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Clover MSDAS v1.10.0 Major Update
  • Identification Routine is now available. It is a new user interface to simplify the identification and the use of all prediction models available for clinical routine.
  • Easily share your home-built prediction models across all users in your organization.
  • SMOTE algorithm is now available. Use it when training prediction models to mitigate issues related with unbalanced datasets. Synthetic samples will be added to complete the smallest categories.
  • PDF reports can now be generated in:
    • Identification modules
    • Validation modules
    • Prediction models training
  • Home Screen:
    • Starred (favourites) peak matrices are now displayed on Home screen.
  • Experiment & Peak matrix Screens
    • Improvements in the UI design of algorithms and categories.
Clover MSDAS v1.8.9
  • KMeans: First version of K-Means Algorithm is now available for all users
  • Identification: A slider with prediction confidence cut-off values to Identification results view is added. Cut-off can be edited and saved
  • Prediction Models improvements:
    • First version of re-train prediction models with new samples is now available for premium users
    • Now optimizaction information, if available, is displayed
  • Users can now uploading zip files with open format files in it. Folder hierarchy is kept
  • Collection: Add editor options to Usage Notes and Abstract fields
  • Training: Youden Index is now available in ROC curve in training.
Clover MSDAS v1.8.4
  • Ribopeaks: First version of Ribopeaks integration in experiment detail view
  • Alignment: Now spectra can be aligned by selecting reference peaks
  • Validation: Users now can compare one category versus the others to obtain all metrics
  • Correlation Analysis: Heatmap is now included in pairwise mode
  • Biomarker Analysis: Wilcoxon-Mann-Whitney test is now available
  • Global Prediction Bases are now available for Premium MALDI users.
Clover MSDAS v1.8 Experiment Pipeline
  • Experiment new workflow: First version of the experiment view redesign project, which includes a data flow pipeline for selecting the three main processes before the peak matrix (Preprocessing, Outlier, and Train/Test set splitting).
  • Outlier: With the new experiment workflow, selected outlier samples will be skipped in subsequent actions.
Clover MSDAS v1.7.2 Task list update
  • Task list: First version of Task list functionality to check the state of the user tasks in the last 2 days
  • Antibiotic Analysis Detection Module: Enabled test module for new Imipenen values
  • Studies: Now studies can be archived
  • Reproducibility tests: ANOVA results are now displayed for analysis with more than two categories
  • Premium/Basic accounts: Now user can distinguish between MALDI and FTIR premium when accesing to the different modules
  • Correlation Analysis: User now can export a unique excel file with the results of all groups
Clover MSDAS v1.7.1 Antibiotic Analysis Detection Module
  • Antibiotic Analysis Detection
    • Module enable for all Premium Users
    • Works with or without multicenter projects
  • Mabritec Central:
    • Mabritec Central is now available for all Premium Users
    • Mabritec Central has now its own box in Bioanalsysis screen
  • Average Spectra from Replicates: Advanced mode is now available. Now samples with the same name but in different folders are not mixed when grouping replicates.
  • Performance: Improvements in “preprocessing” steps and “peak matrix generation” steps performance
Clover MSDAS v1.7 Major Update
  • FTIR: “Extended Polysaccharide” (1300-800) region is now available as preset in FTIR mode
  • Correlation analysis: Correlation analysis is now available with MALDI-TOF data
  • Train/Test datasets:
    • New method for splitting data into train and test datasets is added
    • Info of splitted sets can be download as csv
    • Category table info is now displayed at experiment detail view
    • When params have no changed, a button is now available to resplit the data into two different datasets
  • Find Peaks Algorithm: Dynamic Threshold algorithm is now available
  • Biomarker Analysis:
    • New option to discriminate one category from the rest in ROC analysis is now available
    • Now users can now directly create a new peak matrix in a new step in Biomarker Analsyis with selected peaks
    • Number of samples of each category is now displayed
  • Validation: Now samples categories in categories step of the validation process are now recognized automatically
  • Dendrogram: A toggle button is added to show/hid the cut-off value
  • SVM: Poly Kernel option is now available
  • Correlation/Distance Heatmap: Now color is from blut to red space. Gaps are added between cells
Discrimination between hypervirulent and non-hypervirulent ribotypes of Clostridioides difficile by MALDI-TOF mass spectrometry and machine learning
Clover MSDAS – Mabritec Integration

  • Export and import files to/from Mabritec tool is now available.
  • Imported identification from Mabritec are now displayed in Clover MSDAS.
Clover MSDAS v1.6.6 Minor Update
  • Hierarchical Clustering:
    • Cut-off value can be now calculated in automatic or optimal mode.
    • Features dendrogram is now available when you build a matrix with peaks.
  • Outlier detection:
    • A table with summarized analysis is now added.
    • User can now modify the STD value limits.
    • Samples can now be marked and saved as outliers within an experiment.
Rapid Discrimination of Pseudomonas aeruginosa ST175 Isolates Involved in a Nosocomial Outbreak Using MALDI-TOF Mass Spectrometry and FTIR Spectroscopy Coupled with Machine Learning


