Richard D. Smith

Biological Sciences Division, Pacific Northwest National Laboratory

Affiliated withPacific Northwest National Laboratory

Research Area

ChemistryBiologyBiochemistry

Biography

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JoVE Journal Publications

ArticleTotal : 3	Year
Publication title Cited by 31	2018
Publication title Cited by 5	2018
Publication title Cited by 4	2020

Other Publications

Article	Year
Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1. Journal of virology\| PubMed ID: 22718821	2012
Separation of variant methylated histone tails by differential ion mobility. Analytical chemistry\| PubMed ID: 22812477	2012
DanteR: an extensible R-based tool for quantitative analysis of -omics data. Bioinformatics (Oxford, England)\| PubMed ID: 22815360	2012
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\| PubMed ID: 22865858	2012
Protein analyses using differential ion mobility microchips with mass spectrometry. Analytical chemistry\| PubMed ID: 22889348	2012
A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions. International journal of proteomics\| PubMed ID: 22900174	2012
Cerebrospinal fluid proteome of patients with acute Lyme disease. Journal of proteome research\| PubMed ID: 22900834	2012
Mass spectrometry for translational proteomics: progress and clinical implications. Genome medicine\| PubMed ID: 22943415	2012
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\| PubMed ID: 22949669	2012
A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics\| PubMed ID: 23019139	2013
Improving N-glycan coverage using HPLC-MS with electrospray ionization at subambient pressure. Analytical chemistry\| PubMed ID: 23025344	2012
Enhanced top-down characterization of histone post-translational modifications. Genome biology\| PubMed ID: 23034525	2012
GlycReSoft: a software package for automated recognition of glycans from LC/MS data. PloS one\| PubMed ID: 23049804	2012
Activity-based protein profiling reveals mitochondrial oxidative enzyme impairment and restoration in diet-induced obese mice. PloS one\| PubMed ID: 23110155	2012
A systematic analysis of a deep mouse epididymal sperm proteome. Biology of reproduction\| PubMed ID: 23115268	2012
Ultrasensitive sample quantitation via selected reaction monitoring using CITP/CZE-ESI-triple quadrupole MS. Analytical chemistry\| PubMed ID: 23140208	2012
A multi-omic systems approach to elucidating Yersinia virulence mechanisms. Molecular bioSystems\| PubMed ID: 23147219	2013
Unexpected diversity of signal peptides in prokaryotes. mBio\| PubMed ID: 23169999	2012
Suite of activity-based probes for cellulose-degrading enzymes. Journal of the American Chemical Society\| PubMed ID: 23176123	2012
Normalization and missing value imputation for label-free LC-MS analysis. BMC bioinformatics\| PubMed ID: 23176322	2012
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\| PubMed ID: 23204418	2013
High-resolution differential ion mobility spectrometry of a protein. Analytical chemistry\| PubMed ID: 23244633	2013
In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. Journal of proteome research\| PubMed ID: 23268687	2013
Quantitative Site-specific Reactivity Profiling of S-nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry. Free radical biology & medicine\| PubMed ID: 23277143	2012
Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes. The Journal of experimental medicine\| PubMed ID: 23277452	2013
STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results. Proteomics\| PubMed ID: 23303698	2013
High-definition differential ion mobility spectrometry with resolving power up to 500. Journal of the American Society for Mass Spectrometry\| PubMed ID: 23345059	2013
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Chemistry & biology\| PubMed ID: 23352146	2013
Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. Journal of virology\| PubMed ID: 23365422	2013
RNA type III secretion signals that require Hfq. Journal of bacteriology\| PubMed ID: 23396917	2013
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. BMC bioinformatics\| PubMed ID: 23398735	2013
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\| PubMed ID: 23423792	2013
Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis. Journal of proteome research\| PubMed ID: 23495885	2013
Determination of burn patient outcome by large-scale quantitative discovery proteomics. Critical care medicine\| PubMed ID: 23507713	2013
Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output. PloS one\| PubMed ID: 23554854	2013
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Molecular bioSystems\| PubMed ID: 23559334	2013
Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Applied and environmental microbiology\| PubMed ID: 23584789	2013
Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling. Proteomics. Clinical applications\| PubMed ID: 23589343	2013
Disparate proteome responses of pathogenic and nonpathogenic aspergilli to human serum measured by activity-based protein profiling (ABPP). Molecular & cellular proteomics : MCP\| PubMed ID: 23599423	2013
Multi-omic data integration links deleted in breast cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response. Molecular & cellular proteomics : MCP\| PubMed ID: 23639857	2013
Evaluation of selected binding domains for the analysis of ubiquitinated proteomes. Journal of the American Society for Mass Spectrometry\| PubMed ID: 23649778	2013
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\| PubMed ID: 23720318	2013
Protein co-expression network analysis (ProCoNA). Journal of clinical bioinformatics\| PubMed ID: 23724967	2013
Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion. Journal of proteome research\| PubMed ID: 23763644	2013
Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing. Analytical chemistry\| PubMed ID: 23772796	2013
Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics\| PubMed ID: 23776032	2013
Capillary isotachophoresis-nanoelectrospray ionization-selected reaction monitoring MS via a novel sheathless interface for high sensitivity sample quantification. Analytical chemistry\| PubMed ID: 23789856	2013
A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection. PloS one\| PubMed ID: 23840608	2013
Separation of protein conformers by differential ion mobility in hydrogen-rich gases. Analytical chemistry\| PubMed ID: 23855890	2013
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC systems biology\| PubMed ID: 23895213	2013
Controlled dispensing and mixing of pico- to nanoliter volumes using on-demand droplet-based microfluidics. Microfluidics and nanofluidics\| PubMed ID: 23935562	2013
A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses. PloS one\| PubMed ID: 23935999	2013
Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection. Molecular & cellular proteomics : MCP\| PubMed ID: 23970565	2013
Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans. Molecular & cellular proteomics : MCP\| PubMed ID: 24002365	2013
Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis. Analytical chemistry\| PubMed ID: 24004026	2013
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. Bioinformatics (Oxford, England)\| PubMed ID: 24008421	2013
Gray matter is targeted in first-attack multiple sclerosis. PloS one\| PubMed ID: 24039694	2013
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\| PubMed ID: 24076077	2013
The succinated proteome. Mass spectrometry reviews\| PubMed ID: 24115015	2014
Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30. Molecular bioSystems\| PubMed ID: 24121482	2013
Picoelectrospray ionization mass spectrometry using narrow-bore chemically etched emitters. Journal of the American Society for Mass Spectrometry\| PubMed ID: 24122304	2014
Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. Cancer discovery\| PubMed ID: 24124232	2013
Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium. ACS chemical biology\| PubMed ID: 24168666	2014
A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum. Journal of proteome research\| PubMed ID: 24251762	2014
Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens. Antimicrobial agents and chemotherapy\| PubMed ID: 24277029	2014
Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium. mBio\| PubMed ID: 24281717	2013
Accounting for population variation in targeted proteomics. Journal of proteome research\| PubMed ID: 24320210	2014
Proteomic identification and quantification of S-glutathionylation in mouse macrophages using resin-assisted enrichment and isobaric labeling. Free radical biology & medicine\| PubMed ID: 24333276	2014
The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics. Molecular & cellular proteomics : MCP\| PubMed ID: 24335474	2014
Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications. Nature protocols\| PubMed ID: 24336471	2014
Fast and accurate database searches with MS-GF+Percolator. Journal of proteome research\| PubMed ID: 24344789	2014
Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS. Mass spectrometry (Tokyo, Japan)\| PubMed ID: 24349930	2013
Differential ion mobility separations in up to 100% helium using microchips. Journal of the American Society for Mass Spectrometry\| PubMed ID: 24402673	2014
Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry. Molecular & cellular proteomics : MCP\| PubMed ID: 24403597	2014
Automated data extraction from in situ protein-stable isotope probing studies. Journal of proteome research\| PubMed ID: 24467184	2014
Implementation of dipolar resonant excitation for collision induced dissociation with ion mobility/time-of-flight MS. Journal of the American Society for Mass Spectrometry\| PubMed ID: 24470195	2014
Organelle-specific activity-based protein profiling in living cells. Angewandte Chemie (International ed. in English)\| PubMed ID: 24505022	2014
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\| PubMed ID: 24555535	2014
Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani. PLoS pathogens\| PubMed ID: 24586154	2014
Signatures for mass spectrometry data quality. Journal of proteome research\| PubMed ID: 24611607	2014
Honoring Dr. Jean H. Futrell. Journal of the American Society for Mass Spectrometry\| PubMed ID: 24627182	2014
High and low doses of ionizing radiation induce different secretome profiles in a human skin model. PloS one\| PubMed ID: 24642900	2014
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\| PubMed ID: 24676894	2014
Characterization of individual mouse cerebrospinal fluid proteomes. Proteomics\| PubMed ID: 24677814	2014
Cytomegalovirus pp65 limits dissemination but is dispensable for persistence. The Journal of clinical investigation\| PubMed ID: 24691437	2014
Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Molecular & cellular proteomics : MCP\| PubMed ID: 24719451	2014
Improving ion mobility measurement sensitivity by utilizing helium in an ion funnel trap. Analytical chemistry\| PubMed ID: 24786390	2014
Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements. Journal of the American Society for Mass Spectrometry\| PubMed ID: 24796262	2014
Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. mBio\| PubMed ID: 24846384	2014
Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece. Journal of proteome research\| PubMed ID: 24846609	2014
GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization. Analytical chemistry\| PubMed ID: 24881670	2014
Detecting differential protein expression in large-scale population proteomics. Bioinformatics (Oxford, England)\| PubMed ID: 24928210	2014
