David C. Muddiman

Solution composition and thermal denaturation for the production of single-stranded PCR amplicons: piperidine-induced destabilization of the DNA duplex?

Evaluation of sample preparation techniques for mass measurements of PCR products using ESI-FT-ICR mass spectrometry.

Gas-phase ion unimolecular dissociation for rapid phosphopeptide mapping by IRMPD in a Penning ion trap: an energetically favored process.

Dual-micro-ESI source for precise mass determination on a quadrupole time-of-flight mass spectrometer for genomic and proteomic applications.

Implications of hydrophobicity and free energy of solvation for characterization of nucleic acids by electrospray ionization mass spectrometry.

Advantages of Thermococcus kodakaraenis (KOD) DNA Polymerase for PCR-mass spectrometry based analyses.

Mass spectral determination of skeletal/cardiac actin isoform ratios in cardiac muscle.

Determination of a correction to improve mass measurement accuracy of isotopically unresolved polymerase chain reaction amplicons by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Coordination-driven self-assembly of supramolecular cages: heteroatom-containing and complementary trigonal prisms.

Naturally processed measles virus peptide eluted from class II HLA-DRB1*03 recognized by T lymphocytes from human blood.

Dual electrospray ionization source for confident generation of accurate mass tags using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry.

Identification and characterization of novel, naturally processed measles virus class II HLA-DRB1 peptides.

Enzymatic strategies for the characterization of nucleic acids by electrospray ionization mass spectrometry.

Determination of the relative energies of activation for the dissociation of aromatic versus aliphatic phosphopeptides by ESI-FTICR-MS and IRMPD.

Androgens negatively regulate forkhead transcription factor FKHR (FOXO1) through a proteolytic mechanism in prostate cancer cells.

A method for calculating 16O/18O peptide ion ratios for the relative quantification of proteomes.

Informed use of proteolytic inhibitors in biomarker discovery.

Detection of genetic variants of transthyretin by liquid chromatography-dual electrospray ionization fourier-transform ion-cyclotron-resonance mass spectrometry.

Identification of transthyretin variants by sequential proteomic and genomic analysis.

Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry.

Evaluation of a cleavable stable isotope labeled synthetic peptide for absolute protein quantification using LC-MS/MS.

Analytical performance of a venturi device integrated into an electrospray ionization fourier transform ion cyclotron resonance mass spectrometer for analysis of nucleic acids.

Discovery of ovarian cancer biomarkers in serum using NanoLC electrospray ionization TOF and FT-ICR mass spectrometry.

Analysis of the low molecular weight fraction of serum by LC-dual ESI-FT-ICR mass spectrometry: precision of retention time, mass, and ion abundance.

Effect of post-excitation radius on ion abundance, mass measurement accuracy, and isotopic distributions in Fourier transform ion cyclotron resonance mass spectrometry.

Protein expression profiling of CLL B cells using replicate off-line strong cation exchange chromatography and LC-MS/MS.

Mapping sites of protein phosphorylation by mass spectrometry utilizing a chemical-enzymatic approach: characterization of products from alpha-S1 casein phosphopeptides.

Statistical evaluation of internal and external mass calibration laws utilized in fourier transform ion cyclotron resonance mass spectrometry.

Leveling response factors in the electrospray ionization process using a heated capillary interface.

Evaluation of protein depletion methods for the analysis of total-, phospho- and glycoproteins in lumbar cerebrospinal fluid.

Déjà vu all over again: skin cap still contains a high-potency glucocorticosteroid.

Primary trabecular meshwork cells incubated in human aqueous humor differ from cells incubated in serum supplements.

Quantitative protein expression analysis of CLL B cells from mutated and unmutated IgV(H) subgroups using acid-cleavable isotope-coded affinity tag reagents.

Coordination-driven self-assemblies with a carborane backbone.

Normalization of relative peptide ratios derived from in-gel digests: applications to protein variant analysis at the peptide level.

Accurate mass precursor ion data and tandem mass spectrometry identify a class I human leukocyte antigen A*0201-presented peptide originating from vaccinia virus.

