PeptidomicsDB: a unified resource of endogenous peptidomes for peptide discovery and functional exploration across species and biological contexts
- 1Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, College of Pharmacy, Chongqing Medical University , Chongqing 400016 ,
- 2The First Clinical College of Chongqing Medical University , Chongqing 400016 ,
- 3Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016 ,
Abstract
Endogenous peptides represent a rich source of bioactive molecules that regulate diverse physiological processes and offer opportunities for functional discovery. Mass spectrometry-based peptidomics enables their systematic characterization, yet public datasets remain fragmented and are often processed using heterogeneous tools and parameters, limiting peptide-level retrieval, cross-study exploration, and data reuse. We developed PeptidomicsDB (freely accessible at http://www.inbirg.com/ppd/), a unified resource based on the standardized reanalysis of 151 public peptidomics projects comprising 3992 biological samples from major branches, including global peptidomics, neuropeptidomics, and immunopeptidomics, across species and biological contexts. Using the DeepNovo Peptidome workflow implemented in PEAKS Studio 13.0, which integrates database searching, homology searching, and de novo sequencing, we identified >33 million peptide records representing over 4 million unique peptide sequences, of which >400 000 showed sequence similarity to bioactive peptides curated in public repositories. Analysis of 249 curated pairwise comparison datasets identified 78 910 differentially abundant peptide records, while 14 context-specific datasets yielded 148 175 peptide records enriched in individual tissues, diseases, or cell types. PeptidomicsDB links peptide, precursor-protein, sample, and dataset levels with experimental provenance, quantitative evidence, mass spectrometric data, and functional annotations. Together, these capabilities support peptide discovery and functional exploration.
Related
- Synthesis, characterization, biological activity, density functional theory (DFT) and molecular docking of some new imidazolidin-4-one derivatives
- Bioactive Chitosan Films from Shrimp and Crab Shells: Physicochemical and Functional Properties Associated with Biological Source and Processing History
- From Food Structure to L-Cell Exposure: How Processing and Digestion Shape Endogenous GLP-1 Responses
- Chemical Synthesis of the endogenous metabolite Phosphocitrate and Its Structural Isomer Phosphoisocitrate
- Opto-Covalent Modulators Enable Control of Endogenous Epidermal Growth Factor Receptor Activity in Native Cells
BibTeX
@article{yang2026peptidomicsdb,
title = {{PeptidomicsDB: a unified resource of endogenous peptidomes for peptide discovery and functional exploration across species and biological contexts}},
author = {Fengyuan Yang and Yichen Guo and Peiqi Luo and Yucheng Wu and Yapeng Li and Zishun Zhang and Na Ge and Haihan Yuan and Desi Liu and Jianbo Pan},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag1032},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1032/8986579},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - PeptidomicsDB: a unified resource of endogenous peptidomes for peptide discovery and functional exploration across species and biological contexts
AU - Fengyuan Yang
AU - Yichen Guo
AU - Peiqi Luo
AU - Yucheng Wu
AU - Yapeng Li
AU - Zishun Zhang
AU - Na Ge
AU - Haihan Yuan
AU - Desi Liu
AU - Jianbo Pan
PY - 2026
DA - 2026/10/23
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1032
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1032/8986579
AB - Endogenous peptides represent a rich source of bioactive molecules that regulate diverse physiological processes and offer opportunities for functional discovery. Mass spectrometry-based peptidomics enables their systematic characterization, yet public datasets remain fragmented and are often processed using heterogeneous tools and parameters, limiting peptide-level retrieval, cross-study exploration, and data reuse. We developed PeptidomicsDB (freely accessible at http://www.inbirg.com/ppd/), a unified resource based on the standardized reanalysis of 151 public peptidomics projects comprising 3992 biological samples from major branches, including global peptidomics, neuropeptidomics, and immunopeptidomics, across species and biological contexts. Using the DeepNovo Peptidome workflow implemented in PEAKS Studio 13.0, which integrates database searching, homology searching, and de novo sequencing, we identified >33 million peptide records representing over 4 million unique peptide sequences, of which >400 000 showed sequence similarity to bioactive peptides curated in public repositories. Analysis of 249 curated pairwise comparison datasets identified 78 910 differentially abundant peptide records, while 14 context-specific datasets yielded 148 175 peptide records enriched in individual tissues, diseases, or cell types. PeptidomicsDB links peptide, precursor-protein, sample, and dataset levels with experimental provenance, quantitative evidence, mass spectrometric data, and functional annotations. Together, these capabilities support peptide discovery and functional exploration.
SN - 0305-1048
SN - 1362-4962
ER -