Richard D. Smith Biography Publications JoVE Articles Richard D. Smith has not added a biography. If you are Richard D. Smith and would like to personalize this page please email our Author Liaison for assistance. Publications Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics Cancer Journal (Sudbury, Mass.). May/Jun, 2018 | Pubmed ID: 29794536 An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies International Journal of Mass Spectrometry. Apr, 2018 | Pubmed ID: 29706793 QC-ART: A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data Molecular & Cellular Proteomics : MCP. 04, 2018 | Pubmed ID: 29666158 Subnanogram Proteomics: Impact of LC Column Selection, MS Instrumentation and Data Analysis Strategy on Proteome Coverage for Trace Samples International Journal of Mass Spectrometry. Apr, 2018 | Pubmed ID: 29576737 Characterization of the Ovarian Tumor Peptidome Vitamins and Hormones. 2018 | Pubmed ID: 29544642 Evaluating Lipid Mediator Structural Complexity Using Ion Mobility Spectrometry Combined with Mass Spectrometry Bioanalysis. Mar, 2018 | Pubmed ID: 29494212 Nanodroplet Processing Platform for Deep and Quantitative Proteome Profiling of 10-100 Mammalian Cells Nature Communications. 02, 2018 | Pubmed ID: 29491378 High-throughput Serum Proteomics for the Identification of Protein Biomarkers of Mortality in Older Men Aging Cell. Apr, 2018 | Pubmed ID: 29399943 MERS-CoV and H5N1 Influenza Virus Antagonize Antigen Presentation by Altering the Epigenetic Landscape Proceedings of the National Academy of Sciences of the United States of America. Jan, 2018 | Pubmed ID: 29339515 A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer Using Structures for Lossless Ion Manipulations Journal of the American Society for Mass Spectrometry. Feb, 2018 | Pubmed ID: 29235041 Recent Advances in Lipid Separations and Structural Elucidation Using Mass Spectrometry Combined with Ion Mobility Spectrometry, Ion-molecule Reactions and Fragmentation Approaches Current Opinion in Chemical Biology. Feb, 2018 | Pubmed ID: 29223060 Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses Analytical Chemistry. Jan, 2018 | Pubmed ID: 29220163 A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements Analytical Chemistry. Jan, 2018 | Pubmed ID: 29161511 Pyroptosis by Caspase11/4-gasdermin-D Pathway in Alcoholic Hepatitis in Mice and Patients Hepatology (Baltimore, Md.). May, 2018 | Pubmed ID: 29108122 A Global Survey of ATPase Activity in Asexual Blood Stages and Gametocytes Molecular & Cellular Proteomics : MCP. Jan, 2018 | Pubmed ID: 29079720 Towards Discovery and Targeted Peptide Biomarker Detection Using NanoESI-TIMS-TOF MS Journal of the American Society for Mass Spectrometry. May, 2018 | Pubmed ID: 28889248 A Structural Examination and Collision Cross Section Database for over 500 Metabolites and Xenobiotics Using Drift Tube Ion Mobility Spectrometry Chemical Science. Nov, 2017 | Pubmed ID: 29568436 Multiplexed Targeted Mass Spectrometry Assays for Prostate Cancer-associated Urinary Proteins Oncotarget. Nov, 2017 | Pubmed ID: 29254211 Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis Cell Host & Microbe. Dec, 2017 | Pubmed ID: 29154144 Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues Journal of Proteome Research. Dec, 2017 | Pubmed ID: 29124938 LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers Methods in Molecular Biology (Clifton, N.J.). Nov, 2017 | Pubmed ID: 29116567 Quantification of Mutant SPOP Proteins in Prostate Cancer Using Mass Spectrometry-based Targeted Proteomics Journal of Translational Medicine. Aug, 2017 | Pubmed ID: 28810879 Informed-Proteomics: Open-source Software Package for Top-down Proteomics Nature Methods. Sep, 2017 | Pubmed ID: 28783154 Advances in Microscale Separations Towards Nanoproteomics Applications Journal of Chromatography. A. Nov, 2017 | Pubmed ID: 28765000 An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements Analytical Chemistry. Sep, 2017 | Pubmed ID: 28763190 Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues Analytical Chemistry. Sep, 2017 | Pubmed ID: 28724286 Targeted Proteomic Assays for Quantitation of Proteins Identified by Proteogenomic Analysis of Ovarian Cancer Scientific Data. 07, 2017 | Pubmed ID: 28722704 Changes of Protein Turnover in Aging Molecular & Cellular Proteomics : MCP. Sep, 2017 | Pubmed ID: 28679685 Quantitative Proteomics Identifies Altered O-GlcNAcylation of Structural, Synaptic and Memory-associated Proteins in Alzheimer's Disease The Journal of Pathology. Sep, 2017 | Pubmed ID: 28657654 Distinguishing D- and L-aspartic and Isoaspartic Acids in Amyloid β Peptides with Ultrahigh Resolution