logo ipb
logo ipb mobile
x
  • Deutsch
  • English
Benutzeranmeldung
  • Research
    • Research Mission and Profile

    • Molecular Signal Processing

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Nutrient Sensing
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Symbiosis Signaling
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Jasmonate Signaling
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Bioorganic Chemistry

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Bioactives
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Natural Products & Metabolomics
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Biotechnology
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Biofunctional Synthesis
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Computational Chemistry
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Data & Resources
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Biochemistry of Plant Interactions

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Calcium-dependent Protein Kinases
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Cellular Signaling
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Metabolite-based Defense Mechanisms
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Nuclear Processes in Plant Defense
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Cell and Metabolic Biology

      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Glandular Trichomes and Isoprenoid Biosynthesis
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Jasmonate Function & Mycorrhiza
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Phenylpropanoid Metabolism
          • Projects
          • Staff
          • Publications
          • Collaborations
        • Synthetic Biology
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Independent Junior Research Groups

      • Research Groups
        • Receptor Biochemistry
          • Projects
          • Staff
          • Publications
          • Collaborations
    • Program Center MetaCom

      • Secretariat & All staff
      • Publikationen
      • Our Equipment
      • Research Groups
        • Metabolomics Facility
          • Projects
          • Staff
          • Publications
          • Methods
        • MetaCom Analytical Laboratory
          • Projects
          • Staff
          • Publications
          • Methods
        • Computational Plant Biochemistry
          • Projects
          • Staff
          • Publications
          • Collaborations
        • MetaCom Junior Research Group
          • Projects
          • Staff
    • Publications

    • Good Scientific Practice

    • Research Funding

    • Networks and Collaborative Projects

      • Collaborative Projects as Coordinator
        • Completed Projects as Coordinator
      • Collaborative Projects as Partner
        • Completed Projects as Partner
      • Networks
    • Symposia and Colloquia

      • Lectures
        • IPB Seminars
      • Leibniz Plant Biochemistry Symposia
    • Alumni Research Groups

      • Research Groups
        • Auxin Signaling
          • Projects
          • Publications
        • Bioorganic Chemistry
          • Projects
          • Publications
        • Designer Glycans
          • Projects
          • Publications
        • Jasmonate Mode of Action
          • Publications
        • Protein Recognition and Degradation
          • Projects
          • Publications
        • Regulatory RNAs (MLU-associated group)
          • Projects
          • Publications
        • Signal Integration
          • Projects
          • Publications
        • Ubiquitination in Immunity
          • Projects
          • Publications
        • Cellular Coordination
          • Projects
          • Publications
  • Infrastructure
    • Databases and Tools

      • XCMS
      • Rdisop
      • CAMERA
      • MetShot
      • MassBank
      • MetFrag
      • MetFamily
      • PaCeQuant
      • CytoskeletonAnalyzer
      • GoldenMutagenesis
      • cisHighlight
      • FlagScreen
      • RootDetection
    • Technical Resources

    • Imaging Unit

    • Greenhouses and Phytochambers

    • Library Services

      • OPAC
      • Electronic Journals Library
      • Service for Employees
  • Institute
    • Organizational Chart

    • Management and Boards

      • Board of Trustees
      • Scientific Advisory Board
      • IPB Management / Board of Directors
      • Scientific Council
      • Authorized Representatives of the IPB
      • Staff Council
      • Statutes
    • Administration and Infrastructure

      • Secretariat & All Staff
      • Working Groups
        • Human Resources
        • Finance & Accounting
        • Purchasing
        • IT & Technical Support
        • Experimental Nursery
        • Facility Management
        • Library
        • Digitalization
    • Energy Management

      • Objectives and Measures
      • Energy Management Team
    • Diversity, Family, Equality

      • Diversity
      • Equality
      • Family Support
      • Training and further Education
      • Integration and Health
      • General Equal Treatment Act
    • Public Tendering

