A5008226211- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Plant Reproductive Biology
- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Photosynthetic Processes and Mechanisms
- Protein Structure and Dynamics
- Plant nutrient uptake and metabolism
- Enzyme Catalysis and Immobilization
- Legume Nitrogen Fixing Symbiosis
- Scientific Computing and Data Management
- Soybean genetics and cultivation
- Cloud Computing and Resource Management
- Plant-Microbe Interactions and Immunity
- GABA and Rice Research
- Advanced Biosensing Techniques and Applications
- Bioinformatics and Genomic Networks
- Plant biochemistry and biosynthesis
- Plant Gene Expression Analysis
- Enzyme Structure and Function
- Biotin and Related Studies
- Phytochemicals and Antioxidant Activities
- Potato Plant Research
University of Vienna
2010-2015
Technische Universität Braunschweig
2009-2010
University of Cologne
2009
Max Planck Institute for Molecular Genetics
2000-2002
Scienion (Germany)
2002
Mitogen-activated protein kinase (MPK) cascades are important for eukaryotic signal transduction. They convert extracellular stimuli (e.g. some hormones, growth factors, cytokines, microbe- or damage-associated molecular patterns) into intracellular responses while at the same time amplifying transmitting signal. By doing so, they ensure proper performance, and eventually survival, of a given organism, example in times stress. MPK function via reversible phosphorylation cascade components...
Metabolomics has emerged as a key technique of modern life sciences in recent years. Two major techniques for metabolomics the last 10 years are gas chromatography coupled to mass spectrometry (GC-MS) and liquid (LC-MS). Each platform specific performance detecting subsets metabolites. GC-MS combination with derivatisation preference small polar metabolites covering primary metabolism. In contrast, reversed phase LC-MS covers large hydrophobic predominant secondary Here, we present an...
In the era of fast genome sequencing a critical goal is to develop genome-wide quantitative molecular approaches. Here, we present metaproteogenomic strategy integrate proteomics and metabolomics data for systems level analysis in recently sequenced unicellular green algae Chlamydomonas reinhardtii. To achieve representative proteome coverage analysed different growth conditions with protein prefractionation shotgun proteomics. For identification, annotations as well new gene model...
Proteomics has become a critical tool in the functional understanding of plant processes at molecular level. Proteomics-based studies have also contributed to ever-expanding array data modern biology, with many generating Web portals and online resources that contain incrementally expanding updated information. Many these reflect specialist research areas significant novel information is not currently captured by centralized repositories. The Arabidopsis (Arabidopsis thaliana) community well...
Tomato is a globally important crop grown and consumed worldwide. Its reproductive activity highly sensitive to environmental fluctuations, for instance temperature drought. Here, pollen development one of the most decisive processes. The present study aims identification cell-specific proteins during developmental stages tomato. We have setup protocol stage-specific isolation including microsporocytes (pollen mother cells), tetrads, microspores, polarized mature pollen. Proteins were...
Potentilla anserina L. (Rosaceae) is known for its beneficial effects of prevention pre-menstrual syndrome (PMS). For this reason P. processed into many food supplements and pharmaceutical preparations. Here we analyzed hydroalcoholic reference extracts compared them with various different pharmacies using an integrative metabolomics platform comprising GC-MS LC-MS analysis software toolboxes data alignment (MetMAX Beta 1.0) multivariate statistical (COVAIN 1.0). Multivariate statistics the...
Pollen development in angiosperms is one of the most important processes controlling plant reproduction and thus productivity. At same time, pollen highly sensitive to environmental fluctuations, including temperature, drought, nutrition. Therefore, biology a major focus applied studies breeding approaches for improving productivity globally changing climate. The accessible developmental stages are mature tubes, these frequently analyzed. To reveal complete quantitative proteome map, we...
The use of delayed ion extraction in MALDI time-of-flight mass spectrometry distorts the linear relationship between m/z and square flight time (t2) with consequence that, if a accuracy 10 ppm or better is to be obtained, calibrant signals have fall close analyte signals. If this not possible, systematic errors arise. To eliminate these, higher-order calibration function thus several are required. For internal calibration, however, approach limited by signal suppression effects increasing...
