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Wyświetlanie 1-20 z 48
Tytuł:
Orthogonal proteomics methods to unravel the HOTAIR interactome.
Autorzy:
Delhaye L; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.; OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
De Bruycker E; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
Volders PJ; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.; OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
Fijalkowska D; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
De Sutter D; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
Degroeve S; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
Martens L; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
Mestdagh P; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
Eyckerman S; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. .; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium. .; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium. .
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Źródło:
Scientific reports [Sci Rep] 2022 Jan 27; Vol. 12 (1), pp. 1513. Date of Electronic Publication: 2022 Jan 27.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Proteomics*
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.
Autorzy:
Verheggen K; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biochemistry, Ghent University, Ghent, Belgium.; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
Raeder H; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway.; Department of Pediatrics, Haukeland University Hospital, Bergen, Norway.
Berven FS; Proteomics Unit, Department of Biomedicine, University of Bergen, Norway.
Martens L; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biochemistry, Ghent University, Ghent, Belgium.; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
Barsnes H; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway.; Proteomics Unit, Department of Biomedicine, University of Bergen, Norway.; Computational Biology Unit, Department of Informatics, University of Bergen, Norway.
Vaudel M; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway.; Proteomics Unit, Department of Biomedicine, University of Bergen, Norway.; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.
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Źródło:
Mass spectrometry reviews [Mass Spectrom Rev] 2020 May; Vol. 39 (3), pp. 292-306. Date of Electronic Publication: 2017 Sep 13.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Review
MeSH Terms:
Mass Spectrometry/*methods
Proteins/*chemistry
Proteomics/*methods
Search Engine/*methods
Animals ; Humans ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Cross-linked peptide identification: A computational forest of algorithms.
Autorzy:
Yılmaz Ş; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biochemistry, Ghent University, Ghent, Belgium.
Shiferaw GA; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biochemistry, Ghent University, Ghent, Belgium.
Rayo J; Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KULeuven-University of Leuven, Leuven, Belgium.
Economou A; Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KULeuven-University of Leuven, Leuven, Belgium.
Martens L; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biochemistry, Ghent University, Ghent, Belgium.
Vandermarliere E; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biochemistry, Ghent University, Ghent, Belgium.
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Źródło:
Mass spectrometry reviews [Mass Spectrom Rev] 2018 Nov; Vol. 37 (6), pp. 738-749. Date of Electronic Publication: 2018 Mar 12.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Review
MeSH Terms:
Algorithms*
Cross-Linking Reagents/*chemistry
Mass Spectrometry/*methods
Peptides/*analysis
Proteomics/*methods
Animals ; Humans ; Models, Molecular ; Proteins/analysis
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Quality control in mass spectrometry-based proteomics.
Autorzy:
Bittremieux W; Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.; Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium.
Tabb DL; Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences, Tygerberg Hospital, Cape Town, South Africa.
Impens F; VIB Proteomics Core, Ghent, Belgium.; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.; Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium.
Staes A; VIB Proteomics Core, Ghent, Belgium.; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.; Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium.
Timmerman E; VIB Proteomics Core, Ghent, Belgium.; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.; Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium.
Martens L; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.; Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium.; Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Belgium.
Laukens K; Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.; Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium.
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Źródło:
Mass spectrometry reviews [Mass Spectrom Rev] 2018 Sep; Vol. 37 (5), pp. 697-711. Date of Electronic Publication: 2017 Sep 07.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Review
MeSH Terms:
Quality Control*
Computational Biology/*methods
Mass Spectrometry/*methods
Proteomics/*methods
Chromatography, Liquid/methods ; Humans ; Mass Spectrometry/instrumentation ; Mass Spectrometry/standards ; Proteomics/instrumentation ; Proteomics/standards ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics.
Autorzy:
Vandemoortele G; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Staes A; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Gonnelli G; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Samyn N; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
De Sutter D; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Vandermarliere E; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Timmerman E; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Gevaert K; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Martens L; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Eyckerman S; VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
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Źródło:
Scientific reports [Sci Rep] 2016 Jun 06; Vol. 6, pp. 27220. Date of Electronic Publication: 2016 Jun 06.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Archaeal Proteins/*metabolism
Peptides/*isolation & purification
Proteomics/*methods
Pyrococcus furiosus/*metabolism
Archaeal Proteins/chemistry ; Computer Simulation ; HCT116 Cells ; Humans ; Protein Interaction Maps
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
PeptideShaker enables reanalysis of MS-derived proteomics data sets.
Autorzy:
Vaudel M; 1] Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany. [2] Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
Burkhart JM; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
Zahedi RP; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
Oveland E; 1] Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway. [2] Department of Clinical Medicine, University of Bergen, Bergen, Norway. [3] The KG Jebsen Centre for MS Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
Berven FS; 1] Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway. [2] The KG Jebsen Centre for MS Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway. [3] The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
Sickmann A; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
Martens L; 1] Department of Medical Protein Research, VIB, Ghent, Belgium. [2] Department of Biochemistry, Ghent University, Ghent, Belgium.
Barsnes H; 1] Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway. [2] Computational Biology Unit, University of Bergen, Norway.
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Źródło:
Nature biotechnology [Nat Biotechnol] 2015 Jan; Vol. 33 (1), pp. 22-4.
Typ publikacji:
Letter; Research Support, Non-U.S. Gov't
MeSH Terms:
Proteomics*
Mass Spectrometry/*methods
Peptides/*chemistry
Amino Acid Sequence ; Molecular Sequence Data
Raport
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Autorzy:
Vizcaíno JA; 1] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. [2].
Deutsch EW; 1] Institute for Systems Biology, Seattle, Washington, USA. [2].
