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PXD046201

PXD046201 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePretrained Deep Protein Language Model-Aided Estimation of Collision Cross Section
DescriptionCollision 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.
HostingRepositoryjPOST
AnnounceDate2025-05-03
AnnouncementXMLSubmission_2025-05-02_17:39:24.222.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKosuke Ogata
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListS-carboxamidomethyl-L-cysteine; O4'-phospho-L-tyrosine; O-phospho-L-threonine; O-phospho-L-serine; L-methionine sulfoxide
Instrumentinstrument
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-10-17 21:20:19ID requested
12025-05-02 17:39:24announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Proteomics, Ion mobility, Collision cross section, Protein, Language model
Contact List
Yasushi Ishihama
lab head
Kosuke Ogata
contact affiliationKyoto university
dataset submitter
Full Dataset Link List
jPOST dataset URI
Dataset FTP location
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