| --- |
| license: mit |
| tags: |
| - biology |
| - proteomics |
| - mass-spectrometry |
| - benchmark |
| configs: |
| - config_name: massive_kb_native |
| data_files: |
| - split: train |
| path: data/massive_kb_native/train.parquet |
| - split: validation |
| path: data/massive_kb_native/val.parquet |
| - split: test |
| path: data/massive_kb_native/test.parquet |
| - config_name: massive_kb_canonical |
| data_files: |
| - split: train |
| path: data/massive_kb_canonical/train.parquet |
| - split: validation |
| path: data/massive_kb_canonical/val.parquet |
| - split: test |
| path: data/massive_kb_canonical/test.parquet |
| - config_name: prospect_native |
| data_files: |
| - split: train |
| path: data/prospect_native/train.parquet |
| - split: validation |
| path: data/prospect_native/val.parquet |
| - split: test |
| path: data/prospect_native/test.parquet |
| - config_name: prospect_canonical |
| data_files: |
| - split: train |
| path: data/prospect_canonical/train.parquet |
| - split: validation |
| path: data/prospect_canonical/val.parquet |
| - split: test |
| path: data/prospect_canonical/test.parquet |
| - config_name: ood_native |
| data_files: |
| - split: test |
| path: data/ood_native/*.parquet |
| - config_name: ood_canonical |
| data_files: |
| - split: test |
| path: data/ood_canonical/*.parquet |
| - config_name: sample_data |
| data_files: |
| - split: train |
| path: data/sample_data/*.parquet |
| --- |
| |
| # Overview |
|
|
| PepSpecBench is a unified benchmark dataset designed for peptide MS/MS spectrum prediction. |
|
|
| ## Dataset Formats |
|
|
| To accommodate various modeling architectures and evaluation protocols, the data is provided in two distinct representations: |
|
|
| - **`native`**: The complete, benchmark-ready full-spectrum representation with original m/z and intensity arrays. |
| - **`canonical`**: A processed representation in a standardized 234-dimensional space, specifically designed for uniform benchmark evaluation across heterogeneous model architectures. |
|
|
| ## Repository Contents |
|
|
| The dataset is distributed across three primary data groups, each offered in both `native` and `canonical` formats: |
|
|
| - **`massive_kb`**: Benchmark-ready data tables derived from MassIVE-KB (train/validation/test splits). |
| - **`prospect`**: Benchmark-ready data tables derived from the PROSPECT dataset (train/validation/test splits). |
| - **`ood`**: Cross-species out-of-distribution (OOD) evaluation tables (7 species-specific subsets). |
| |
| ## Quick Start / Sample Data |
| |
| The full dataset release exceeds 4 GB. For rapid preliminary inspection of the schema, post-translational modification (PTM) normalization, and overall data formatting, a lightweight sample package is provided in the `sample_data` config. |
| |
