Changelog

  1. 3.2.0

      -  August 13, 2022
    • Added  -  Simple factor-of-lowest intensity mass detector (Robin Schmid)
    • Updated  -  IMS expander improved memory and threading (Steffen Heuckeroth)
    • Updated  -  Redesign ImageVisualizer (Robin Schmid)
    • Updated  -  Speedup advanced mzML import (with mass detection for lower memory usage) 6x (Robin Schmid)
    • Fixed  -  imzML import (Robin Schmid)
    • Fixed  -  File type detection was too slow (Robin Schmid)
    • Fixed  -  Mass calibration setup (Olena Mokshyna)
    • Fixed  -  NIST MS search (Kevin Murray)
    • Fixed  -  Fix spectral deconvolution (Aleksandr Smirnov)

  2. 3.1.0-beta

      -  June 18, 2022
    • Added  -  Metadata support (Kirill Ponomarov)
    • Added  -  Set location for taskmanager or hide (Robin Schmid)
    • Added  -  Spectral library search in batch wizard (Robin Schmid)
    • Added  -  LC + Image feature list aligner (Steffen Heuckeroth)
    • Added  -  Normalized images in feature table and export (Steffen Heuckeroth)
    • Added  -  Compound database match results in tab (Steffen Heuckeroth)
    • Updated  -  Scan histogram (Robin Schmid)
    • Updated  -  Harmonize style of spectra and chromatogram plots and raw data overview in general (Robin Schmid)
    • Fixed  -  Rows filter (Robin Schmid)
    • Fixed  -  Major netagive mode ions in IIN refinement (Robin Schmid)
    • Fixed  -  Same range gap filling (Steffen Heuckeroth)
    • Fixed  -  Ransac aligner (Steffen Heuckeroth)
    • Fixed  -  Baseline resolver (Steffen Heuckeroth)
    • Fixed  -  Linear normaizer and RT calibration (Steffen Heuckeroth)

  3. 3.0.21-beta

      -  March 9, 2022
    • Added  -  PRM import from Bruker timsTOF tdf files (Steffen Heuckeroth)
    • Added  -  Error message on old project load (Steffen Heuckeroth)
    • Updated  -  Update links to new documentation (Steffen Heuckeroth)
    • Updated  -  Export ion identity edges for all selected feature lists with naming pattern (Amol Singh, sanbit876)
    • Fixed  -  Major adduct refinement for negative mode data (was deleting all IIN in negative mode) (Robin Schmid)
    • Fixed  -  Baseline cut-off resolver (Steffen Heuckeroth)
    • Fixed  -  Linear normalizer (Steffen Heuckeroth)
    • Fixed  -  RT calibration (Steffen Heuckeroth)
    • Fixed  -  RANSAC aligner (Steffen Heuckeroth)

  4. 3.0.11-beta

      -  March 9, 2022
    • Added  -  Binning in IMS raw data overview (Steffen Heuckeroth)
    • Added  -  Add ion mobility to CSV export (legacy MZmine2 format; GNPS FBMN/IIMN)(Robin Schmid)
    • Updated  -  Improve ion mobility segments data model (Steffen Heuckeroth)
    • Updated  -  Sorting of features in feature resolver preview (Steffen Heuckeroth)
    • Updated  -  Speed up feature resolver preview (Robin Schmid)
    • Updated  -  Spectral library matching more performant, more options (Robin Schmid)
    • Fixed  -  Waters RAW import (select parent folder or drag and drop) (Robin Schmid)
    • Fixed  -  Zip data import (.mzML.zip and .mzML.gz files) (Steffen Heuckeroth)
    • Fixed  -  Feature lists default sorting by retention time (Robin Schmid)
    • Fixed  -  MS/MS scatter plot (Robin Schmid)
    • Fixed  -  Chart freeze on invalid paint scale range for empty data (Steffen Heuckeroth)

