v2.0.0

What's Changed

This version now enabled using the new rust search backend.
It is superior in speed and performance, and recommended for Thermo and Sciex data (cf. the proteobench results for the performance-equivalent version v1.12.1).

However, some features are not yet available:

• transfer learning
• multiplexing
• processing Bruker files

It also comes with a series of breaking changes, both in the input (config) and in the output (column names).

New features

• Enable rust backend @mschwoer in #713
• Add parameter search functionality to gui by @mschwoer in #689

Breaking Changes

• The default output file format is now “parquet” instead of “tsv”
• Many output column names have been changed (see here)

[relevant for expert users only] The following config parameters have been renamed:

• fdr.competetive_scoring -> fdr.competitive_scoring
• search_initial.initial_num_candidates -> search_initial.num_candidate
• search_initial.initial_ms1_tolerance -> search_initial.ms1_tolerance
• search_initial.initial_ms2_tolerance -> search_initial.ms2_tolerance
• search_initial.initial_mobility_tolerance -> search_initial.mobility_tolerance
• search_initial.initial_rt_tolerance -> search_initial.rt_tolerance

[relevant for expert users only]In addition, some internal algorithmic parameters have been changed:
fdr.enable_nn_hyperparameter_tuning is now true by default
search_output.peptide_level_lfq and search_output.precursor_level_lfq are now true by default

• Add intensity to precursor table by @GeorgWa in #687
• Change config defaults by @mschwoer in #720
• rename competetive -> competitive by @mschwoer in #718
• Rename initial parameters in configuration files for consistency by @mschwoer in #719
• add semantic output names by @GeorgWa in #709
• Semantic stat keys by @GeorgWa in #726
• change stats by @GeorgWa in #729

Other Changes / unlabeled

• improve config comments by @mschwoer in #721
• fix test on windows: The key is that we exit the with block (which cl… by @mschwoer in #717
• log more system information including OS and Python details by @mschwoer in #716
• fix formatting by @mschwoer in #723
• output refactoring by @GeorgWa in #707
• Refactoring to isolate qouant output loading and building by @GeorgWa in #708
• bump version of rust backend by @mschwoer in #724
• Get rid of weird chars in windows GUI by @mschwoer in #693
• add rust dependency by @mschwoer in #725
• renaming by @mschwoer in #728
• fix: update intensity column mappings in output configuration by @mschwoer in #730
• fix: update output format for commitish_to_test in e2e testing workflow by @mschwoer in #731

unit/integration tests ran here: https://github.com/MannLabs/alphadia/actions/runs/18969706236
E2E tests ran here: https://github.com/MannLabs/alphadia/actions/runs/18970580325/job/54177201160

The linux installer was broken and has been removed, is fixed in this (functionally equivalent) release: https://github.com/MannLabs/alphadia/releases/tag/v2.0.1

Full Changelog: v1.12.2...v2.0.0