Browsing Bergen Open Research Archive by Author "Berven, Frode"
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Anatomy and evolution of database search engines — a central component of mass spectrometry based proteomic workflows
Verheggen, Kenneth; Ræder, Helge; Berven, Frode; Martens, Lennart Martens; Barsnes, Harald; Vaudel, Marc (Peer reviewed; Journal article, 2017-09-13)Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass ... -
The Capacity of Long-Term In Vitro Proliferation of Acute Myeloid Leukemia Cells Supported Only by Exogenous Cytokines Is Associated with a Patient Subset with Adverse Outcome
Brenner, Annette; Aasebø, Elise; Hernandez-Valladares, Maria; Selheim, Frode; Berven, Frode; Grønningsæter, Ida Sofie; Bartaula-Brevik, Sushma; Bruserud, Øystein (Peer reviewed; Journal article, 2019-01-10)Acute myeloid leukemia (AML) is an aggressive malignancy, which is highly heterogeneous with regard to chemosensitivity and biological features. The AML cell population is organized in a hierarchy that is reflected in the ... -
Characterization of glomerular extracellular matrix in IgA nephropathy by proteomic analysis of laser-captured microdissected glomeruli
Paunas, Flavia Teodora Ioana; Finne, Kenneth; Leh, Sabine Maria; Osman, Tarig Al-Hadi; Marti, Hans-Peter; Berven, Frode; Vikse, Bjørn Egil (Peer reviewed; Journal article, 2019-11-14)Background IgA nephropathy (IgAN) involves mesangial matrix expansion, but the proteomic composition of this matrix is unknown. The present study aimed to characterize changes in extracellular matrix in IgAN. Methods In ... -
Detecting single amino acids and small peptides by combining isobaric tags and peptidomics
Burger, Bram; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald (Peer reviewed; Journal article, 2019)Single amino acids and small endogenous peptides play important roles in maintaining a properly functioning organism. These molecules are however currently only routinely identified in targeted approaches. In a small ... -
Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis
Guldbrandsen, Astrid; Lereim, Ragnhild Reehorst; Jacobsen, Mari; Garberg, Hilde Kristin; Kroksveen, Ann Cathrine; Barsnes, Harald; Berven, Frode (Journal article; Peer reviewed, 2020)Background: Verification of cerebrospinal fluid (CSF) biomarkers for multiple sclerosis and other neurological diseases is a major challenge due to a large number of candidates, limited sample material availability, disease ... -
Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM
Kroksveen, Ann Cathrine; Aasebø, Elise; Vethe, Heidrun; van Pesch, Vincent; Franciotta, Diego; Teunissen, Charlotte E.; Ulvik, Rune Johan; Vedeler, Christian A.; Myhr, Kjell-Morten; Barsnes, Harald; Berven, Frode (Peer reviewed; Journal article, 2013-01)In the present study, we aimed to discover cerebrospinal fluid (CSF) proteins with significant abundance difference between early multiple sclerosis patients and controls, and do an initial verification of these proteins ... -
Epac1-deficient mice have bleeding phenotype and thrombocytes with decreased GPIbβ expression
Nygaard, Gyrid; Herfindal, Lars; Åsrud, Kathrine Sivertsen; Bjørnstad, Ronja; Kopperud, Reidun Kristin; Oveland, Eystein; Berven, Frode; Myhren, Lene Elisabeth; Høivik, Erling Andre; Lunde, Turid Helen Felli; Bakke, Marit; Døskeland, Stein Ove; Selheim, Frode (Peer reviewed; Journal article, 2017)Epac1 (Exchange protein directly activated by cAMP 1) limits fluid loss from the circulation by tightening the endothelial barrier. We show here that Epac1−/− mice, but not Epac2−/− mice, have prolonged bleeding time, ... -
Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR)
Guldbrandsen, Astrid; Farag, Yehia Mohamed Mokhtar; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald (Peer reviewed; Journal article, 2019)Every year, a large number of published studies present biomarkers for various neurological disorders. Many of these studies are based on mass spectrometry proteomics data and describe comparison of the abundance of proteins ... -
Exploring the potential of public proteomics data
Vaudel, Marc; Verheggen, Kenneth; Csordas, Attila; Ræder, Helge; Berven, Frode; Martens, Lennart; Vizcaíno, Juan Antonio; Barsnes, Harald (Peer reviewed; Journal article, 2016)In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS‐based proteomics data has ... -
The extracellular bone marrow microenvironment — a proteomic comparison of constitutive protein release by in vitro cultured osteoblasts and mesenchymal stem cells
Aasebø, Elise; Birkeland, Even; Selheim, Frode; Berven, Frode; Brenner, Annette; Bruserud, Øystein (Journal article; Peer reviewed, 2021)Mesenchymal stem cells (MSCs) and osteoblasts are bone marrow stromal cells that contribute to the formation of stem cell niches and support normal hematopoiesis, leukemogenesis and development of metastases from distant ... -