Gentle protein ionization assisted by high-velocity gas flow.

Quantitative mass spectral evidence for the absence of circulating brain natriuretic peptide (BNP-32) in severe human heart failure.

Identification of class II HLA-DRB1*03-bound measles virus peptides by 2D-liquid chromatography tandem mass spectrometry.

Identification of subunit-subunit interactions in bacteriophage P22 procapsids by chemical cross-linking and mass spectrometry.

"Lewis and Clark" proteomics.

Chromatin assembly factor 1 interacts with histone H3 methylated at lysine 79 in the processes of epigenetic silencing and DNA repair.

Reproducibility of retention time using a splitless nanoLC coupled to an ESI-FTICR mass spectrometer.

Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry.

Molecular architecture via coordination: self-assembly of nanoscale hexagonal metallodendrimers with designed building blocks.

Incorporation of 2,6-di(4,4'-dipyridyl)-9-thiabicyclo[3.3.1]nonane into discrete 2D supramolecules via coordination-driven self-assembly.

Generation and detection of multiply-charged peptides and proteins by matrix-assisted laser desorption electrospray ionization (MALDESI) Fourier transform ion cyclotron resonance mass spectrometry.

Sub parts-per-million mass measurement accuracy of intact proteins and product ions achieved using a dual electrospray ionization quadrupole fourier transform ion cyclotron resonance mass spectrometer.

Direct high-resolution peptide and protein analysis by desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

A method for automatically interpreting mass spectra of 18O-labeled isotopic clusters.

Elevated levels of phosphorylated fibrinogen-alpha-isoforms and differential expression of other post-translationally modified proteins in the plasma of ovarian cancer patients.

Coordination-driven self-assembly of metallodendrimers possessing well-defined and controllable cavities as cores.

Effect of matrix crystal structure on ion abundance of carbohydrates by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

Direct characterization of intact polypeptides by matrix-assisted laser desorption electrospray ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometry.

Understanding the influence of post-excite radius and axial confinement on quantitative proteomic measurements using Fourier transform ion cyclotron resonance mass spectrometry.

Detection of attomole amounts of analyte by desorption electrospray ionization mass spectrometry (DESI-MS) determined using fluorescence spectroscopy.

Parts-per-billion mass measurement accuracy achieved through the combination of multiple linear regression and automatic gain control in a Fourier transform ion cyclotron resonance mass spectrometer.

Epithelial ovarian cancer: disease etiology, treatment, detection, and investigational gene, metabolite, and protein biomarkers.

Remote mass spectrometric sampling of electrospray- and desorption electrospray-generated ions using an air ejector.

Details of the structure determination of the sulfated steroids PSDS and PADS: new components of the sea lamprey (petromyzon marinus) migratory pheromone.

Quantitative comparison of a flared and a standard heated metal capillary inlet with a voltage-assisted air amplifier on an electrospray ionization linear ion trap mass spectrometer.

Differential protein expression in male and female human lumbar cerebrospinal fluid using iTRAQ reagents after abundant protein depletion.

Probing the mechanisms of an air amplifier using a LTQ-FT-ICR-MS and fluorescence spectroscopy.

Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer.

Carbohydrate analysis by desorption electrospray ionization fourier transform ion cyclotron resonance mass spectrometry.

A highly efficient approach to the self-assembly of hexagonal cavity-cored tris[2]pseudorotaxanes from several components via multiple noncovalent interactions.

A new family of multiferrocene complexes with enhanced control of structure and stoichiometry via coordination-driven self-assembly and their electrochemistry.

Synthesis, characterization, and application of iodoacetamide derivatives utilized for the ALiPHAT strategy.

Human Proteinpedia enables sharing of human protein data.

Investigations with O-linked protein glycosylations by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

Coordination-driven self-assembly of cavity-cored multiple crown ether derivatives and poly[2]pseudorotaxanes.

Mass measurement accuracy comparisons between a double-focusing magnetic sector and a time-of-flight mass analyzer.

