What’s new in Mnova 15.0.0
Mnova 15 is a major release that incorporates many new features in NMR, MSChrom, Mgears, ElViS, DB, new product versions such as Chrom Reaction Optimization 1.1, QC Profiling 1.2 and Multiplet Report 1.1, and the usual bunch of bugs fixes! You can find a summary of our selected top features here.
1Audit Trail
- Peak Picking information noted in the Audit Trail is now the same for both manual and automatic peak picking processing.
2Chemometrics
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 additional tools such as CCSD, ECHOS, and PROFILE.
3Data Analysis
- The Report Table to CSV function within the Data Analysis dialog now allows users to save data in CSV files, making it possible to open the CSV file in the same format as saved in Mnova.
- A new Delete Function button has been added to remove custom functions in the Model Function dialogue.
4DB
- DB queries are now available 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 have been 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 have been implemented in the DB Browser.
- The DB Browser now allows users to add clickable links in the HTML Display Mode.
- Users can customize the order and height of the rows in the Fields Table and save their preferences.
- The combined search process has been improved to reduce the time taken to return results.
- An option to Show Password Button has been added in the connection panel of the Database settings.
- In the Search Results dialogue, columns are sorted numerically 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.
- A Before Paste option has been added to the Database – Record View menu in the DB Browser.
- Improvements in user management of the DB allow users to change their passwords themselves in the Database toolbar under Database > Management > Change Password.
- A new "Keep the Scale" button has been implemented to maintain the scale of the spectra in the Spectral View of the DB Browser.
5DB Server
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:
- Facilitates the distribution of databases, as well as moving, copying, and managing backups and restores.
- Allows for easy modification of database information.
- Creating or deleting user accounts.
- Assigning user roles.
- Handling passwords.
- This allows for more secure validations in active directory environments.
6ElViS ( Electronic & Vibrational Spectroscopies)
- A PLS-based baseline correction tool (IarPLS) has been implemented with a button to automatically compute a near-optimal value for 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.
7Gears Chrom Reaction Optimization 1.1
- The settings dialog has been revamped and is now organized into four tabs: Input, Analysis, Quality Controls, and Output, offering a more logical and intuitive user experience.
- Warning messages and tooltips have been added to enhance the user experience and ensure smoother interactions with the plugin.
- A warning message now prevents duplicate component names when defining reaction components, 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 values (e.g., MZ or Molecular formula) for the same components to improve peak assignment accuracy.
- Multiple assignments are better managed by selecting the best assignment based on input type and match scores or parameters.
- The plugin now supports detecting and analyzing traces in both positive and negative Total Ion Chromatograms (TICs), improving compatibility for compounds that typically ionize negatively.
- The Peak Picking and Mol Match settings are now accessible within the plugin, enabling streamlined configuration and saving of distinct settings for different experiments.
- Two new options for quality control tests allow users to detect samples with multiple peaks in a specified RT range or when MS data matches diverge from the specified RT input.
- Users can now create custom output values using formulas based on default outputs, utilizing a predefined set of parameters, including component areas, total area, and concentrations (if calibration data is available).
- You can now name the CSV file based on the results folder name rather than the default "results.csv," enhancing data organization and identification.
- A new "Unknowns (Area)" field in the CSV output allows assessment of the total area of unidentified peaks. To use this feature, enable the "Evaluate Unknowns" option in the settings.
- The Chrom Reaction Optimization user guide is now accessible from within the brick's settings.
- The settings file (.data) is now presented in a more user-friendly format.
8Gears QC Profiling 1.2
- 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.
9IUPAC Name
- The time to generate the IUPAC Name has been reduced.
10Licensing
- The starting time when using Mnova offline from the campus network has been improved.
11Line Fitting
- The Levenberg-Marquardt algorithm has been updated to the latest stable version.
- A new Conformer Generator has been implemented within the molecule plugin, allowing users to combine different engines (GMMX, RDKit, and Balloon) to create a list of 3D conformers. This list can be reduced via Kmeans clustering or RMSD to produce a smaller list of the most relevant conformers.
12Mgears 2.5
- The Input tab now offers the selection of 15N and 31P experiment types, with configurable 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 configured masks has been improved to prevent the detection of multiple files for the same experiment, 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 now be optionally 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.
13Mnova
- 32-bit support has been removed in Windows.
- A new shortcut has been added to launch the Run Script action: Ctrl+Shift+R.
- The size of the report, such as peaks report, can be adjusted manually or automatically to fit within the canvas.
- Two new buttons allow users to move the scripting directories up and down in Scripting Preferences.
- In the spectrum metadata table, it is now possible to add clickable links, such as HTTPS, email addresses, or file paths from the user's local data.
- A new NMR converter has been added to import and export JSON files, with options to export only the FID, the spectrum, or both, and to include the imaginary part, peaks, multiplets, and integrals from the spectrum.