  5. 3.0.0-beta

      -  March 1, 2022
    • Added  -  Advanced data and spectral library import (Robin Schmid)
    • Added  -  Batch wizard simplifying batch setup (Steffen Heuckeroth)
    • Added  -  Create batch from any feature list with applied methods (Steffen Heuckeroth)
    • Added  -  Raw data overview (Steffen Heuckeroth)
    • Added  -  IMS data support (Steffen Heuckeroth, Ansgar Korf)
    • Added  -  Native timsTOF-MS data support (Steffen Heuckeroth, Ansgar Korf)
    • Added  -  IMS feature data model (Steffen Heuckeroth)
    • Added  -  Mobility-MZ Visualizer plot (Steffen Heuckeroth)
    • Added  -  CCS-MZ Visualizer plot (Steffen Heuckeroth)
    • Added  -  CCS Calculation for TIMS, DTIMS, TWIMS (Steffen Heuckeroth)
    • Added  -  Mass defect rows filter (Steffen Heuckeroth)
    • Added  -  Feature list blank subtraction (Steffen Heuckeroth)
    • Added  -  Ion mobility trace builder (Ansgar Korf, Steffen Heuckeroth)
    • Added  -  Recursive IMS builder (Steffen Heuckeroth)
    • Added  -  Ims expander (Steffen Heuckeroth)
    • Added  -  Mobilogram smoothing (Steffen Heuckeroth)
    • Added  -  Mobilogram resolving (Steffen Heuckeroth)
    • Added  -  Mobilogram binning (Steffen Heuckeroth)
    • Added  -  IMS Gap filling (Steffen Heuckeroth)
    • Added  -  Loess smoothing algorithm (Steffen Heuckeroth)
    • Added  -  Comprehensive CSV data export (Robin Schmid)
    • Added  -  Ion Identity Molecular Networking (Robin Schmid)
    • Added  -  Isotope finder to detect possible isotope signals (Robin Schmid)
    • Added  -  13C isotope filter (Robin Schmid)
    • Added  -  Options to keep all features with MS2 spectrum (Robin Schmid)
    • Updated  -  Project save with small option (without data files) or portable (Steffen Heckeroth)
    • Updated  -  Lipid identification modules (Ansgar Korf)
    • Updated  -  Join aligner now multi-threaded (Steffen Heuckeroth, Robin Schmid)
    • Updated  -  Gap-filling now multi-threaded (Robin Schmid)
    • Updated  -  Speed gains and memory efficiency (Robin Schmid, Steffen Heuckeroth)
    • Updated  -  Modernized and overhauled Graphical user interfaces (Roman Bushuiev, Steffen Heuckeroth, Robin Schmid)
    • Updated  -  Feature data model (Robin Schmid)
    • Updated  -  Feature raw model (Steffen Heuckeroth)
    • Updated  -  Adapted compound database data model (Steffen Heuckeroth)
    • Updated  -  Spectral library matching more performant, more options (Robin Schmid)
    • Updated  -  Gaussian fit in isotope pattern preview (Steffen Heuckeroth)
    • Fixed  -  Harmonized ADAP chromatogram builder with other parts (Robin Schmid)
    • Updated  -  Build pipeline (Tomáš Pluskal)
    • Updated  -  Continuous integration and testing (Robin Schmid, Steffen Heuckeroth)

  6. 2.53

      -  December 13, 2019
    • Fixed  -  Missing dependencies for ADAP modules (Tomáš Pluskal)
    • Fixed  -  Spectral database export module (Tomáš Pluskal)
    • Updated  -  File open dialogs (Tomáš Pluskal)
    • Updated  -  New icon for upcoming MZmine 3 (Tomáš Pluskal)

