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Publications

Journal publications provide an important mechanism of communication and dissemination, and we aim to rigorously publish our work as soon as possible, targeting venues having both expert and non-expert audiences.  Our overall aim is to promote, advertise, and make available our enabling technologies to the biomedical research community.

Additional resources can also be found at the Biomedical Technology Resources portal, an NIH innovative technology resource.

When appropriate, please acknowledge our support in publications and presentations: “This work was supported in part by the National Institutes of Health grant P41GM108538.”

All Publications

Click on the links below for further reading on our research

Publication Library

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1483-P: Identifying Conditional Dependence of Proteins Regulating Islet Biology with Machine Learning

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High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan

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Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags

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LipiDex 2 Integrates MSn Tree-Based Fragmentation Methods and Quality Control Modules to Improve Discovery Lipidomics

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Chemical Proteomics Strategies for Analyzing Protein Lipidation Reveal the Bacterial O-Mycoloylome

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Offline Two-dimensional Liquid Chromatography-Mass Spectrometry for Deep Annotation of the Fecal Metabolome

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Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer

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Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry

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Succinate dehydrogenase–complex II regulates skeletal muscle cellular respiration and contractility but not muscle mass in genetically induced pulmonary emphysema

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RNA sequestration in P-bodies sustains myeloid leukemia

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The prolyl isomerase FKBP11 is a secretory translocon accessory factor

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Regulated N-glycosylation controls chaperone function and receptor trafficking

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High-throughput relative quantification of fatty acids by 12-plex isobaric labeling and microchip capillary electrophoresis – Mass spectrometry

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Post-GWAS multiomic functional investigation of the TNIP1 locus in Alzheimer’s disease highlights a potential role for GPX3

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Signaling through the nicotinic acetylcholine receptor in the liver protects against the development of metabolic dysfunction-associated steatohepatitis

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A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

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Cell type specific gene therapy confers protection against motor neuron disease caused by a TFG variant

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In-Depth Chemical Analysis of the Brain Extracellular Space Using In Vivo Microdialysis with Liquid Chromatography-Tandem Mass Spectrometry

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Preparation of high-efficiency HILIC capillary columns utilizing slurry packing at 2100 bar

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Recent Advances in Labeling-Based Quantitative Glycomics: From High-Throughput Quantification to Structural Elucidation

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12-Plex Isobaric Multiplex Labeling Reagents for Carbonyl-Containing Compound (SUGAR) Tag-Enabled High-Throughput Quantitative Glycomics

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sn-Position-Resolved Quantification of Aminophospholipids by Isotopic N, N-Dimethyl Leucine Labeling and High-Resolution Ion Mobility Mass Spectrometry

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6-Plex mdSUGAR Isobaric-Labeling Guide Fingerprint Embedding for Glycomics Analysis

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CHRISTMAS: Chiral Pair Isobaric Labeling Strategy for Multiplexed Absolute Quantitation of Enantiomeric Amino Acids

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Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue

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Pptc7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy

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Plasma metabolomics supports non-fasted sampling for metabolic profiling across a spectrum of glucose tolerance in the Nile rat model for type 2 diabetes

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MmuPV1 E6 induces cell proliferation and other hallmarks of cancer

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A transcriptional network governing ceramide homeostasis establishes a cytokine-dependent developmental process

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Hem25p is required for mitochondrial IPP transport in fungi

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HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B

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Decreased plasma cartilage acidic protein 1 in COVID-19

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DiLeu Isobaric Labeling Coupled with Limited Proteolysis Mass Spectrometry for High-Throughput Profiling of Protein Structural Changes in Alzheimer’s Disease

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Regulation of DNA damage and transcriptional output in the vasculature through a cytoglobin-HMGB2 axis

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Development of novel isobaric tags enables accurate and sensitive multiplexed proteomics using complementary ions

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Improved Structural Characterization of Glycerophospholipids and Sphingomyelins with Real-Time Library Searching

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Systematic analysis of metabolic bottlenecks in the methylerythritol 4-phosphate (MEP) pathway of Zymomonas mobilis

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The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse

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PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae

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Mass Spectrometry-Based Multi-omics Integration with a Single Set of C. elegans Samples

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DNA-Compatible Copper/TEMPO Oxidation for DNA-Encoded Libraries

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Evaluation of Orbitrap Ascend Tribrid Mass Spectrometer for Shotgun Proteomics

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Large‐scale proteome and metabolome analysis of CSF implicates altered glucose and carbon metabolism and succinylcarnitine in Alzheimer’s disease

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Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae

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N-glycoproteomics of brain synapses and synaptic vesicles