    • Patents and Licensing

    • The IPB Welcoming Culture

    • Guest Houses

    • IPB Site Map

    • Brief IPB History

      • Bildergalerie zur Historie
      • Alte Filmsequenzen zum Institut
      • Historischer Massenspektrograph
    • Alumni Network

      • The IPB as a career launching pad
  • Career
    • Data protection information for applicants

    • PhD Program

      • PhD Student Representatives
      • DoCou - Doctoral Training Courses
      • PSSC
    • Postdocs

    • Berufsausbildung

  • Public Relations
    • News

      • 2024
      • 2023
      • 2022
      • Archiv Aktuelles
        • 2021
        • 2020
        • 2019
        • 2018
        • 2017
        • 2016
        • 2015
        • 2014
        • vor 2014
    • News Ticker Science

      • News Ticker 2024
      • News Ticker 2023
      • News Ticker 2022
      • News Ticker Archive
        • News Ticker 2021
        • News Ticker 2020
        • News Ticker 2019
    • Press Releases

      • 2024
      • 2023
      • 2022
      • Archive Press Releases
        • 2021
        • 2020
        • 2019
        • 2018
        • 2017
        • 2016
        • 2015
        • 2014
        • 2013
        • 2012
        • 2011
        • 2010
        • 2009
        • 2008
        • 2007
        • 2006
        • 2005
        • 2004
        • 2003
        • 2002
    • IPB Pressespiegel

    • LANGE NACHT, DIE WISSEN SCHAFFT: PROGRAMM

    • IPB Newsletter

    • Printed / Information Material

    • Scientific Reports / Research Highlights

    • Events

      • 2024 Long Night of Sciences
      • 2024 Leibniz Plant Biochemistry Symposium
      • Archiv Veranstaltungen
    • Cover Art

    • Citizen Science: Pilzberatung

      • Das Reich der Pilze
      • Pilzberatung
      • Forschung an Pilzen
  • Contact
    • Directions for Visitors

    • Staff Directory

    • Imprint

    • Data Protection

    • Accessibility

  1. IPB Halle
  2. Research
  3. Publications

    • Research Mission and Profile
    • Trenner 0
    • Molecular Signal Processing
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Nutrient Sensing
        • Symbiosis Signaling
        • Jasmonate Signaling
    • Bioorganic Chemistry
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Bioactives
        • Natural Products & Metabolomics
        • Biotechnology
        • Biofunctional Synthesis
        • Computational Chemistry
        • Data & Resources
    • Biochemistry of Plant Interactions
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Calcium-dependent Protein Kinases
        • Cellular Signaling
        • Metabolite-based Defense Mechanisms
        • Nuclear Processes in Plant Defense
    • Cell and Metabolic Biology
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Glandular Trichomes and Isoprenoid Biosynthesis
        • Jasmonate Function & Mycorrhiza
        • Phenylpropanoid Metabolism
        • Synthetic Biology
    • Independent Junior Research Groups
      • Research Groups
        • Receptor Biochemistry
    • Program Center MetaCom
      • Secretariat & All staff
      • Publikationen
      • Our Equipment
      • Research Groups
        • Metabolomics Facility
        • MetaCom Analytical Laboratory
        • Computational Plant Biochemistry
        • MetaCom Junior Research Group
    • Trenner 1
    • Publications
    • Good Scientific Practice
    • Research Funding
    • Trenner
    • Networks and Collaborative Projects
      • Collaborative Projects as Coordinator
        • Completed Projects as Coordinator
      • Collaborative Projects as Partner
        • Completed Projects as Partner
      • Networks
    • Symposia and Colloquia
      • Lectures
        • IPB Seminars
      • Leibniz Plant Biochemistry Symposia
    • Trenner
    • Alumni Research Groups
      • Research Groups
        • Auxin Signaling
        • Bioorganic Chemistry
        • Designer Glycans
        • Jasmonate Mode of Action
        • Protein Recognition and Degradation
        • Regulatory RNAs (MLU-associated group)
        • Signal Integration
        • Ubiquitination in Immunity
        • Cellular Coordination

