MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics

ABSTRACT: Breakthroughs in artificial intelligence (AI) for natural language processing and computer vision have been largely driven by high-quality, large-scale datasets such as OpenWebText and ImageNet. Inspired by this, we present MassNet, a foundational resource for proteomics designed to accelerate deep learning applications. MassNet is the largest known corpus of data-dependent acquisition (DDA) mass spectrometry (MS) data, derived from ∼30 TB of raw files and comprising 1.54 billion MS/MS spectra, resulting in 558 million peptide-spectrum matches (PSMs) across 35 species, including animals, plants, and microorganism. Within the human subset, MassNet includes more than 1.7 million precursors and 19,966 proteins, covering 98% of annotated human proteins. To enable efficient AI training, we developed the Mass Spectrometry Data Tensor (MSDT), a structured format based on Parquet that enables standardized, high-performance batch access and seamless integration with GPU and TPU platforms for distributed training.

INSTRUMENT(S):

ORGANISM(S): Legionella Pneumophila Acinetobacter Baumannii Staphylococcus Epidermidis Saccharomyces Cerevisiae (baker's Yeast) Bacillus Subtilis Chlamydomonas Reinhardtii Sus Scrofa Domesticus (domestic Pig) Glycine Max Drosophila Melanogaster (fruit Fly) Streptomyces Coelicolor Escherichia Coli Bacillus Cereus Staphylococcus Aureus Trypanosoma Brucei Capsicum Annuum Arabidopsis Thaliana (mouse-ear Cress) Zea Mays (maize) Coffea Arabica (arabian Coffee) Rattus Norvegicus (rat) Equus Caballus (horse) Zymomonas Mobilis Caenorhabditis Elegans Danio Rerio (zebrafish) (brachydanio Rerio) Oryza Sativa (rice) Pseudomonas Aeruginosa Canis Familiaris (dog) (canis Lupus Familiaris) Moorella Thermoacetica Homo Sapiens (human) Bos Taurus (bovine) Toxoplasma Gondii Gallus Gallus (chicken) Oryctolagus Cuniculus (rabbit) Rhodopseudomonas Palustris Callithrix Jacchus Mus Musculus (mouse)

SUBMITTER: Tiannan Guo  

LAB HEAD: Tiannan Guo

PROVIDER: PXD071590 | Pride | 2026-10-20

REPOSITORIES: Pride