  7. 2.52

      -  November 20, 2019
    • Added  -  Manual graphical integration of peaks (Steffen Heuckeroth)
    • Added  -  Kovats Index extraction tool (Robin Schmid)
    • Added  -  GC-GNPS export (Robin Schmid)
    • Fixed  -  Exception in ADAP hierarchical clustering (Robin Schmid)
    • Fixed  -  jmzTab limit on number of columns (Nils Hoffmann)
    • Fixed  -  Missing scans from Waters instrument mzML files (Alex Smirnov)
    • Updated  -  GNPS export module and documentation (Robin Schmid, Louis-Félix Nothias)
    • Updated  -  Automatic spectra processing in the spectrum visualizer (Steffen Heuckeroth)
    • Updated  -  Lipid search classes (Ansgar Korf)
    • Updated  -  Formula information in Van Krevelen plots (Ansgar Korf)
    • Updated  -  Spectra similarity check in Join Aligner (Ansgar Korf)
    • Updated  -  Passwords not saved in project files, config file saved to home directory (Markus Fleischauer)

  8. 2.51

      -  September 3, 2019
    • Fixed  -  A bug in spectra merging for SIRIUS export (Tomáš Pluskal)
    • Fixed  -  Added missing libraries for raw file import on Windows (Tomáš Pluskal)
    • Fixed  -  Added a missing manual.pdf and license to the release (Tomáš Pluskal)
    • Fixed  -  Made the Linux and macOS startup scripts executable again (Tomáš Pluskal)

  9. 2.50

      -  September 2, 2019
    • Added  -  New 3D visualizer based on JavaFX (Akshaj Gupta)
    • Added  -  New build system using Gradle (Tomáš Pluskal)
    • Added  -  Minor GUI enhancements for task bar and dock (Tomáš Pluskal)
    • Updated  -  Help windows (Tomáš Pluskal)
    • Fixed  -  Isotope pattern preview (Steffen Heuckeroth)

  10. 2.42

      -  August 22, 2019
    • Updated  -  MSP export to include more details (Alex Smirnov)
    • Updated  -  Spectral database search (Robin Schmid)
    • Fixed  -  Isotope pattern viewing after chemical formula prediction (Tomáš Pluskal)
    • Fixed  -  Mass detection messages about centroid/profile spectra (Tomáš Pluskal)
    • Fixed  -  ADAP aligner - progress, missing spectra (Alex Smirnov)

  11. 2.41.2

      -  July 28, 2019
    • Fixed  -  SIRIUS search on Windows (Tomáš Pluskal)

  12. 2.41.1

      -  July 26, 2019
    • Fixed  -  Loading & saving of project files (Tomáš Pluskal)

  13. 2.41

      -  July 25, 2019
    • Added  -  Color blindness aware color palettes (Robin Schmid)
    • Added  -  Spectral DB search for single peak list row (Ansgar Korf)
    • Added  -  Kendrick mass defect filter (Ansgar Korf)
    • Updated  -  ADAP aligner and wavelet deconvolution (Alex Smirnov, Du lab)
    • Updated  -  Automatic spectra processing in the spectrum visualizer (Steffen Heuckeroth)
    • Updated  -  Van Krevelen diagrams (Ansgar Korf)
    • Fixed  -  Spectra merging for SIRIUS and GNPS export (Kai Dürkhop)

  14. 2.40.1

      -  June 3, 2019
    • Fixed  -  GNPS library submission/creation (Robin Schmid)
    • Fixed  -  Compatibility with Java 8 (Tomáš Pluskal)

