CHANGELOG.md

Changelog

Follow the changelog format from https://keepachangelog.com/en/1.0.0/.

For later changes, see the GitHub releases.

1.1.0

Added

• Support transfer learning based on DIA search results.
• Add peptdeep cmd-flow CLI command for CLI users, see README for details.
• Add ThermoTOF and Astral instrument type for Astral

Changed

• other_modification_mapping to psm_modification_mapping in yaml.
• Removed rescore in CLI and removed percolator in global_settings.

1.0.2

Added

• Enable speclib_tsv for transfer learning in CLI and GUI.

1.0.1 - 2023.01.20

Fixed

• Fatal: transfer learning failed in match_psms() with error "... match_psms() takes 0 arguments but 1 were given ..." in GUI and CLI.

Added

• 'protein_reverse' decoy, see https://alphabase.readthedocs.io/en/latest/protein/protein_level_decoy.html
• Enabled multi-target prediction, all targets will store in one column as np.array object
• Enabled attention_mask and fixed sequence length
• Tested torch.jit.trace to compile the JIT model

1.0.0 - 2023.01.09 (key changes of previous versions)

Changed

• Multiprocessing with spawn for different OS systems to prevent hangs on Linux.
• Using constant values as defaults params of class methods or functions instead of global_settings[xxx] values. Using global_settings[xxx] values as defaults params does not update once global_settings changes, this is dangerous.

Added

• Testing on Python 3.10
• fixed_sequence_len with padding zeros for sequence models.
• GUI: it is able to delete tasks in the task queue.
• user_defined_modifications in peptdeep/constants/global_settings.yaml for CLI and GUI, it allows us to define our own modifications.
• other_modification_mapping in peptdeep/constants/global_settings.yaml for CLI and GUI, it allows us to read arbitrary PTMs from other search engines.
• special_mods in global_settings for special modifications like GlyGly@K or Phospho.
• labeling_channels in global_settings.
• MS2/RT/CCS models for Dimethyl-labeled peptides, see https://github.com/MannLabs/alphapeptdeep/releases/tag/dimethyl-models.

Fixed

• "No match found for given type params" for IntPtr.__overloads__[Int64] in pythonnet>=3 for DotNetArrayToNPArray(), see https://github.com/MannLabs/alphapeptdeep/blob/main/peptdeep/legacy/thermo_raw/pyrawfilereader.py#L77

0.4.0 - 2022.12.28

Added

• Test the model after transfer learning (MS2/RT/CCS), and the metrics will be logged.

Changed

• frag_end_idx->frag_stop_idx

0.3.0 - 2022.12.27

Added

• More features (mostly about modifications) in GUI.
• Peptide labeling and special modifications in peptdeep.protein.fasta.PredictSpecLibFasta.
• Use queue system in peptdeep/webui/serve.py to reduce conflicts of prediction.

Changed

• Use sphinx and readthedocs for documentation, nbdev_test for unit tests.
• Plan to move thermo_raw to AlphaRaw.

0.2.0

• First official release

0.1.3

• FIXED in GUI: keep_only_important_modloss -> modloss_importance_level

0.1.2

• First release

0.0.1

• FEAT: Initial creation of peptdeep