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Details	EV-TRACK ID	Experiment nr.	Species	Sample type	Separation protocol	First author	Year	EV-METRIC
	EV231008	1/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	75%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 75% (90th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 1 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: CD9/ CD81/ Flotillin-1/ Flotillin-2 non-EV: Apolipoprotein A-1/ Albumin/ Calreticulin/ GM130/ PMP70/ Argonaute-2/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Western Blot Detected EV-associated proteins CD9/ CD81/ Flotillin-1/ Flotillin-2 Detected contaminants Apolipoprotein A-1 Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ GM130/ PMP70/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 188±24 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	2/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	75%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 75% (90th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 1 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: CD9/ CD81/ Flotillin-1/ Flotillin-2 non-EV: Apolipoprotein A-1/ Albumin/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Argonaute-2/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Western Blot Detected EV-associated proteins CD9/ CD81/ Flotillin-1/ Flotillin-2 Detected contaminants Apolipoprotein A-1 Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ GM130/ PMP70/ Prohibitin Not detected contaminants Argonaute-2/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 689±205 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	3/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	75%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 75% (90th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 2 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: CD9/ CD81/ Flotillin-1/ Flotillin-2 non-EV: Apolipoprotein A-1/ Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Western Blot Detected EV-associated proteins CD9/ CD81/ Flotillin-1/ Flotillin-2 Detected contaminants Apolipoprotein A-1 Proteomics database ProteomeXchange Detected contaminants Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 200±3 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	4/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	75%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 75% (90th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 2 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: CD9/ CD81/ Flotillin-1/ Flotillin-2 non-EV: Apolipoprotein A-1/ Albumin/ Calreticulin/ PMP70/ Prohibitin/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Western Blot Detected EV-associated proteins CD9/ CD81/ Flotillin-1/ Flotillin-2 Detected contaminants Apolipoprotein A-1 Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 1009±417 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	5/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	67%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 67% (72nd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 3 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 403±47 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	6/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	67%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 67% (72nd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 3 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 730±158 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	7/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	67%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 67% (72nd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 4 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 222±22 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	8/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	67%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 67% (72nd percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 4 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis DLS Report type Mean±SD Reported size (nm) 509±115 Used for determining EV concentration? Yes EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	9/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	50%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 50% (56th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 5 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	10/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	50%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 50% (56th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 5 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	11/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	50%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 50% (56th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 6 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Argonaute-2/ Calreticulin/ GM130/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Cryo-EM Image type Close-up, Wide-field

	EV231008	12/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 6 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	13/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 7 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	14/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 7 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	15/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 8 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	16/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 8 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Prohibitin/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Prohibitin/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	17/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 9 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Prohibitin/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Prohibitin/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	18/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 9 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ PMP70/ Apolipoprotein A-1/ Argonaute-2/ Calreticulin/ GM130/ Prohibitin/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ PMP70/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ Calreticulin/ GM130/ Prohibitin/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	19/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 10 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	20/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 10 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	21/27	Homo sapiens	malignant ascites	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 11 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	22/27	Homo sapiens	malignant ascites	(d)(U)C UF qEV	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (25th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type malignant ascites Sample origin ovarian cancer (HGSC) patient 11 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Ultrafiltration qEV Protein markers EV: None non-EV: Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1/ Argonaute-2/ GM130/ Tamm-Horsfall protein Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type malignant ascites Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Pelleting performed No Ultra filtration Cut-off size (kDa) 10 Membrane type Polyethersulfone (PES) Commercial kit qEV Other Name other separation method qEV Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Detected contaminants Albumin/ Calreticulin/ PMP70/ Prohibitin/ Apolipoprotein A-1 Not detected contaminants Argonaute-2/ GM130/ Tamm-Horsfall protein Characterization: Lipid analysis No Characterization: Particle analysis None

