PXD045682

PXD045682 is an original dataset announced via ProteomeXchange.

Title	[HPP-2.0] A tyrosine phosphoproteome analysis approach enabled by selective dephosphorylation with protein tyrosine phosphatase
Description	Protein tyrosine phosphorylation (pTyr) plays a prominent role in signal transduction and regulation in all eukaryotic cells. In conventional immunoaffinity purification (IP) methods, phosphotyrosine peptides are isolated from the digest of cellular protein extracts with a phosphotyrosine-specific antibody and are identified by tandem mass spectrometry. However, the low sensitivity, poor reproducibility and cost-prohibitive are universal concerns for IP approaches. In this study, we presented an antibody-free approach to identify phosphortyrosine peptides by using protein tyrosine phosphatase (PTP). It was found that most of PTPs including PTP1B, TCPTP and SHP1 can efficiently and selectively dephosphorylated phosphotyrosine peptides. We then designed a workflow by combining two Ti4+-IMAC-based phosphopeptide enrichment steps with PTP catalyzed dephosphorylation for tyrosine phosphoproteomics analysis. This workflow was firstly validated by selectively detection of phosphotyrosine peptides from semi-complex sample and then applied to analyze the tyrosine phosphoproteome of Jurkat T cells. Around 1000 putative former phosphotyrosine peptides were identified from less than 500 μg of cell lysate. The tyrosine phosphosites on majority of these peptides could be unambiguously determined for over 70% of them possess only one tyrosine residue. It was also found that the tyrosine sites identified by this method was highly complementary to these identified by SH2 superbinder based method. Therefore, the combination of Ti4+-IMAC enrichment with PTP dephosphorylation provides an alternative and cost-effective approach for tyrosine phosphoproteomics analysis.
HostingRepository	iProX
AnnounceDate	2023-09-26
AnnouncementXML	Submission_2024-05-21_00:51:22.773.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zheng Fang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-25 20:22:08	ID requested
1	2023-09-25 20:22:16	announced
⏵ 2	2024-05-21 00:51:23	announced	2024-05-21: Update information.

Liu X, Dong M, Yao Y, Wang Y, Mao J, Hu L, Yao L, Ye M, A Tyrosine Phosphoproteome Analysis Approach Enabled by Selective Dephosphorylation with Protein Tyrosine Phosphatase. Anal Chem, 94(10):4155-4164(2022) [pubmed]

submitter keyword: Phospho-Proteome

Mingliang Ye
contact affiliation	Dalian Institute of Chemical Physics, Chinese Academy of Sciences
contact email	mingliang@dicp.ac.cn
lab head
Zheng Fang
contact affiliation	Dalian Institute of Chemical Physics, Chinese Academy of Sciences
contact email	zhengfang@dicp.ac.cn
dataset submitter

iProX dataset URI