any category. All comments fields are editable, enabling users to provide comprehensive comments while reviewing results.
• The total area of the peaks is now evaluated alongside the peak intensity to determine the presence of data in the sample.
• Colored pie charts and bar charts are generated for more intuitive result visualization.
• Charts to display the control results are now automatically generated, making it easy to spot flagged items by inspecting the well plate.
• The log file information has been improved, including more notifications regarding the start and end of the evaluation, recalculation, etc.
• An additional result viewer named the "QC Profiling Viewer" is now available and includes a table with the input masses that can be displayed alongside the results, making it easier to analyze and interpret the analysis results.
• The QC Profiling Viewer allows the user to input new m/z values or delete those provided by the input CSV.
• The QC Profiling settings can now be directly accessed from the results viewer, enabling convenient changes to settings and recalculation of results.
• The settings file (.data) is now presented in a more user-friendly format.

• The time to generate the IUPAC Name has been reduced.

• The starting time when using Mnova offline from the campus network has been improved.

• Levenberg-Marquadt algorithm has been updated to the latest stable version.
• A new Conformer Generator has been implemented within the molecule plugin. This allows users to combine different engines: GMMX, RDKit, and Balloon to create a list of 3D conformers. This list can then be reduced via Kmeans clustering or RMSD, to produce a small list of the most relevant conformers.

• The Input tab now offers the selection of 15N and 31P experiment types, with the ability to configure corresponding processing and design templates.
• A new option allows you to copy files to the output folder in batch or real-time without opening, processing, or analyzing them. Enabling this option hides the processing and analysis-related tabs and options.
• You can now add LC/GC-MS blind regions to hide specific portions of chromatograms that you don't want included in data analysis.
• The automatic detection of data files using the configured masks has been enhanced to prevent the detection of multiple files for the same experiment, thus avoiding sample duplication.
• A new feature has been introduced to efficiently handle input data organized in multiple subfolders. When enabled, this option creates a distinct HTML report for each subfolder, facilitating the review of individual results.
• Mnova and PDF reports can optionally be sorted into subfolders named after the corresponding input subfolders.
• The Mgears Viewer now displays the ten most recent result sets that have been opened.
• Data can now be visualized as a heat map in the results viewer.
• Mgears batch and real-time processes are now executable from the command line or any other application.
• Mgears settings are now exported in a user-friendly format.

• 32-bit support has been removed in Windows.
• A new shortcut has been added to launch Run Script action: Ctrl+Shift+r.
• The size of the report, i.e., peaks report, can be adjusted manually or automatically to provide users with the best fit within the canvas.
• Two new buttons allow the user to move the scripting directories up and down in Scripting Preferences.
• Now, in the spectrum metadata table, it is possible to add clickable links as https, email addresses, or file paths from the user local data.
• A new NMR converter has been added to import and export JSON files. This includes the option to export only the FID, the Spectrum, or Both. Additionally, the user can choose to export the imaginary part, peaks, multiplets and the integrals from the spectrum.
• The Export – Split Document… function has been improved, and the script now also exports NMR spectra from pages that include additional items such as molecules.

• Biosequence Tools, a new tool to draw amino acid chains such as polypeptides, offers a list of standard and non-standard amino acids list, L or D configuration, data handle as .mol file, extendable structures, splitting and more functions.
• Scripted function has been added to Import v3000 mol files.
• A new parameter has been implemented to the NMR Assignment atom label macro which allows users to set the display mode for multiple shifts ({smrassignment,,rng} to display the shift list as a range with ellipsis if there are more than two values, {smrassignment,,avg} to display the average shift).
• Carbon assignment values are observed in the Assignments Table when loading the attached .sdf files in Mnova imported from nmrshiftdb2.
• If Mnova presents a problem with InChi string, and the problem may represent a different molecule, a warning message is displayed.
• NMR Predictor has been improved to reduce the calculation time of large molecules spectra.
• Some improvements were implemented in the Molecule toolbar, including adjustments to button size and location. Additionally, InChI and SMILES options are now grouped into two new drop-down menus.

• The Mnova MS plugin has been renamed MSChrom in Mnova 15.
• 32-bit support has been removed for Windows. Check the updated list of Supported Formats.
• Enhanced Peak Picking is a new and robust peak picking algorithm developed to be an alternative to the Classic algorithm. Includes option to change the sensitivity of the peak detection, integration type, overlap level, signal smoothing, baseline correction or identify saturated peaks.
• Blind Regions replaces Excluding Regions function. It is an upgrade which allows users to exclude regions to the peak picking calculation in any part of the chromatogram. The limits can be managed graphically over the chromatogram.
• A Background Subtraction function has been implemented to subtract MS/UV chromatograms. It includes the option to apply a normalization.
• Improved mass chromatogram peak splitting to maintain the original baseline by default.
• Now, it is possible to add a set of rules in the Mass Preferences dialog to configure Blind Regions when opening a new MS dataset.
• The user can set up The Memory Cache Byte Limit in the Mass Preferences dialog.
• Now, the Chromatogram Fractions Table is accessible by right-clicking over a fraction.

