Zhi Sun

The paper creates a high-confidence human methylation atlas and develops a deep learning model for methylated peptide detection.

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

The paper presents the E. coli PeptideAtlas build, a comprehensive pan-proteome resource covering 4,755 proteins and over 10,000 PTM sites from 40 datasets.

The paper provides an updated Candida albicans PeptideAtlas proteomics resource with detailed PTM data and tools for analysis.

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

The paper identifies sulfotyrosine (sY) sites in the human phosphoproteome by distinguishing them from phosphorylation using mass error shifts and filters out false positives, finding 31 convincing sY sites.

The paper develops the Maize PeptideAtlas resource to analyze maize proteomes using MS/MS data, identifying peptides and proteins across diverse genetic backgrounds and conditions.

This paper performs a meta-analysis of 11 phosphoproteomics datasets to identify phosphorylated sites in Plasmodium falciparum and related species, revealing sequence motifs, conservation patterns, and structural context of phosphosites.

This study analyzes rice phosphoproteomics data to identify phosphosite variations across the rice pan-genome and their functional implications.

The paper estimates the false discovery rate of phosphosites in public databases and predicts a more realistic count of true phosphosites in the human proteome.

The paper examines organ-specific proteins in mice across different genetic backgrounds to assess their diversity and define robustness scores for quality assessment.

The paper introduces the Universal Spectrum Identifier (USI) to standardize referencing mass spectra in proteomics repositories, enabling transparent traceability of spectral evidence in publications.

PTMProphet provides localization confidence for post-translational modifications in proteomics data, improving accuracy for downstream analysis.