A5086646667- Metabolomics and Mass Spectrometry Studies
- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- Plant Gene Expression Analysis
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Mass Spectrometry Techniques and Applications
- Genomics, phytochemicals, and oxidative stress
- Plant biochemistry and biosynthesis
- Microbial Metabolic Engineering and Bioproduction
- Molecular Biology Techniques and Applications
- Analytical Chemistry and Chromatography
- Lipid metabolism and biosynthesis
- Plant-Microbe Interactions and Immunity
- Photosynthetic Processes and Mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- Cancer, Hypoxia, and Metabolism
- Biochemical and biochemical processes
- Immunodeficiency and Autoimmune Disorders
- Fermentation and Sensory Analysis
- Plant Parasitism and Resistance
- Lymphoma Diagnosis and Treatment
- Coconut Research and Applications
- Mitochondrial Function and Pathology
- Mycorrhizal Fungi and Plant Interactions
European Molecular Biology Laboratory
2022-2024
European Molecular Biology Laboratory
2021-2024
Max Planck Institute of Molecular Plant Physiology
2017-2023
University of Copenhagen
2017
Heidelberg University
2017
University of Cambridge
2015-2016
Abstract Knowledge of the subcellular distribution proteins is vital for understanding cellular mechanisms. Capturing proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning to niches low resolution and/or accuracy. Here we introduce hyperLOPIT, method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry multivariate data analysis. We apply hyperLOPIT pluripotent stem cell population whose...
Abstract Metabolomics has grown into one of the major approaches for systems biology studies, in part driven by developments mass spectrometry (MS), providing high sensitivity and coverage metabolome at throughput. Untargeted metabolomics allows investigation metabolic phenotypes involving several hundreds to thousands metabolites. In this approach, all signals a chromatogram are processed an unbiased way, allowing deeper phenotypes, but also resulting significantly more complex data...
Dark-induced senescence provokes profound metabolic shifts to recycle nutrients and guarantee plant survival. To date, research on these processes has largely focused characterizing mutants deficient in individual pathways. Here, we adopted a time-resolved genome-wide association-based approach characterize dark-induced by evaluating the photochemical efficiency content of primary lipid metabolites at beginning, or after 3 6 days darkness. We discovered six patterns identified 215...
Vanillin is the most important flavor compound in vanilla pod. Vanilla planifolia vanillin synthase (VpVAN) catalyzes conversion of ferulic acid and glucoside into glucoside, respectively. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) pod sections demonstrates that preferentially localized within mesocarp placental laminae whereas mesocarp. VpVAN present as mature form (25 kDa) but, depending on tissue isolation procedure, small amounts immature unprocessed (40...
The emergence of type III polyketide synthases (PKSs) was a prerequisite for the conquest land by green lineage. Within PKS superfamily, chalcone (CHSs) provide entry point reaction to flavonoid pathway, while LESS ADHESIVE POLLEN 5 and 6 (LAP5/6) constituents outer exine pollen wall. To study deep evolutionary history this key family, we conducted phylogenomic synteny network phylogenetic analyses whole-genome data from 126 species spanning lineage including Arabidopsis thaliana, tomato...
Metabolomic and proteomic analyses of human plasma serum samples harbor the power to advance our understanding disease biology. Pre-analytical factors may contribute variability bias in detection analytes, especially when multiple labs are involved, caused by sample handling, processing time, differing operating procedures. To better understand impact pre-analytical that relevant implementing a unified metabolomic approach clinical setting, we assessed influence temperature, sitting times,...
A major bottleneck of mass spectrometric metabolomic analysis is still the rapid detection and annotation unknown m/ z features across biological matrices. This kind especially cumbersome for complex samples with hundreds to thousands features. Traditionally, was done manually imposing constraints in reproducibility automatization. Furthermore, different tools are typically used at steps which requires parsing data changing environments. We present here MetNet, implemented R programming...
Abstract Understanding the interplay of proteome and metabolome helps to understand cellular regulation response. To enable robust inferences from such multi-omics analyses, we introduced evaluated a workflow for combined analysis starting single sample. Specifically, integrated established individually optimized protocols metabolomic proteomic profiling (EtOH/MTBE autoSP3, respectively) into unified (termed MTBE-SP3), took advantage fact that protein residue sample can be used as direct...
Plant chemical diversity is largely owing to a number of enzymes which catalyse reactions involved in the assembly, and subsequent modifications, core structures major classes plant specialized metabolites. One such reaction acylation. With this mind, study deep evolutionary history BAHD serine-carboxypeptidase-like (SCPL) acyltransferase genes, we assembled phylogenomic synteny networks based on large-scale inference analysis orthologues across whole-genome sequences 126 species spanning...
Among the main challenges in metabolomics are rapid dereplication of previously characterized metabolites across a range biological samples and structural prediction unknowns from MS/MS data. Here, we developed MetCirc to comprehensively align calculate pairwise similarity scores among spectral data visualize these samples. comprises functionalities interactively organize according compound familial groupings accelerate discovery shared hypothesis formulation for unknowns. As such, provides...
Rice with panicle-blast resistance is needed for stable rice production. Although we have previously demonstrated that OsGF14b underlies a quantitative trait locus positively regulates panicle blast resistance, the mechanism still unknown. In this study, multi-omics approach was used to investigate possible downstream signaling pathway regulated by OsGF14b. both strongly activated gibberellin biosynthetic during pathogen infection and reprogrammed lignin pathway. Reduced accumulation...
Abstract Plants synthesize specialized metabolites to facilitate environmental and ecological interactions. During evolution, plants diversified in their potential these metabolites. Quantitative differences metabolite levels of natural Arabidopsis (Arabidopsis thaliana) accessions can be employed unravel the genetic basis for metabolic traits using genome-wide association studies (GWAS). Here, we performed GWAS on seeds a panel 315 A. thaliana accessions, including reference genotypes C24...
Multiple factors can impact accuracy and reproducibility of mass spectrometry data. There is a need to integrate quality assessment control into data analytic workflows.The MsQuality package calculates 43 low-level metrics based on the controlled mzQC vocabulary defined by HUPO-PSI single spectrometry-based measurement sample. It helps identify low-quality measurements track quality. Its use community-standard facilitates comparability (QA/QC) criteria across datasets.The R available through...
Abstract Motivation First-line data quality assessment and exploratory analysis are integral parts of any workflow. In high-throughput quantitative omics experiments (e.g. transcriptomics, proteomics metabolomics), after initial processing, the typically presented as a matrix numbers (feature IDs × samples). Efficient standardized metrics calculation visualization key to track within-experiment these rectangular types guarantee for high-quality datasets subsequent biological question-driven...
The plant kingdom is thought to encompass about one million unique metabolite structures. Whilst considerable advances have been made with regard quantification, annotation trails behind. Computational workflows, as demonstrated here, can pave a route forward. High-resolution mass spectrometry (MS) data are generated (A) and processed (B); tandem MS (MS/MS) spectra matched against experimental or in silico databases (e.g., similarity) (C); matching scores used select potential hits (D);...
Abstract The emergence of type III polyketide synthases (PKSs) was a pre-requisite for the conquest land by green lineage. To study deep evolutionary history this key family, we used phylogenomic synteny network and phylogenetic analyses whole-genome data from 126 species spanning This thereby combined genomic location context with changes in gene sequences. We found that two major clades, CHS LAP5/6 homologs, evolved early segmental duplication event prior to divergence Bryophytes...