  15. 2.40

      -  June 2, 2019
    • Added  -  Support for MoNA, GNPS, NIST spectral database file formats (Robin Schmid)
    • Added  -  Support for JCAMP-DX spectral database file format (Ansgar Korf)
    • Added  -  Different spectral similarity algorithms for spectral search (Robin Schmid)
    • Added  -  Automatic spectra processing in the spectrum visualizer (Steffen Heuckeroth)
    • Added  -  Mirror plot for spectral database hit visualization (Ansgar Korf, Robin Schmid)
    • Added  -  Spectral matching in the spectrum visualizer (Ansgar Korf)
    • Updated  -  Local MS2 library search (Ansgar Korf, Robin Schmid)
    • Updated  -  MS2 spectra export to GNPS (Robin Schmid)
    • Updated  -  Changed Student's t-test to ANOVA test (Alex Smirnov, Du lab)
    • Updated  -  Spectra merging for SIRIUS and GNPS export (Kai Dürkhop)
    • Updated  -  Performance improvement for centroid mass detector (Kai Dürkhop)
    • Updated  -  New functions in Kendrick Mass plot (Ansgar Korf)

  16. 2.39

      -  April 28, 2019
    • Added  -  Local MS2 library search (Robin Schmid)
    • Added  -  MS2 spectra export to GNPS (Robin Schmid)
    • Added  -  Utility module to associate MS2 spectra with detected features (Robin Schmid)
    • Added  -  Sparse hierarchical clustering for spectral deconvolution (Alex Smirnov, Du lab)
    • Added  -  Student's t-test and log fold-change for two groups (Alex Smirnov, Du lab)
    • Updated  -  Peak list table - opening compound URL (Robin Schmid)
    • Fixed  -  Neutral loss filter (Steffen Heuckeroth, Robin Schmid)
    • Fixed  -  Avoid exporting empty scans for SIRIUS (Tomáš Pluskal)

  17. 2.38

      -  February 5, 2019
    • Added  -  Diagnostic Fragmentation Filter plot (Shawn Hoogstra)
    • Added  -  Custom database search for spectra (Ansgar Korf)
    • Added  -  Multiple MS/MS spectra plot (Robin Schmid, Ansgar Korf)
    • Updated  -  Spectra annotation for online DB and lipid search (Ansgar Korf)
    • Updated  -  Isotope pattern preview tool (Steffen Heuckeroth)
    • Updated  -  Spectra selection for SIRIUS export (Robin Schmid)
    • Fixed  -  Kendrick mass plots and Van Krevelen diagram labels and paint scales (Ansgar Korf)
    • Fixed  -  MassBank, PubChem, YMDB online DB search (Tomáš Pluskal)

  18. 2.37

      -  November 29, 2018
    • Added  -  A selection of methods for m/z value calculation during chromatogram deconvolution (Robin Schmid)
    • Added  -  Direct submission to GNPS (Robin Schmid)
    • Updated  -  Formula prediction sorting by mass deviation (Ansgar Korf)
    • Fixed  -  SIRIUS search (Tomáš Pluskal)

  19. 2.36

      -  November 16, 2018
    • Added  -  Export of multiple mzML files (Robin Schmid)
    • Added  -  Raw data file merge function (Robin Schmid)
    • Updated  -  SIRIUS search updated to new version(Tomáš Pluskal)
    • Updated  -  Isotope pattern preview tool (Steffen Heuckeroth)
    • Fixed  -  A bug in ADAP Chromatogram builder (Alex Smirnov)

  20. 2.35

      -  October 26, 2018
    • Updated  -  ChemSpider search to new Web API (Tomáš Pluskal)
    • Updated  -  Peak list row filter and duplicate peak filter (Robin Schmid)
    • Fixed  -  SIRIUS export (Tomáš Pluskal)
    • Fixed  -  Multithreaded peak finder in batch mode (Robin Schmid)

  21. 2.34

      -  September 19, 2018
    • Added  -  SIRIUS/CSI-FingerID structure prediction module (Evgeniy Sorokin)
    • Added  -  Multi-threaded gap filling (Robin Schmid and Mingxun Wang)
    • Added  -  Isotope pattern preview (Steffen Heuckeroth)
    • Added  -  m/z histogram (Robin Schmid)
    • Added  -  Lipid search module (Ansgar Korf)
    • Updated  -  JfreeChart plots (Robin Schmid)

