├── .github ├── dependabot.yml └── workflows │ └── CICD.yml ├── .gitignore ├── .pre-commit-config.yaml ├── Dockerfile ├── LICENSE ├── README.md ├── docs ├── API reference │ └── PepTransformerModel.md ├── CLI reference │ └── cli.qmd ├── README.md ├── img │ ├── data_flow.mermaid │ ├── data_flow.svg │ ├── mermaid-diagram-20210823221411.png │ ├── schematic.png │ └── spectrum.png └── quickstart.qmd ├── elfragmentador ├── __init__.py ├── cli.py ├── config │ ├── __init__.py │ └── default_config.toml ├── data │ ├── converter.py │ ├── datamodules.py │ ├── predictor.py │ └── torch_datasets.py ├── math_utils.py ├── metrics.py ├── model │ ├── __init__.py │ ├── ms_transformer_layers.py │ ├── nn_encoding.py │ ├── peptransformer.py │ ├── transformer_layers.py │ └── visualization.py ├── named_batches.py ├── train.py ├── utils.py └── version.py ├── evaluation ├── .gitignore ├── AcetylStrep.html ├── Arabidopsis.html ├── CElegansGG.html ├── EcoliTMT.html ├── HLApeptides.html ├── PhospoAHLFQ.html ├── PhospoTMT.html ├── README.md ├── external │ ├── run.yml │ └── snakefile.smk ├── poetry.lock ├── pyproject.toml ├── reference_files │ └── comet.params.new ├── results │ ├── AcetylStrep │ │ └── mokapot │ │ │ ├── mokapot.peptides.txt.evaluation.csv │ │ │ └── mokapot.peptides.txt.evaluation.log │ ├── Arabidopsis │ │ └── mokapot │ │ │ ├── mokapot.peptides.txt.evaluation.csv │ │ │ └── mokapot.peptides.txt.evaluation.log │ ├── CElegansGG │ │ └── mokapot │ │ │ ├── mokapot.peptides.txt.evaluation.csv │ │ │ └── mokapot.peptides.txt.evaluation.log │ ├── EcoliTMT │ │ └── mokapot │ │ │ ├── mokapot.peptides.txt.evaluation.csv │ │ │ └── mokapot.peptides.txt.evaluation.log │ ├── HLApeptides │ │ └── mokapot │ │ │ ├── mokapot.peptides.txt.evaluation.csv │ │ │ └── mokapot.peptides.txt.evaluation.log │ ├── PhospoAHLFQ │ │ └── mokapot │ │ │ ├── mokapot.peptides.txt.evaluation.csv │ │ │ └── mokapot.peptides.txt.evaluation.log │ └── PhospoTMT │ │ └── mokapot │ │ ├── mokapot.peptides.txt.evaluation.csv │ │ └── mokapot.peptides.txt.evaluation.log ├── scripts │ └── psms_to_ssl.py ├── template.qmd └── training_sequences │ ├── tainseqs_strip.txt.gz │ └── train_seqs.txt.gz ├── mkdocs.yml ├── notebooks ├── README.md ├── docs │ ├── render.bash │ ├── visualize_attention.qmd │ ├── visualize_embeddings.ipynb │ └── visualize_embeddings.qmd └── etc │ └── bayes_architecture_search.qmd ├── poetry.lock ├── pyproject.toml ├── requirements.txt └── tests ├── __init__.py ├── data ├── 01625b_GA1-TUM_first_pool_1_01_01-2xIT_2xHCD-1h-R1 │ ├── 01625b_GA1-TUM_first_pool_1_01_01-2xIT_2xHCD-1h-R1.elfragmentador.pin │ ├── 01625b_GA1-TUM_first_pool_1_01_01-2xIT_2xHCD-1h-R1.mzML │ ├── 01625b_GA1-TUM_first_pool_1_01_01-2xIT_2xHCD-1h-R1.pep.xml │ ├── 01625b_GA1-TUM_first_pool_1_01_01-2xIT_2xHCD-1h-R1.pin │ ├── README.md │ ├── TUM_first_pool_1_contam.decoy.fasta │ └── comet.params.high_high ├── FTMS_HCD_20_annotated_2019-11-12_filtered.msp ├── dlib │ └── small_yeast.dlib ├── fasta │ ├── P0DTC4.fasta │ └── 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