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Ovarian cancer mouse model tissue LC-MSMS

ABSTRACT: For this project N-glycosylated peptides were extracted from tissue of a mouse model for ovarian cancer tissue and matched control mice. The extracted N-glycosites were analyzed by LC-MSMS

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Oocyte

DISEASE(S): Malignant Neoplasm Of Ovary

SUBMITTER: Ruth Huttenhain

LAB HEAD: Ruth Huttenhain

PROVIDER: PXD005665 | Pride | 2019-07-01

REPOSITORIES: pride

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Dataset's files

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			Action	DRS
	B08-05030_TS03_C1_c.mzXML	Mzxml
	B08-05030_TS03_C1_c.pep.xml	Pepxml
	B08-05031_TS03_C1_c.mzXML	Mzxml
	B08-05031_TS03_C1_c.pep.xml	Pepxml
	B08-05032_TS03_C1_c.mzXML	Mzxml

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Publications

A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer.

Hüttenhain Ruth R Choi Meena M Martin de la Fuente Laura L Oehl Kathrin K Chang Ching-Yun CY Zimmermann Anne-Kathrin AK Malander Susanne S Olsson Håkan H Surinova Silvia S Clough Timothy T Heinzelmann-Schwarz Viola V Wild Peter J PJ Dinulescu Daniela M DM Niméus Emma E Vitek Olga O Aebersold Ruedi R

Molecular & cellular proteomics : MCP 20190709 9

Protein biomarkers for epithelial ovarian cancer are critical for the early detection of the cancer to improve patient prognosis and for the clinical management of the disease to monitor treatment response and to detect recurrences. Unfortunately, the discovery of protein biomarkers is hampered by the limited availability of reliable and sensitive assays needed for the reproducible quantification of proteins in complex biological matrices such as blood plasma. In recent years, targeted mass spec ...[more]

PMID: 31289117

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CPTAC High-grade serous ovarian carcinoma SWATH-MS

Project description:Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) is a DIA method whose use in proteomic studies has increased considerably within the past five years. SWATH-MS acquires a complete and permanent digital record for all the detectable MS/MS spectra of a sample using DIA. After their generation, the SWATH-MS maps can be used for iterative analyses of candidate proteins. As with any analytical methodology that has potential widespread use, several studies have been conducted to optimize and evaluate the performance of SWATH-MS. The present dataset was acquired from 103 tissue samples of high-grade serous ovarian carcinoma collected and processed in the context of the CPTAC initiative and analyzed via bottom-up SWATH mass spectrometry.

2020-07-14 | PXD010437 | Pride

Site-specific N- and O-glycosylation Analysis of Human Plasma Fibronectin

Project description:Human plasma fibronectin is an adhesive protein that plays a crucial role in wound healing. Many studies had indicated that glycans may mediate the expression and functions of fibronectin, yet a comprehensive understanding of its glycosylation is still missing. Here, we performed a comprehensive N- and O-glycosylation mapping of human plasma fibronectin, and quantified the occurrence of each glycoform in a site-specific manner. Intact N-glycopeptides were enriched by zwitterionic hydrophilic interaction chromatography, and N-glycosites sites were localized by the 18O-labeling method. O-glycopeptide enrichment and O-glycosite identification were achieved by an enzyme-assisted site-specific extraction method. An RP–LC–MS/MS system functionalized with Collision-Induced Dissociation and stepped normalized collision energy (sNCE)-HCD tandem mass was applied to analyze the glycoforms of fibronectin. A total of 6 N-glycosites and 53 O-glycosites were identified, which were occupied by 3842 N-glycoforms and 16 O-glycoforms, respectively. Furthermore, 81.4% of N-glycans were either fucosylated, sialylated, or with both modifications77.31% of N-glycans were sialylated, while O-glycosylation was dominated by the sialyl-T antigen. These site-specific glycosylation patterns on human fibronectin can facilitate functional analyses of fibronectin and therapeutics development.

2022-02-17 | PXD025886 | Pride

Comprehensive analysis of platelet glycoprotein Ibα glycosylation.

