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Lipidomics, Proteomics and Metabolomics

A major advantage of the -omics movement is the capacity to sample many features in a single experiment, establishing a global snapshot of the molecules that govern biology. Still, a fundamental challenge remains in establishing the biological relevance for features identified in these large-scale screens.

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.”

Lipidomics

Lipidomics

In discovery lipidomics, complex lipid mixtures are separated using high-flow separations, micro-electrospray ionization, and tandem MS. The primary goal is to produce fatty acid level lipid characterization for as many unique species as possible. By developing integrated lipid identification tools, such as LipiDex, we now routinely detect up to 1,000 such species per 30-min experiment.
Check out our custom Lipid identification software and web-based tools

LipiDex

A free and open-source software package which unifies all stages of LC-MS/MS lipid identification, empowering intelligent data filtering to greatly reduce manual result curation and increase identification confidence.

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LipiDex Library Forge
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LipidGenie

An interactive, query-able resource to facilitate lipid identification, provide evidence for gene function, and when queried for either lipid ID or gene ID, reveal acyl-chain specificity for ABHD1 and ABHD2, respectively.

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Advancing Liquid-phase Peptide Separations

Advancing Liquid-phase Peptide Separations

To increase sampling depth for the same unit time and keep up with modern MS/MS acquisition rates, we have developed technology for packing nano LC columns with smaller particles and at higher pressures.

We also explored capillary zone electrophoresis (CZE) and documented remarkable performance for both single-shot CZE and CZE coupled with our MS systems for shotgun proteomics. We are well-positioned not only to increase the speed and depth of analysis but also to make impactful contributions to applications demanding extreme sensitivity.

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Tools for Multi-omic Data Exploration

Tools for Multi-omic Data Exploration

To enable faster and simpler exploration of complex data sets we conceived and developed web-based data tools where researchers can upload project-specific data directly to a browser using generic spreadsheets. Check out our custom software and web-based tools

Argonaut

A simple, code-free, and user-friendly platform for creation of interactive data-hosting websites. Argonaut conducts real-time statistical analysis of measured bio molecules,visualizes data using popular plots, and can be securely shared with and explored by collaborators across the globe.

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COVID-19 Multi-Omics Dashboard

A web-based tool enabling interactive exploration of published data and a machine learning approach for prediction of COVID-19 severity.

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Metandem

A free data analysis platform for mass spectrometry-based isobaric labeling metabolomics. It allows users to upload and process MS or hyphenated MS data files for isobaric-labeling-based quantitative and qualitative metabolomics analyses, including feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, parameter optimization, median normalization, and statistical analysis. Results can be downloaded or visualized online.

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Technology – Training Link

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Fast and sensitive proteome analysis

Fast and Sensitive Proteome Analysis

In a 2014 publication, we described a method for the near complete analysis of the yeast proteome in just one hour. However, achieving a comparable coverage of mammalian proteomes requires spending hours or even days of analysis time. Improved peptide separation technologies, along with advancements in MS hardware, will be essential for achieving this goal. We and others are actively working towards improving the speed, depth, and sensitivity at which proteomes can be measured.

Interactive Peptide Spectral Annotator (IPSA)

A web-based utility for the annotation of shotgun proteomics mass spectrometry data. IPSA generates interactive visualizations from bottom-up proteomic workflows. These visualizations can be exported in SVG format and annotated fragment ions and additional metrics can be exported in CSV format.

Manuscript Get the Software

MS-Helios

An easy to use command line tool with multiple built-in data processing functions, allowing non-expert users to construct circular proteome maps. MS-Helios automatically generates data and configuration files to create high quality and publishable circular plots with Circos.

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Compass

A free and open-source software pipeline for high-throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. COMPASS supports all functions required for searching proteomics data including: FASTA database creation, peptide-spectral matching, calculation of false discovery rates, and protein grouping.

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-Omics Publication Library

-Omics Publication Library

 

Lipidomics

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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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Accelerating Lipidomic Method Development through in Silico Simulation

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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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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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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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LipiDex: A software package for lipid identification

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

Proteomics

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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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Pilot Proteomic Analysis of Cerebrospinal Fluid in Alzheimer’s Disease

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

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

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Maximizing Tandem MS Acquisition Rates for Shotgun Proteomics

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

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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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Proteomic Atlas of the Human Brain in Alzheimer’s Disease

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

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

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HOTMAQ Quantification Method for Targeted Proteomics

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Proteomics needs better chromatography

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NeuCode proteomics reveals Bap1 regulation of metabolism

Multi-omics

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

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Urinary Amine Metabolomics Characterization with Custom 12-plex Isobaric DiLeu Labeling

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

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Tailoring a Global Iron Regulon to a Uropathogen

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

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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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An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis

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

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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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Relative quantification of N-glycans

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

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A Combined Isobaric and Mass Difference Quantification Strategy (mdDiLeu)

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, 425 Henry Mall, Madison, WI
Li Lab, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI
Pagliarini Lab, Washington University School of Medicine, 4523 Clayton Ave, St. Louis, MO