PXD025038

PXD025038 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Peptide probes containing a non-hydrolyzable phosphotyrosine-mimetic residue as a tool for tyrosine phosphatomics
Description	Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate intracellular tyrosine phosphorylation levels, and their dysfunction is associated with various diseases. However, due to the low abundance of PTPs in cells, comprehensive analysis requires an enrichment step prior to liquid chromatography/tandem mass spectrometry (LC/MS/MS). In this study, we designed and synthesized peptide probes for PTP pulldown assay using a non-hydrolyzable phosphotyrosine mimetic, 4-[difluoro(phosphono)methyl]-L-phenylalanine (F2Pmp). We found that different F2Pmp probes can enrich different PTPs, depending on the probe sequence. Furthermore, proteins containing a Src homology 2 (SH2) domain were enriched together. Importantly, probes containing phosphotyrosine instead of F2Pmp failed to enrich PTPs due to dephosphorylation during the pulldown step. This enrichment approach using peptides containing F2Pmp could be a generic tool for tyrosine phosphatome analysis without the use of antibodies.
HostingRepository	jPOST
AnnounceDate	2021-10-27
AnnouncementXML	Submission_2022-09-18_03:08:44.742.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kazuya Tsumagari
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxymethyl-L-cysteine; L-methionine sulfoxide; alpha-amino dimethylated residue; Dimethyl:2H(4)13C(2); N6,N6-dimethyl-L-lysine; 2x(13)C,4x(2)H labeled dimethylated L-lysine; alpha-amino acetylated residue; S-carboxamidomethyl-L-cysteine
Instrument	Orbitrap Fusion Lumos; instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-27 10:12:24	ID requested
1	2021-10-27 01:50:08	announced
2	2021-11-09 20:44:18	announced	2021-11-10: Updated PubMed.
⏵ 3	2022-09-18 03:08:45	announced	2022-09-18: Updated FTP location.

Publication List

Tsumagari K, Niinae T, Otaka A, Ishihama Y, Peptide probes containing a non-hydrolyzable phosphotyrosine-mimetic residue for enrichment of protein tyrosine phosphatases. Proteomics, 22(4):e2100144(2022) [pubmed]

Tsumagari K, Niinae T, Otaka A, Ishihama Y, Peptide probes containing a non-hydrolyzable phosphotyrosine-mimetic residue for enrichment of protein tyrosine phosphatases. Proteomics, 22(4):e2100144(2022) [pubmed]

Keyword List

submitter keyword: F2Pmp, peptide pulldown, phosphatomics, phosphatase, tyrosine phosphatase, PTP

submitter keyword: F2Pmp, peptide pulldown, phosphatomics, phosphatase, tyrosine phosphatase, PTP

Contact List

Yasushi Ishihama
lab head
Kazuya Tsumagari
contact affiliation	Keio University
dataset submitter

Full Dataset Link List

jPOST dataset URI
Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST000491/

jPOST dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST000491/