PXD056746-1

PXD056746 is an original dataset announced via ProteomeXchange.

Title	SCASP-PTM multiple PTM enrichment method
Description	Multiple post-translational modification (PTM) proteomics generally relies on combining the enrichment of various PTMs with multiplex isobaric labeling and extensive peptide fractionation. However, effective methods for sequentially enriching multiple PTMs from a single sample for data-independent acquisition mass spectrometry (DIA-MS) are still lacking. Here, we present SCASP-PTM, a novel approach enabling desalting-free enrichment of diverse PTMs—including phosphopeptides, ubiquitinated peptides, acetylated peptides, glycopeptides, and biotinylated peptides. SCASP-PTM utilizes SDS for protein denaturation, which is sequestered by cyclodextrins before trypsin digestion, allowing sequential PTM enrichment without additional purification steps. By combing SCASP-PTM with DIA-MS, we quantified the proteome, ubiquitinome, phosphoproteome, and glycoproteome from 18 poly(I:C)-treated HeLa-S3 cell samples, identifying serine 28 phosphorylation as the key driver of poly(I:C)-induced p62 degradation. Additionally, this method enabled the quantification of proteome, ubiquitinome, acetylomes, phosphoproteome, and glycoproteome from 32 clinical tissue samples, revealing that ubiquitination/acetylation of lysine 330 on ALDOA is critical for tumor progression. In summary, SCASP-PTM is a robust method by enabling desalting-free, sequential enrichment of multiple PTMs from a single sample, offering a streamlined workflow for comprehensive PTM analysis when combined with DIA-MS in both basic research and clinical application.
HostingRepository	iProX
AnnounceDate	2024-10-12
AnnouncementXML	Submission_2024-10-11_20:42:53.093.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chuanqi Zhong
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	phosphorylated residue; ubiquitination signature dipeptidyl lysine; acetylated residue
Instrument	Orbitrap Fusion Lumos; timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-11 20:40:25	ID requested
⏵ 1	2024-10-11 20:42:53	announced

Dataset with its publication pending

submitter keyword: Post-translational modifications, Data-Independent Acquisition, diaPASEF

Chuanqi Zhong
contact affiliation	Xiamen Univerisity
contact email	zhongcq@xmu.edu.cn
lab head
Chuanqi Zhong
contact affiliation	Xiamen University
contact email	zhongcq@xmu.edu.cn
dataset submitter

iProX dataset URI