	EV231008	23/27	Homo sapiens	non-malignant peritoneal effusions	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (50th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type non-malignant peritoneal effusions Sample origin follicular fluid. control 1 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: None Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type non-malignant peritoneal effusions Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field

	EV231008	24/27	Homo sapiens	non-malignant peritoneal effusions	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (50th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type non-malignant peritoneal effusions Sample origin non-malignant ascites (OHSS). control 2 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: None Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type non-malignant peritoneal effusions Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field

	EV231008	25/27	Homo sapiens	non-malignant peritoneal effusions	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (50th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type non-malignant peritoneal effusions Sample origin follicular fluid. control 3 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: None Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type non-malignant peritoneal effusions Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field

	EV231008	26/27	Homo sapiens	non-malignant peritoneal effusions	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (50th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type non-malignant peritoneal effusions Sample origin cystic fluid. control 4 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: None Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type non-malignant peritoneal effusions Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field

	EV231008	27/27	Homo sapiens	non-malignant peritoneal effusions	(d)(U)C DC	Vyhlídalová Kotrbová A	2024	33%
Study summary Full title Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. All authors Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V Journal J Extracell Vesicles Abstract High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type (show more...)High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics. (hide) EV-METRIC 33% (50th percentile of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type non-malignant peritoneal effusions Sample origin follicular fluid. control 5 Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture (Differential) (ultra)centrifugation Density cushion Protein markers EV: None non-EV: None Proteomics yes Show all info Study aim Identification of content (omics approaches)/Technical analysis comparing/optimizing EV-related methods Sample Species Homo sapiens Sample Type non-malignant peritoneal effusions Separation Method (Differential) (ultra)centrifugation dUC: centrifugation steps Below or equal to 800 g Between 800 g and 10,000 g Between 10,000 g and 50,000 g Between 100,000 g and 150,000 g Pelleting performed No Density cushion Density medium Sucrose Sample volume 34 Cushion volume 4 Density of the cushion 30% Centrifugation time 70 Centrifugation speed 100,000 Characterization: Protein analysis Protein Concentration Method Not determined Proteomics database ProteomeXchange Characterization: Lipid analysis No Characterization: Particle analysis EM EM-type Transmission-EM Image type Close-up, Wide-field

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EV-TRACK ID	EV231008
species	Homo sapiens
sample type	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	malignant ascites	non-malignant peritoneal effusions	non-malignant peritoneal effusions	non-malignant peritoneal effusions	non-malignant peritoneal effusions	non-malignant peritoneal effusions
condition	ovarian cancer (HGSC) patient 1	ovarian cancer (HGSC) patient 1	ovarian cancer (HGSC) patient 2	ovarian cancer (HGSC) patient 2	ovarian cancer (HGSC) patient 3	ovarian cancer (HGSC) patient 3	ovarian cancer (HGSC) patient 4	ovarian cancer (HGSC) patient 4	ovarian cancer (HGSC) patient 5	ovarian cancer (HGSC) patient 5	ovarian cancer (HGSC) patient 6	ovarian cancer (HGSC) patient 6	ovarian cancer (HGSC) patient 7	ovarian cancer (HGSC) patient 7	ovarian cancer (HGSC) patient 8	ovarian cancer (HGSC) patient 8	ovarian cancer (HGSC) patient 9	ovarian cancer (HGSC) patient 9	ovarian cancer (HGSC) patient 10	ovarian cancer (HGSC) patient 10	ovarian cancer (HGSC) patient 11	ovarian cancer (HGSC) patient 11	follicular fluid. control 1	non-malignant ascites (OHSS). control 2	follicular fluid. control 3	cystic fluid. control 4	follicular fluid. control 5
separation protocol	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ Ultrafiltration/ qEV	dUC/ DC	dUC/ DC	dUC/ DC	dUC/ DC	dUC/ DC
Exp. nr.	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27
EV-METRIC %	75	75	75	75	67	67	67	67	50	50	50	33	33	33	33	33	33	33	33	33	33	33	33	33	33	33	33

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