PXD000061-2
PXD000061 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Proteome-wide purification of O-GlcNAc proteins |
Description | Global O-GlcNAc profiling: proteome-wide purification and identification of O-GlcNAc proteins using GlcNAz metabolic labeling in combination with Click chemistry and label-free LC-MS/MS-based quantification. OGA inhibition: same workflow as 'Global O-GlcNAc profiling'; inhibition of O-GlcNAcase by a small molecule inhibitor. O-GlcNAc sites: identification of O-GlcNAc sites by metabolic labeling/Click chemistry followed by beta elimination Bioinformatics workflow of Global O-GlcNAc profiling and OGA inhibition experiments: Raw mass spectrometry files have been processed using Progenesis LC-MS (4.0) and exported as Mascot generic format for subsequent Mascot (2.3) database search. Mascot search results were processed using Mascot Percolator and the results have been imported back into Progenesis as well as imported to Scaffold (3.5.1). The Progenesis peptide quantification report has been exported as Excel file. Bioinformatics workflow of O-GlcNAc site identification: Raw mass spectrometry files have been processed using Mascot Distiller 2.3 and searched with Mascot. Mascot search results were processed using the Mascot Percolator and imported into Scaffold (3.5.1). After manual validation, peptide and protein identifications (Scaffold file) were imported into Scaffold PTM 2.0 for the estimation of site localization probabilities. |
HostingRepository | PRIDE |
AnnounceDate | 2013-07-29 |
AnnouncementXML | Submission_2013-07-29_04:07:47.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Hannes Hahne |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | O-(N-acetylamino)glucosyl-L-threonine; O-(N-acetylamino)glucosyl-L-serine |
Instrument | LTQ Orbitrap; LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2012-10-31 07:49:13 | ID requested | |
1 | 2013-01-10 06:44:38 | announced | |
1 | 2014-07-25 00:42:44 | announced | |
⏵ 2 | 2013-07-29 04:07:47 | announced | Add reference |
Publication List
Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B, Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry. J Proteome Res, 12(2):927-36(2013) [pubmed] |
Keyword List
submitter keyword: O-GlcNAc, proteomics, metabolic labeling, Click chemistry |
Contact List
Hannes Hahne | |
---|---|
contact affiliation | Chair of Proteomics and Bioanalytics, TU München |
contact email | hannes.hahne@tum.de |
Full Dataset Link List
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.pride.ebi.ac.uk/2013/01/PXD000061 |