The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environmental microbiology reports\| PubMed ID: 24992538	2014
Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria. Frontiers in microbiology\| PubMed ID: 25071738	2014
Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry. International journal of mass spectrometry\| PubMed ID: 25089116	2013
Proteome-wide light/dark modulation of thiol oxidation in cyanobacteria revealed by quantitative site-specific redox proteomics. Molecular & cellular proteomics : MCP\| PubMed ID: 25118246	2014
Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry. Analytical chemistry\| PubMed ID: 25118826	2014
Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements. Molecular & cellular proteomics : MCP\| PubMed ID: 25129695	2014
A method to determine lysine acetylation stoichiometries. International journal of proteomics\| PubMed ID: 25143833	2014
Expediting SRM assay development for large-scale targeted proteomics experiments. Journal of proteome research\| PubMed ID: 25145539	2014
Experimental evaluation and optimization of structures for lossless ion manipulations for ion mobility spectrometry with time-of-flight mass spectrometry. Analytical chemistry\| PubMed ID: 25152066	2014
Characterization of ion dynamics in structures for lossless ion manipulations. Analytical chemistry\| PubMed ID: 25152178	2014
Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid. Analytical and bioanalytical chemistry\| PubMed ID: 25192788	2014
Mobility-resolved ion selection in uniform drift field ion mobility spectrometry/mass spectrometry: dynamic switching in structures for lossless ion manipulations. Analytical chemistry\| PubMed ID: 25222548	2014
High sensitivity combined with extended structural coverage of labile compounds via nanoelectrospray ionization at subambient pressures. Analytical chemistry\| PubMed ID: 25222651	2014
Simulation of electric potentials and ion motion in planar electrode structures for lossless ion manipulations (SLIM). Journal of the American Society for Mass Spectrometry\| PubMed ID: 25257188	2014
Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics\| PubMed ID: 25263569	2014
Antibody-independent targeted quantification of TMPRSS2-ERG fusion protein products in prostate cancer. Molecular oncology\| PubMed ID: 25266362	2014
On the ionization and ion transmission efficiencies of different ESI-MS interfaces. Journal of the American Society for Mass Spectrometry\| PubMed ID: 25267087	2015
Brain insulin lowers circulating BCAA levels by inducing hepatic BCAA catabolism. Cell metabolism\| PubMed ID: 25307860	2014
Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes. Journal of proteome research\| PubMed ID: 25350482	2015
Rectangular ion funnel: a new ion funnel interface for structures for lossless ion manipulations. Analytical chemistry\| PubMed ID: 25409343	2015
Proteomic approaches for site-specific O-GlcNAcylation analysis. Bioanalysis\| PubMed ID: 25411699	2014
HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa. PLoS genetics\| PubMed ID: 25412208	2014
Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Molecular & cellular proteomics : MCP\| PubMed ID: 25433089	2014
Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis. Journal of proteome research\| PubMed ID: 25496566	2015
Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment. Analytical chemistry\| PubMed ID: 25517423	2015
Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle. BMC genomics\| PubMed ID: 25547186	2014
Perturbations in the urinary exosome in transplant rejection. Frontiers in medicine\| PubMed ID: 25593928	2014
Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer. Journal of mass spectrometry : JMS\| PubMed ID: 25601704	2015
Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO₂. Scientific reports\| PubMed ID: 25633131	2015
Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. Journal of proteome research\| PubMed ID: 25855118	2015
Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods. Journal of translational medicine\| PubMed ID: 25889691	2015
Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus. Virology\| PubMed ID: 25965799	2015
Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations. Analytical chemistry\| PubMed ID: 25971536	2015
A comprehensive collection of systems biology data characterizing the host response to viral infection. Scientific data\| PubMed ID: 25977790	2014
An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics. Journal of the American Society for Mass Spectrometry\| PubMed ID: 26015166	2015
Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics\| PubMed ID: 26046661	2015
Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadrupole Mass Spectrometry. Analytical chemistry\| PubMed ID: 26107611	2015
Lipidomic and proteomic analysis of Caenorhabditis elegans lipid droplets and identification of ACS-4 as a lipid droplet-associated protein. Biochimica et biophysica acta\| PubMed ID: 26121959	2015
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\| PubMed ID: 26140287	2015
Identification of Salmonella Typhimurium Deubiquitinase SseL Substrates by Immunoaffinity Enrichment and Quantitative Proteomic Analysis. Journal of proteome research\| PubMed ID: 26147956	2015
Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics. Journal of proteome research\| PubMed ID: 26151086	2015
Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer. International journal of mass spectrometry\| PubMed ID: 26185483	2015
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Molecular & cellular proteomics : MCP\| PubMed ID: 26217018	2015
Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes. Cell metabolism\| PubMed ID: 26244933	2015
Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch. The Analyst\| PubMed ID: 26289106	2015
The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. Scientific data\| PubMed ID: 26306205	2015
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\| PubMed ID: 26317212	2015
Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling. Biotechnology for biofuels\| PubMed ID: 26413155	2015
Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations. Analytical chemistry\| PubMed ID: 26510005	2015
The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification. Expert review of proteomics\| PubMed ID: 26581546	2016
Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85. PloS one\| PubMed ID: 26629814	2015
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer. Molecular & cellular proteomics : MCP\| PubMed ID: 26631509	2016
Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. Journal of proteome research\| PubMed ID: 26653538	2016
Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function during Nanoparticle-Induced Oxidative Stress. ACS nano\| PubMed ID: 26700264	2016
SerpinB1 Promotes Pancreatic β Cell Proliferation. Cell metabolism\| PubMed ID: 26701651	2016
Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clinical chemistry\| PubMed ID: 26719571	2016
Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. The Analyst\| PubMed ID: 26734689	2016
SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities. Endocrinology\| PubMed ID: 26745641	2016
Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations. Analytical chemistry\| PubMed ID: 26752262	2016
Surprising impact of remote groups on the folding--unfolding and dimer-chain equilibria of bifunctional H-bonding unimers. Chemical communications (Cambridge, England)\| PubMed ID: 26830456	2016
Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence. Cell chemical biology\| PubMed ID: 26853625	2016
Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell host & microbe\| PubMed ID: 26867183	2016
Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 26867747	2016
Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 26867748	2016
Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences\| PubMed ID: 26868616	2016
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\| PubMed ID: 26925055	2016
The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. Expert review of proteomics\| PubMed ID: 26960075	2016
Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations. The Journal of clinical endocrinology and metabolism\| PubMed ID: 27007693	2016
Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations. The New England journal of medicine\| PubMed ID: 27007809	2016
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC genomics\| PubMed ID: 27029936	2016
Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry. Journal of the American Society for Mass Spectrometry\| PubMed ID: 27052738	2016
A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation. Journal of the American Society for Mass Spectrometry\| PubMed ID: 27098413	2016
Mining the human urine proteome for monitoring renal transplant injury. Kidney international\| PubMed ID: 27165815	2016
Advances in targeted proteomics and applications to biomedical research. Proteomics\| PubMed ID: 27302376	2016
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell\| PubMed ID: 27372738	2016
Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. Science signaling\| PubMed ID: 27405981	2016
Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. PloS one\| PubMed ID: 27434306	2016
Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations. Analytical chemistry\| PubMed ID: 27479234	2016
Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module. Analytical chemistry\| PubMed ID: 27531027	2016
The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nature microbiology\| PubMed ID: 27573103	2016
Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses. Analytical and bioanalytical chemistry\| PubMed ID: 27604268	2017
Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. eLife\| PubMed ID: 27623010	2016
FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans. Cell reports\| PubMed ID: 27626670	2016
Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry. Molecular & cellular proteomics : MCP\| PubMed ID: 27670688	2016
The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates. Molecular ecology\| PubMed ID: 27696597	2016
Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations. Analytical chemistry\| PubMed ID: 27715008	2016
Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142. Applied and environmental microbiology\| PubMed ID: 27742679	2016
MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. mSystems\| PubMed ID: 27822525	2016
Proteome Remodeling in Response to Sulfur Limitation in " Pelagibacter ubique". mSystems\| PubMed ID: 27822545	2016
Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction. Molecular & cellular proteomics : MCP\| PubMed ID: 27836980	2017
Position-dependent termination and widespread obligatory frameshifting in Euplotes translation. Nature structural & molecular biology\| PubMed ID: 27870834	2017
Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go? Bioanalysis\| PubMed ID: 27921453	2017
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\| PubMed ID: 27934097	2016
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\| PubMed ID: 27958645	2017
Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation. Analytical chemistry\| PubMed ID: 27966901	2017
Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples. Scientific reports\| PubMed ID: 28004771	2016
