Dataset Information

Human urinary protein and glycopeotein LC-MSMS

ABSTRACT: N-glycosylation is one of the most common and important post-translational modifications, and plays a vital role in the control of many biological processes. The increasing discovery of abnormal alterations of N-linked glycans associated with many diseases leads to greater demands for rapid and efficient N-glycosylation profiling in large-scale clinical samples. In the workflow of global N-glycosylation analysis, enzymatic digestion is the main rate-limiting step, including both protease digestion and PNGase F deglycosylation.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

SUBMITTER: Zhiya Fan

LAB HEAD: Weijie Qin

PROVIDER: PXD024639 | Pride | 2022-02-17

REPOSITORIES: Pride

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Publications

An Ultrafast N-Glycoproteome Analysis Method Using Thermoresponsive Magnetic Fluid-Immobilized Enzymes.

Fan Zhiya Z Liu Tong T Zheng Fei F Qin Weijie W Qian Xiaohong X

Frontiers in chemistry 20210426

N-Glycosylation is one of the most common and important post-translational modification methods, and it plays a vital role in controlling many biological processes. Increasing discovery of abnormal alterations in N-linked glycans associated with many diseases leads to greater demands for rapid and efficient N-glycosylation profiling in large-scale clinical samples. In the workflow of global N-glycosylation analysis, enzymatic digestion is the main rate-limiting step, ...[more]

PMID: 33981677

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Project description:Protein O-glycosylation has long been recognized to be closely associated with many diseases, particularly with tumor proliferation, invasion and metastasis. The ability to efﬁciently proﬁle the variation of O-glycosylation in large-scale clinical samples provides an important approach for the development of biomarkers for cancer diagnosis and for therapeutic response evaluation. Therefore, mass spectrometry (MS)-based techniques for high throughput, in-depth and reliable elucidation of protein O-glycosylation in large clinical cohorts are in high demand. However, the wide existence of serine and threonine residues in the proteome and the tens of mammalian O-glycan types lead to extremely large searching space composed of millions of theoretical combinations of peptides and O-glycans for intact O-glycopeptide database searching. As a result, exceptionally long time is required for database searching which is a major obstacle in O-glycoproteome studies of large clinical cohorts. More importantly, due to the low abundance and poor ionization of intact O-glycopeptides and the stochastic nature of data-dependent MS2 acquisition, substantially elevated missing data levels are inevitable as the sample number increases, which undermines the quantitative comparison across samples. Therefore, we report a new MS data processing strategy that integrates glycoform-specific database searching, reference library-based MS1 feature matching and MS2 identification propagation for fast identification, in-depth and reproducible label-free quantification of O-glycosylation of human urinary proteins. This strategy increases the database searching speeds by up to 20-fold and leads to a 30-40% enhanced intact O-glycopeptide quantification in individual samples with an obviously improved reproducibility. In total, we obtained quantitative information for 1068 intact O-glycopeptides across 36 healthy human urine samples with a 30-40% reduction in the amount of missing data. This is currently the largest dataset of urinary O-glycoproteome and demonstrates the application potential of this new strategy in large-scale clinical investigations.

			Action	DRS
	Free_PNGF_1.raw	Raw
	Free_PNGF_2.raw	Raw
	Free_PNGF_3.raw	Raw
	Free_Trypsin_1.raw	Raw
	Free_Trypsin_2.raw	Raw

Dataset Information

Human urinary protein and glycopeotein LC-MSMS

Dataset's files

Publications

An Ultrafast <i>N-</i>Glycoproteome Analysis Method Using Thermoresponsive Magnetic Fluid-Immobilized Enzymes.

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