PATCH NOTES

This page lists the changes made to the MOREPEAKS program. Please note that confidentially issues may force us to be nebulous about certain details. In these cases this will be indicated and the details will be made available at a later stage.

1.06 – IMPROVEMENT ON PEAK TRACKING
Relative retention and search windows are made more robust.
 
Major updates
  • Peak tracking
    • Mass spectra are used to assess search windows.
    • Relative retention is now used when evaluating unpaired peaks.
    • Paired peaks will always be shown on chromatograms, eventhough the chromatogram is edited by the user.
    • When no peak pairs are found, MOREPEAKS no longer tries to save the non-existing data.
    • The minimal extracted prominence of a peak is calculated from the maximum extracted signal times a certain percentage. The user is free to determine this threshold.

Minor updates

  • Loading-message are made universal.
  • It is now possible to select Pareto points of a previous optimization for comparison.
  • When adjusting the baseline of a two-dimensional chromatogram, MOREPEAKS will prevent negative time values. The user is shown a message when this is happening.
  • When overwriting imported data, MOREPEAKS updates the graphical user interface accordingly.
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1.05 – DATA TYPE UPDATE
Loading data is made more robust and new MS datafiles can be loaded in.
 
Major updates
  • It is now possible to load mass spectrum data with the extension .cdf.
  • The search algorithm for solvent peaks has been made more robust when tracking peaks.
Minor updates
  • Mass spectra from different types suppliers can be imported more robust when the datafiles are converted to .mzXML.
  • Fixed a bug where the Analyte Database couldn’t be exported for three parameter models.
  • Visualizing an extracted ion chromatogram has been made significantly faster.
  • Retention plots for normal-phase liquid chromatography and ion exchange chromatography are now shown on a logarithmic scale.
1.04 – IMPROVED 1D PEAK TRACKING
A number of the improvements to the two-dimensional peak-tracking algorithm have been transfer to the 1D peak-tracking algorithm.
 
Major updates
  • Peak tracking 1D
    • The GUI to view pairing performance was completely revamped. The GUI and algorithms now feature the improvements released previously for the 2D peak tracking GUI.
    • Algorithm now involves all statistical moments for peak tracking.
Minor updates
  • The retention plot in the Analyte Database GUI no longer shows inactive (i.e. non-selected) analytes, unless the analyte is selected.
  • Fixed a bug where the Analyte Database couldn’t be exported for three parameter models.
  • The quadratic model will use a maximum of 100 steps in the Simpson’s Approximation to save time.
  • Viscosity now has the unit Pa.s, added as label.
  • Corrected a number of minor spelling  and display-related errors.
  • MOREPEAKS will produce a warning when trying to fit modifier fractions above 1 when not using ion exchange.
  • Prevented user from fitting just two data sets on a three parameter model.
  • Using the Bruker raw data import function now locks MOREPEAKS until it the program has finished converting the files.
1.03 – MINOR IMPROVEMENTS (17 September 2019)
A number of critical bugs and improvements were made.
 
Minor updates
  • Analyte database now has an option to export the data table
  • Names can now be loaded in from the first column of a peaktable.
  • Added retention plots to the Analyte database
  • Peak detection in 1D Visualization and Analysis tab can now be turned off.
  • Check for updates button has been enabled and when clicked, will guide the user to https://morepeaks.org/software/