Ion Mobility Spectrometry Chemical Communications (Cambridge, England). Jul, 2017 | Pubmed ID: 28654112 Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in MBio. 06, 2017 | Pubmed ID: 28634240 Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions Journal of the American Society for Mass Spectrometry. Jul, 2017 | Pubmed ID: 28560562 PIXiE: an Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation Using Global Data Association Bioinformatics (Oxford, England). Sep, 2017 | Pubmed ID: 28505286 Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM) Analytical Chemistry. Jun, 2017 | Pubmed ID: 28497957 2016 ASMS Workshop Review: Next Generation LC/MS: Critical Insights and Future Perspectives Journal of the American Society for Mass Spectrometry. Jul, 2017 | Pubmed ID: 28417304 Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS Using Structures for Lossless Ion Manipulations Analytical Chemistry. Apr, 2017 | Pubmed ID: 28332832 Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research. Jul, 2017 | Pubmed ID: 28316103 Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses Annual Review of Analytical Chemistry (Palo Alto, Calif.). Jun, 2017 | Pubmed ID: 28301728 Structural Elucidation of Cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry The Journal of Physical Chemistry Letters. Apr, 2017 | Pubmed ID: 28267339 New Frontiers for Mass Spectrometry Based Upon Structures for Lossless Ion Manipulations The Analyst. Mar, 2017 | Pubmed ID: 28262893 Phycobilisome Truncation Causes Widespread Proteome Changes in Synechocystis Sp. PCC 6803 PloS One. 2017 | Pubmed ID: 28253354 Ion Elevators and Escalators in Multilevel Structures for Lossless Ion Manipulations Analytical Chemistry. Feb, 2017 | Pubmed ID: 28208272 LIQUID: An-open Source Software for Identifying Lipids in LC-MS/MS-based Lipidomics Data Bioinformatics (Oxford, England). Jun, 2017 | Pubmed ID: 28158427 Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations International Journal of Molecular Sciences. Jan, 2017 | Pubmed ID: 28106768 MPLEx: a Method for Simultaneous Pathogen Inactivation and Extraction of Samples for Multi-omics Profiling The Analyst. Jan, 2017 | Pubmed ID: 28091625 High-resolution Ultrahigh-pressure Long Column Reversed-phase Liquid Chromatography for Top-down Proteomics Journal of Chromatography. A. May, 2017 | Pubmed ID: 28077236 Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation Analytical Chemistry. Jan, 2017 | Pubmed ID: 27966901 Comparing Identified and Statistically Significant Lipids and Polar Metabolites in 15-year Old Serum and Dried Blood Spot Samples for Longitudinal Studies Rapid Communications in Mass Spectrometry : RCM. Mar, 2017 | Pubmed ID: 27958645 Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go? Bioanalysis. Jan, 2017 | Pubmed ID: 27921453 Position-dependent Termination and Widespread Obligatory Frameshifting in Euplotes Translation Nature Structural & Molecular Biology. 01, 2017 | Pubmed ID: 27870834 Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction Molecular & Cellular Proteomics : MCP. Jan, 2017 | Pubmed ID: 27836980 Enhancing Glycan Isomer Separations with Metal Ions and Positive and Negative Polarity Ion Mobility Spectrometry-mass Spectrometry Analyses Analytical and Bioanalytical Chemistry. Jan, 2017 | Pubmed ID: 27604268 SPE-IMS-MS: An Automated Platform for Sub-sixty Second Surveillance of Endogenous Metabolites and Xenobiotics in Biofluids Clinical Mass Spectrometry (Del Mar, Calif.). Dec, 2016 | Pubmed ID: 29276770 Ion Mobility Separations of Isomers Based Upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry ChemistrySelect. Jul, 2016 | Pubmed ID: 28936476 Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform Analytical Chemistry. Dec, 2016 | Pubmed ID: 28193022 An Efficient Method for Native Protein Purification in the Selected Range from Prostate Cancer Tissue Digests Chinese Clinical Oncology. Dec, 2016 | Pubmed ID: 28061542 Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples Scientific Reports. Dec, 2016 | Pubmed ID: 28004771 Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming Analytical Chemistry. Dec, 2016 | Pubmed ID: 27934097 Proteome Remodeling in Response to Sulfur Limitation in " Pelagibacter Ubique" MSystems. Jul-Aug, 2016 | Pubmed ID: 27822545 MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses MSystems. May-Jun, 2016 | Pubmed ID: 27822525 Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece Sp. Strain ATCC 51142 Applied and Environmental Microbiology. Dec, 2016 | Pubmed ID: 27742679 Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations Analytical Chemistry. Oct, 2016 | Pubmed ID: 27715008 The Fungal Cultivar of Leaf-cutter Ants Produces Specific Enzymes in Response to Different Plant Substrates Molecular Ecology. Nov, 2016 | Pubmed ID: 27696597 Simultaneous Proteomic Discovery and Targeted Monitoring Using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Molecular & Cellular Proteomics : MCP. Dec, 2016 | Pubmed ID: 27670688 FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans Cell Reports. 