metadata
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.