Richard D. Smith

Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1.

Separation of variant methylated histone tails by differential ion mobility.

DanteR: an extensible R-based tool for quantitative analysis of -omics data.

Multiplexed activity-based protein profiling of the human pathogen Aspergillus fumigatus reveals large functional changes upon exposure to human serum.

Protein analyses using differential ion mobility microchips with mass spectrometry.

A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions.

Cerebrospinal fluid proteome of patients with acute Lyme disease.

Mass spectrometry for translational proteomics: progress and clinical implications.

Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum.

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.

Improving N-glycan coverage using HPLC-MS with electrospray ionization at subambient pressure.

Enhanced top-down characterization of histone post-translational modifications.

GlycReSoft: a software package for automated recognition of glycans from LC/MS data.

Activity-based protein profiling reveals mitochondrial oxidative enzyme impairment and restoration in diet-induced obese mice.

A systematic analysis of a deep mouse epididymal sperm proteome.

Ultrasensitive sample quantitation via selected reaction monitoring using CITP/CZE-ESI-triple quadrupole MS.

A multi-omic systems approach to elucidating Yersinia virulence mechanisms.

Unexpected diversity of signal peptides in prokaryotes.

Suite of activity-based probes for cellulose-degrading enzymes.

Normalization and missing value imputation for label-free LC-MS analysis.

Proteome analyses of strains ATCC 51142 and PCC 7822 of the diazotrophic cyanobacterium Cyanothece sp. under culture conditions resulting in enhanced H₂ production.

High-resolution differential ion mobility spectrometry of a protein.

In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics.

Quantitative Site-specific Reactivity Profiling of S-nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry.

Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes.

STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

High-definition differential ion mobility spectrometry with resolving power up to 500.

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.

Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells.

RNA type III secretion signals that require Hfq.

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking.

Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis.

Determination of burn patient outcome by large-scale quantitative discovery proteomics.

Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output.

Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.

Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.

Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling.

Disparate proteome responses of pathogenic and nonpathogenic aspergilli to human serum measured by activity-based protein profiling (ABPP).

Multi-omic data integration links deleted in breast cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response.

Evaluation of selected binding domains for the analysis of ubiquitinated proteomes.

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.

Protein co-expression network analysis (ProCoNA).

Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion.

Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing.

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies.

Capillary isotachophoresis-nanoelectrospray ionization-selected reaction monitoring MS via a novel sheathless interface for high sensitivity sample quantification.

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection.

Separation of protein conformers by differential ion mobility in hydrogen-rich gases.

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice.

Controlled dispensing and mixing of pico- to nanoliter volumes using on-demand droplet-based microfluidics.

A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses.

Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection.

Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans.

Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis.

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

Gray matter is targeted in first-attack multiple sclerosis.

Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger.

The succinated proteome.

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30.

Picoelectrospray ionization mass spectrometry using narrow-bore chemically etched emitters.

Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium.

Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium.

A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum.

Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens.

Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium.

Accounting for population variation in targeted proteomics.

Proteomic identification and quantification of S-glutathionylation in mouse macrophages using resin-assisted enrichment and isobaric labeling.

The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics.

Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications.

Fast and accurate database searches with MS-GF+Percolator.

Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS.

Differential ion mobility separations in up to 100% helium using microchips.

Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry.

Automated data extraction from in situ protein-stable isotope probing studies.

Implementation of dipolar resonant excitation for collision induced dissociation with ion mobility/time-of-flight MS.

Organelle-specific activity-based protein profiling in living cells.

LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism.

Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani.

Signatures for mass spectrometry data quality.

Honoring Dr. Jean H. Futrell.

High and low doses of ionizing radiation induce different secretome profiles in a human skin model.

Improving the sensitivity of mass spectrometry by using a new sheath flow electrospray emitter array at subambient pressures.

Characterization of individual mouse cerebrospinal fluid proteomes.

Cytomegalovirus pp65 limits dissemination but is dispensable for persistence.

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.

Improving ion mobility measurement sensitivity by utilizing helium in an ion funnel trap.

Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements.

Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses.

Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece.

GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization.

Detecting differential protein expression in large-scale population proteomics.

The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation.

Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria.

Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry.

Proteome-wide light/dark modulation of thiol oxidation in cyanobacteria revealed by quantitative site-specific redox proteomics.

Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry.

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements.

A method to determine lysine acetylation stoichiometries.

Expediting SRM assay development for large-scale targeted proteomics experiments.

Experimental evaluation and optimization of structures for lossless ion manipulations for ion mobility spectrometry with time-of-flight mass spectrometry.

Characterization of ion dynamics in structures for lossless ion manipulations.

Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid.

Mobility-resolved ion selection in uniform drift field ion mobility spectrometry/mass spectrometry: dynamic switching in structures for lossless ion manipulations.

High sensitivity combined with extended structural coverage of labile compounds via nanoelectrospray ionization at subambient pressures.

Simulation of electric potentials and ion motion in planar electrode structures for lossless ion manipulations (SLIM).

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data.

Antibody-independent targeted quantification of TMPRSS2-ERG fusion protein products in prostate cancer.

On the ionization and ion transmission efficiencies of different ESI-MS interfaces.

Brain insulin lowers circulating BCAA levels by inducing hepatic BCAA catabolism.

Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes.

Rectangular ion funnel: a new ion funnel interface for structures for lossless ion manipulations.

Proteomic approaches for site-specific O-GlcNAcylation analysis.

HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa.

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis.

Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment.

Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle.

Perturbations in the urinary exosome in transplant rejection.

Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer.

Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO₂.

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics.

Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods.

Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus.

Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations.

A comprehensive collection of systems biology data characterizing the host response to viral infection.

An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics.

Enhancing bottom-up and top-down proteomic measurements with ion mobility separations.

Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadrupole Mass Spectrometry.

Lipidomic and proteomic analysis of Caenorhabditis elegans lipid droplets and identification of ACS-4 as a lipid droplet-associated protein.

Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (μFAIMS/IMS-MS) separations.

Identification of Salmonella Typhimurium Deubiquitinase SseL Substrates by Immunoaffinity Enrichment and Quantitative Proteomic Analysis.

Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics.

Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer.

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.

Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes.

Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch.

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.

Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants.

Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling.

Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations.

The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification.

Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.

Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function during Nanoparticle-Induced Oxidative Stress.

SerpinB1 Promotes Pancreatic β Cell Proliferation.

Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.

Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry.

SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities.

Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations.

Surprising impact of remote groups on the folding--unfolding and dimer-chain equilibria of bifunctional H-bonding unimers.

Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence.

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS.

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids.

Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium.

The current state of the art of quantitative phosphoproteomics and its applications to diabetes research.

Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations.

Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations.

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry.

A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation.

Mining the human urine proteome for monitoring renal transplant injury.

Advances in targeted proteomics and applications to biomedical research.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.

Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations.

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module.

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses.

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes.

FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans.

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry.

The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates.

Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations.

Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142.

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.

Proteome Remodeling in Response to Sulfur Limitation in " Pelagibacter ubique".

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.

Position-dependent termination and widespread obligatory frameshifting in Euplotes translation.

Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?

Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming.

Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies.

Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation.

Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples.

An efficient method for native protein purification in the selected range from prostate cancer tissue digests.

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics.

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.

Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations.

LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data.

Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform.

Ion Elevators and Escalators in Multilevel Structures for Lossless Ion Manipulations.

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803.

New frontiers for mass spectrometry based upon structures for lossless ion manipulations.

Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry.

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses.

Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics.

Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations.

2016 ASMS Workshop Review: Next Generation LC/MS: Critical Insights and Future Perspectives.

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).

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.

Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions.

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in .

Distinguishing d- and l-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry.

Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.

Changes of Protein Turnover in Aging .

Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer.

Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues.

An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements.

Advances in microscale separations towards nanoproteomics applications.

Informed-Proteomics: open-source software package for top-down proteomics.

Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics.

Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS.

Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry.

A Global Survey of ATPase Activity in Asexual Blood Stages and Gametocytes.

Pyroptosis by caspase11/4-gasdermin-D pathway in alcoholic hepatitis in mice and patients.

LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers.

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues.

Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis.

A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements.

Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses.

Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches.

A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer Using Structures for Lossless Ion Manipulations.

Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids.

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape.

High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men.

Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells.

Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry.

Characterization of the Ovarian Tumor Peptidome.

A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry.

Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples.

QC-ART: A tool for real-time quality control assessment of mass spectrometry-based proteomics data.

An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies.

Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics.