PXD046201

PXD046201 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Pretrained Deep Protein Language Model-Aided Estimation of Collision Cross Section
Description	Collision cross section (CCS) of peptide ions provides an important separation dimension in liquid chromatography/tandem mass spectrometry-based proteomics that incorporates ion mobility spectrometry (IMS), and its accurate prediction is the basis for advanced proteomics workflows. We constructed an experimental peptide CCS dataset using phosphoproteome data. To obtain a unique set of peptides, we digested HeLa cell extracts with seven proteases (trypsin, LysargiNase, Lys-C, Lys-N, Glu-C, Asp-N, and chymotrypsin), enriched phosphopeptides from the digests, and fractionated the resulting phospho peptides with SCX-StageTip. We then dephosphorylated the phosphopeptides using calf intestine alkaline phosphatase to generate non-phosphorylated peptides with more missed cleavages.
HostingRepository	jPOST
AnnounceDate	2025-05-03
AnnouncementXML	Submission_2025-05-02_17:39:24.222.xml
DigitalObjectIdentifier
ReviewLevel	Non 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
Instrument	instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-17 21:20:19	ID requested
⏵ 1	2025-05-02 17:39:24	announced

Publication List

Dataset with its publication pending

Dataset with its publication pending

Keyword List

submitter keyword: Proteomics, Ion mobility, Collision cross section, Protein, Language model

submitter keyword: Proteomics, Ion mobility, Collision cross section, Protein, Language model

Contact List

Yasushi Ishihama
lab head
Kosuke Ogata
contact affiliation	Kyoto university
dataset submitter

Full Dataset Link List

jPOST dataset URI
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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/JPST002337/