  22. 2.33

      -  July 2, 2018
    • Added  -  Spectral Deconvolution/Blind Source Separation method (Xiuxia Du lab)
    • Updated  -  Targeted peak detection - added MS level (Andrius Chaleckis)
    • Fixed  -  HMDB search (Tomáš Pluskal)

  23. 2.32

      -  April 1, 2018
    • Added  -  Hierarchical clustering aligner (Gauthier Boaglio)
    • Added  -  Quick search bars to peaklist table (Akshaj Gupta)
    • Added  -  Van-Krevelen diagrams (Ansgar Korf)
    • Updated  -  Kendrick mass plots (Ansgar Korf)
    • Fixed  -  MetaCyc search in case no record is found (Tomáš Pluskal)

  24. 2.31

      -  February 11, 2018
    • Added  -  Kendrick mass plots (Ansgar Korf)
    • Added  -  Lots of new features for visualization plots (Robin Schmid)
    • Updated  -  Replaced PlantCyc search with MetaCyc using REST API (Tomáš Pluskal)
    • Fixed  -  Fixed access to MassBank Europe (Tomáš Pluskal)

  25. 2.30

      -  November 24, 2017
    • Added  -  RCaller as an option for R backend (Gauthier Boaglio)
    • Added  -  Single feature export from peak list table for SIRIUS (Kai Dürkhop)
    • Updated  -  Peak list SIRIUS export (Kai Dürkhop)
    • Updated  -  Peak list GNPS export (Pieter Dorrestein lab)
    • Fixed  -  MS2 similarity search peaklist selection (Tim Fallon)

  26. 2.29

      -  September 21, 2017
    • Added  -  A second module for GC-MS spectral deconvolution (Xiuxia Du lab)
    • Added  -  Added mzML and netcdf raw data export via MSDK (Tomáš Pluskal)
    • Updated  -  MS2 similarity search (Tim Fallon)
    • Updated  -  Sirius export (Kai Dürkhop)
    • Updated  -  GNPS export (Pieter Dorrestein lab)
    • Updated  -  CSV export with peak identifications (Tomáš Pluskal)
    • Fixed  -  netCDF import for 32-bit precision files (Tomáš Pluskal)
    • Fixed  -  Peak area calculation in the chromatogram smoothing module (Tomáš Pluskal)
    • Fixed  -  Targeted peak detection module in case the input CSV file contains a byte order mark (Tomáš Pluskal)
    • Fixed  -  HMDB online database search (Tomáš Pluskal)

  27. 2.28

      -  July 21, 2017
    • Updated  -  GNPS and Sirius export (Pieter Dorrestein lab)
    • Fixed  -  R-based modules using latest R release (Gauthier Boaglio)

  28. 2.27

      -  June 24, 2017
    • Updated  -  ADAP feature detection module (Xiuxia Du lab)
    • Updated  -  MS/MS scan detection in chromatogram deconvolution (Pieter Dorrestein lab)
    • Fixed  -  File open dialog filters under JDK 8 (Tomáš Pluskal)
    • Fixed  -  Temporary file creating on certain Windows versions (Tomáš Pluskal)
    • Fixed  -  Temporary file locking on network filesystems (Tomáš Pluskal)
    • Fixed  -  Scatter plot tooltips (Tomáš Pluskal)
    • Fixed  -  Memory detection under Linux in different locale settings (Sergio Oller)

  29. 2.26

      -  May 10, 2017
    • Updated  -  GNPS and Sirius export options (Pieter Dorrestein lab)
    • Updated  -  Chemical formular prediction, now much faster thanks to CDK update (Tomáš Pluskal)

  30. 2.25

      -  May 6, 2017
    • Added  -  A new ADAP module for spectral deconvolution of GC/MS data (Xiuxia Du lab)
    • Added  -  GNPS and Sirius export options (Pieter Dorrestein lab)
    • Updated  -  Peak list filter module (Pieter Dorrestein lab)
    • Fixed  -  CSV export in batch mode (Tomáš Pluskal)