Advanced Search

  • Type of publication
    • Publication (5)
  • Year
    • 1999 (1)
      2005 (1)
      2006 (3)
      2007 (6)
      2008 (5)
      2010 (5)
      2011 (2)
      2012 (5)
      2013 (11)
      2014 (7)
      2015 (11)
      2016 (11)
      2017 (6)
      2018 (10)
      2019 (11)
      2020 (5)
      2021 (7)
      2022 (8)
      2023 (8)
      2024 (1)
      2025 (1)
  • Journal / Volume / Preprint Server Sorted by frequency and by alphabetical order
    • Anal. Chem. (2)
      Mol. Cell. Proteomics (1)
      Nat. Biotechnol. (1)
      Nat. Genet. (1)
  • Author Sorted by frequency and by alphabetical order
    • Wessjohann, L. A. (21)
      Schmidt, J. (10)
      Wessjohann, L. (10)
      Arnold, N. (8)
      Eschen-Lippold, L. (8)
      Westermann, B. (8)
      Brandt, W. (7)
      Hause, B. (7)
      Porzel, A. (6)
      Scheel, D. (6)
      Tissier, A. (6)
      Farag, M. A. (5)
      Lee, J. (5)
      Neumann, S. (5)
      Weissenborn, M. J. (5)
      Ali, N. A. A. (4)
      Böttcher, C. (4)
      Flitsch, S. L. (4)
      Neves Filho, R. A. W. (4)
      Quint, M. (4)
      Rosahl, S. (4)
      Stark, S. (4)
      Šardzík, R. (4)
      Abbas, M. (3)
      Bouyer, D. (3)
      Brauch, S. (3)
      Dissmeyer, N. (3)
      Fellenberg, C. (3)
      Franke, K. (3)
      Handrick, V. (3)
      Harashima, H. (3)
      Hause, G. (3)
      Henze, M. (3)
      Lindhorst, T. K. (3)
      Miersch, O. (3)
      Palm-Forster, M. A. T. (3)
      Pecher, P. (3)
      Schnittger, A. (3)
      Setzer, W. N. (3)
      Stenzel, I. (3)
      Vogt, T. (3)
      Wasternack, C. (3)
      Wehner, J. W. (3)
      Zhao, X. (3)
      Antolín-Llovera, M. (2)
      Bethke, G. (2)
      Bette, M. (2)
      Boland, W. (2)
      Breithaupt, C. (2)
      Brusniak, M.-Y. (2)
      Bräuer, U. (2)
      Clausnitzer, D. (2)
      Deutsch, E. W. (2)
      Eyers, C. E. (2)
      Fandrich, U. (2)
      Forner, S. (2)
      Frolov, A. (2)
      Gabriel, L. (2)
      Glazebrook, J. (2)
      Goetz, S. (2)
      Gray, C. J. (2)
      Görlich, S. (2)
      Heilmann, I. (2)
      Hellwege, A. (2)
      Hoehenwarter, W. (2)
      Jaenecke, F. (2)
      Knogge, W. (2)
      Landgraf, R. (2)
      Lindequist, U. (2)
      Moritz, R. L. (2)
      Nowack, M. K. (2)
      Parniske, M. (2)
      Parthier, C. (2)
      Rausch, F. (2)
      Ried, M. K. (2)
      Rivera, D. G. (2)
      Sallaud, C. (2)
      Schulze, S. (2)
      Smolka, U. (2)
      Steinborn, D. (2)
      Strnad, M. (2)
      Stubbs, M. T. (2)
      Trujillo, M. (2)
      Ullrich, K. K. (2)
      Vasilev, D. (2)
      Wehmeier, U. F. (2)
      Weimer, A. K. (2)
      Wirthmueller, L. (2)
      van Berkel, S. S. (2)
      van Berkel, S. S. (2)
      Abdala, G. (1)
      Aebersold, R. (1)
      Agus, D. B. (1)
      Al-Didamony, G. (1)
      Al-Fatimi, M. A. (1)
      Alhaj, M. (1)
      Amado, E. (1)
      Amaral-Zettler, L. (1)
      Amodei, D. (1)
      Anderson, R. G. (1)
  • Year
  • Type of publication
Search narrowed by: Year: 2012 Author Sorted by frequency and by alphabetical order: Neumann, S. Remove all filters
Displaying results 1 to 5 of 5.
  • Results as:
  • Print view
  • Endnote (RIS)
  • BibTeX
  • Table: CSV | HTML
Results per page:
  • 1