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Global detection of human variants and isoforms by deep proteome sequencing

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Recent advances in isobaric labeling and applications in quantitative proteomics

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Systematic analysis of metabolic bottlenecks in the methylerythritol 4-phosphate (MEP) pathway of Zymomonas mobilis

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Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut

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Rapid multi-omics sample preparation for mass spectrometry

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DiLeu: Enhanced Isobaric N,N-Dimethyl Leucine Tagging Strategy for a Comprehensive Quantitative Glycoproteomic Analysis

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Novel Isobaric Tagging Reagent Enabled Multiplex Quantitative Glycoproteomics via Electron-Transfer/Higher-Energy Collisional Dissociation (EThcD) Mass Spectrometry

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Structure and functionality of a multimeric human COQ7:COQ9 complex

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Spatial Snapshots of Amyloid Precursor Protein Intramembrane Processing via Early Endosome Proteomics

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Isotopic N,N-dimethyl leucine tags for absolute quantification of clustering and apolipoprotein E in Alzheimer’s disease

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The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium

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12-Plex DiLeu Isobaric Labeling Enabled High-Throughput Investigation of Citrullination Alterations in the DNA Damage Response

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Multiplexed quantitative neuropeptidomics via DiLeu isobaric tagging

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Rapid and Gentle Immunopurification of Brain Synaptic Vesicles

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Increased expression of SLC25A1/CIC causes an autistic-like phenotype with altered neuron morphology

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SLC13A5/sodium-citrate co-transporter overexpression causes disrupted white matter integrity and an autistic-like phenotype

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IQGAP1 and RNA Splicing in the Context of Head and Neck via Phosphoproteomics

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Maximizing MS/MS Acquisition for Lipidomics Using Capillary Separation and Orbitrap Tribrid Mass Spectrometer

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Defining mitochondrial protein 1 functions through deep multi-omic profiling

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Tcof1 hHploinsufficiency Promotes Early T Cell Precursor-like Leukemia in NrasQ61R/+ Mice

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High-fat Diet Disrupts REG3γ and Gut Microbial Rhythms
Promoting Metabolic Dysfunction

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Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States

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Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation

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High-Throughput, Comprehensive Single-Cell Proteomic Analysis of Xenopus laevis Embryos at the 50-Cell Stage Using a Microplate-Based MICROFASP System

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Practical Effects of Intramolecular Hydrogen Rearrangement in Electron Transfer Dissociation-Based Proteomics

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Lipidomic analysis of tissue culture cells, tissues, and purified organelles

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Developing mass spectrometry for the quantitative analysis of neuropeptides

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Proteomic and metabolomic profiling of acute and chronic stress events associated with military exercises

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Rapid preparation of human blood plasma for bottom-up proteomics analysis

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DNA-Scaffolded Synergistic Catalysis

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UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae

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TTcof1 haploinsufficiency promotes early T cell precursor-like leukemia in NrasQ61R/+ mice

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The molecular and metabolic program for adaptation of white adipocytes to cool physiologic temperatures

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PKM2-TMEM33 axis regulates lipid homeostasis in cancer cells by controlling SCAP stability

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Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy

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A multi-omic investigation of male lower urinary tract symptoms: Potential role for JC virus

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SDH Subunit C Regulates Muscle Oxygen Consumption and Fatigability in an Animal Model of Pulmonary Emphysema

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DiLeuPMP: a multiplexed isobaric labeling method for quantitative analysis of O-glycans

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Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway

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Proteome-wide and matrisome-specific alterations during human pancreas development and maturation

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A Deep Analysis of the Proteomic and Phosphoproteomic Alterations that Occur in Skeletal Muscle after the Onset of Immobilization

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Defining intermediates and redundancies in coenzyme Q precursor biosynthesis

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Pilot Proteomic Analysis of Cerebrospinal Fluid in Alzheimer’s Disease

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Unique inflammatory profile is associated with higher SARS-CoV-2 acute respiratory distress syndrome (ARDS) mortality

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Metabolomic Biomarkers Differentiate Soy Sauce Freshness under
Conditions of Accelerated Storage

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Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

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Mapping of the contraction-induced phosphoproteome identifies TRIM28 as a significant regulator of skeletal muscle size and function

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PCarbomer-based adjuvant elicits CD8 T-cell immunity by inducing a distinct metabolic state in cross-presenting dendritic cells

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Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation

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Large-Scale Multi-omic Analysis of COVID-19 Severity

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Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis

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A large-scale genome–lipid association map guides lipid identification

