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Changes made in v1.2.0.3¶

General¶

The underlying codebase of ORIGAMI has been improved to make it more readable and more responsive

Improved Item font color will be automatically adjusted to ensure best contrast from the background color in various lists in the GUI

Changed Logging of events was temporarily disabled as it appears to be causing some issues. I haven't been able to figure out why it crashes the program (yet).

Tandem MS :star¶

Added Added support to load .mgf and .mzIdentML file formats to visualise tandem mass spectrometry results. Menu -> Open open-source files... to load .mgf files. You can then annotate the tandem MS with peptide fragments. See Figure 1 for example.

Interactive panel¶

Added Started adding support for individual modification of parameters for interactive plots (double-clicking on an item in the list)

Fixed Issue that prevent proper showing of toolbar has been removed

Peaklist panel¶

Added Added 'Extract automatically' check tool (Peaklist -> Toolbar -> Extract...)

Improved Added a lot of new shortcuts for easier plotting

Text file panel¶

Added Added 'Extract automatically' check tool (Peaklist -> Toolbar -> Extract...)

Fixed Removed an issue that would incorrectly remove documents from the text file list

Multiple MS files panel¶

Added The average mass spectrum can be re-binned/re-processed based on new parameters (Process -> Average mass spectra (current document))

Fixed Removed an issue that prevented typing-in numerical values in the 'variable' colument when using laptop keyboards. I have only ever encountered this issue once... Let me know if it still occurs!

Document tree¶

Added Double-clicking on the document header will now clear all plots and show the most basic plots for that document (e.g. MS, DT, RT, etc). You can also do this by Right-click -> Refresh document.

Improved Significant improvements to the right-click menus (most notably for UniDec/Annotations)

Plots panel¶

Added Some images can now be rotated by 90 degrees (mainly 2D)

Wheel-zoom in the X-dimensions has been improved (works like on maps now)

Data extraction¶

Added You can now extract mass spectra from the '2D' panel. Hold CTRL on your keyboard and drag the mouse in the plot area. Only works when standard plot is shown (e.g. Drift time (bins) vs Scans/Time)

Improved Extracted mass spectra extracted in the DT and RT windows will be now shown in an area beneath the extraction plot (for convenience)

MS annotations¶

Added Peaks can now be annotated with an arrow (also available when exporting in an interactive format)

Improved Selection of a peak in the MS window using the mouse (Annotating: On) will automatically try to determine the charge state based on the peaks isotopic distribution. You can change the error tolerance in Action -> Customise other settings -> Charge prediction value (default: 0.05).

UniDec settings¶

Added Plots can now be customised using settings editor. (Settings: UniDec -> Customise plots...)

Added You can switch between tabbed view where each plot is in a separate tab OR continuous view where all plots are available on the same page (Customise plots... -> Panel view)

Improved Deconvolution is now done in a multi-threaded mode. Should stop program from hanging

Improved All deconvolution results will be now stored in a temporary_data folder (found in ORIGAMI directory). This should keep your HDDs a little bit tidier. All files will be deleted at the end of the session.

MS comparison¶

Added You can now assign your own label to the plot.

Improved You can now compare ALL available mass spectra and not just those that were hidden under 'Mass Spectra' tag. (This includes: Mass Spectra, Mass Spectrum, Mass Spectrum (processed)). To open comparison panel: Menu -> View -> Open MS comparison panel...)

Peak detection¶

Improved Works in multi-threaded mode. Should stop program from hanging.