  31. 2.24

      -  April 10, 2017
    • Added  -  New ADAP modules for EIC construction and EIC peak picking (Xiuxia Du lab)
    • Fixed  -  A bug in spectrum visualizer (Tomáš Pluskal)
    • Fixed  -  PubChem search module (Tomáš Pluskal)

  32. 2.23

      -  December 12, 2016
    • Fixed  -  A bug in peak list row filter (Tomáš Pluskal)
    • Fixed  -  Version number (Tomáš Pluskal)

  33. 2.22

      -  December 9, 2016
    • Updated  -  MS2 similarity search (Tim Fallon)
    • Fixed  -  Metaboanalyst export format (Tomáš Pluskal)
    • Fixed  -  CSV export with multiple IDs (Tomáš Pluskal)

  34. 2.21

      -  July 3, 2016
    • Added  -  A simple module for feature comparison by MS2 similarity (Tim Fallon)
    • Updated  -  Minor updates to CSV export (Gauthier Boaglio)
    • Fixed  -  A bug in reading some Waters RAW files (Tomáš Pluskal)
    • Fixed  -  Mac OS X script should work in case there is not JDK installed, only JRE (Tomáš Pluskal)
    • Fixed  -  Occasional exceptions in linear normalizer and scatter plot (Tomáš Pluskal)

  35. 2.20

      -  March 3, 2016
    • Added  -  A "Round resample filter" to the scan by scan filtering methods (Gauthier Boaglio)
    • Added  -  Peak-to-peak comparison filter, e.g. by fold-change (Tim Fallon)
    • Updated  -  Spectrum export dialog remembers last open directory (Tomáš Pluskal)
    • Updated  -  Chemical formula prediction shows ppm errors (Tim Fallon)
    • Updated  -  More options in peak list row filter (Tim Fallon)
    • Updated  -  CSV export to handle multiple peaklists (Gauthier Boaglio)
    • Fixed  -  Polarity and precursor recognition for Thermo RAW files (Tomáš Pluskal)
    • Fixed  -  Peak shape component shows MS2 traces properly (Tomáš Pluskal)
    • Fixed  -  Saving of RT start and ends into project files (Tomáš Pluskal)

  36. 2.19

      -  February 1, 2016
    • Added  -  MassBank.eu search (Tobias Schulze)
    • Added  -  Close all windows menu item (Tomáš Pluskal)
    • Added  -  Import of zipped and gzipped raw data files (Tomáš Pluskal)
    • Updated  -  Import of multiple mzTab files (Tomáš Pluskal)
    • Updated  -  Minor improvements in parameter setting components (Tomáš Pluskal)
    • Updated  -  Chemical formula input more robust to whitespace (Tim Fallon)
    • Updated  -  Chromatogram deconvolution can handle polarity switching data (Tomáš Pluskal)
    • Fixed  -  Speed issues when importing mzML files from network shares (Tomáš Pluskal)
    • Fixed  -  startMZmine.bat failure when executed from a different folder (Gauthier Boaglio)

  37. 2.18.3

      -  January 15, 2016
    • Fixed  -  A bug in mzML export (Tomáš Pluskal)
    • Fixed  -  A bug in m/z range parameter component (Tomáš Pluskal)
    • Updated  -  Numerical parameter components ignore whitespace (Tim Fallon)

    2.18.2

      -  December 18, 2015
    • Added  -  Option to export spectra to mzML from the spectra visualizer (Tim Fallon)
    • Fixed  -  Loading of mzML files that contain UV data (Tomáš Pluskal)
    • Fixed  -  Chromatogram builder on polarity-switching datasets (Tomáš Pluskal)
    • Fixed  -  Minor bugs in scatter plot, intensity plot, and PubChem search (Tomáš Pluskal)