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Survival Following Traumatic Brain Injury in Drosophila Is Increased by Heterozygosity for a Mutation of the NF-κB Innate Immune Response Transcription Factor Relish

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Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer

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Quantitative shotgun proteome analysis by direct infusion

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Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration

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Integrated Label-Free and 10-plex DiLeu Isobaric Tag Quantitative Methods for Profiling Changes in the Mouse Hypothalamic Neuropeptidome and Proteome: Assessment of the Impact of the Gut Microbiome

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Optical Fiber-Enabled Photoactivation of Peptides and Proteins

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Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD)

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Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

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Mass Defect-based DiLeu Tagging for Multiplexed Data-Independent Acquisition

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Highly multiplexed quantitative proteomic and phosphoproteomic analyses in vascular smooth muscle cell dedifferentiation

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Isobaric labeling strategy utilizing 4-plex N,N-dimethyl leucine (DiLeu) tags reveals proteomic changes induced by chemotherapy in cerebrospinal fluid of children with B-cell acute lymphoblastic leukemia

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Established biomarkers of COPD reflect skeletal muscle integrity’s response to exercise in an animal model of pulmonary emphysema

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Urinary metabolomic and proteomic analyses in a mouse model of prostatic inflammation

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21-plex DiLeu Isobaric Tags for High-throughput Quantitative Proteomics

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Tailoring a Global Iron Regulon to a Uropathogen

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Spatiotemporal proteomics reveals the molecular consequences of hormone treatment in a mouse model of lower urinary tract dysfunction

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In utero and lactational 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure exacerbates urinary dysfunction in hormone-treated C57BL/6J mice…

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Proteomic modulation in the dorsal spinal cord following spinal cord stimulation therapy in an in vivo neuropathic pain model

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Quantitative Capillary Zone Electrophoresis-Mass Spectrometry Reveals the N-glycome Developmental Plan during Vertebrate Embryogenesis

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Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogene

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Ribonucleic acid sequence characterization by negative electron transfer dissociation mass spectrometry

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A Genetic Toggle for Chemical Control of Individual Plk1 Substrates

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The Genetic Basis of Aneuploidy Tolerance in Wild Yeast

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High-Resolution Enabled 5-plex Mass Defect-based N,N-Dimethyl Leucine Tags for Quantitative Proteomics

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In-depth Quantification of Extracellular Matrix Proteins from Human Pancreas

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IL13-driven pulmonary emphysema leads to skeletal muscle dysfunction attenuated by endurance exercise

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A Strategy for Discovery and Verification of Candidate Biomarkers in Cerebrospinal Fluid of Preclinical Alzheimer’s Disease

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Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts

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High CO2 down-regulates skeletal muscle protein anabolism via AMPKα2-mediated depressed ribosomal biogenesis

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Metandem: An online software tool for mass spectrometry-basedisobaric labeling metabolomics

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Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis

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Polo-like Kinase 4 Maintains Centriolar Satellite Integrity By Phosphorylation Of Centrosomal Protein 131 (CEP131)

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Accelerating Lipidomic Method Development through in Silico Simulation

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Acetyl-CoA Flux Regulates the proteome and Acetyl-Proteome to Maintain Intracellular Metabolic Crosstalk

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Metabolic Remodeling During Biofilm Development of Bacillus Subtilis

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Maximizing Tandem MS Acquisition Rates for Shotgun Proteomics

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Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry Produces Over 4400 Phosphopeptide Identifications from 220 ng Sample

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Interactive Peptide Spectral Annotator: A Versatile Web-Based Tool for Proteomic Applications

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Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics

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Quantitative Proteomics for Analyses of Multiple Samples in Parallel with Chemical Perturbation

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Quantitative Proteomic Analysis of a Genetically Induced Prostate Inflammation Mouse Model via Custom 4-plex DiLeu Isobaric Labeling

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S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability of cancer stem cells

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Coenzyme Q proteins assemble in a substrate-dependent manner at ER-mitochondria contacts

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Proteomic Atlas of the Human Brain in Alzheimer’s Disease

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GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism

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Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries

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An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis

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Capturing Site-Specific Heterogeneity With Large-Scale N-Glycoproteome Analysis

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MS-Helios: A Circos Wrapper To Visualize Multi-Omic Datasets

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Systems Analyses Reveal Physiological Roles and Genetic Regulators of Liver Lipid Species

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Genetic Regulation of Plasma Lipid Species and Their Association with Metabolic Phenotypes

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The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins

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Single Shot Electrophoresis-Mass Spectrometry Produces Over 27,000 Peptide and Nearly 4,400 Protein Identifications