Publications

Kuhl, C.; Tautenhahn, R.; Böttcher, C.; Larson, T. R.; Neumann, S.; CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets Anal. Chem. 84 283-289 (2012) DOI: 10.1021/ac202450g
  • Abstract
  • BibText
  • RIS

Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottleneck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion modes, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. We demonstrate the utility of CAMERA in two different, easily adoptable plant metabolomics experiments, where the application of CAMERA drastically reduced the amount of manual analysis.

Publications

Schymanski, E. L.; Gallampois, C. M. J.; Krauss, M.; Meringer, M.; Neumann, S.; Schulze, T.; Wolf, S.; Brack, W.; Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties Anal. Chem. 84 3287-3295 (2012) DOI: 10.1021/ac203471y
  • Abstract
  • BibText
  • RIS

This article explores consensus structure elucidation on the basis of GC/EI-MS, structure generation, and calculated properties for unknown compounds. Candidate structures were generated using the molecular formula and substructure information obtained from GC/EI-MS spectra. Calculated properties were then used to score candidates according to a consensus approach, rather than filtering or exclusion. Two mass spectral match calculations (MOLGEN-MS and MetFrag), retention behavior (Lee retention index/boiling point correlation, NIST Kovat’s retention index), octanol–water partitioning behavior (log Kow), and finally steric energy calculations were used to select candidates. A simple consensus scoring function was developed and tested on two unknown spectra detected in a mutagenic subfraction of a water sample from the Elbe River using GC/EI-MS. The top candidates proposed using the consensus scoring technique were purchased and confirmed analytically using GC/EI-MS and LC/MS/MS. Although the compounds identified were not responsible for the sample mutagenicity, the structure-generation-based identification for GC/EI-MS using calculated properties and consensus scoring was demonstrated to be applicable to real-world unknowns and suggests that the development of a similar strategy for multidimensional high-resolution MS could improve the outcomes of environmental and metabolomics studies.

Publications

Sansone, S.-A.; Rocca-Serra, P.; Field, D.; Maguire, E.; Taylor, C.; Hofmann, O.; Fang, H.; Neumann, S.; Tong, W.; Amaral-Zettler, L.; Begley, K.; Booth, T.; Bougueleret, L.; Burns, G.; Chapman, B.; Clark, T.; Coleman, L.-A.; Copeland, J.; Das, S.; de Daruvar, A.; de Matos, P.; Dix, I.; Edmunds, S.; Evelo, C. T.; Forster, M. J.; Gaudet, P.; Gilbert, J.; Goble, C.; Griffin, J. L.; Jacob, D.; Kleinjans, J.; Harland, L.; Haug, K.; Hermjakob, H.; Sui, S. J. H.; Laederach, A.; Liang, S.; Marshall, S.; McGrath, A.; Merrill, E.; Reilly, D.; Roux, M.; Shamu, C. E.; Shang, C. A.; Steinbeck, C.; Trefethen, A.; Williams-Jones, B.; Wolstencroft, K.; Xenarios, I.; Hide, W.; Toward interoperable bioscience data Nat. Genet. 44 121-126 (2012) DOI: 10.1038/ng.1054
  • Abstract
  • BibText
  • RIS

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

Publications

Deutsch, E. W.; Chambers, M.; Neumann, S.; Levander, F.; Binz, P.-A.; Shofstahl, J.; Campbell, D. S.; Mendoza, L.; Ovelleiro, D.; Helsens, K.; Martens, L.; Aebersold, R.; Moritz, R. L.; Brusniak, M.-Y.; TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists Mol. Cell. Proteomics 11 R111.015040 (2012) DOI: 10.1074/mcp.R111.015040
  • Abstract
  • BibText
  • RIS

Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more preparation in the form of selecting appropriate signatures for the proteins and peptides that are to be targeted. There is a growing number of software programs and resources for selecting optimal transitions and the instrument settings used for the detection and quantification of the targeted peptides, but the exchange of this information is hindered by a lack of a standard format. We have developed a new standardized format, called TraML, for encoding transition lists and associated metadata. In addition to introducing the TraML format, we demonstrate several implementations across the community, and provide semantic validators, extensive documentation, and multiple example instances to demonstrate correctly written documents. Widespread use of TraML will facilitate the exchange of transitions, reduce time spent handling incompatible list formats, increase the reusability of previously optimized transitions, and thus accelerate the widespread adoption of targeted proteomics via selected reaction monitoring.

Publications

Chambers, M. C.; Maclean, B.; Burke, R.; Amodei, D.; Ruderman, D. L.; Neumann, S.; Gatto, L.; Fischer, B.; Pratt, B.; Egertson, J.; Hoff, K.; Kessner, D.; Tasman, N.; Shulman, N.; Frewen, B.; Baker, T. A.; Brusniak, M.-Y.; Paulse, C.; Creasy, D.; Flashner, L.; Kani, K.; Moulding, C.; Seymour, S. L.; Nuwaysir, L. M.; Lefebvre, B.; Kuhlmann, F.; Roark, J.; Rainer, P.; Detlev, S.; Hemenway, T.; Huhmer, A.; Langridge, J.; Connolly, B.; Chadick, T.; Holly, K.; Eckels, J.; Deutsch, E. W.; Moritz, R. L.; Katz, J. E.; Agus, D. B.; MacCoss, M.; Tabb, D. L.; Mallick, P.; A cross-platform toolkit for mass spectrometry and proteomics Nat. Biotechnol. 30 918-920 (2012) DOI: 10.1038/nbt.2377
  • BibText
  • RIS

0

  • 1

Print

  • IPB Halle
  • News
  • Lectures
  • Publications
  • Public Tendering
  • IPB Remote & Mail
  • Imprint
  • Data Protection
  • Accessibility
  • Die Leibniz-Gemeinschaft
  • Wege zu einer pflanzenbasierten Wirtschaft
  • Martin-Luther Universität Halle
  • Erfolgsfaktor Familie
  • TOTAL E-QUALITY
  • Research
    • Research Mission and Profile

    • Molecular Signal Processing

    • Bioorganic Chemistry

    • Biochemistry of Plant Interactions

    • Cell and Metabolic Biology

    • Independent Junior Research Groups

    • Program Center MetaCom

    • Publications

    • Good Scientific Practice

    • Research Funding

    • Networks and Collaborative Projects

    • Symposia and Colloquia

    • Alumni Research Groups

  • Infrastructure
    • Databases and Tools

    • Technical Resources

    • Imaging Unit

    • Greenhouses and Phytochambers

    • Library Services

  • Institute
    • Organizational Chart

    • Management and Boards

    • Administration and Infrastructure

    • Energy Management

    • Diversity, Family, Equality

    • Public Tendering

    • Patents and Licensing

    • The IPB Welcoming Culture

    • Guest Houses

    • IPB Site Map

    • Brief IPB History

    • Alumni Network

  • Career
    • Data protection information for applicants

    • PhD Program

    • Postdocs

    • Berufsausbildung

  • Public Relations
    • News

    • News Ticker Science

    • Press Releases

    • IPB Pressespiegel

    • LANGE NACHT, DIE WISSEN SCHAFFT: PROGRAMM

    • IPB Newsletter

    • Printed / Information Material

    • Scientific Reports / Research Highlights

    • Events

    • Cover Art

    • Citizen Science: Pilzberatung

  • IPB Remote & Mail