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Chris-young-2004/PepSpecBench

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… See the full description on the dataset page: https://huggingface.co/datasets/Chris-young-2004/PepSpecBench.

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Dataset Card

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.