09, 2016 | Pubmed ID: 27626670 Hypothalamic Transcriptomes of 99 Mouse Strains Reveal Trans EQTL Hotspots, Splicing QTLs and Novel Non-coding Genes ELife. Sep, 2016 | Pubmed ID: 27623010 The Abundant Marine Bacterium Pelagibacter Simultaneously Catabolizes Dimethylsulfoniopropionate to the Gases Dimethyl Sulfide and Methanethiol Nature Microbiology. 05, 2016 | Pubmed ID: 27573103 Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 M Serpentine Path Length Structures for Lossless Ion Manipulations Module Analytical Chemistry. Sep, 2016 | Pubmed ID: 27531027 Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations Analytical Chemistry. Sep, 2016 | Pubmed ID: 27479234 Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas Pusilla PloS One. 2016 | Pubmed ID: 27434306 Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the EGFR-MAPK Pathway Science Signaling. 07, 2016 | Pubmed ID: 27405981 Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer Cell. Jul, 2016 | Pubmed ID: 27372738 Advances in Targeted Proteomics and Applications to Biomedical Research Proteomics. 08, 2016 | Pubmed ID: 27302376 Mining the Human Urine Proteome for Monitoring Renal Transplant Injury Kidney International. 06, 2016 | Pubmed ID: 27165815 A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation Journal of the American Society for Mass Spectrometry. Jul, 2016 | Pubmed ID: 27098413 Spatial Ion Peak Compression and Its Utility in Ion Mobility Spectrometry Journal of the American Society for Mass Spectrometry. Jun, 2016 | Pubmed ID: 27052738 Evidence-based Green Algal Genomics Reveals Marine Diversity and Ancestral Characteristics of Land Plants BMC Genomics. Mar, 2016 | Pubmed ID: 27029936 Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations The New England Journal of Medicine. Apr, 2016 | Pubmed ID: 27007809 Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations The Journal of Clinical Endocrinology and Metabolism. 05, 2016 | Pubmed ID: 27007693 The Current State of the Art of Quantitative Phosphoproteomics and Its Applications to Diabetes Research Expert Review of Proteomics. 2016 | Pubmed ID: 26960075 Comparative Proteomic Analysis of Desulfotomaculum Reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium Frontiers in Microbiology. 2016 | Pubmed ID: 26925055 Contributions of Immunoaffinity Chromatography to Deep Proteome Profiling of Human Biofluids Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. May, 2016 | Pubmed ID: 26868616 Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS Methods in Molecular Biology (Clifton, N.J.). 2016 | Pubmed ID: 26867748 Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays Methods in Molecular Biology (Clifton, N.J.). 2016 | Pubmed ID: 26867747 Integrated Omics Analysis of Pathogenic Host Responses During Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism Cell Host & Microbe. Feb, 2016 | Pubmed ID: 26867183 Systematic Survey of Serine Hydrolase Activity in Mycobacterium Tuberculosis Defines Changes Associated with Persistence Cell Chemical Biology. Feb, 2016 | Pubmed ID: 26853625 Surprising Impact of Remote Groups on the Folding--unfolding and Dimer-chain Equilibria of Bifunctional H-bonding Unimers Chemical Communications (Cambridge, England). Mar, 2016 | Pubmed ID: 26830456 Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations Analytical Chemistry. Feb, 2016 | Pubmed ID: 26752262 SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities Endocrinology. Mar, 2016 | Pubmed ID: 26745641 Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry The Analyst. Mar, 2016 | Pubmed ID: 26734689 Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays Clinical Chemistry. Jan, 2016 | Pubmed ID: 26719571 SerpinB1 Promotes Pancreatic β Cell Proliferation Cell Metabolism. Jan, 2016 | Pubmed ID: 26701651 Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function During Nanoparticle-Induced Oxidative Stress ACS Nano. Jan, 2016 | Pubmed ID: 26700264 Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts Journal of Proteome Research. Mar, 2016 | Pubmed ID: 26653538 An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer Molecular & Cellular Proteomics : MCP. Mar, 2016 | Pubmed ID: 26631509 The Clinical Impact of Recent Advances in LC-MS for Cancer Biomarker Discovery and Verification Expert Review of Proteomics. 