PXD019746

PXD019746 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry
Description	The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge states. However, it is necessary to know how phosphate groups affect the peptide collision cross sections (CCS) in order to accurately predict phosphopeptide CCS values and to maximize the usefulness of IMS. In this work, we systematically characterized the CCS values of 4,433 pairs of mono-phosphopeptide and corresponding unphosphorylated peptide ions using trapped ion mobility spectrometry (TIMS). Nearly one-third of the mono-phosphopeptide ions evaluated here showed smaller CCS values than their unphosphorylated counterparts, even though phosphorylation results in a mass increase of 80 Da. Significant changes of CCS upon phosphorylation occurred mainly in structurally extended peptides with large numbers of basic groups, possibly reflecting intramolecular interactions between phosphate and basic groups.
HostingRepository	jPOST
AnnounceDate	2021-01-14
AnnouncementXML	Submission_2022-09-18_03:33:35.196.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kosuke Ogata
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; O4'-phospho-L-tyrosine; O-phospho-L-threonine; O-phospho-L-serine; L-methionine sulfoxide; alpha-amino acetylated residue
Instrument	instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-14 09:00:11	ID requested
1	2021-01-24 17:30:07	announced
2	2021-02-04 16:53:29	announced	2021-02-04: Updated FTP location.
3	2021-02-24 08:12:30	announced	2021-02-25: Updated PubMed.
⏵ 4	2022-09-18 03:33:36	announced	2022-09-18: Updated FTP location.

Publication List

Ogata K, Chang CH, Ishihama Y, Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry. Mass Spectrom (Tokyo), 10():A0093(2021) [pubmed]

Ogata K, Chang CH, Ishihama Y, Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry. Mass Spectrom (Tokyo), 10():A0093(2021) [pubmed]

Keyword List

submitter keyword: Phosphopeptides, LC/IMS/MS/MS, Trapped ion mobility spectrometry, Collision cross section, Proteomics

submitter keyword: Phosphopeptides, LC/IMS/MS/MS, Trapped ion mobility spectrometry, Collision cross section, Proteomics

Contact List

Yasushi Ishihama
lab head
Kosuke Ogata
contact affiliation	Kyoto 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/JPST000848/

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/JPST000848/