ProteomicsDB: a multi-omics and multi-organism resource for life science research.

Autor: Samaras P; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany., Schmidt T; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany., Frejno M; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany., Gessulat S; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.; Innovation Center Network, SAP SE, Potsdam, Germany., Reinecke M; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany., Jarzab A; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany., Zecha J; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany., Mergner J; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany., Giansanti P; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany., Ehrlich HC; Innovation Center Network, SAP SE, Potsdam, Germany., Aiche S; Innovation Center Network, SAP SE, Potsdam, Germany., Rank J; Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.; SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany., Kienegger H; Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.; SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany., Krcmar H; Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.; SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany., Kuster B; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, Bavaria, Germany., Wilhelm M; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2020 Jan 08; Vol. 48 (D1), pp. D1153-D1163.

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning.

Autor: Gessulat S; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.; SAP SE, Potsdam, Germany., Schmidt T; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany., Zolg DP; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany., Samaras P; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany., Schnatbaum K; JPT Peptide Technologies GmbH, Berlin, Germany., Zerweck J; JPT Peptide Technologies GmbH, Berlin, Germany., Knaute T; JPT Peptide Technologies GmbH, Berlin, Germany., Rechenberger J; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany., Delanghe B; Thermo Fisher Scientific, Bremen, Germany., Huhmer A; Thermo Fisher Scientific, San Jose, CA, USA., Reimer U; JPT Peptide Technologies GmbH, Berlin, Germany., Ehrlich HC; SAP SE, Potsdam, Germany., Aiche S; SAP SE, Potsdam, Germany., Kuster B; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany. kuster@tum.de.; Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany. kuster@tum.de., Wilhelm M; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany. mathias.wilhelm@tum.de.

Publikováno v: Nature methods [Nat Methods] 2019 Jun; Vol. 16 (6), pp. 509-518. Date of Electronic Publication: 2019 May 27.

The target landscape of clinical kinase drugs.

Autor: Klaeger S; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany., Heinzlmeir S; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany., Wilhelm M; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Polzer H; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany., Vick B; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany., Koenig PA; Institut für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany., Reinecke M; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany., Ruprecht B; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Petzoldt S; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany., Meng C; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Zecha J; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany., Reiter K; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany., Qiao H; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Helm D; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Koch H; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany., Schoof M; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Canevari G; Oncology, Nerviano Medical Sciences Srl, Milan, Italy., Casale E; Oncology, Nerviano Medical Sciences Srl, Milan, Italy., Depaolini SR; Oncology, Nerviano Medical Sciences Srl, Milan, Italy., Feuchtinger A; Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany., Wu Z; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Schmidt T; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Rueckert L; SAP SE, Potsdam, Germany., Becker W; SAP SE, Potsdam, Germany., Huenges J; SAP SE, Potsdam, Germany., Garz AK; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany., Gohlke BO; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany., Zolg DP; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Kayser G; Institute of Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany., Vooder T; Center of Thoracic Surgery, Krefeld, Germany.; Estonian Genome Center, University of Tartu, Tartu, Estonia.; Tartu University Hospital, Tartu, Estonia., Preissner R; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany., Hahne H; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Tõnisson N; Estonian Genome Center, University of Tartu, Tartu, Estonia.; Tartu University Hospital, Tartu, Estonia., Kramer K; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Götze K; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany., Bassermann F; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany., Schlegl J; SAP SE, Walldorf, Germany., Ehrlich HC; SAP SE, Potsdam, Germany., Aiche S; SAP SE, Potsdam, Germany., Walch A; Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany., Greif PA; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany., Schneider S; Department of Chemistry, TUM, Garching, Germany.; Center For Integrated Protein Science Munich (CIPSM), Munich, Germany., Felder ER; Oncology, Nerviano Medical Sciences Srl, Milan, Italy., Ruland J; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Institut für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany., Médard G; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany., Jeremias I; German Cancer Consortium (DKTK), Heidelberg, Germany.; Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany.; Department of Pediatrics, Dr von Hauner Children's Hospital, LMU, Munich, Germany., Spiekermann K; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany., Kuster B; Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany. kuster@tum.de.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.; Center For Integrated Protein Science Munich (CIPSM), Munich, Germany.; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany.

Publikováno v: Science (New York, N.Y.) [Science] 2017 Dec 01; Vol. 358 (6367).

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

Autor: Röst HL; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.; Department of Genetics, Stanford University, Stanford, California, USA., Sachsenberg T; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany., Aiche S; Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany., Bielow C; Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.; Metabolomics Core Facility, Berlin Institute of Health, Berlin, Germany., Weisser H; Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK., Aicheler F; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany., Andreotti S; Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany., Ehrlich HC; Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany., Gutenbrunner P; Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK., Kenar E; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany.; Quantitative Biology Center, University of Tübingen, Tübingen, Germany., Liang X; International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC), Berlin, Germany., Nahnsen S; Quantitative Biology Center, University of Tübingen, Tübingen, Germany., Nilse L; Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany., Pfeuffer J; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany., Rosenberger G; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Rurik M; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany., Schmitt U; ID Scientific IT Services, ETH Zurich, Zurich, Switzerland., Veit J; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany., Walzer M; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany., Wojnar D; Quantitative Biology Center, University of Tübingen, Tübingen, Germany., Wolski WE; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.; Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland., Schilling O; Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany., Choudhary JS; Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK., Malmström L; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland., Aebersold R; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.; Faculty of Science, University of Zurich, Zurich, Switzerland., Reinert K; Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.; Max Planck Institute for Molecular Genetics, Berlin, Germany., Kohlbacher O; Department of Computer Science, University of Tübingen, Tübingen, Germany.; Center for Bioinformatics, University of Tübingen, Tübingen, Germany.; Quantitative Biology Center, University of Tübingen, Tübingen, Germany.; Faculty of Medicine, University of Tübingen, Tübingen, Germany.; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Publikováno v: Nature methods [Nat Methods] 2016 Aug 30; Vol. 13 (9), pp. 741-8.

Searching for recursively defined generic chemical patterns in nonenumerated fragment spaces.

Autor: Ehrlich HC; University of Hamburg, Bundestraße 43, 20146 Hamburg, Germany., Henzler AM, Rarey M

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2013 Jul 22; Vol. 53 (7), pp. 1676-88. Date of Electronic Publication: 2013 Jul 09.