A5044938404- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Physiological and biochemical adaptations
- Metabolomics and Mass Spectrometry Studies
- Infant Nutrition and Health
- Molecular Biology Techniques and Applications
- Protein Hydrolysis and Bioactive Peptides
- Advanced Glycation End Products research
- Insect and Pesticide Research
- Insect and Arachnid Ecology and Behavior
- Salmonella and Campylobacter epidemiology
- Fatty Acid Research and Health
- Food Allergy and Anaphylaxis Research
- Streptococcal Infections and Treatments
- Connexins and lens biology
- Biotin and Related Studies
- Inflammasome and immune disorders
- Phosphodiesterase function and regulation
- Hepatitis Viruses Studies and Epidemiology
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Genetics, Aging, and Longevity in Model Organisms
- Probiotics and Fermented Foods
- Biosensors and Analytical Detection
- vaccines and immunoinformatics approaches
Danone (Netherlands)
2018-2025
Danone Nutricia Research (Netherlands)
2018-2019
Nutricia Research (Netherlands)
2018-2019
University of British Columbia
2011-2015
Utrecht University
2005-2010
University of Southern Denmark
2008-2009
Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of technology is closed nature and slow development cycle vendor-supplied software solutions. We have created an open source environment, called MSQuant, which allows visualization validation peptide identification results directly raw mass spectrometric data. MSQuant iteratively recalibrates MS thereby significantly increasing accuracy leading to fewer false...
Reversible protein phosphorylation ranks among the most important post-translational modifications, and elucidation of sites is essential to understand regulation key cellular processes such as signal transduction. Enrichment phosphorylated peptides a prerequisite for successful analysis due their low stoichiometry, heterogeneity, abundance. often performed manually, which inherently labor-intensive major hindrance in large-scale analyses. Automation enrichment method would vastly improve...
In the biological sciences, model organisms have been used for many decades and enabled gathering of a large proportion our present day knowledge basic processes their derailments in disease. Although these studies using organisms, focus has primarily on genetics genomics approaches, it is important that methods become available to extend this relevant protein level. Mass spectrometry-based proteomics increasingly becoming standard comprehensively analyze proteomes. An transition made...
The dicistrovirus intergenic region internal ribosome entry site (IRES) utilizes a unique mechanism, involving P-site tRNA mimicry, to directly assemble 80S ribosomes and initiate translation at specific non-AUG codon in the ribosomal A site. subgroup of genomes contains an additional stem-loop 5′-adjacent IRES short open reading frame (ORFx) that overlaps viral structural polyprotein ORF (ORF2) +1 frame. Using mass spectrometry extensive mutagenesis, we show that, besides directing ORF2...
Bacteria can release membrane-derived nanoparticles made of lipid bilayers, so-called extracellular vesicles (EVs), which carry diverse cargo and are important for microbe-microbe microbe-host interactions. Here, we studied the production EVs by Streptococcus thermophilus 065, protein composition EVs, how produced impact immune response in vitro. Cultures S. grown 6 h at 40 °C M17 broth with 2% lactose reached high biomass yields a level quantified lipophilic fluorescent dye staining....
B cells play an essential role in the immune response. Upon activation they may differentiate into plasma that secrete specific antibodies against potentially pathogenic non-self antigens. To identify cellular proteins are important for efficient production of these we set out to study cell differentiation process at proteome level. We performed in-depth proteomic quantify dynamic relative protein expression patterns several hundreds five consecutive time points after...
Abstract Bacillus subtilis has been developed as a model system for physiological proteomics. However, thus far these studies have mainly limited to cytoplasmic, extracellular, and cell‐wall attached proteins. Although being certainly important cell physiology, the membrane protein fraction not studied in comparable depth due inaccessibility by traditional 2‐DE‐based workflows limitations reliable quantification. In this study, we now compare potential of stable isotope labeling with amino...