    2.18.1

      -  December 14, 2015
    • Fixed  -  A bug in executing R-based modules, e.g. XCMS and CAMERA (Tomáš Pluskal)

    2.18

      -  December 12, 2015
    • Added  -  Peak selector component for parameter setup dialogs (Tomáš Pluskal)
    • Fixed  -  Batch mode processing of tasks that do not produce any new data (Tomáš Pluskal)

  38. 2.17

      -  September 24, 2015
    • Fixed  -  Bug in heat map plot (Tomáš Pluskal)
    • Fixed  -  Bugs Thermo and Waters raw data import (Tomáš Pluskal)

  39. 2.16

      -  September 3, 2015
    • Added  -  Option to export spectra to text formats (MGF, MSP & TXT) (Thomas F. Dyrlund)
    • Added  -  FWHM, Tailing factor and Asymmetry factor to peak lists and exports (Thomas F. Dyrlund)
    • Added  -  Peak filter module for filtering individual peaks in peak lists (Thomas F. Dyrlund)
    • Updated  -  Progress tracking for project loading and saving (Tomáš Pluskal)
    • Updated  -  Chromatogram builder parameters to include scan selection option (Tomáš Pluskal)
    • Updated  -  Scan selector component to include scan definition option (Tomáš Pluskal)
    • Updated  -  More options in Crop filter (Tomáš Pluskal)
    • Fixed  -  Issue with mzTab import and export (Thomas F. Dyrlund)
    • Fixed  -  Error in chromatogram builder in case scans are not sorted by RT (Tomáš Pluskal)
    • Fixed  -  Bugs in heat map plot (Tomáš Pluskal)
    • Fixed  -  Bugs in PCA plot (Tomáš Pluskal)
    • Fixed  -  Bugs in logratio plot (Thomas F. Dyrlund)

  40. 2.15

      -  August 4, 2015
    • Added  -  RT start, RT end and # data points to the CSV and SQL exports (Thomas F. Dyrlund)
    • Added  -  EMF and EPS vector image save options to plots (Thomas F. Dyrlund)
    • Added  -  Tracking of MZmine module usage in Google Analytics (Thomas F. Dyrlund)
    • Added  -  Scan selector component, so methods can be applied to selected types of scans (e.g. only positive polarity) (Tomáš Pluskal)
    • Added  -  IDA visualizer module (Thomas F. Dyrlund)
    • Updated  -  Rserve is now used for integration with R - this should fix many of the R issues and speed up analysis (Gauthier Boaglio)
    • Updated  -  General clean-up of start-up scripts (Thomas F. Dyrlund)
    • Updated  -  The CSV export can now export all identification results for a peak (Thomas F. Dyrlund)
    • Fixed  -  Issue with newly opened peak list tables being hidden behind main window (Tomáš Pluskal)
    • Fixed  -  Bugs in the heat map module (Tomáš Pluskal)
    • Fixed  -  Bug in standard compound normalizer (Thomas F. Dyrlund)

  41. 2.14.2

      -  April 14, 2015
    • Fixed  -  Java3D dependency conflict in the 3D visualizer (Tomáš Pluskal)

    2.14.1

      -  April 9, 2015
    • Fixed  -  Version number was incorrectly reported as 0.0 (Tomáš Pluskal)
    • Fixed  -  Minor fixes in the TIC visualizer (Tomáš Pluskal)

