DIA-NN 2.0-series Updates

[vdemichev]

Updates on DIA-NN 2.0-series.

• 2025-03-25: DIA-NN 2.1.0 Release Notes:
  Note: versions 2.0 - 2.1.0 generate compatible .quant files and spectral libraries, i.e. a later version can be used to summarise the processing results of an earlier version.

  • Built-in support for Thermo .raw on both Windows and Linux.
  • Reduced memory usage spikes when loading Sciex .wiff files.
  • Identification performance improvements (minimal).
  • More robust towards any issues with instrument calibration.
  • Significantly expanded QC metrics plots in the PDF report, allowing assessment of both MS1/MS2 calibration, peak width (PWHM), RT & IM alignment, recovery of hydrophilic/hydrophobic peptides in each run, presence of highly abundant peptides, peptide charge & peptides/protein distributions.
  • Added a new PDF report showing trends across the experiment (in the order of runs as specified in the GUI).
  • The script used to generate the PDF reports (diann-stats.py) is now included in the Linux distribution.
  • Fixed an issue with --channel-run-norm not working correctly, do not rely on plexDIA cross-run normalisation in previous versions with this setting (within-run ratios are not affected).
  • Fixed an issue with site localisation algorithm failing when considering distinct modifications potentially occupying the same site.
  • Fixed an issue with localisation confidence not being reported for C-terminal modifications.
  • Site quantities matrices now produced for all modifications declared as variable, not just phosphorylation. The quantities for sites are still based on top 1 precursor approach, but precursors are now quantified by summing the top 3 library fragments intensities.
  • Fixed issues with incorrect decoy peptide handling and reannotation when converting libraries to .parquet format.
  • Ability to save full raw file names in the main report using --report-file-name.
  • Apex MS2 scan index now also saved to the main report when using --export-quant for query by downstream tools.
  • Numbers of all/proteotypic sequences matching the protein group added to the protein group matrices.
  • Added a note to the user guide on --export-quant being potentially useful for MRM/PRM assay design.

• 2025-02-14: DIA-NN 2.0.2 Release Notes:

  • Somewhat faster neural network training. This update also fixes the issue of DIA-NN getting stuck at NN training with <=4 CPU threads.
  • No functional changes, i.e. all output is identical.

• 2025-02-12: DIA-NN 2.0.1 Release Notes:

  • Speed optimisation for very large spectra. Up to fold-change speed up for certain scenarious, in particular when analysing long-gradient 1F Slice-PASEF runs. No difference for most workflows.
  • Ability to set a narrower RT window for further speed up, details in https://github.com/vdemichev/DiaNN?tab=readme-ov-file#speed-optimisation.
  • Fixed incorrect export of decoys when exporting a .parquet library to .parquet format, this is relevant when applying in silico modifications to DIA-NN-generated empirical libraries.
  • Different treatment of occasions when an in silico generated decoy in an empirical library has the same sequence and charge as one of other target or decoy precursors, this change has a negligible effect on protein q-value calculation with empirical libraries.

• 2025-01-29: DIA-NN-2.0-Academia.msi installer repackaged to include the updated version of the mimalloc .dll, this fixes compatibility issues introduced on some systems with Windows 11 24H2 update.