A5051218655- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Metabolomics and Mass Spectrometry Studies
- Enzyme Production and Characterization
- RNA and protein synthesis mechanisms
- Mitochondrial Function and Pathology
- Microfluidic and Capillary Electrophoresis Applications
- Analytical Chemistry and Chromatography
- Enzyme Catalysis and Immobilization
- Cellular transport and secretion
- Advanced Battery Materials and Technologies
- Adipose Tissue and Metabolism
- Fungal and yeast genetics research
- Epigenetics and DNA Methylation
- Advancements in Battery Materials
- Chronic Myeloid Leukemia Treatments
- Genomics and Phylogenetic Studies
- Eosinophilic Disorders and Syndromes
- Hemoglobinopathies and Related Disorders
- Erythrocyte Function and Pathophysiology
- Asthma and respiratory diseases
- Biochemical Acid Research Studies
- Glycosylation and Glycoproteins Research
McGill University
2023-2025
University of Wisconsin–Madison
2015-2024
Quantitative BioSciences
2024
Energy Center of Wisconsin
2011-2023
Great Lakes Bioenergy Research Center
2016-2023
Janssen (United States)
2021
Morgridge Institute for Research
2020
Dalhousie University
2017
Madison Group (United States)
2017
New York Genome Center
2015
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...
Initiating the DNA base excision repair pathway, glycosylases find and hydrolytically excise damaged bases from DNA. While some exhibit narrow specificity, others remove multiple forms of damage. Human thymine glycosylase (hTDG) cleaves mutagenic G·T mispairs, recognizes many additional lesions, has a strong preference for nucleobases paired with guanine rather than adenine. Yet, hTDG avoids cytosine, despite million-fold excess normal G·C pairs over mispairs. The mechanism this remarkable...
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...
Abstract Protein arginine methyltransferases (PRMTs) introduce methylation, a post-translational modification with the increasingly eminent role in normal physiology and disease. PRMT4 or coactivator-associated methyltransferase 1 (CARM1) is propitious target for cancer therapy; however, few CARM1 substrates are known, its mechanism of substrate recognition poorly understood. Here we employed quantitative mass spectrometry approach to globally profile breast cell lines. We identified >130...
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...
The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production renewable bioenergy. Despite extensive knowledge regulatory networks controlling carbon metabolism in yeast, little is known about how reprogram S. ferment at rates comparable glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses identify characterize responsible mutations series evolved strains capable...
Abstract Capillary zone electrophoresis (CZE)–tandem mass spectrometry (MS/MS) has recently attracted attention as a tool for shotgun proteomics. However, its performance this analysis so far fallen below that of reversed‐phase liquid chromatography (RPLC)–MS/MS. The use CZE method with wide separation window (up to 90 min) and high peak capacity (ca. 300) is reported. This was coupled an Orbitrap Fusion spectrometer through electrokinetically pumped sheath‐flow interface the complex...
Extreme sample complexity is an inherent challenge in shotgun proteomics that positions quality of chromatographic separations as one the key determinants attainable proteome coverage. In search better separations, macroscopic physical characteristics capillary columns, i.e., length and properties stationary phase particles, are typically considered optimized, while significance packing bed morphology frequently underappreciated. Here, we describe a technology enables columns at excess...
Imidazolium ionic liquids (IILs) underpin promising technologies that generate fermentable sugars from lignocellulose for future biorefineries. However, residual IILs are toxic to fermentative microbes such as Saccharomyces cerevisiae, making IIL-tolerance a key property strain engineering. To enable rational engineering, we used chemical genomic profiling understand the effects of on S. cerevisiae. We found likely target mitochondria their profiles closely resembled mitochondrial membrane...
A system-wide understanding of biological processes requires a comprehensive knowledge the proteins in system. The eosinophil is type granulocytic leukocyte specified early hematopoietic differentiation that participates barrier defense, innate immunity, and allergic disease. proteome largely unannotated with under 500 identified. We now report map nonstimulated peripheral blood assembled using two-dimensional liquid chromatography coupled high-resolution mass spectrometry. Our analysis...
Mechanical signals play a critical role in the regulation of muscle mass, but molecules that sense mechanical and convert this stimulus into biochemical events regulate mass remain ill-defined. Here we report spectrometry-based workflow to study changes protein phosphorylation occur mouse skeletal 1 h after bout electrically evoked maximal-intensity contractions (MICs). Our dataset provides first comprehensive map MIC-regulated phosphoproteome. Using unbiased bioinformatics approaches,...
Modern ion trap mass spectrometers are capable of collecting up to 60 tandem MS (MS/MS) scans per second, in theory providing acquisition speeds that can sample every eluting peptide precursor presented the system. In practice, however, sampling capacity enabled by these ultrafast rates is often underutilized due a host reasons (e.g., long injection times and wide analyzer ranges). One overlooked reason for this underutilization instrument exhausts all features it identifies as suitable...
Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. strains have been completely sequenced found to contain 2–8 native plasmids. However, systematic verification of predicted plasmid genes their contribution cell fitness has not hitherto addressed. Moreover, the precise number identities plasmids in model strain ZM4 unclear. The lack functional information about impedes ongoing studies for this biofuel-producing strain....
We introduce neutron-encoded (NeuCode) amino acid labeling of mice as a strategy for multiplexed proteomic analysis in vivo. Using NeuCode, we characterize an inducible knockout mouse model Bap1, tumor suppressor and deubiquitinase whose vivo roles outside cancer are not well established. NeuCode proteomics revealed altered metabolic pathways following Bap1 deletion, including profound elevation cholesterol biosynthetic machinery coincident with reduced expression gluconeogenic lipid...