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The cellular economy of the Saccharomyces cerevisiae zinc proteome

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Islet proteomics reveals genetic variation in dopamine production resulting in altered insulin secretion

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The GIS2 Gene Is Repressed by a Zinc-Regulated Bicistronic RNA in Saccharomyces cerevisiae

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Ultra-high pressure packing of capillary columns enhances depth of shotgun proteomic

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Comprehensive single-shot proteomics with faims

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5-plex Mass Defect-based N,N-Dimethyl Leucine Tags for Proteomics

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In-depth Quantification of Extracellular Matrix Proteins from Human Pancreas

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HOTMAQ Quantification Method for Targeted Proteomics

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Increased N,N-Dimethyl Leucine Isobaric Tag Multiplexing

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Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

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ATM directs DNA damage responses and proteostasis via genetically separable pathways

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Phosphorylation dynamics dominate the regulated proteome during early xenopus development

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GATA factor-regulated Samd14 enhancer confers red blood cell regeneration in severe anemia

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Large-Scale Differentiation and Site Specific Discrimination of Hydroxyproline Isomers by EThcD Mass Spectrometry

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LipiDex: A software package for lipid identification

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Caloric restriction engages hepatic RNA processing mechanisms in rhesus monkeys

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Multi-omics reveal specific targets of the RNA-binding protein Puf3p in mitochondrial biogenesis

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Multi-omic mitoprotease profiling defines a role for Oct1p in coenzyme Q production

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An autophagy-independent role for ATG41 in sulfur metabolism during zinc deficiency

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Protocol: Proteome analysis with neutron-encoded isotope labeling

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A molecular portrait of de novo genes in yeasts

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A split-Abl kinase for direct activation in cells

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Relative quantitation of neuropeptides using N, N-dimethyl leucine isobaric tags

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Relative quantification of N-glycans

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Erythropoietin signaling regulates heme biosynthesis

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Ptc7p dephosphorylates select mitochondrial proteins to enhance metabolic function

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Multi-omics evidence for inheritance of energy pathways in red blood cells

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Proteomics needs better chromatography

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NeuCode proteomics reveals Bap1 regulation of metabolism

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Site-specific characterization and quantitation of N-glycopeptides (EThcD)

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PKM2 methylation by CARM1 activates aerobic glycolysis

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Improving data quality for isobaric tag-based quantitative proteomics

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NANOG Is Multiply Phosphorylated and Directly Modified by ERK2 and CDK1 In Vitro

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Expanding DiLeu to Eight Quantitative Channels

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DiLeu Allows for Multiplex Quantification of Urinary Proteins in Men

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Further Multiplexing with Quantitative Proteomics Enabled by Mass Defect and High Resolution MS

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Further Multiplexing with Quantitative Proteomics Enabled by Mass Defect and High Resolution MS

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Absolute Quantification with isotopic DiLeu (iDiLeu)

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Absolute Quantification with isotopic DiLeu (iDiLeu)

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Utilizing DiLeu for Quantifying Amine-Containing Metabolites

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Exploring Other Dimethylated Amino Acids

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A Combined Isobaric and Mass Difference Quantification Strategy (mdDiLeu)

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NeuCode Labeling for Top-Down Protein Quantification

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In Vivo Mouse Labeling in Just a Few Weeks Using NeuCode

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Multi-Plexed, Absolute Protein Quantification Using NeuCode

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NeuCode Offers a Route for Multi-Plexed Quantification with Data-Independent Acquisition 

 

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NeuCode Signatures Can be Used to Facilitate Peptide ID & De Noro Sequencing 

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Product Ion Annotation Using NeuCode

 

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A Simple Approach for NeuCode Chemical Labeling

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Neucode Labels for Metabolite Quantification

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Patents

    

Patents

Another key avenue to promoting developed technologies is patenting. Patent protection is often needed for an industrial partner to license a newly developed technology and make it commercially available. The patent protection allows them to invest their own capitol in taking the proof-of-concept work, done in the academic lab, and making the method robust and suitable for general use.  We work with the  Wisconsin Alumni Research Foundation (WARF), a private, nonprofit patent and licensing organization for the University of Wisconsin–Madison.  Several patents from the center’s current activities are pending.

Contact

For additional information about NCQBCS please send your contact details using the form below.
Note, if you are interested in training, please use the form on our training page.

Contact

For additional information about NCQBCS please send your contact details (name, institution, email) along with a short description of how we can help to laura[dot]vantoll[at]wisc[dot]edu.

Note, if you are interested in training, please use the form on our training page.

Coon Lab, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI
Li Lab, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI