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@lukasz-migas lukasz-migas released this 03 Jan 19:49
· 2 commits to main since this release
v0.2.0
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Learn about vigilant mode.

This is a substantial release with a lot of new functionality

New

  • Complete revamp of the user interface, making it easier to edit tasks.
  • Added Add reference project…` and Remove reference project… options to allow creation of ‘multi-project’ projects when dealing with a lot of data.
  • Added `P: Create a merged project from a select single-datasets (merged-project) task, which will create a merged dataset based on your selection.
  • Added P: Skyline mass spectrum (single-dataset) task, which will create a skyline mass spectrum (instead of average) - this can be used in any other task that uses mass spectra.
  • Added Filter ion centroids (single-/multi-dataset), which will help reduce the number of isotopic ions from your peaklists.
  • Added W: XGBoost training (single/merged-project) task, which is a more specialized supervised classification workflow that does multi-iteration training + SHAP.
  • Added W: Annotate average mass spectrum (merged-project) task, which will provide annotations for the average mass spectrum of each dataset in a merged project.
  • Added P: Normalization (merged-project) task, which will provide normalizations based on a subset of datasets.
  • Added m/zs (must be used in calibration) to the calibration task. This will ensure that the RANSAC model used during calibration ‘overfits’ on the specified m/z. It is very useful when an internal standard or lockmass is used.
  • Enabled automatic SNR detection for all Annotation tasks. This is based on a simple knee rule where we try to find optimal SNR based on the number of peaks detected. When knee is detected, SNR is assumed to be optimal.
  • Added Enable filtering rules to all Annotation tasks. This will enable rules defined by Maddie.
  • Added Group statistics of mass spectra and Group statistics of ion centroids which will enable generation of dataset or mask distribution plots.
  • Added a Creating/Editing field to the statusbar to indicate which action is taking place.
  • When opening a project, the retrieval of metadata information is performed in another thread, so it should no longer block the UI.
  • There is now an option to disable instance validation, which substantially speeds up task addition. Tasks are always validated during export.

Changed

  • Added a few extra adducts to the Annotation adduct selection (M+Ag, M+Li, M+H-H2O).
  • The Quality control task has now been separated into W: Compute quality control metrics and W: Visualise quality control metrics to reduce the amount of data duplication.
  • Separated export of the mass spectrum to a separate task due to a design flaw (stupidly, mass spectra were exported before calibration, which is not particularly helpful). If you want to have mass spectrum, please add E: Export mass spectrum task to the queue.
  • Tasks are no longer appended to the end of the queue but rather inserted in the appropriate location according to their priority (execution order).
  • Many of the tasks now have improved defaults.

Fixed

  • Many small bugs.
  • Even more big bugs.
  • Filtering of tasks is better now.
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