We also determine protein-protein interactions after co-immunoprecipitation or affinity enrichment. A MALDI-TOF based method has been developed for the rapid identification and de-replication of microorganisms isolated from plant and environmental samples, based on their intact protein profiles. We also use mass spectrometry-based imaging (MSI) for spatial mapping of metabolites in plant tissues. The proteomics facility supports the complete proteomic workflow, starting from project planning, sample preparation, data acquisition and data analysis up to the publication of results. Our method and instrument portfolios are frequently extended and updated.

For further information and project discussions please contact us at SSP@igzev.de.

External cooperation partners
Hochschule Geisenheim University (HGU), Geisenheim (Germany)
Julius Kühn Institute (JKI), Quedlinburg (Germany)
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany)
Nicolaus Copernicus Universität Torun, Torun (Poland)
University of Silesia in Katowice, Katowice (Poland)
Indian Institute of Science Education and Research, Tirupati (India)
University of Santo Tomas in Manila, Manila (Philippines)
Cairo University, Cairo (Egypt)

Offering high resolution and accuracy, it is one of the widely used techniques employed in metabolomics, with the fundamental aim of providing a comprehensive view of the metabolites involved in the organism´s cellular processes, such as growth, development, adaptation and ecological interactions. 
The LC-MS-based metabolomics facility contributes to method development, data acquisition, data processing, multivariate data analysis, dereplication, compound annotation, identification, and data interpretation. Project design, training, education and scientific communication are also part of the core facility activities.

For further information and project discussions please contact us at SSP@igzev.de.

External cooperation partners
​​​Indian Institute of Technology Delhi, Department of Biochemical Engineering and Biotechnology, Delhi (India)
University of São Paulo (Brazil)
Leibniz Institute for Plant Biochemistry (IPB), Halle (Germany)
University Hohenheim, Stuttgart (Germany)

Here at IGZ, we collect plant VOCs by headspace sampling where the VOCs are released in gas chromatography via thermal desorption. We also collect VOCs from dry biomass by non-polar solvent extraction. In a number of projects, we are involved in designing the collection of emitted and endogenous VOCs and also in the development of instrumental methods for the precise identification and analysis of plant VOCs.

We have an infrastructural facility of single quadrupole GC-MS for performing untargeted analysis of chemical compounds as well as triple quadrupole GC-MS/MS for detecting trace amounts of compounds. We also have GC-Q-TOF (quadrupole time of flight) for obtaining accurate mass spectra of compounds for precise identification and profiling of chemical compounds.

The GC-MS facility at the IGZ supports the complete workflow for the analysis of both targeted and untargeted VOC metabolites, starting from project planning, sample preparation, data processing and analysis to the publication of results. Our method and instrument portfolios are frequently extended and updated.

For further information and project discussions please contact us at SSP@igzev.de.

External cooperation partners
Helmholtz Centre for Environmental Research – UFZ, Leipzig (Germany)

We provide de novo and reference-based approaches for genome and transcriptome assembly to facilitate the identification of novel genes and isoforms. We also perform functional enrichment analyses to help identifying important gene sets and biological pathways involved in biological processes.

To provide a deeper knowledge of complex biological relationships and molecular processes, our pipelines also make pathway analysis and molecular networking easier. We provide extensive systems-level insights into plant biology by integrating data from several omics layers, providing possibilities for data-driven discoveries in sustainable plant-based agrifood systems.

Furthermore, we develop and implement machine learning models for a range of applications, such as mass spectrum grouping, sample classification, gene and protein interaction analysis, and metabolite structure prediction. This extends the area of study and ensures that our bioinformatics platform supports a variety of biological research questions.

Ensuring data standards and interoperability is crucial to our bioinformatics work, as it facilitates data administration and sharing both within the IGZ and with external partners. In addition, we supply and manage the bioinformatics infrastructure required to handle omics- related workloads , effectively and facilitate reproducible research.

Where existing solutions are insufficient to fulfill specific research demands, this architecture allows the development of pipelines and new tools. Through interactive workshops, mentorship programmes, and hands-on education, we also aim to empower researchers and students to use bioinformatics tools efficiently, making the latest approaches accessible and useful for their studies.

We develop partnerships within the scientific community to encourage innovation and knowledge exchange in cooperation with other bioinformatics groups.

For further information and project discussions, please contact us at SSP@igzev.de.

External cooperation partners

Leibniz Institute for Plant Biochemistry (IPB), Halle (Germany)