Project description:Background: Platelet glycoprotein (GP) Ibα is the major ligand-binding subunit of the GPIb-IX-V complex that binds von Willebrand Factor (VWF). GPIbα is heavily glycosylated, and its glycans have been proposed to play key roles in platelet clearance, VWF binding, and as target antigens in immune thrombocytopenia syndromes. Despite its importance in platelet biology, the glycosylation profile of GPIbα is not well characterized. Objectives: The aim of this study was to comprehensively analyze GPIbα amino acid sites of glycosylation (glycosites) and glycan structures. Methods: GPIbα ectodomain that was recombinantly expressed or that was purified from human platelets was analyzed by Western blot, mass spectrometry (MS) glycomics, and MS glycoproteomics to define glycosites and the structures of the attached glycans. Results: We identified a diverse repertoire of N- and O-glycans, including sialoglycans, Tn antigen, T antigen, and ABH blood group antigens. In the analysis of the recombinant protein, we identified 62 unique O-glycosites. In the analysis of the endogenous protein purified from platelets, we identified at least 48 unique O-glycosites and 1 N-glycosite. The GPIbα mucin domain is densely O-glycosylated. Glycosites are also located within the macroglycopeptide domain and mechanosensory domain (MSD). Conclusions: This comprehensive analysis of GPIbα glycosylation lays the foundation for further studies to determine the functional and structural roles of GPIbα glycans.

2023-02-09 | PXD035030 | Pride

N-glycosite mapping in Brugia malayi female worms, male worms, and microfilariae

Project description:N-linked glycosylation is a critical post translational modification of eukaryotic proteins. N-linked glycans are present on surface and secreted filarial proteins that play a role in host parasite interactions. Examples of glycosylated Brugia malayi proteins have been previously identified but there has not been a systematic study of the N-linked glycoproteome of this or any other filarial parasite. In this study, we applied an enhanced N-glyco FASP protocol using an engineered carbohydrate-binding protein, Fbs1, to enrich N-glycosylated peptides for analysis by LC-MS/MS. We then mapped the N-glycosites on proteins from three host stages of the parasite: adult female, adult male and microfilariae. Fbs1 enrichment of N-glycosylated peptides enhanced the identification of N-glycosites. Our data identified 582 N-linked glycoproteins with 1273 N-glycosites. Gene ontology and cell localization prediction of the identified N-glycoproteins indicated that they were mostly membrane and extracellular proteins. Comparing results from adult female worms, adult male worms, and microfilariae, we find variability in N-glycosylation at the protein level as well as at the individual N-glycosite level. These variations are highlighted in cuticle N-glycoproteins and adult worm restricted N-glycoproteins as examples of proteins at the host parasite interface that are well positioned as potential therapeutic targets or biomarkers.

2023-04-23 | PXD039002 | Pride

Lymph node macrophages drive immune tolerance and resistance to cancer therapy by expression of the immune-regulatory cytokine IL-33 [RNA-seq]

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Lymph node macrophages drive immune tolerance and resistance to cancer therapy by expression of the immune-regulatory cytokine IL-33 [scRNA-seq]

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2010-06-19 | E-GEOD-12976 | biostudies-arrayexpress

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Project description:The densely glycosylated spike (S) proteins that are highly exposed on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitate viral attachment, entry, and membrane fusion. We have previously reported all the 22 N-glycosites and site-specific N-glycans in the S protein protomer. Herein, we report the comprehensive site-specific O-glycosylation landscapes of SARS-CoV-2 S proteins, which were characterized using high-resolution mass spectrometry. Following digestion using trypsin and trypsin/Glu-C, and de-N-glycosylation using PNGase F, we determined the mucin-type (GalNAc-type) O-glycosylation pattern of S proteins, including O-glycosites and the 6 most common O-glycans occupying them, via Byonic identification and manual validation. Finally, 43 O-glycosites were identified by higher energy collision-induced dissociation (HCD), and 11 O-glycosites were verified by electron transfer/higher energy collision-induced dissociation (EThcD) in the insect cell-expressed S protein. Most glycosites were modified by non-sialylated O-glycans such as HexNAc(1) and HexNAc(1)Hex(1). In contrast, 30 O-glycosites were identified by HCD, and 14 O-glycosites were verified by EThcD in the human cell-expressed S protein S1 subunit. Most glycosites were modified by sialylated O-glycans such as HexNAc(1)Hex(1)NeuAc(1) and HexNAc(1)Hex(1)NeuAc(2). Our results are the first to reveal that the SARS-CoV-2 S protein is a mucin-type glycoprotein; clustered O-glycans often occur in the N- and the C-termini of the S protein, and the O-glycosite and O-glycan compositions vary with the host cell type. These site-specific O-glycosylation landscapes of the SARS-CoV-2 S protein are expected to provide novel insights into the viral binding mechanism and present a strategy for the development of vaccines and targeted drugs.

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