Changelog

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

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