In matrix-assisted laser desorption/ionization (MALDI) analyses of small oligosaccharides a very large increase in sensitivity (by factor 1000) may be obtained by introducing quaternary ammonium center ('quaternization'). Such introduced into the saccharide reaction with commercially available glycidyltrimethylammonium chloride (GTMA), or using Girard's reagent T (Naven and Harvey, Rapid Commun. Mass Spectrom. 1996; 10: 829). GTMA reacts alcohol functionalities, whereas is specific for...
Comparative proteomics has emerged as a powerful approach to determine differences in protein abundance between biological samples. The introduction of stable-isotopes internal standards especially paved the road for quantitative comprehensive approaches accurately dynamics. Metabolic labeling with 15N isotopes is applied an increasing number organisms, including Drosophila, C. elegans, and rats. However, 15N-enrichment often suboptimal (<98%), which may hamper identification quantitation...
An important hallmark in embryonic development is characterized by the maternal-to-zygotic transition (MZT) where zygotic transcription activated a maternally controlled environment. Post-transcriptional and translational regulation critical for this has been investigated considerable detail at gene level. We used proteomics approach using metabolic labeling of Drosophila to quantitatively assess changes protein expression levels before after MZT. By combining stable isotope fruit flies vivo...
Failure to induce oral tolerance may result in food allergy. Hydrolysed cow's milk-based infant formulas are recommended subjects with a high risk of developing allergic disease. Presentation T cell epitopes is prerequisite generate regulatory cells that could contribute tolerance.To investigate whether specific hydrolysed whey-based formula contains peptides function as support the development whey.First, novel liquid chromatography-mass spectrometry (LC-MS) method was developed...
ABSTRACT The transcription factors HilA and SsrB activate expression of two type III secretion systems (T3SSs) cognate effectors that reprogram host cell functions to benefit infecting Salmonella in the host. These factors, systems, are all encoded by horizontally acquired genes. Using quantitative proteomics, we quantified abundance 2,149 proteins from hilA or ssrB vitro . Our results suggest regulon does not extend significantly beyond known be involved direct interactions with intestinal...
A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, presents specific technical challenges, including complexity dynamic range member taxa, need for well-annotated metagenomic databases, high inter-protein sequence redundancy similarity. In this study, an approach developed assessment biological phenotype metabolic status, as functional...
Abstract Inhibitors of phosphodiesterase 5 (PDE5) are widely used for the treatment erectile dysfunction and pulmonary hypertension. The commercially available inhibitors effective, well‐tolerated drugs, but differ in their specificity. To explore manipulate specificity PDE5 inhibitors, a small library four was synthesized using structure known as scaffold. Their inhibitory potency towards related family members evaluated. Next, they were immobilized on matrix to perform affinity pull‐down...
Nontyphoidal Salmonella enterica (NTS) infections are a major burden to global public health, as they lead diseases ranging from gastroenteritis systemic and there is currently no vaccine available. Here, we describe highly effective component against S. serovar Typhimurium in both murine infection models. We devised an approach generate supernatants of Typhimurium, organism that abundant virulence factors. Immunization mice with this supernatant resulted dramatic protection challenge...
Electron transfer dissociation (ETD) of peptide ions has been introduced as a tool for mass spectrometry based sequencing, complementary to the commonly used collision induced (CID). It proposed that ETD may have better performance than CID more highly charged and/or larger peptides. Here, we compare and on data generated in large-scale proteomics experiment. First, tryptic proteolytic peptides Drosophila melanogaster oocytes were off-line separated their insolution net charge state using...
Recent declines in honey bee (Apis mellifera L., 1758) populations worldwide have spurred significant research into the impact of pathogens on colony health. The role Israeli acute paralysis virus (IAPV) hive mortality has become particular concern since being correlated with losses. However, molecular interactions between IAPV and its host remain largely unknown. To investigate changes protein expression during infection, mass-spectrometry-based quantitative proteomics was used to compare...