Wang R; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Csordas A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Reisinger F; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Ríos D; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Dianes JA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Sun Z; Institute for Systems Biology, Seattle, Washington, USA.
Farrah T; Institute for Systems Biology, Seattle, Washington, USA.
Bandeira N; Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA.
Binz PA; Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
Xenarios I; 1] Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland. [2] University of Lausanne, Lausanne, Switzerland, and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. [3] Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Eisenacher M; Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
Mayer G; Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
Gatto L; Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
Campos A; Integromics SL, Santiago Grisolia, Madrid, Spain.
Chalkley RJ; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.
Kraus HJ; Wiley-VCH Verlag, Weinheim, Germany.
Albar JP; ProteoRed-ISCIII, National Center for Biotechnology-CSIC, Madrid, Spain.
Martinez-Bartolomé S; ProteoRed-ISCIII, National Center for Biotechnology-CSIC, Madrid, Spain.
Apweiler R; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Omenn GS; 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
Martens L; 1] Department of Medical Protein Research, VIB, Ghent, Belgium. [2] Department of Biochemistry, Ghent University, Ghent, Belgium.
Jones AR; Institute of Integrative Biology, University of Liverpool, UK.
Hermjakob H; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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Źródło:
Nature biotechnology [Nat Biotechnol] 2014 Mar; Vol. 32 (3), pp. 223-6.
Typ publikacji:
Letter; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:
Database Management Systems*
Databases, Protein*
Internet*
Mass Spectrometry*
Proteomics*
Software*
Animals ; Humans ; International Cooperation ; Mice
Raport
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Getting intimate with trypsin, the leading protease in proteomics.
Autorzy:
Vandermarliere E; Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
Mueller M
Martens L
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Źródło:
Mass spectrometry reviews [Mass Spectrom Rev] 2013 Nov-Dec; Vol. 32 (6), pp. 453-65. Date of Electronic Publication: 2013 Jun 15.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Review
MeSH Terms:
Proteome/*analysis
Proteomics/*methods
Trypsin/*metabolism
Animals ; Humans ; Models, Molecular ; Peptides/analysis ; Peptides/metabolism ; Protein Conformation ; Proteome/metabolism ; Trypsin/chemistry
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Towards a human proteomics atlas.
Autorzy:
Gonnelli G; Department of Medical Protein Research, VIB, Ghent, Belgium.
Hulstaert N
Degroeve S
Martens L
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Źródło:
Analytical and bioanalytical chemistry [Anal Bioanal Chem] 2012 Sep; Vol. 404 (4), pp. 1069-77. Date of Electronic Publication: 2012 Mar 25.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Databases, Protein*
Proteomics*
Proteins/*chemistry
Humans ; Mass Spectrometry ; Proteins/genetics ; Proteins/metabolism ; Software
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Autorzy:
Wang R
Fabregat A
Ríos D
Ovelleiro D
Foster JM
Côté RG
Griss J
Csordas A
Perez-Riverol Y
Reisinger F
Hermjakob H
Martens L
Vizcaíno JA
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Źródło:
Nature biotechnology [Nat Biotechnol] 2012 Feb 08; Vol. 30 (2), pp. 135-7. Date of Electronic Publication: 2012 Feb 08.
Typ publikacji:
Letter; Research Support, Non-U.S. Gov't
MeSH Terms:
Proteomics*
Software*
Information Storage and Retrieval/*methods
Databases, Protein ; Humans ; Mass Spectrometry/methods ; Statistics as Topic/methods
Raport
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Combining quantitative proteomics data processing workflows for greater sensitivity.
Autorzy:
Colaert N; Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium.
Van Huele C
Degroeve S
Staes A
Vandekerckhove J
Gevaert K
Martens L
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Źródło:
Nature methods [Nat Methods] 2011 Jun; Vol. 8 (6), pp. 481-3. Date of Electronic Publication: 2011 May 08.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Electronic Data Processing/*methods
Proteomics/*statistics & numerical data
Algorithms ; Computational Biology ; Databases, Protein ; Humans ; Proteomics/standards ; Quality Control ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
compomics-utilities: an open-source Java library for computational proteomics.
Autorzy:
Barsnes H; Proteomics Unit, Department of Biomedicine, University of Bergen, Norway.
Vaudel M
Colaert N
Helsens K
Sickmann A
Berven FS
Martens L
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2011 Mar 08; Vol. 12, pp. 70. Date of Electronic Publication: 2011 Mar 08.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Databases, Protein*
Software*
Proteomics/*methods
Computational Biology/methods ; Proteins/analysis
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
PRIDE Converter: making proteomics data-sharing easy.
Autorzy:
Barsnes H
Vizcaíno JA
Eidhammer I
Martens L
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Źródło:
Nature biotechnology [Nat Biotechnol] 2009 Jul; Vol. 27 (7), pp. 598-9.
Typ publikacji:
Comment; Letter; Research Support, Non-U.S. Gov't
MeSH Terms:
Databases, Protein*
Proteomics*
Software*
Information Storage and Retrieval/*methods
Internet ; User-Computer Interface
Raport
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis.
Autorzy:
Van Damme P; Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Belgium.
Martens L
Van Damme J
Hugelier K
Staes A
Vandekerckhove J
Gevaert K
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Źródło:
Nature methods [Nat Methods] 2005 Oct; Vol. 2 (10), pp. 771-7.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Apoptosis*
Caspases/*metabolism
Peptides/*chemistry
Proteins/*chemistry
Proteins/*metabolism
Proteomics/*methods
Amino Acid Sequence ; Chromatography/methods ; Humans ; Jurkat Cells ; Molecular Sequence Data ; Peptides/analysis ; Peptides/isolation & purification ; Substrate Specificity ; fas Receptor/metabolism
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Wyświetlanie 1-20 z 48

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