A5007686133- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Analytical Chemistry and Chromatography
- Ion-surface interactions and analysis
- Microfluidic and Capillary Electrophoresis Applications
- Mitochondrial Function and Pathology
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- Microbial Metabolic Engineering and Bioproduction
- Legume Nitrogen Fixing Symbiosis
- Advanced Electron Microscopy Techniques and Applications
- Electrohydrodynamics and Fluid Dynamics
- Plant nutrient uptake and metabolism
- Fungal and yeast genetics research
- Electron and X-Ray Spectroscopy Techniques
- Photosynthetic Processes and Mechanisms
- Advanced biosensing and bioanalysis techniques
- Mechanical and Optical Resonators
- Molecular Biology Techniques and Applications
- Coenzyme Q10 studies and effects
- Biochemical Acid Research Studies
- Adipose Tissue and Metabolism
- Bioinformatics and Genomic Networks
University of Wisconsin–Madison
2015-2024
Quantitative BioSciences
2019-2024
Energy Center of Wisconsin
2011-2020
New York Genome Center
2015
Division of Chemistry
2012
Thermo Fisher Scientific (United States)
2010
Selected reaction monitoring on a triple quadrupole mass spectrometer is currently experiencing renaissance within the proteomics community for its, as yet, unparalleled ability to characterize and quantify set of proteins reproducibly, completely, with high sensitivity. Given immense benefit that resolution accurate instruments have brought discovery field, we wondered if highly measurement capabilities could be leveraged provide benefits in targeted domain well. Here, propose new paradigm...
We describe the comprehensive analysis of yeast proteome in just over one hour optimized analysis. achieve this expedited characterization with improved sample preparation, chromatographic separations, and by using a new Orbitrap hybrid mass spectrometer equipped filter, collision cell, high-field analyzer, and, finally, dual cell linear ion trap analyzer (Q-OT-qIT, Fusion). This system offers high MS2 acquisition speed 20 Hz detects up to 19 peptide sequences within single second operation....
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 Protein glycosylation is a highly important, yet poorly understood protein post-translational modification. Thousands of possible glycan structures and compositions create potential for tremendous site heterogeneity. A lack suitable analytical methods large-scale analyses intact glycopeptides has limited our abilities both to address the degree heterogeneity across glycoproteome understand how this contributes biologically complex systems. Here we show that N-glycoproteome...
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...
Symbiotic associations between legumes and rhizobia usually commence with the perception of bacterial lipochitooligosaccharides, known as Nod factors (NF), which triggers rapid cellular molecular responses in host plants. We report here deep untargeted tandem mass spectrometry-based measurements NF-induced changes phosphorylation status 13,506 phosphosites 7739 proteins from model legume Medicago truncatula. To place these within a biological context, quantitative phosphoproteomic RNA...
Significance Coenzyme Q (CoQ) is a requisite component of the mitochondrial oxidative phosphorylation machinery that produces more than 90% cellular ATP. Despite discovery CoQ 50 years ago, many aspects its biosynthesis remain obscure. These include functions uncharacterized CoQ-related proteins whose disruption can cause human diseases. Our work reveals one such protein, COQ9, lipid-binding protein enables through physical and functional interaction with COQ7, via stabilization entire...
Lysine acetylation is rapidly becoming established as a key post-translational modification for regulating mitochondrial metabolism. Nonetheless, distinguishing regulatory sites from among the thousands identified by mass spectrometry and elucidating how these modifications alter enzyme function remain primary challenges. Here, we performed multiplexed quantitative to measure changes in mouse liver acetylproteome response acute chronic alterations nutritional status, integrated data sets...
We describe a synthesis strategy for the preparation of lysine isotopologues that differ in mass by as little 6 mDa. demonstrate incorporation these molecules into proteomes actively growing cells does not affect cellular proliferation, and we discuss how to use embedded signatures (neutron encoding (NeuCode)) multiplexed proteome quantification means high-resolution spectrometry. NeuCode SILAC amalgamates quantitative accuracy with multiplexing isobaric tags and, doing so, offers up new...
ADP-ribosylation (ADPr) is a post-translational modification that plays pivotal roles in wide range of cellular processes. Mass spectrometry (MS)-based analysis ADPr under physiological conditions, without relying on genetic or chemical perturbation, has been hindered by technical limitations. Here, we describe the applicability activated ion electron transfer dissociation (AI-ETD) for MS-based proteomics using our unbiased Af1521 enrichment strategy. To benchmark AI-ETD, profile 9,000...
Abstract Native mass spectrometry (MS) is increasingly used to provide complementary data electron microscopy (EM) for protein structure characterization. Beyond the ability measurements of gas-phase biomolecular ions, MS instruments offer purify, select, and precisely control spatial location these ions. Here we present a modified Orbitrap system capable depositing native ion beam onto EM grids. We further describe use chemical landing matrix that preserves structural integrity deposited...
Owing to its roles in cellular signal transduction, protein phosphorylation plays critical myriad cell processes. That said, detecting and quantifying has remained a challenge. We describe the use of novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) achieve rapid deep analysis human mouse phosphoproteomes. With this method, we map approximately 30,000 unique sites within half-hour data collection. The technology is benchmarked other state-of-the-art MS...
The charge state of ions produced in electrospray ionization (ESI) was reduced a controlled manner to yield predominantly singly charged species by exposure the aerosol bipolar ionizing gas. Analysis resulting on an orthogonal time-of-flight mass spectrometer yielded spectra greatly simplified compared with conventional ESI spectra. decreased spectral complexity afforded reduction facilitates analysis mixtures spectrometry.
A new mass spectrometric technique, charge reduction electrospray spectrometry (CREMS), allowing the analysis of complex mixtures biological molecules is described. The state ions produced by ionization may be reduced in a controlled manner to yield predominantly singly charged through reactions with bipolar (i.e., both positively and negatively charged) generated using 210Po α particle source. electrospray-generated multiply undergo "neutralization chamber" positioned before entrance nozzle...
The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier economical production lignocellulosic biofuels. Although genetic approaches have enabled engineering S. convert efficiently into ethanol in defined lab medium, few strains are able from hydrolysates absence oxygen. This limited conversion believed result small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress impair...