Dataset Information

Proteome-wide purification of O-GlcNAc proteins

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap, LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Hannes Hahne

PROVIDER: PXD000061 | Pride | 2013-01-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Global_profiling_combined_IDs.mzid	Mzid
	Global_profiling_combined_IDs.sf3	Other
	Global_profiling_combined_peaklists.mgf	Mgf
	Global_profiling_raw_GlcNAz_labelled_00469_C08_P003386_B00_F01_R1.raw	Raw
	Global_profiling_raw_unlabelled_background_00469_D08_P003387_B00_F01_R1.raw	Raw

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Publications

Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.

Hahne Hannes H Sobotzki Nadine N Nyberg Tamara T Helm Dominic D Borodkin Vladimir S VS van Aalten Daan M F DM Agnew Brian B Kuster Bernhard B

Journal of proteome research 20130118 2

The post-translational modification of proteins with N-acetylglucosamine (O-GlcNAc) is involved in the regulation of a wide variety of cellular processes and associated with a number of chronic diseases. Despite its emerging biological significance, the systematic identification of O-GlcNAc proteins is still challenging. In the present study, we demonstrate a significantly improved O-GlcNAc protein enrichment procedure, which exploits metabolic labeling of cells by azide-modified GlcNAc and copp ...[more]

PMID: 23301498

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