Introducing PandaNovo for practical large-scale de novo peptide sequencing

preprint · bioRxiv · 2023

preprint · bioRxiv · 2023. Tingpeng Yang et al. De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of…
Date 2023-07-15
Type preprint
Venue bioRxiv
Publisher Cold Spring Harbor Laboratory
Contribution algorithm
DOI 10.1101/2023.07.15.549133
Citations (OpenAlex) 3

Peer-reviewed version: Introducing π-HelixNovo for practical large-scale de novo peptide sequencing (2024-02-10, Briefings in Bioinformatics)

Abstract

De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing model{pi} -HelixNovo based on Transformer architecture.{pi} -HelixNovo outperforms other state-of-the-art models and enhances the taxonomic resolution of gut metaproteome, taking a significant step forward in de novo sequencing.

Authors

  1. Tingpeng Yang · Peng Cheng Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University
  2. Tianze Ling · Beijing Institute of Lifeomics, State Key Laboratory of Medical Proteomics, Tsinghua University
  3. Boyan Sun · Beijing Institute of Lifeomics, State Key Laboratory of Medical Proteomics
  4. Zhendong Liang · Peng Cheng Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University
  5. Fan Xu · Peng Cheng Laboratory
  6. Xiansong Huang · Peng Cheng Laboratory
  7. Linhai Xie · Beijing Institute of Lifeomics, International Academy of Phronesis Medicine (Guangdong), State Key Laboratory of Medical Proteomics
  8. Yonghong He · Peng Cheng Laboratory, Tsinghua University
  9. Leyuan Li · Beijing Institute of Lifeomics, State Key Laboratory of Medical Proteomics
  10. Fuchu He · Beijing Institute of Lifeomics, International Academy of Phronesis Medicine (Guangdong), National Center for Protein Sciences (Beijing), State Key Laboratory of Medical Proteomics
  11. Yu Wang · Peng Cheng Laboratory
  12. Cheng Chang · Beijing Institute of Lifeomics, International Academy of Phronesis Medicine (Guangdong), National Center for Protein Sciences (Beijing), State Key Laboratory of Medical Proteomics

Methods and tools

Data used

  • BALF proteomics - In-depth proteomic analysis of human bronchoalveolar lavage fluid towards the biomarker discovery for (as deposited) · PXD012645
  • Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic β-cells (as deposited) · PXD012979
  • High-resolution spatially-resolved proteome mapping using automated, sacrificial liquid-mediated sample transfer from la (as deposited) · PXD008844
  • Low-density lipoprotein receptor-related protein 1 (LRP1)-derived peptides protect against aggregation of LDL and choles (as deposited) · PXD011246
  • MassIVE-KB (v1) · MSV000081142
  • Mining waste streams of food production for bioactive plant polysaccharides that affect the fitness and expressed activi (as deposited) · MSV000082287
  • Proteome of the rodent malaria parasite Plasmodium berghei liver stage merosomes (as deposited) · PXD010559
  • Proteomic analysis of six different tissues from the Atlantic bottlenose dolphin (Tursiops truncatus) (as deposited) · PXD008808

Cites (7)

Cited by (24)

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