2016 | Pubmed ID: 26581546 Evaluating Models of Cellulose Degradation by Fibrobacter Succinogenes S85 PloS One. 2015 | Pubmed ID: 26629814 Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations Analytical Chemistry. Nov, 2015 | Pubmed ID: 26510005 Advancing Understanding of Microbial Bioenergy Conversion Processes by Activity-based Protein Profiling Biotechnology for Biofuels. 2015 | Pubmed ID: 26413155 Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus Gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants PloS One. 2015 | Pubmed ID: 26317212 The Pacific Northwest National Laboratory Library of Bacterial and Archaeal Proteomic Biodiversity Scientific Data. 2015 | Pubmed ID: 26306205 Ion Manipulations in Structures for Lossless Ion Manipulations (SLIM): Computational Evaluation of a 90° Turn and a Switch The Analyst. Oct, 2015 | Pubmed ID: 26289106 Preserved DNA Damage Checkpoint Pathway Protects Against Complications in Long-Standing Type 1 Diabetes Cell Metabolism. Aug, 2015 | Pubmed ID: 26244933 Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data Molecular & Cellular Proteomics : MCP. Sep, 2015 | Pubmed ID: 26217018 Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer International Journal of Mass Spectrometry. Feb, 2015 | Pubmed ID: 26185483 Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics Journal of Proteome Research. Aug, 2015 | Pubmed ID: 26151086 Identification of Salmonella Typhimurium Deubiquitinase SseL Substrates by Immunoaffinity Enrichment and Quantitative Proteomic Analysis Journal of Proteome Research. Sep, 2015 | Pubmed ID: 26147956 Enhancing Biological Analyses with Three Dimensional Field Asymmetric Ion Mobility, Low Field Drift Tube Ion Mobility and Mass Spectrometry (μFAIMS/IMS-MS) Separations The Analyst. Oct, 2015 | Pubmed ID: 26140287 Lipidomic and Proteomic Analysis of Caenorhabditis Elegans Lipid Droplets and Identification of ACS-4 As a Lipid Droplet-associated Protein Biochimica Et Biophysica Acta. Oct, 2015 | Pubmed ID: 26121959 Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadrupole Mass Spectrometry Analytical Chemistry. Jul, 2015 | Pubmed ID: 26107611 Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations Proteomics. Aug, 2015 | Pubmed ID: 26046661 An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics Journal of the American Society for Mass Spectrometry. Dec, 2015 | Pubmed ID: 26015166 Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations Analytical Chemistry. Jun, 2015 | Pubmed ID: 25971536 Proteomic Analysis Reveals Down-regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus Virology. Sep, 2015 | Pubmed ID: 25965799 Analytical Platform Evaluation for Quantification of ERG in Prostate Cancer Using Protein and MRNA Detection Methods Journal of Translational Medicine. Feb, 2015 | Pubmed ID: 25889691 Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-based Label-free Global Proteomics Journal of Proteome Research. May, 2015 | Pubmed ID: 25855118 Synechococcus Elongatus UTEX 2973, a Fast Growing Cyanobacterial Chassis for Biosynthesis Using Light and CO₂ Scientific Reports. Jan, 2015 | Pubmed ID: 25633131 Improved Ion Optics for Introduction of Ions into a 9.4-T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Journal of Mass Spectrometry : JMS. Jan, 2015 | Pubmed ID: 25601704 Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells Without Affinity Enrichment Analytical Chemistry. Jan, 2015 | Pubmed ID: 25517423 Changes in Protein Expression Across Laboratory and Field Experiments in Geobacter Bemidjiensis Journal of Proteome Research. Mar, 2015 | Pubmed ID: 25496566 Rectangular Ion Funnel: a New Ion Funnel Interface for Structures for Lossless Ion Manipulations Analytical Chemistry. Jan, 2015 | Pubmed ID: 25409343 Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes Journal of Proteome Research. Jan, 2015 | Pubmed ID: 25350482 On the Ionization and Ion Transmission Efficiencies of Different ESI-MS Interfaces Journal of the American Society for Mass Spectrometry. Jan, 2015 | Pubmed ID: 25267087 A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection Scientific Data. 2014 | Pubmed ID: 25977790 Perturbations in the Urinary Exosome in Transplant Rejection Frontiers in Medicine. 2014 | Pubmed ID: 25593928 Transcriptomic and Proteomic Dynamics in the Metabolism of a Diazotrophic Cyanobacterium, Cyanothece Sp. PCC 7822 During a Diurnal Light-dark Cycle BMC Genomics. Dec, 2014 | Pubmed ID: 25547186 Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Molecular & Cellular Proteomics : MCP. Dec, 2014 | Pubmed ID: 25433089 HAM-5 Functions As a MAP Kinase Scaffold During Cell Fusion in Neurospora Crassa PLoS Genetics. Nov, 2014 | Pubmed ID: 25412208 Proteomic Approaches for Site-specific O-GlcNAcylation Analysis Bioanalysis. 