A5033409837- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Bioinformatics and Genomic Networks
- Ferroptosis and cancer prognosis
- Metabolomics and Mass Spectrometry Studies
- Cancer, Lipids, and Metabolism
- Nutrition, Genetics, and Disease
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Ubiquitin and proteasome pathways
- Gene expression and cancer classification
- Molecular Biology Techniques and Applications
- Biosensors and Analytical Detection
- RNA and protein synthesis mechanisms
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Radiomics and Machine Learning in Medical Imaging
- Cell Image Analysis Techniques
- Genomics and Rare Diseases
- Oral microbiology and periodontitis research
- Glycosylation and Glycoproteins Research
- CRISPR and Genetic Engineering
- Salivary Gland Disorders and Functions
- Advanced Biosensing Techniques and Applications
Max Planck Institute of Biochemistry
2015-2025
Max Planck Society
2008-2020
Genentech
2015
Dublin City University
2012
Novo Nordisk Foundation
2010
University of Copenhagen
2010
Mass spectrometry-based proteomics has greatly benefitted from enormous advances in high resolution instrumentation recent years. In particular, the combination of a linear ion trap with Orbitrap analyzer proven to be popular instrument configuration. Complementing this hybrid trap-trap instrument, as well standalone termed Exactive, we here present coupling quadrupole mass filter an analyzer. This "Q Exactive" features currents because S-lens, and fast high-energy collision-induced...
Shotgun proteomics entails the identification of as many peptides possible from complex mixtures. Here we investigate how are detectable by high resolution MS in standard LC runs cell lysate and them accessible to data-dependent MS/MS. Isotope clusters were determined MaxQuant stringently filtered for charge states retention times typical peptides. This resulted more than 100 000 likely peptide features, which only about 16% had been targeted Three instrumental attributes determine...
Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated other types quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation enrichment, which compares from any two 'omics' in context categorical or genes. Suitable categories are membership biochemical pathways, their with gene ontology terms, sub-cellular localization, presence...
PHOSIDA http://www.phosida.com, a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics various species. For each phosphosite, lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, also predicts phosphosites.
Phasing-in quality control in the nucleus The fundamental process of protein is not well understood. contains several non–membrane-bound subcompartments forming liquid-like condensates. largest these nucleolus, site ribosome biogenesis. Frottin et al. found that metastable nuclear proteins misfold upon heat stress enter nucleolus. In they avoid irreversible aggregation and remain competent for shock 70–dependent refolding recovery from stress. Prolonged or uptake associated with...
Yeast remains an important model for systems biology and evaluating proteomics strategies. In-depth shotgun studies have reached nearly comprehensive coverage, rapid, targeted approaches been developed this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns gradients coupled to a linear ion trap Orbitrap instrument had unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J.,...
Although only a few years old, the combination of linear ion trap with an Orbitrap analyzer has become one standard mass spectrometers to characterize proteins and proteomes. Here we describe novel version this instrument family, Elite, which is improved in three main areas. The transfer optics path that blocks line sight achieve more robust operation. tandem MS acquisition speed dual cell now exceeds 12 Hz. Most importantly, resolving power been increased twofold for same transient length...
In-depth MS-based proteomics has necessitated fractionation of either proteins or peptides both, often requiring considerable analysis time. Here we employ long liquid chromatography runs with high resolution coupled to an instrument fast sequencing speed investigate how much the proteome is directly accessible chromatography-tandem MS characterization without any prefractionation steps. Triplicate single-run analyses identified 2990 yeast proteins, 68% total measured in a comprehensive...
Abstract Systems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray sequencing techniques. Marked developments in proteomic technologies now enable very deep clinical samples, with high identification quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 triple negative tumours reached a quantitative depth >10,000 proteins. These profiles identified functional differences between subtypes, related to energy...
Modern software platforms enable the analysis of shotgun proteomics data in an automated fashion resulting high quality identification and quantification results. Additional understanding underlying can be gained with help advanced visualization tools that allow for easy navigation through large LC‐MS/MS datasets potentially consisting terabytes raw data. The updated MaxQuant version has a map component steers users mass retention time‐dependent spectrometric signals. It used to monitor...
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout day. These methods hold significant promise for future discovery, when combined with computational modeling. However, genome-scale experiments are costly laborious, yielding “big data” that conceptually statistically difficult analyze. There is no obvious consensus...
Identifying the building blocks of mammalian tissues is a precondition for understanding their function. In particular, global and quantitative analysis proteome would point to tissue-specific mechanisms place function each protein in whole-organism perspective. We performed proteomic analyses 28 mouse using high-resolution mass spectrometry used mix labeled via stable isotope labeling with amino acids cell culture as "spike-in" internal standard accurate quantification across these tissues....
The oral cavity is home to one of the most diverse microbial communities human body and a major entry portal for pathogens. Its homeostasis maintained by saliva, which fulfills key functions including lubrication food, pre-digestion, bacterial defense. Consequently, disruptions in saliva secretion changes microbiome contribute conditions such as tooth decay respiratory tract infections. Here we set out quantitatively map proteome great depth with rapid in-depth mass spectrometry-based...
Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over last decades greatly evolved terms achievable resolution, accuracy, and dynamic range. The Bruker impact platform QTOF instruments takes advantage these developments here we develop evaluate II for shotgun proteomics applications. Adaption our heated liquid chromatography system achieved very narrow peptide elution peaks. equipped...