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 боуменова пространства в мышей, облегчается 2 фотона микроскопия 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 MPLEx протокол для мульти omic анализ образцов почвы 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 боуменова пространства в мышей, облегчается 2 фотона микроскопия 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
MPLEx протокол для мульти omic анализ образцов почвы 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