2014 | Pubmed ID: 25411699 Brain Insulin Lowers Circulating BCAA Levels by Inducing Hepatic BCAA Catabolism Cell Metabolism. Nov, 2014 | Pubmed ID: 25307860 Antibody-independent Targeted Quantification of TMPRSS2-ERG Fusion Protein Products in Prostate Cancer Molecular Oncology. Oct, 2014 | Pubmed ID: 25266362 Proteogenomic Strategies for Identification of Aberrant Cancer Peptides Using Large-scale Next-generation Sequencing Data Proteomics. Dec, 2014 | Pubmed ID: 25263569 Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM) Journal of the American Society for Mass Spectrometry. Nov, 2014 | Pubmed ID: 25257188 High Sensitivity Combined with Extended Structural Coverage of Labile Compounds Via Nanoelectrospray Ionization at Subambient Pressures Analytical Chemistry. Oct, 2014 | Pubmed ID: 25222651 Mobility-resolved Ion Selection in Uniform Drift Field Ion Mobility Spectrometry/mass Spectrometry: Dynamic Switching in Structures for Lossless Ion Manipulations Analytical Chemistry. Oct, 2014 | Pubmed ID: 25222548 Microscale Depletion of High Abundance Proteins in Human Biofluids Using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid Analytical and Bioanalytical Chemistry. Nov, 2014 | Pubmed ID: 25192788 Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations Analytical Chemistry. Sep, 2014 | Pubmed ID: 25152178 Experimental Evaluation and Optimization of Structures for Lossless Ion Manipulations for Ion Mobility Spectrometry with Time-of-flight Mass Spectrometry Analytical Chemistry. Sep, 2014 | Pubmed ID: 25152066 Expediting SRM Assay Development for Large-scale Targeted Proteomics Experiments Journal of Proteome Research. Oct, 2014 | Pubmed ID: 25145539 A Method to Determine Lysine Acetylation Stoichiometries International Journal of Proteomics. 2014 | Pubmed ID: 25143833 Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Molecular & Cellular Proteomics : MCP. Aug, 2014 | Pubmed ID: 25129695 Polysialylated N-glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations, and Electrospray Ionization-mass Spectrometry Analytical Chemistry. Sep, 2014 | Pubmed ID: 25118826 Proteome-wide Light/dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-specific Redox Proteomics Molecular & Cellular Proteomics : MCP. Dec, 2014 | Pubmed ID: 25118246 Characterization of Protein Redox Dynamics Induced During Light-to-dark Transitions and Nutrient Limitation in Cyanobacteria Frontiers in Microbiology. 2014 | Pubmed ID: 25071738 The Fungus Gardens of Leaf-cutter Ants Undergo a Distinct Physiological Transition During Biomass Degradation Environmental Microbiology Reports. Aug, 2014 | Pubmed ID: 24992538 Detecting Differential Protein Expression in Large-scale Population Proteomics Bioinformatics (Oxford, England). Oct, 2014 | Pubmed ID: 24928210 GlyQ-IQ: Glycomics Quintavariate-informed Quantification with High-performance Computing and GlycoGrid 4D Visualization Analytical Chemistry. Jul, 2014 | Pubmed ID: 24881670 Proteomic Profiles of Five Strains of Oxygenic Photosynthetic Cyanobacteria of the Genus Cyanothece Journal of Proteome Research. Jul, 2014 | Pubmed ID: 24846609 Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-stimulated Gene Responses MBio. May, 2014 | Pubmed ID: 24846384 Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-mass Spectrometry Measurements Journal of the American Society for Mass Spectrometry. Dec, 2014 | Pubmed ID: 24796262 Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel Trap Analytical Chemistry. Jun, 2014 | Pubmed ID: 24786390 Ischemia in Tumors Induces Early and Sustained Phosphorylation Changes in Stress Kinase Pathways but Does Not Affect Global Protein Levels Molecular & Cellular Proteomics : MCP. Jul, 2014 | Pubmed ID: 24719451 Cytomegalovirus Pp65 Limits Dissemination but is Dispensable for Persistence The Journal of Clinical Investigation. May, 2014 | Pubmed ID: 24691437 Characterization of Individual Mouse Cerebrospinal Fluid Proteomes Proteomics. May, 2014 | Pubmed ID: 24677814 Improving the Sensitivity of Mass Spectrometry by Using a New Sheath Flow Electrospray Emitter Array at Subambient Pressures Journal of the American Society for Mass Spectrometry. Dec, 2014 | Pubmed ID: 24676894 High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model PloS One. 2014 | Pubmed ID: 24642900 Honoring Dr. Jean H. Futrell Journal of the American Society for Mass Spectrometry. May, 2014 | Pubmed ID: 24627182 Signatures for Mass Spectrometry