PXD061213-1

PXD061213 is an original dataset announced via ProteomeXchange.

Title	Identification of Unknown Biological Toxin Protein Using Mass Spectrometry: A Case Study on De Novo Sequencing of Ricin
Description	Currently, the genomes of many toxin proteins remain unsequenced. Characterizing these toxin proteins and their active peptide segments is crucial for the development of detoxification agents and for discovering proteins with potential therapeutic applications. Existing methods for identifying and detecting toxin proteins primarily focus on known proteins, making them less applicable for identifying toxins from unknown sources. In this study, we employed a combination of multiple enzymatic digestion techniques, de novo mass spectrometry sequencing, and sequence assembly methods based on graph theory to perform high-precision, full-length sequencing of multi-subunit toxin proteins. After de novo sequencing and identifying Ricin toxin proteins, we utilized a strategy based on multiple alignments and error correction through the construction of overlapping scaffolds to differentiate between homologous isomers I and L and to detect unexpected post-translational modifications. This approach, referred to as the Heuristic Denovo protein sequencing(HDPS), facilitated the rapid hydrolysis and identification of proteins. The method achieved a 100% coverage rate for protein/peptide biological toxins and an amino acid-level accuracy of over 95%. Through de novo sequencing of Ricin toxin, this study provides a stable and reliable solution for identifying highly mutated proteins and those from unknown sequence sources.
HostingRepository	PRIDE
AnnounceDate	2025-12-01
AnnouncementXML	Submission_2025-11-30_16:09:15.544.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yubo Song
SpeciesList	scientific name: Ricinus communis; NCBI TaxID: NEWT:3988;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-26 00:00:58	ID requested
⏵ 1	2025-11-30 16:09:16	announced

10.3390/toxins17110564;

Song Y, Wang H, Wen J, Xu J, Zhu S, Wang F, Zhang Y, Identification of Unknown Biological Toxin Proteins Using Mass Spectrometry: A Case Study on De Novo Sequencing of Ricin. Toxins (Basel), 17(11):(2025) [pubmed]

ProteomeXchange project tag: Toxicoproteomics (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: Unknown biological toxin protein, Heuristic Denovo protein sequencing, Ricin toxin, De novo sequencing,Mass spectrometry

Fuli Wang
contact affiliation	State Key Laboratory of NBC Protection for Civilian
contact email	wangfuli5728@163.com
lab head
Yubo Song
contact affiliation	Beijing Institute of Technology
contact email	3220235200@bit.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD061213
     1. Label: PRIDE project
     2. Name: Identification of Unknown Biological Toxin Protein Using Mass Spectrometry: A Case Study on De Novo Sequencing of Ricin