• The widgets within the Multiplet Report dialog have been reorganized and grouped into more clearly defined sections.
• A new Mnova capability, "Report J Coupled Assigned Atoms," has been integrated into the multiplet report settings.

• Mnova 15 ensures seamless integration with peak lists from NMR software such as CARA, CCPN, Sparky and TopSpin, enhancing NMR Data Handling Capabilities.
• The 3D Spectrum Viewer is a new tool for visualizing 3D spectra, conventional 2D spectra, and arrayed NMR experiments (i.e., pseudo 2D), such as DOSY spectra.
• The Zero filling and LP dialog for 2D spectra has been improved, now, it incorporates buttons for selecting f1 or f2 These buttons enable the user to switch more quickly between dimensions without closing the dialog.
• A new option, Add assigned coupling atoms has been added to the Setup Multiplet Report dialog, within the Report Js section. This option is unchecked by default, and it is only enabled or applied when Report Js is checked. The option is also accessible from the Script Multiplets in Tools > Scripting > Report or when the Setup Multiplet Report dialog is opened from a report already reported in the canvas. This is accessible by right-clicking on the spectrum and selecting Properties from the menu.
• A new option, Show PCA in Axes option is now available at View menu in the PCA Workspace. It is checked by default.
• Behavior of several functions over multiplets has been modified, including those in the Multiplets dialog, Multiplet Manager. An Opacity Factor option has been added to the NMR Spectrum Properties dialog, and some Scripting engines for handling multiplets data were improved.
• Some new improvements in NMR Blind Regions include the ability for Blind Regions to be imported into all selected pages in the document and to be copied and pasted independently.
• A new script, Assignments to Spectrum, has been added to the Tools > Scripts > NMR tools menu. This script allows users to generate a synthetic spectrum by entering the desired spectral parameters in the Assignments to Spectrum dialogue.
• MLDCON peak picking has been integrated into the Method menu within the Peak Picking Options dialogue.
• A new 2D contour plotting algorithm, Fast Quadtree, has been added to the Contour Drawing Mode dropdown menu, in NMR Preferences dialogue.
• The peak multiplicity property is accessible from the scripting engine in both read and write options.
• A new function for Sum and Edited Sum integral methods has been implemented, allowing the user to graphically modify the baseline using handlers at both ends.

NMR -  Assignments

• Atoms with labile protons are not highlighted in Assisted mode, and the multiplets are not highlighted if the user is hovering the mouse over a labile proton.
• A new functionality Deduce in Active is available in Assignments ribbon when there are assignments in the active molecule to deduce correlation only in the active spectrum.
• A new button, Rename, has been added to the Assignments ribbon. When this button is clicked, the active spectrum multiples are renamed with the assigned atoms information, and a new link is added between each multiplet and the corresponding nucleus.
• A new button, Gets Js, has been added to the NMR Assignments Table, it reads the J coupling of two multiplets and tries to create pairs of similar J values.
• A new option, Add assigned coupling atoms, has been added to the Setup Multiplet Report dialog, in Report Js section, the functionality is the same as the Gets Js button.
• In the Setup Assignments Report dialog is possible to customize the number of decimals for the J coupling constants.
• Added a new property Quality to the AtomNMRAssignmentData object.
• The checkboxes of the correlation arrows in the Assignments ribbon are always enabled in the presence of an active molecule.

NMR -  DOSY/Diffusion

• We have redefined algorithms to achieve more precise DOSY spectra computation, integrating improved error analysis, Weighted and Monte Carlo fitting. Both were implemented into the DOSY transform dialogue. This includes expanded support for a wider variety of PFG experiments.
• Implemented a new DOSY Peaks panel with several options to display fit curve plots and tables, including parameters data, spectra list, and diffusion values. Various viewing options are available to manage all plot and data windows. This versatile tool facilitates the retrieval of information about each peak used in the DOSY analysis.
• The Inverse Laplace method has been refactored to improve performance.
• A new scale section has been added to the DOSY transform dialogue, providing two options, Manual or Auto Scale Detect. The Auto Scale Detect option automatically helps the user achieve a better fit spectrum transformation on the canvas.
• The Use exiting peaks and GSD analysis options have been removed from the DOSY transform dialogue. In their place, a new label has been added to indicate a message informing users whether an automatic peak picking will be performed or if the already picked peaks will be used.

• The action Get From Assignments is now able to read the ¹³C chemical shifts such as for ¹H spectra in Spin Simulation.
• Charge option has been removed from the settings, when running a new prediction only Fast Increments will be used.