Data Quality Journal of Proteome Research. Apr, 2014 | Pubmed ID: 24611607 Metabolic Reprogramming During Purine Stress in the Protozoan Pathogen Leishmania Donovani PLoS Pathogens. Feb, 2014 | Pubmed ID: 24586154 LC-MS Proteomics Analysis of the Insulin/IGF-1-deficient Caenorhabditis Elegans Daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism Journal of Proteome Research. Apr, 2014 | Pubmed ID: 24555535 Organelle-specific Activity-based Protein Profiling in Living Cells Angewandte Chemie (International Ed. in English). Mar, 2014 | Pubmed ID: 24505022 Implementation of Dipolar Resonant Excitation for Collision Induced Dissociation with Ion Mobility/time-of-flight MS Journal of the American Society for Mass Spectrometry. Apr, 2014 | Pubmed ID: 24470195 Automated Data Extraction from in Situ Protein-stable Isotope Probing Studies Journal of Proteome Research. Mar, 2014 | Pubmed ID: 24467184 Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry Molecular & Cellular Proteomics : MCP. Apr, 2014 | Pubmed ID: 24403597 Differential Ion Mobility Separations in Up to 100% Helium Using Microchips Journal of the American Society for Mass Spectrometry. Mar, 2014 | Pubmed ID: 24402673 Fast and Accurate Database Searches with MS-GF+Percolator Journal of Proteome Research. Feb, 2014 | Pubmed ID: 24344789 Resin-assisted Enrichment of Thiols As a General Strategy for Proteomic Profiling of Cysteine-based Reversible Modifications Nature Protocols. Jan, 2014 | Pubmed ID: 24336471 The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics Molecular & Cellular Proteomics : MCP. Feb, 2014 | Pubmed ID: 24335474 Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-assisted Enrichment and Isobaric Labeling Free Radical Biology & Medicine. Feb, 2014 | Pubmed ID: 24333276 Accounting for Population Variation in Targeted Proteomics Journal of Proteome Research. Jan, 2014 | Pubmed ID: 24320210 Phosphate-containing Polyethylene Glycol Polymers Prevent Lethal Sepsis by Multidrug-resistant Pathogens Antimicrobial Agents and Chemotherapy. 2014 | Pubmed ID: 24277029 A Highly Sensitive Targeted Mass Spectrometric Assay for Quantification of AGR2 Protein in Human Urine and Serum Journal of Proteome Research. Feb, 2014 | Pubmed ID: 24251762 Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium ACS Chemical Biology. Jan, 2014 | Pubmed ID: 24168666 Picoelectrospray Ionization Mass Spectrometry Using Narrow-bore Chemically Etched Emitters Journal of the American Society for Mass Spectrometry. Jan, 2014 | Pubmed ID: 24122304 The Succinated Proteome Mass Spectrometry Reviews. Mar-Apr, 2014 | Pubmed ID: 24115015 Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry International Journal of Mass Spectrometry. Nov, 2013 | Pubmed ID: 25089116 Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS Mass Spectrometry (Tokyo, Japan). 2013 | Pubmed ID: 24349930 Proteomic and Transcriptomic Analyses of "Candidatus Pelagibacter Ubique" Describe the First PII-independent Response to Nitrogen Limitation in a Free-living Alphaproteobacterium MBio. Nov, 2013 | Pubmed ID: 24281717 Connecting Genomic Alterations to Cancer Biology with Proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium Cancer Discovery. Oct, 2013 | Pubmed ID: 24124232 Activity-based Protein Profiling of Secreted Cellulolytic Enzyme Activity Dynamics in Trichoderma Reesei QM6a, NG14, and RUT-C30 Molecular BioSystems. Dec, 2013 | Pubmed ID: 24121482 Impact of Alg3 Gene Deletion on Growth, Development, Pigment Production, Protein Secretion, and Functions of Recombinant Trichoderma Reesei Cellobiohydrolases in Aspergillus Niger Fungal Genetics and Biology : FG & B. Dec, 2013 | Pubmed ID: 24076077 Gray Matter is Targeted in First-attack Multiple Sclerosis PloS One. 2013 | Pubmed ID: 24039694 LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility and Mass Spectrometry Features in Complex Datasets Bioinformatics (Oxford, England). Nov, 2013 | Pubmed ID: 24008421 Long-gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis Analytical Chemistry. Oct, 2013 | Pubmed ID: 24004026 Reduced Insulin/insulin-like Growth Factor-1 Signaling and Dietary Restriction Inhibit Translation but Preserve Muscle Mass in Caenorhabditis Elegans Molecular & Cellular Proteomics : MCP. Dec, 2013 | Pubmed ID: 24002365 Comparative Phosphoproteomics Reveals Components of Host Cell Invasion and Post-transcriptional Regulation During Francisella Infection Molecular & Cellular Proteomics : MCP. Nov, 2013 | Pubmed ID: 23970565 A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses PloS One. 2013 | Pubmed ID: 23935999 Controlled Dispensing and Mixing of Pico- to Nanoliter Volumes Using On-demand Droplet-based Microfluidics Microfluidics and Nanofluidics. Jul, 2013 | Pubmed ID: 23935562 Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice BMC Systems Biology. Jul, 2013 | Pubmed ID: 23895213 Separation of Protein Conformers by Differential Ion Mobility in Hydrogen-rich Gases Analytical Chemistry. Jul, 2013 | Pubmed ID: 23855890 A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection PloS One. 2013 | Pubmed ID: 23840608 Capillary Isotachophoresis-nanoelectrospray Ionization-selected Reaction Monitoring MS Via a Novel Sheathless Interface for High Sensitivity Sample Quantification Analytical Chemistry. Aug, 2013 | Pubmed ID: 23789856 Amino Acid Treatment Enhances Protein Recovery from Sediment and Soils for Metaproteomic Studies Proteomics. Oct, 2013 | Pubmed ID: 23776032 Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing Analytical Chemistry. Jul, 2013 | Pubmed ID: 23772796 Targeted Quantification of Low Ng/mL Level Proteins in Human Serum Without Immunoaffinity Depletion Journal of Proteome Research. Jul, 2013 | Pubmed ID: 23763644 Protein Co-expression Network Analysis (ProCoNA) Journal of Clinical Bioinformatics. Jun, 2013 | Pubmed ID: 23724967 Top-down Proteomics Reveals a Unique Protein S-thiolation Switch in Salmonella Typhimurium in Response to Infection-like Conditions Proceedings of the National Academy of Sciences of the United States of America. Jun, 2013 | Pubmed ID: 23720318 Evaluation of Selected Binding Domains for the Analysis of Ubiquitinated Proteomes Journal of the American Society for Mass Spectrometry. Aug, 2013 | Pubmed ID: 23649778 Multi-omic Data Integration Links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response Molecular & Cellular Proteomics : MCP. Aug, 2013 | Pubmed ID: 23639857 Disparate Proteome Responses of Pathogenic and Nonpathogenic Aspergilli to Human Serum Measured by Activity-based Protein Profiling (ABPP) Molecular & Cellular Proteomics : MCP. Jul, 2013 | Pubmed ID: 23599423 Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling Proteomics. Clinical Applications. Aug, 2013 | Pubmed ID: 23589343 Leucoagaricus Gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-cutter Ant Fungus Gardens Applied and Environmental Microbiology. Jun, 2013 | Pubmed ID: 23584789 Salmonella Modulates Metabolism During Growth Under Conditions That Induce Expression of Virulence Genes Molecular BioSystems. Jun, 2013 | Pubmed ID: 23559334 Assigning Quantitative Function to Post-translational Modifications Reveals Multiple Sites of Phosphorylation That Tune Yeast Pheromone Signaling Output PloS One. 2013 | Pubmed ID: 23554854 Determination of Burn Patient Outcome by Large-scale Quantitative Discovery Proteomics Critical Care Medicine. Jun, 2013 | Pubmed ID: 23507713 Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis Journal of Proteome Research. May, 2013 | Pubmed ID: 23495885 Mixed-isotope Labeling with LC-IMS-MS for Characterization of Protein-protein Interactions by Chemical Cross-linking Journal of the American Society for Mass Spectrometry. Mar, 2013 | Pubmed ID: 23423792 MultiAlign: a Multiple LC-MS Analysis Tool for Targeted Omics Analysis BMC Bioinformatics. Feb, 2013 | Pubmed ID: 23398735 RNA Type III Secretion Signals That Require Hfq Journal of Bacteriology. May, 2013 | Pubmed ID: 23396917 Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells Journal of Virology. Apr, 2013 | Pubmed ID: 23365422 Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium Tuberculosis Chemistry & Biology. Jan, 2013 | Pubmed ID: 23352146 High-definition Differential Ion Mobility Spectrometry with Resolving Power Up to 500 Journal of the American Society for Mass Spectrometry. Jan, 2013 | Pubmed ID: 23345059 STEPS: a Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results Proteomics. Mar, 2013 | Pubmed ID: 23303698 Serum Proteomics Reveals Systemic Dysregulation of Innate Immunity in Type 1 Diabetes The Journal of Experimental Medicine. Jan, 2013 | Pubmed ID: 23277452 In-source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics Journal of Proteome Research. Feb, 2013 | Pubmed ID: 23268687 High-resolution Differential Ion Mobility Spectrometry of a Protein Analytical Chemistry. Jan, 2013 | Pubmed ID: 23244633 Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece Sp. Under Culture Conditions Resulting in Enhanced H₂ Production Applied and Environmental Microbiology. Feb, 2013 | Pubmed ID: 23204418 A Multi-omic Systems Approach to Elucidating Yersinia Virulence Mechanisms Molecular BioSystems. Jan, 2013 | Pubmed ID: 23147219 A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments Proteomics. Feb, 2013 | Pubmed ID: 23019139 Quantitative Site-specific Reactivity Profiling of S-nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry Free Radical Biology & Medicine. Dec, 2012 | Pubmed ID: 23277143 Normalization and Missing Value Imputation for Label-free LC-MS Analysis BMC Bioinformatics. 