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 |
Keyword List
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 |
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/ |