- The Export – Split Document… function has been improved, and the script now exports NMR spectra from pages that include additional items such as molecules.
14Molecules
- Biosequence Tools, a new tool to draw amino acid chains such as polypeptides, offers a list of standard and non-standard amino acids, L or D configuration, data handled as .mol files, extendable structures, splitting, and more functions.
- A scripted function has been added to import v3000 mol files.
- A new parameter has been implemented in the NMR Assignment atom label macro, allowing users to set the display mode for multiple shifts: {smrassignment,,rng} to display shifts as a range with ellipsis for more than two values, or {smrassignment,,avg} to display the average shift.
- Carbon assignment values are observed in the Assignments Table when loading attached .sdf files in Mnova imported from nmrshiftdb2.
- If Mnova encounters a problem with an InChi string that may represent a different molecule, a warning message is displayed.
- NMR Predictor has been improved to reduce the calculation time of large molecule spectra.
- Improvements have been made to the Molecule toolbar, including adjustments to button size and location, and grouping InChI and SMILES options into two new drop-down menus.
15MSChrom
- The Mnova MS plugin has been renamed to 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 as an alternative to the Classic algorithm. It includes options to change the sensitivity of peak detection, integration type, overlap level, signal smoothing, baseline correction, or to identify saturated peaks.
- Blind Regions replaces the Excluding Regions function, allowing users to exclude regions from the peak picking calculation anywhere in the chromatogram. The limits can be managed graphically over the chromatogram.
- A Background Subtraction function has been implemented to subtract MS/UV chromatograms, with the option to apply normalization.
- Improved mass chromatogram peak splitting now maintains the original baseline by default.
- It is now 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.
- The Chromatogram Fractions Table is now accessible by right-clicking over a fraction.
16Multiplet Report 1.1
- 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.
17NMR
- 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 (e.g., pseudo 2D), such as DOSY spectra.
- The Zero filling and LP dialog for 2D spectra has been improved, incorporating buttons for selecting f1 or f2, enabling quicker switching 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 only enabled when Report Js is checked. It is also accessible from the Script Multiplets in Tools > Scripting > Report or when the Setup Multiplet Report dialog is opened from a report already on the canvas, accessible by right-clicking on the spectrum and selecting Properties.
- A new "Show PCA in Axes" option is now available in the View menu of the PCA Workspace and is checked by default.
- The behavior of several functions over multiplets has been modified, including those in the Multiplets dialog and 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.
- New improvements in NMR Blind Regions include the ability to import Blind Regions into all selected pages in the document and to copy and paste them independently.
- A new script, "Assignments to Spectrum," has been added to the Tools > Scripts > NMR tools menu, allowing 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 the NMR Preferences dialogue.
- The peak multiplicity property is now 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 users to graphically modify the baseline using handlers at both ends.
- Atoms with labile protons are not highlighted in Assisted mode, and the multiplets are not highlighted when the mouse is hovered over a labile proton.
- A new functionality, "Deduce in Active," is available in the Assignments ribbon when there are assignments in the active molecule to deduce correlations only in the active spectrum.
- A new button, "Rename," has been added to the Assignments ribbon. When clicked, it renames the active spectrum multiplets with the assigned atom information and creates a link 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 attempts to create pairs of similar J values.
- A new option, "Add assigned coupling atoms," has been added to the Setup Multiplet Report dialog in the Report Js section, with the same functionality as the "Gets Js" button.
- In the Setup Assignments Report dialog, it is now possible to customize the number of decimals for the J coupling constants.
- A new property, "Quality," has been added to the AtomNMRAssignmentData object.
- The checkboxes for the correlation arrows in the Assignments ribbon are always enabled when an active molecule is present.
- Redefined algorithms have been developed for more precise DOSY spectra computation, integrating improved error analysis, Weighted and Monte Carlo fitting. Both methods have been implemented in the DOSY transform dialogue, with expanded support for a wider variety of PFG experiments.
- A new DOSY Peaks panel has been implemented with options to display fit curve plots and tables, including parameter data, spectra lists, and diffusion values. Various viewing options are available to manage all plot and data windows, facilitating 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, offering Manual or Auto Scale Detect options. The Auto Scale Detect option automatically helps the user achieve a better fit spectrum transformation on the canvas.
- The "Use existing peaks" and "GSD analysis" options have been removed from the DOSY transform dialogue. Instead, a new label informs users whether automatic peak picking will be performed or if already picked peaks will be used.
18NMRPredict
- The action "Get From Assignments" can now read 13C chemical shifts, similar to how it does for 1H spectra in Spin Simulation.
- The Charge option has been removed from the settings; when running a new prediction, only Fast Increments will be used.
Please contact support@mestrelab.com if you previously reported any bugs that are still unresolved in this version.
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