Bug fixes

  • Fixed a bug where Peak Tracking in 2D would look for value that where higher than the length of the relative times.
  • Fixed a bug where 2D chromatograms of filetype CSV weren’t loaded in correctly.
  • Fixed interaction to program a two step shifted plot.
  • Fixed folder direction for when saving results sets.
1.02 – PEAK TRACKING 2.0 PROTOTYPE 2
This update features an extensive improvement to the peak-tracking algorithm for multi-dimensional chromatography.
Major updates
  • Peak-tracking for multi-dimensional chromatography
    • Algorithm now utilizes statistical moments to increase tracking accuracy
      • 0th moment: area
      • 1st moment (normalized): center of gravity / retention time
      • 2nd moment (normalized, centralized): variance
      • 3rd moment (normalized, centralized, corrected): skew
      • 4th moment (normalized, centralized, corrected): kurtosis
    • All moments may be modified in the algorithm. Details about this and the exact decision tree will be made available once the algorithm has been published. Evaluate unpaired peaks now takes in the MomentScore instead of only the nearest peak.
    • A new window was added where the detailed results of the peak tracking is presented to the user.
      • TOTAL PLOT: Average score of each feature is plotted as a line in color. The actual overall, weighted score of each tracked peak is plotted as a scatter plot in black.
      • FEATURE ANALYSIS: Histograms can be prompted where the occurrence of scores are plotted per feature.
      • SUSPECT TABLE: A table is presented containing all peaks where the algorithm was inconclusive (<40%).
      • COMPLETE TABLE: A comprehensive table detailing all found peaks, their mass values and individual similarity scores can be prompted by the user.
    • The statistical moments are differently assessed for the first -and second dimension. In addition, the state in both dimensions of an individual peak also influences the computations. Details will be made available once the algorithm is published.
    • Pattern recognition pre-search tool was improved.
    • Peak-tracking algorithm can decide to improve its computations by consulting the extracted ion-current chromatograms.
  • Retention modelling
    • Added an expert fitting   tool to load extremely large quantities of input chromatograms to (improve the) fit (of) retention parameters.
    • A graphical user interface was added to facilitate this.
Minor updates
  • Detecting new peaks when pairing is already done, now gives the
    user the choice to cancel or to delete the pairing information.
  • The functions to generate multi-dimensional extracted ion-current chromatograms have been significantly optimized and should be much faster.
  • A number of general & technical improvements were made.
Bug fixes
  • The peak-tracking algorithm now prevents its own activation if the peak-detection algorithm was not correctly applied.
  • When changing the number of data sets in Import Data, the 2D
    gradients tables are also updated, UpdateImportDataTwoDim.m was edited
  • A new function SaveSettings.m will save the current settings as a
    file called Settings.mp. MOREPEAKS startup function will load this file
    to use it as default settings.
  • Fixed a bug where loading raw data was impossible if the data contained no detectable peaks.
  • A number of improvements to the design of the graphical user interface were made.

1.01 – PEAK TRACKING 2.0 PROTOTYPE 1, GENERAL IMPROVEMENTS & BUG FIXES

This patch introduces the first prototype of the peak-tracking algorithm for two-dimensional chromatography (LC×LC-MS and GC×GC-MS). In addition, a number of general improvements and bug fixes are featured.

Major updates

  • Peak-tracking for multi-dimensional chromatography
    • The Import Data tab now features the option to automatically track peaks.
    • Upon execution, a special window can be opened by the user to view detailed results of the peak tracking.
    • All relevant information, such as the similarity of mass spectra, can be prompted by the user.
    • The peak-tracking algorithm utilizes area and mass spectra to track peaks.

Minor updates

  • Data analysis of two-dimensional data
    • Baseline correction function added to two-dimensional chromatographic data analysis tab.
    • Slider GUI component added to adjust the colormap intensity of the chromatogram.
  • For the generation of extraction ion-current chromatograms (XIC) a threshold value can now be supplied. This was needed for reduced datafiles where not the whole MS spectrum is available. 
  • Peak detection
    • The speed of the peak-detection algorithm was significantly enhanced.
    • Algorithm can be individually called.
    • The peak-detection algorithm no longer principally removes peaks suffering from first-dimension undersampling. Instead the decision is left with the end-user and a warning is generated. A future version will feature a setting option to turn this on or off.
  • The status indicator of MOREPEAKS now more accurately tracks computation status.
  • A number of general & technical improvements were made.

Bug fixes

  • Fixed the occurrence of a crash in the Method Parameters tab of the Optimization window, where the program tried to find variables that didn’t exist yet when loading in a datafile from the user.
  • Fixed failure of loading previous sessions where in addition a chromatogram was loaded with a different database than the underlying session.
  • Fixed case where the function which folds the one-dimensional chromatography into a two-dimensional chromatographic space, inaccurately located the start of the modulation.
1.0 – BASE VERSION
  • Major features
    • Complete overhaul of PIOTR v1.32. The program has been completely rewritten and is now referred to as MOREPEAKS.
    • The program now utilizes MATLAB’s APP framework. No longer GUIDE.