2012 | Pubmed ID: 23176322 Suite of Activity-based Probes for Cellulose-degrading Enzymes Journal of the American Chemical Society. Dec, 2012 | Pubmed ID: 23176123 Unexpected Diversity of Signal Peptides in Prokaryotes MBio. Nov, 2012 | Pubmed ID: 23169999 Ultrasensitive Sample Quantitation Via Selected Reaction Monitoring Using CITP/CZE-ESI-triple Quadrupole MS Analytical Chemistry. Dec, 2012 | Pubmed ID: 23140208 A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome Biology of Reproduction. Jun, 2012 | Pubmed ID: 23115268 Activity-based Protein Profiling Reveals Mitochondrial Oxidative Enzyme Impairment and Restoration in Diet-induced Obese Mice PloS One. 2012 | Pubmed ID: 23110155 GlycReSoft: a Software Package for Automated Recognition of Glycans from LC/MS Data PloS One. 2012 | Pubmed ID: 23049804 Enhanced Top-down Characterization of Histone Post-translational Modifications Genome Biology. Oct, 2012 | Pubmed ID: 23034525 Improving N-glycan Coverage Using HPLC-MS with Electrospray Ionization at Subambient Pressure Analytical Chemistry. Nov, 2012 | Pubmed ID: 23025344 Antibody-free, Targeted Mass-spectrometric Approach for Quantification of Proteins at Low Picogram Per Milliliter Levels in Human Plasma/serum Proceedings of the National Academy of Sciences of the United States of America. Sep, 2012 | Pubmed ID: 22949669 Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications Genome Medicine. 2012 | Pubmed ID: 22943415 Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease Journal of Proteome Research. Oct, 2012 | Pubmed ID: 22900834 A Comprehensive Subcellular Proteomic Survey of Salmonella Grown Under Phagosome-Mimicking Versus Standard Laboratory Conditions International Journal of Proteomics. 2012 | Pubmed ID: 22900174 Protein Analyses Using Differential Ion Mobility Microchips with Mass Spectrometry Analytical Chemistry. Sep, 2012 | Pubmed ID: 22889348 Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus Fumigatus Reveals Large Functional Changes Upon Exposure to Human Serum The Journal of Biological Chemistry. Sep, 2012 | Pubmed ID: 22865858 DanteR: an Extensible R-based Tool for Quantitative Analysis of -omics Data Bioinformatics (Oxford, England). Sep, 2012 | Pubmed ID: 22815360 Separation of Variant Methylated Histone Tails by Differential Ion Mobility Analytical Chemistry. Aug, 2012 | Pubmed ID: 22812477 Reevaluation of the Coding Potential and Proteomic Analysis of the BAC-derived Rhesus Cytomegalovirus Strain 68-1 Journal of Virology. Sep, 2012 | Pubmed ID: 22718821 Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells JoVE 61797 Biochemistry Micropuncture של השטח של באומן בעכברים בהנחייתם של מיקרוסקופיית פוטון 2 Katsuyuki Matsushita1, Kirsti Golgotiu1, Daniel J. Orton2, Richard D. Smith2, Karin D. Rodland2, Paul D. Piehowski2, Michael P. Hutchens1,3 1Anesthesiology & Perioperative Medicine, Oregon Health & Science University, 2Environmental and Biological Services Division, Pacific Northwest National Laboratory, 3Operative Care Division, Portland Veterans Affairs Medical Center JoVE 58206 Biology פרוטוקול MPLEx עבור ניתוחים מולטי-omic של דגימות אדמה Carrie D. Nicora*1, Kristin E. Burnum-Johnson*1, Ernesto S. Nakayasu1, Cameron P. Casey1, Richard A. White III1, Taniya Roy Chowdhury1, Jennifer E. Kyle1, Young-Mo Kim1, Richard D. Smith1, Thomas O. Metz1, Janet K. Jansson1, Erin S. Baker1 1Biological Sciences Division, Pacific Northwest National Laboratory JoVE 57343 Chemistry
Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells JoVE 61797 Biochemistry
Micropuncture של השטח של באומן בעכברים בהנחייתם של מיקרוסקופיית פוטון 2 Katsuyuki Matsushita1, Kirsti Golgotiu1, Daniel J. Orton2, Richard D. Smith2, Karin D. Rodland2, Paul D. Piehowski2, Michael P. Hutchens1,3 1Anesthesiology & Perioperative Medicine, Oregon Health & Science University, 2Environmental and Biological Services Division, Pacific Northwest National Laboratory, 3Operative Care Division, Portland Veterans Affairs Medical Center JoVE 58206 Biology
פרוטוקול MPLEx עבור ניתוחים מולטי-omic של דגימות אדמה Carrie D. Nicora*1, Kristin E. Burnum-Johnson*1, Ernesto S. Nakayasu1, Cameron P. Casey1, Richard A. White III1, Taniya Roy Chowdhury1, Jennifer E. Kyle1, Young-Mo Kim1, Richard D. Smith1, Thomas O. Metz1, Janet K. Jansson1, Erin S. Baker1 1Biological Sciences Division, Pacific Northwest National Laboratory JoVE 57343 Chemistry