Fast hyperbaric decompression after heliox saturation altered the brain proteome in rats
Bjørkum, Alvhild Alette; Oveland, Eystein; Stuhr, Linda Elin Birkhaug; Havnes, Marianne Bjordal; Berven, Frode; Grønning, Marit; Hope, Arvid (Peer reviewed; Journal article, 2017-10-04)Better understanding of the physiological mechanisms and neurological symptoms involved in the development of decompression sickness could contribute to improvements of diving procedures. The main objective of the present ... -
Glomerular abundance of complement proteins characterized by proteomic analysis of laser-captured microdissected glomeruli associates with progressive disease in IgA nephropathy
Paunas, Flavia Teodora Ioana; Finne, Kenneth; Leh, Sabine Maria; Marti, Hans-Peter; Mollnes, Tom Eirik; Berven, Frode; Vikse, Bjørn Egil (Peer reviewed; Journal article, 2017-08-14)Background: The clinical course of IgA nephropathy (IgAN) is variable and complement activation may predict prognosis. The present study investigated whether glomerular abundance of complement proteins associates with ... -
In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis: presenting a comprehensive picture of pathways and processes affected by multiple sclerosis
Kroksveen, Ann Cathrine; Guldbrandsen, Astrid; Vaudel, Marc; Lereim, Ragnhild Reehorst; Barsnes, Harald; Myhr, Kjell-Morten; Torkildsen, Øivind; Berven, Frode (Peer reviewed; Journal article, 2017)In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry ... -
In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR)
Guldbrandsen, Astrid; Vethe, Heidrun; Farag, Yehia Mohamed Mokhtar; Oveland, Eystein; Garberg, Hilde Kristin; Berle, Magnus Foldal; Myhr, Kjell-Morten; Opsahl, Jill Anette; Barsnes, Harald; Berven, Frode (Peer reviewed; Journal article, 2014-11)In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF ... -
Practical considerations for omics experiments in biomedical sciences
Vaudel, Marc; Barsnes, Harald; Bjerkvig, Rolf; Bikfalvi, Andreas; Selheim, Frode; Berven, Frode; Daubon, Thomas (Peer reviewed; Journal article, 2016)Modern analytical techniques provide an unprecedented insight to biomedical samples, allowing an in depth characterization of cells or body fluids, to the level of genes, transcripts, peptides, proteins, metabolites, or ... -
The progression of acute myeloid leukemia from first diagnosis to chemoresistant relapse: A comparison of proteomic and phosphoproteomic profiles
Aasebø, Elise; Berven, Frode; Hovland, Randi; Doskeland, Stein Ove; Bruserud, Øystein; Selheim, Frode; Hernandez-Valladares, Maria (Journal article; Peer reviewed, 2020)Acute myeloid leukemia (AML) is an aggressive hematological malignancy. Nearly 50% of the patients who receive the most intensive treatment develop chemoresistant leukemia relapse. Although the leukemogenic events leading ... -
Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action
Hernandez-Valladares, Maria; Wangen, Rebecca; Berven, Frode; Guldbrandsen, Astrid (Peer reviewed; Journal article, 2019)Background: Post-translational modification (PTM) crosstalk is a young research field. However, there is now evidence of the extraordinary characterization of the different proteoforms and their interactions in a biological ... -
Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia
Aasebø, Elise; Berven, Frode; Bartaula-Brevik, Sushma; Stokowy, Tomasz; Hovland, Randi; Vaudel, Marc; Døskeland, Stein Ove; Mc Cormack, Emmet; Batth, Tanveer S; Olsen, Jesper V; Bruserud, Øystein; Selheim, Frode; Hernandez-Valladares, Maria (Journal article; Peer reviewed, 2020)Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly ... -
Proteomic Profiling of Primary Human Acute Myeloid Leukemia Cells Does Not Reflect Their Constitutive Release of Soluble Mediators
Aasebø, Elise; Hernandez-Valladares, Maria; Selheim, Frode; Berven, Frode; Brenner, Annette; Bruserud, Øystein (Peer reviewed; Journal article, 2018-12-20)Acute myeloid leukemia (AML) is a heterogeneous disease, and communication between leukemic cells and their neighboring leukemia-supporting normal cells is involved in leukemogenesis. The bone marrow cytokine network is ... -
Quantitative analyses of the hepatic proteome of methylmercury-exposed Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on cellular energy metabolism
Yadetie, Fekadu; Bjørneklett, Silje; Garberg, Hilde K; Oveland, Eystein; Berven, Frode; Goksøyr, Anders; Karlsen, Odd André (Peer reviewed; Journal article, 2016-08-05)Background: Methylmecury (MeHg) is a widely distributed environmental pollutant with considerable risk to both human health and wildlife. To gain better insight into the underlying mechanisms of MeHg-mediated toxicity, we ...