An efficient method for native protein purification in the selected range from prostate cancer tissue digests. Chinese clinical oncology\| PubMed ID: 28061542	2016
High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics. Journal of chromatography. A\| PubMed ID: 28077236	2017
MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. The Analyst\| PubMed ID: 28091625	2017
Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations. International journal of molecular sciences\| PubMed ID: 28106768	2017
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinformatics (Oxford, England)\| PubMed ID: 28158427	2017
Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform. Analytical chemistry\| PubMed ID: 28193022	2016
Ion Elevators and Escalators in Multilevel Structures for Lossless Ion Manipulations. Analytical chemistry\| PubMed ID: 28208272	2017
Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803. PloS one\| PubMed ID: 28253354	2017
New frontiers for mass spectrometry based upon structures for lossless ion manipulations. The Analyst\| PubMed ID: 28262893	2017
Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry. The journal of physical chemistry letters\| PubMed ID: 28267339	2017
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.)\| PubMed ID: 28301728	2017
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\| PubMed ID: 28316103	2017
Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations. Analytical chemistry\| PubMed ID: 28332832	2017
2016 ASMS Workshop Review: Next Generation LC/MS: Critical Insights and Future Perspectives. Journal of the American Society for Mass Spectrometry\| PubMed ID: 28417304	2017
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 Ma... Analytical chemistry\| PubMed ID: 28497957	2017
PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. Bioinformatics (Oxford, England)\| PubMed ID: 28505286	2017
Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions. Journal of the American Society for Mass Spectrometry\| PubMed ID: 28560562	2017
Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in . mBio\| PubMed ID: 28634240	2017
Distinguishing d- and l-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry. Chemical communications (Cambridge, England)\| PubMed ID: 28654112	2017
Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease. The Journal of pathology\| PubMed ID: 28657654	2017
Changes of Protein Turnover in Aging . Molecular & cellular proteomics : MCP\| PubMed ID: 28679685	2017
Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. Scientific data\| PubMed ID: 28722704	2017
Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues. Analytical chemistry\| PubMed ID: 28724286	2017
An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements. Analytical chemistry\| PubMed ID: 28763190	2017
Advances in microscale separations towards nanoproteomics applications. Journal of chromatography. A\| PubMed ID: 28765000	2017
Informed-Proteomics: open-source software package for top-down proteomics. Nature methods\| PubMed ID: 28783154	2017
Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics. Journal of translational medicine\| PubMed ID: 28810879	2017
Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS. Journal of the American Society for Mass Spectrometry\| PubMed ID: 28889248	2018
Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry. ChemistrySelect\| PubMed ID: 28936476	2016
A Global Survey of ATPase Activity in Asexual Blood Stages and Gametocytes. Molecular & cellular proteomics : MCP\| PubMed ID: 29079720	2018
Pyroptosis by caspase11/4-gasdermin-D pathway in alcoholic hepatitis in mice and patients. Hepatology (Baltimore, Md.)\| PubMed ID: 29108122	2018
LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 29116567	2017
Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. Journal of proteome research\| PubMed ID: 29124938	2017
Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis. Cell host & microbe\| PubMed ID: 29154144	2017
A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements. Analytical chemistry\| PubMed ID: 29161511	2018
Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses. Analytical chemistry\| PubMed ID: 29220163	2018
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\| PubMed ID: 29223060	2018
A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer Using Structures for Lossless Ion Manipulations. Journal of the American Society for Mass Spectrometry\| PubMed ID: 29235041	2018
Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins. Oncotarget\| PubMed ID: 29254211	2017
SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids. Clinical mass spectrometry (Del Mar, Calif.)\| PubMed ID: 29276770	2016
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\| PubMed ID: 29339515	2018
High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men. Aging cell\| PubMed ID: 29399943	2018
Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells. Nature communications\| PubMed ID: 29491378	2018
Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry. Bioanalysis\| PubMed ID: 29494212	2018
Characterization of the Ovarian Tumor Peptidome. Vitamins and hormones\| PubMed ID: 29544642	2018
A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry. Chemical science\| PubMed ID: 29568436	2017
Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. International journal of mass spectrometry\| PubMed ID: 29576737	2018
QC-ART: A tool for real-time quality control assessment of mass spectrometry-based proteomics data. Molecular & cellular proteomics : MCP\| PubMed ID: 29666158	2018
An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies. International journal of mass spectrometry\| PubMed ID: 29706793	2018
Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics. Cancer journal (Sudbury, Mass.)\| PubMed ID: 29794536	2018