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Changelog

1.1.15

  • FIX: Allow to use multiple modifications for the prediction of peptide properties.

1.1.14

  • FIX: Fix the m/z fragment calculation for the modified peptides.
  • FIX: Fix the extraction of the protein names and sequences for the protein groups in DIA-NN.
  • FEAT: Use deep learning prediction for raw files without having to provide output.
  • STYLE: Update the tutorial and add a notebook demonstrating the use of the predict mode.

1.1.13

  • FEAT: Enable fine-tuning of retention times for predictions.
  • FEAT: Add the predicted retention time and ion mobility values to the "Main tab" of the dashboard.
  • FIX: Correct the mass calculation for modified peptides in prediction mode.
  • FIX: After selecting a new protein, always show the first page of the peptide table.
  • STYLE: Update the AlphaViz logo.

1.1.2

  • FIX: Correct the bug with MS2 intensity prediction using deep learning.
  • FIX: Correct the hover information/color for the MS2 spectrum for the predicted ion intensities.
  • FIX: Fix the behaviour of the "Previous/Next frame" & "Overlay frames" buttons for DDA data analyzed by MaxQuant.

1.1.0

  • FEAT: Integrate the AlphaPeptDeep package into AlphaViz to predict the peptide properties, such as the MS2 intensity prediction for DDA data and retention time/ion mobility prediction for DIA data.
  • FEAT: Update the Quality Control tab to make it lighter than the previous version. Variables for plots (m/z, im, rt, length, etc. distributions) can now be selected.
  • FEAT: Reorganize the Settings panel and add more customization options.
  • DOCS: Extend Jupyter notebooks for manual visual inspection of timsTOF DDA and DIA data analyzed by MaxQuant and DIA-NN, respectively.

1.0.5

  • FEAT: Enable the possibility to read DIA data analysed by the DIA-NN software analysis tool.
  • FEAT: Extend the "Quality Control" tab with a summary statistics table and additional plots.
  • FEAT: Add a "Targeted Mode" tab to work with raw data only.
  • DOCS: Update the AlphaViz tutorial with all functionality implemented.
  • FEAT: Create detailed notebooks demonstrating visualisation of DDA and DIA data analysed with MaxQuant and DIA-NN respectively.
  • FIX: Correct the error when reading the MQ output files (missing columns).

0.0.1

  • FEAT: Initial creation of alphaviz.
  • FEAT: Read DDA Bruker data processed with MaxQuant software.