A5031630272- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Lipid Membrane Structure and Behavior
- Advanced biosensing and bioanalysis techniques
- Bioinformatics and Genomic Networks
- Alzheimer's disease research and treatments
- Analytical Chemistry and Chromatography
- Biosensors and Analytical Detection
- Cellular transport and secretion
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Metabolism and Genetic Disorders
- SARS-CoV-2 and COVID-19 Research
- Genetic Associations and Epidemiology
- Gene expression and cancer classification
- Long-Term Effects of COVID-19
- Neurological diseases and metabolism
- RNA and protein synthesis mechanisms
- COVID-19 Clinical Research Studies
- Mitochondrial Function and Pathology
- Lipid metabolism and biosynthesis
Morgridge Institute for Research
2020-2024
University of Wisconsin–Madison
2018-2024
Quantitative BioSciences
2020
Energy Center of Wisconsin
2019
We performed RNA-seq and high-resolution mass spectrometry on 128 blood samples from COVID-19-positive COVID-19-negative patients with diverse disease severities outcomes. Quantified transcripts, proteins, metabolites, lipids were associated clinical outcomes in a curated relational database, uniquely enabling systems analysis cross-ome correlations to molecules patient prognoses. mapped 219 molecular features high significance COVID-19 status severity, many of which involved complement...
Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between nanoelectrospray ionization (nanoESI) emitter an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot data with comparable depth that...
Abstract An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual are typically identified by peptide sequences representing small fraction of their total amino acids. Hence, an fails to distinguish different protein variants and isoforms. Deeper proteome sequencing is therefore required for the global discovery Using six cell lines, proteases, deep fractionation three tandem mass spectrometry fragmentation methods, we...
We describe deep analysis of the human proteome in less than one hour. achieve this expedited characterization by leveraging state-of-the-art sample preparation, chromatographic separations, data tools, and using new Orbitrap Astral mass spectrometer equipped with a quadrupole filter, high-field analyzer, an asymmetric track lossless (Astral) analyzer. The system offers high MS/MS acquisition speed 200 Hz detects hundreds peptide sequences per second within independent- or data-dependent...
Here we present IPSA, an innovative web-based spectrum annotator that visualizes and characterizes peptide tandem mass spectra. A tool for the scientific community, IPSA can visualize peptides collected using a wide variety of experimental instrumental configurations. Annotated spectra are customizable via selection interactive features be exported as editable scalable vector graphics to aid in production publication-quality figures. Single analyzed through provided web forms, whereas data...
Abstract Degradation and recycling of plasma membrane proteins occurs via the endolysosomal system, wherein endosomes bud into cytosol from subsequently mature degradative lysosomal compartments. While methods have been developed for rapid selective capture lysosomes (Lyso-IP), analogous isolation early endosome intermediates are lacking. Here, we develop an approach early/sorting through affinity endosome-associated protein EEA1 (Endo-IP) provide proteomic lipidomic snapshots EEA1-positive...
We performed RNA-Seq and high-resolution mass spectrometry on 128 blood samples from COVID-19 positive negative patients with diverse disease severities. Over 17,000 transcripts, proteins, metabolites, lipids were quantified associated clinical outcomes in a curated relational database, uniquely enabling systems analysis cross-ome correlations to molecules patient prognoses. mapped 219 molecular features high significance status severity, many involved complement activation, dysregulated...
Monoclonal antibodies (mAbs) are important therapeutic glycoproteins, but their large size and structural complexity make them difficult to rapidly characterize. Top-down mass spectrometry (MS) has the potential overcome challenges of other common approaches by minimizing sample preparation preserving endogenous modifications. However, comprehensive mAb characterization requires generation many, well-resolved fragments remains challenging. While ETD retains modifications cleaves disulfide...
Modified oligonucleotides represent a promising avenue for drug development, with small interfering RNAs (siRNA) and microRNAs gaining traction in the therapeutic market. Mass spectrometry (MS)-based analysis offers many benefits characterizing modified nucleic acids. Negative electron transfer dissociation (NETD) has proven valuable sequencing oligonucleotide anions, particularly because it can retain modifications while generating sequence-informative fragments. We show that NETD be...
Mass spectrometry (MS)-based proteomics is a powerful technology to globally profile protein abundances, activities, interactions, and modifications. The extreme complexity of samples, which often contain hundreds thousands analytes, necessitates continuous development MS techniques instrumentation improve speed, sensitivity, precision, accuracy, among other analytical characteristics. Here, we systematically evaluated the Orbitrap Ascend Tribrid mass spectrometer in context shotgun...
As lipidomics experiments increase in scale and complexity, data processing tools must support workflows for new liquid chromatography–mass spectrometry (LC-MS) methods while simultaneously supporting quality controls to maximize the confidence lipid identifications. LipiDex 2 improves algorithms from 1 introduces spectral matching peak annotation functions, with improvements speed user-friendliness. In silico library generation now supports tandem mass (MSn) tree-based fragmentation...
Researchers now generate large multi-omic datasets using increasingly mature mass spectrometry techniques at an astounding pace, facing new challenges of "Big Data" dissemination, visualization, and exploration. Conveniently, web-based data portals accommodate the complexity experiments many experts involved. However, developing these tailored companion resources requires programming expertise knowledge web server architecture—a substantial burden for most. Here, we describe Argonaut, a...
Liquid chromatography-mass spectrometry (LC-MS) is a typical strategy for lipidomics analysis. Although capillary LC-MS common analytical technique proteomics analysis, its application to has been limited. In this study, we aim at improving lipid identifications achieved in single analysis by 3-fold approach: LC and nanoelectrospray enhanced ionization, ion trap higher sensitivity tandem MS, parallelization of mass analyzers increased speed acquisition on an Orbitrap hybrid system. By...
While much effort has been placed on comprehensive quantitative proteome analysis, certain applications demand the measurement of only a few target proteins from complex systems. Traditional approaches to targeted proteomics rely nanoliquid chromatography (nLC) and mass spectrometry (MS) methods, e.g., parallel reaction monitoring (PRM). However, time requirement for nLC can limit throughput proteomics. To achieve rapid high-throughput here we show that separations be eliminated replaced...
In mass spectrometry-based lipidomics, complex lipid mixtures undergo chromatographic separation, are ionized, and detected using tandem MS (MSn) to simultaneously quantify structurally characterize eluting species. The reported structural granularity of these identified lipids is strongly reliant on the analytical techniques leveraged in a study. For example, identifications from traditional collisionally activated data-dependent acquisition experiments often at either species level or...
Advances in tandem mass spectrometry (MS/MS) acquisition rate have steadily led to increased performance shotgun proteomics experiments. To that end, contemporary spectrometers are outfitted with multiple analyzers allowing for the simultaneous collection of survey (MS1) and MS/MS spectra. In latest generation Orbitrap hybrid, scans can be acquired at a high using dual cell linear ion trap analyzer, all while next precursor is being dissociated collision MS1 scan occurring Orbitrap. Often...