Recently, we have developed a quantitative shotgun proteomics strategy called mass accuracy precursor alignment (MAPA). The MAPA algorithm uses high to bin mass-to-charge (m/z) ratios of ions from LC–MS analyses, determines their intensities, and extracts sample versus m/z ratio data matrix multitude samples. Here, introduce novel feature this that allows the extraction proteotypic peptide or any other target complex for accurate quantification unique proteins. This circumvents problem...
The ProMEX database is one of the main collection annotated tryptic peptides in plant proteomics. objective Database to provide experimental MS/MS-based information for cell type-specific or subcellular proteomes Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Lotus japonicus, corniculatus, Phaseolus vulgaris, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Glycine max, Zea mays, Bradyrhizobium japonicum and Sinorhizobium meliloti. Direct links at protein...
A new strategy for identifying proteins by MALDI-TOF-MS peptide mapping is reported. In contrast to current approaches, the does not rely on a good relative or absolute mass accuracy as criterion that discriminates false positive results. The protein sequence database first searched all match minimum five of submitted masses within maximum expected errors when default externally determined calibration constants are used, instance, ±500 ppm. Typically, this search retrieves many thousand...
A new strategy for identifying proteins in sequence databases by MALDI-MS peptide mapping is reported. The corrects systematic deviations of determined molecular masses using information contained the opened database and thereby renders unnecessary internal spectrum calibration. As a result, data acquisition simplified less error prone. Performance demonstrated identification set recombinant, human cDNA expression products as well native isolated from crude mouse brain extracts 2-D...
Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers shotgun proteomics analyses on personal computer in matter hours. We compared 183 LC-MS more than 2 million MS/MS spectra could define separate proteomic phenotypes field grown tubers 12 tetraploid cultivars crop plant Solanum tuberosum. Protein isoforms patatin as well other major gene families such lipoxygenase cysteine protease inhibitor...
Most legume species establish a symbiotic association with soil bacteria. The plant accommodates the differentiated rhizobia in specialized organs, root nodules. In this environment, microsymbiont reduces atmospheric nitrogen (N) making it available for metabolism. Symbiotic N-fixation is driven by respiration of host photosynthates and thus constitutes an additional carbon sink plant. Molecular phenotypes non-symbiotic Medicago truncatula are identified. implication nodule symbiosis on...
A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system, e.g., drug design, metabolic network reconstruction system biology. When scientists the above mentioned wish to unambiguously refer an its function, EC number introduced by Nomenclature Committee International Union Biochemistry Molecular Biology (IUBMB) is used. However, each every one these applications critically dependent upon consistency reliability underlying...
Abstract Background: Enzymes are classified in a numerical classification scheme introduced by the Nomenclature Committee of IUBMB based on overall reaction chemistry. Due to manifold enzymatic reactions system has become highly complex. Assignment enzymes enzyme classes requires detailed knowledge and manual analysis. Frequently rearrangements deletions sub-subclasses necessary. Results: We use Dugundji–Ugi model for coding biochemical which is electron shift patterns occurring during...
Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be challenging task, due to the inherent complexity biological samples. With partial metabolic labeling experiments this increases as result emergence additional isotopic peaks. Automated extraction subsequent protein calculations enable analysis...
We describe the technical feasibility and methodology to characterize a protein by minimal set of structural information generated matrix assisted laser desorption/ionization (MALDI)-mass spectrometry, termed "minimal Identifier" (MPI). MPIs can be determined for proteins from two-dimensional gels recombinant used compare identify these sources.
The molecular systems biology community has to deal with an increasingly growing amount of data.A recent programming model that addresses the data deluge is MapReduce which facilitates processing huge volumes on large sets computing resources.However, availability appropriate local resources often limited.Cloud this issue by providing virtually infinite demand, usually following a pay per use model.In paper we present our cloud based high throughput infrastructure combines Software as...