OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data.

Autor: Pfeuffer J; Algorithmic Bioinformatics, Freie Universität Berlin, Berlin, Germany.; Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany., Bielow C; Bioinformatics Solution Center, Institut für Mathematik und Informatik, Freie Universität Berlin, Berlin, Germany., Wein S; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Jeong K; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Netz E; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Walter A; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Alka O; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Nilse L; Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany., Colaianni PD; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark., McCloskey D; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.; BioMed X Institute, Heidelberg, Germany., Kim J; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Rosenberger G; Department of Systems Biology, Columbia University, New York, NY, USA., Bichmann L; Yale Center for Systems and Engineering Immunology and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA., Walzer M; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), , Wellcome Trust Genome Campus, Hinxton, UK., Veit J; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Boudaud B; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark., Bernt M; Department of Computational Biology, Helmholtz Centre for Environmental Research GmbH-UFZ, Leipzig, Germany., Patikas N; Evergrande Center for Immunologic Diseases Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA., Pilz M; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Startek MP; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.; Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany., Kutuzova S; Department of Computer Science/Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark., Heumos L; Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Oberschleißheim, Germany.; Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Center for Lung Research (DZL), Munich, Germany.; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany., Charkow J; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.; The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada., Sing JC; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.; The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada., Feroz A; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Siraj A; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany., Weisser H; STORM Therapeutics Limited, Cambridge, UK., Dijkstra TMH; Department for Women's Health, University Clinic Tübingen, Tübingen, Germany.; Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany., Perez-Riverol Y; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), , Wellcome Trust Genome Campus, Hinxton, UK., Röst H; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.; The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada., Kohlbacher O; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany.; Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany., Sachsenberg T; Applied Bioinformatics, Department of Computer Science, University of Tuebingen, Tübingen, Germany. timo.sachsenberg@uni-tuebingen.de.; Institute for Bioinformatics and Medical Informatics, University of Tuebingen, Tübingen, Germany. timo.sachsenberg@uni-tuebingen.de.

Publikováno v: Nature methods [Nat Methods] 2024 Mar; Vol. 21 (3), pp. 365-367.

Spectral entropy as a measure of the metaproteome complexity.

Autor: Duan H; School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada., Ning Z; School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada., Zhang A; School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada., Figeys D; School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada.

Publikováno v: Proteomics [Proteomics] 2024 Aug; Vol. 24 (16), pp. e2300570. Date of Electronic Publication: 2024 May 25.

OpenMS - A platform for reproducible analysis of mass spectrometry data.

Autor: Pfeuffer J; Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany. Electronic address: pfeuffer@informatik.uni-tuebingen.de., Sachsenberg T; Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany., Alka O; Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany., Walzer M; Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom., Fillbrunn A; Chair for Bioinformatics and Information Mining, Department of Computer and Information Science, University of Konstanz, Germany., Nilse L; Institute of Molecular Medicine and Cell Research, Freiburg University, Stefan-Meier-Str. 17, 79104 Freiburg, Germany., Schilling O; Institute of Molecular Medicine and Cell Research, Freiburg University, Stefan-Meier-Str. 17, 79104 Freiburg, Germany., Reinert K; Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany., Kohlbacher O; Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Center for Quantitative Biology, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tuebingen, Germany. Electronic address: kohlbacher@informatik.uni-tuebingen.de.

Publikováno v: Journal of biotechnology [J Biotechnol] 2017 Nov 10; Vol. 261, pp. 142-148. Date of Electronic Publication: 2017 May 27.

PFΔScreen — an open-source tool for automated PFAS feature prioritization in non-target HRMS data.

Autor: Zweigle, Jonathan¹ (AUTHOR) jonathan.zweigle@uni-tuebingen.de, Bugsel, Boris¹ (AUTHOR), Fabregat-Palau, Joel² (AUTHOR), Zwiener, Christian¹ (AUTHOR) christian.zwiener@uni-tuebingen.de

Publikováno v: Analytical & Bioanalytical Chemistry. Jan2024, Vol. 416 Issue 2, p349-362. 14p.

Yeast membrane proteomics using leucine metabolic labelling: Bioinformatic data processing and exemplary application to the ER-intramembrane protease Ypf1.

Autor: Nilse L; Institute of Molecular Medicine and Cell Research, University of Freiburg, D-79104 Freiburg, Germany., Avci D; Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany., Heisterkamp P; Institute of Molecular Medicine and Cell Research, University of Freiburg, D-79104 Freiburg, Germany., Serang O; Freie Universität Berlin, Department of Informatik, Takustr. 9, 14195 Berlin, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelsee 310, 12587 Berlin, Germany., Lemberg MK; Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany. Electronic address: m.lemberg@zmbh.uni-heidelberg.de., Schilling O; Institute of Molecular Medicine and Cell Research, University of Freiburg, D-79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany. Electronic address: oliver.schilling@mol-med.uni-freiburg.de.

Publikováno v: Biochimica et biophysica acta [Biochim Biophys Acta] 2016 Oct; Vol. 1864 (10), pp. 1363-71. Date of Electronic Publication: 2016 Jul 15.