Clover MSDAS v1.6 Major Hierarchical Clustering & Dendrogram Update
  • Hierarchical Clustering & Dendrogram
    • PCA at HC: Now PCA data is displayed when retrieving HC
    • Size plot and graphs can be now edited by the user
    • Dendrogram: Color squares can be now edited by the user
    • Cut-off: User can set a custom cutoff value to detect the clusters
    • Summary Table: A new table is displayed summarizing the content of the detected cluster and how the actual categories/classes are distributed
    • Categories as Dendrogram Metadata: One or several columns can be displayed next to the dendrogram. Each column has one coloured rectangle per spectrum. Each rectangle color matches one of the actual categories/classes labelled for the spectrum. This way, it is easy to visually check the detected clusters (unsupervised) and the actual clusters (supervised categories/classes)
  • Dual Tech: MALDI & FTIR
    • Now you can add your preferred technology at SignUp view
    • At User Profile section you can change now your preferred technology
    • Filter in Study List so MALDI-TOF or FTIR can be selected
  • Antibiotic Hydrolysis Analysis
    • Support for Meropenem
Clover Garden Repository release

Clover MSDAS v1.5 Major Update: Features & Improvements
  • Premium users mode is now activated. All module and features are now unlimited for premium users.
  • FT-IR data.
    • FTIR Quality Control Module: First version of QC test for FTIR data.
    • Inclusion of new default ranges and internal improvements in range selection with FTIR data.
    • FTIR Reproducibility Module: First Version of reproducibility Analysis for FTIR data.
  • Algorithms.
    • Balanced Accuracy metric at confusion matrix is now calculated and displayed in confusion matrices.
    • PCA: Edit size, color and shape of displayed dots.
  • Analysis.
    • t-test is now available in biomarker analysis as univariate analysis.
    • MALDI Biomarker Analysis Module have been redesigned.
    • SNP pairwise distance heatmap: First version of Single Nucleotide Polymorphism heatmap.
Direct Detection of Carbapenemase-Producing Klebsiella pneumoniae by MALDI-TOF Analysis of Full Spectra Applying Machine Learning


Automatic discrimination of species within the Enterobacter cloacae complex using MALDI-TOF Mass Spectrometry and supervised algorithms
Clover MSDAS v1.4 FTIR Upgrade: Features & Improvements
  • Armonisation between FTIR workflow and Clover MSDAS have been updated.
  • Rubberband algorithm has been added as Baseline correction algorithm.
  • New normalization algorithms:
    • Vector Normalization
    • Amide I Normalization
    • Amide II Normalization
  • Predefined ranges for absorbance mass filtering:
    • Membrane lipids [3000-2800]
    • Proteins [1800-1500]
    • Polysaccharides [1200-900]
Identification of Mycobacterium abscessus Subspecies by MALDI-TOF Mass Spectrometry and Machine Learning


Clover MSDAS v1.3 Features & Improvements
  • Outliers Detection Module first version release. PCA Reconstruction and Spectra Correlation analysis have been implemented.
  • Shapley Values plot includes now a bar plot to show the shapley values mean.
  • New file size upload limit is upgrade to 300MB.
  • Validation & Identification modules run now asynchronously. You can leave the screen and recover the result later.
  • Hyperparameters at classification can be now choosen manually or calculated via autotune algorithm.
  • ROC and Precision-Recall curves displayed up to 4 decimals for AUC values and can be downloaded in CSV format.
  • Error Rate have been added as a metric.
  • LightGBM have been adjusted on how hyperparameters are optimized.
  • In the ROC curve table at Biomarker Analysis module, you can click now on the table rows for selecting masses. Once they are selected, a peak matrix can be automatically generated by using those masses.
Stable version v1.0 of Clover MS Data Analysis Software


Major updates

  • Multitask mode: Now supervised classifiers run in asynchronous mode. Therefore, the user can leave or close the page/tab safely or work in other tasks, because the result will be there next time the classifier page is accessed.
  • Performance improvements: Algorithms now work in dedicated processes.
  • Random Forest: Newly optimized hyperparameters are: number of estimators, max features, max tree depth, min split size, min number of samples per leaf.
  • LightGBM: Adjustments on hyperparameters optimization. Shapley feature importances optimization.
  • Biomarker Analysis: In the ROC curve table, the user can click on the table rows for selecting masses. Once they are selected, a peak matrix can be automatically generated by using those masses as biomarkers.

Minor updates

  • TIC normalization: is now performed using the area under the entire spectrum.
  • Find Peaks Graph: The user can click on a detected peak for displaying a label with the mass value.
  • Biomarker Analysis: When a row is clicked in the ROC curve table, now it is also filtered in the Peak Distribution table.


Contact Information | Clover Bioanalytical Software

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