    2.14

      -  April 3, 2015
    • Added  -  Option to highlight samples in plots (Thomas F. Dyrlund)
    • Added  -  Noise level cut-off to the targeted peak detection module (Thomas F. Dyrlund)
    • Added  -  Option to remove common prefix in names when importing raw data files (Thomas F. Dyrlund)
    • Added  -  Text search options to the row filter (Tomáš Pluskal)
    • Added  -  Workaround for the issue that editing of compound identity was not possible if some of the first 3 columns were hidden (Tomáš Pluskal)
    • Updated  -  Chromatogram renamed to TIC, Base peak chromatogram, XIC and XIC (base peak) (Thomas F. Dyrlund)
    • Fixed  -  Bugs in peak duration calculations in the targeted peak detection and gap filling modules (Thomas F. Dyrlund)
    • Fixed  -  Error with the batch mode when using the row filter module (Thomas F. Dyrlund)
    • Fixed  -  Error with rounding of m/z ranges for XIC graphs (Thomas F. Dyrlund)
    • Fixed  -  Crash of Waters reader when function contains no scans (Tomáš Pluskal)
    • Fixed  -  Selection of data files or peak lists are kept after sorting (Tomáš Pluskal)

  42. 2.13.1

      -  February 9, 2015
    • Added  -  Two new modules for sorting files and peak lists alphabetically (Tomáš Pluskal)
    • Added  -  Tool to strip extensions from raw data file names (Thomas F. Dyrlund)
    • Updated  -  2D rendering of molecules was improved in database search (Tomáš Pluskal)
    • Fixed  -  Severe bug in project loading (precursor m/z values were lost) (Tomáš Pluskal)

    2.13

      -  February 3, 2015
    • Added  -  Ability to read Waters RAW folders on Windows (Tomáš Pluskal)
    • Added  -  Scan polarity is now recognized and indicated in the GUI (Tomáš Pluskal)
    • Added  -  Import and export from/to mzTab files (Thomas F. Dyrlund)
    • Updated  -  Thermo RAW file import does not require installation of MSFileReader anymore (Tomáš Pluskal)
    • Updated  -  Java3D installation is not required anymore (Tomáš Pluskal)
    • Updated  -  Better recognition of centroided/profile spectra (Tomáš Pluskal)
    • Updated  -  Improved SQL database export (Thomas F. Dyrlund)

  43. 2.12

      -  December 2, 2014
    • Added  -  Option to sort raw data files or peak lists alphabetically (Tomáš Pluskal)
    • Added  -  New algorithms in the Baseline correction module (Gauthier Boaglio)
    • Added  -  MZmine now automatically checks for newer versions (Thomas F. Dyrlund)
    • Updated  -  Improved reporting in the startMZmine script (Tomáš Pluskal)
    • Updated  -  Improved reporting of errors in case of problems with connection to R (Thomas F. Dyrlund)
    • Updated  -  Improved zooming options in TIC visualizer (Thomas F. Dyrlund)
    • Fixed  -  Windows now remember their sizes and positions (Tomáš Pluskal)
    • Fixed  -  Bug that caused freezing when reading certain types of mzML files (Tomáš Pluskal)
    • Fixed  -  Bug in Targeted peak detection module that caused peak areas to be negative (Tomáš Pluskal)
    • Fixed  -  Bugs in Manual peak picker (Thomas F. Dyrlund)

  44. 2.11

      -  August 15, 2014
    • Added  -  New 2D peak detection module called GridMass (Victor Trevino)
    • Added  -  Option to export charges to the CSV export module (Tomáš Pluskal)
    • Updated  -  GUI changed from MDI style to multi-window style, to support operation on multiple screens (Tomáš Pluskal)
    • Updated  -  The online search modules to reflect the current database websites (Tomáš Pluskal)
    • Fixed  -  Bug in Join Aligner where the m/z weight variable was ignored (Tomáš Pluskal)
    • Fixed  -  Operation of Targeted peak detection in batch mode (Tomáš Pluskal)
    • Fixed  -  Export of peak duration in the CSV export module (Tomáš Pluskal)
    • Fixed  -  Reading precursor charge from newer versions of Thermo RAW files (Tomáš Pluskal)
    • Fixed  -  Operation of Dataset filtering module in batch mode (Gauthier Boaglio)
    • Fixed  -  Steps reordering in the batch setup (Gauthier Boaglio)
    • Fixed  -  Peak area calculation in the Peak extender module (Gauthier Boaglio)