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N-GlycositeAtlas, a database resource for mass spectrometry-based human N-linked glycoproteins and glycosylation sites

ABSTRACT: N-Linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focus mainly on the analysis of specific sample type, and lack integration of each glycoproteomic data from different tissues, body fluids or cell types. In this study, we established N-GlycositeAtlas, a comprehensive database resource of human N-linked glycoproteins and their glycosylation sites identified by mass spectrometry. N-GlycositeAtlas contains more than 30,000 glycosite-containing peptides (representing >14,000 N-glycosylation sites) from more than 7,000 N-glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies. The entire human N-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website at nglycositeatlas.biomarkercenter.org.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine, Blood Platelet, T Cell, Cell Culture, Blood Serum, Breast Cancer Cell, Macrophage

DISEASE(S): Prostate Adenocarcinoma,Human Immunodeficiency Virus Infectious Disease,Breast Cancer

SUBMITTER: Shisheng Sun

LAB HEAD: Shisheng Sun

PROVIDER: PXD005232 | Pride | 2022-02-23

REPOSITORIES: Pride

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			Action	DRS
	SunS_1_BreastCancerXenografts_Deglycopeptides_HumanMouseDB_All36.xlsx	Xlsx
	SunS_1_BreastCancerXenografts_Desialoglycopeptides_ModifiedSPEG_F10.raw	Raw
	SunS_1_BreastCancerXenografts_Desialoglycopeptides_ModifiedSPEG_F11.raw	Raw
	SunS_1_BreastCancerXenografts_Desialoglycopeptides_ModifiedSPEG_F12.raw	Raw
	SunS_1_BreastCancerXenografts_Desialoglycopeptides_ModifiedSPEG_F2.raw	Raw

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Project description:Large-scale identification of N-linked intact glycopeptides by liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) in human serum is challenging due to the wide dynamic range of serum protein abundances, the lack of a complete serum N-Glycan database and the existence of non-specifically digested peptides and numerous modifications. In this regard, a spectral library search method was presented for serum N-linked intact glycopeptides identification with target-decoy and motif-specific false discovery rate (FDR) control. Low-abundant glycoproteins were firstly separated from high-abundant proteins by acetonitrile (ACN) precipitation. After digestion, the N-linked intact glycopeptides were enriched by hydrophilic interaction liquid chromatography (HILIC) column and a portion of the enriched N-linked intact glycopeptides were processed by N-Glycosidase F (PNGase F) to generate de-glycopeptides. Both N-linked intact glycopeptides and de-glycopeptides were analyzed by LC-MS/MS. From N-linked de-glycopeptides datasets, 764 N-linked glycoproteins, 1,699 N-linked glycosites and 3,328 unique N-linked de-glycopeptides were identified. The spectra of these N-linked de-glycopeptides were utilized for N-linked de-glycopeptides library construction and identification of N-linked intact glycopeptides. Four types of N-linked glycosylation motifs (NXS/T/C/V, X≠P) were used to recognize the N-linked de-glycopeptides, and two different N-Glycan mass databases including 27 modified N-Glycan masses and 712 unmodified N-Glycan masses were combined and utilized during spectral library search for identification of N-linked intact glycopeptides. In total, from the N-linked intact glycopeptides datasets, 526 N-linked glycoproteins, 1,036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-Glycan masses were identified under 1% FDR, representing the most in-depth serum N-glycoproteome identified by LC-MS/MS at N-linked intact glycopeptide level and N-linked de-glycopeptides level.

Dataset Information

N-GlycositeAtlas, a database resource for mass spectrometry-based human N-linked glycoproteins and glycosylation sites

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