Studying O-linked protein glycosylations in human plasma.

Effect of plasma protein depletion on BNP-32 recovery.

Coordination-driven face-directed self-assembly of trigonal prisms. Face-based conformational chirality.

Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer.

Ambient aerodynamic ionization source for remote analyte sampling and mass spectrometric analysis.

Temperature-dependent regulation of proteins in Aspergillus flavus: whole organism stable isotope labeling by amino acids.

Calibration laws based on multiple linear regression applied to matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

Development and characterization of an ionization technique for analysis of biological macromolecules: liquid matrix-assisted laser desorption electrospray ionization.

Construction of a versatile high precision ambient ionization source for direct analysis and imaging.

Generation of multiply charged peptides and proteins by radio frequency acoustic desorption and ionization for mass spectrometric detection.

Development of a nanoLC LTQ orbitrap mass spectrometric method for profiling glycans derived from plasma from healthy, benign tumor control, and epithelial ovarian cancer patients.

Intact and top-down characterization of biomolecules and direct analysis using infrared matrix-assisted laser desorption electrospray ionization coupled to FT-ICR mass spectrometry.

Absolute quantification of C-reactive protein in human plasma derived from patients with epithelial ovarian cancer utilizing protein cleavage isotope dilution mass spectrometry.

Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides.

Synthesis of six-component metallodendrimers via [3 + 3] coordination-driven self-assembly.

Utilizing artificial neural networks in MATLAB to achieve parts-per-billion mass measurement accuracy with a fourier transform ion cyclotron resonance mass spectrometer.

Development of a robust and high throughput method for profiling N-linked glycans derived from plasma glycoproteins by NanoLC-FTICR mass spectrometry.

Atmospheric pressure infrared (10.6 microm) laser desorption electrospray ionization (IR-LDESI) coupled to a LTQ Fourier transform ion cyclotron resonance mass spectrometer.

Characterization of charge separation in the Array of Micromachined UltraSonic Electrospray (AMUSE) ion source for mass spectrometry.

Proteomics characterization of cell membrane blebs in human retinal pigment epithelium cells.

Evaluation of the ALiPHAT method for PC-IDMS and correlation of limits-of-detection with nonpolar surface area.

Tandem mass spectrometry of thiolate-protected Au nanoparticles Na(x)Au25(SC2H4Ph)(18-y)(S(C2H4O)5CH3)(y).

Improving limits of detection for B-type natriuretic peptide using PC-IDMS: an application of the ALiPHAT strategy.

Increasing the hydrophobicity and electrospray response of glycans through derivatization with novel cationic hydrazides.

Detection of alternative splice variants at the proteome level in Aspergillus flavus.

Binding site on human immunoglobulin G for the affinity ligand HWRGWV.

The effects of abundant plasma protein depletion on global glycan profiling using nanoLC FT-ICR mass spectrometry.

Quantitative top-down proteomics of SILAC labeled human embryonic stem cells.

Study of the ionization mechanism in hybrid laser based desorption techniques.

Interplay of permanent charge and hydrophobicity in the electrospray ionization of glycans.

Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality.

Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma.

Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics.

Self-assembly of dendritic tris(crown ether) hexagons and their complexation with dibenzylammonium cations.

Utilizing spectral counting to quantitatively characterize tandem removal of abundant proteins (TRAP) in human plasma.

Retrospective. John Bennett Fenn (1917-2010).

Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS.

Improving proteome coverage on a LTQ-Orbitrap using design of experiments.

Design, Modeling, Fabrication, and Evaluation of the Air Amplifier for Improved Detection of Biomolecules by Electrospray Ionization Mass Spectrometry.

Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600).

Capitalizing on the hydrophobic bias of electrospray ionization through chemical modification in mass spectrometry-based proteomics.

Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms.

Stable-isotope labeled hydrophobic hydrazide reagents for the relative quantification of N-linked glycans by electrospray ionization mass spectrometry.

Comparison of stable-isotope labeling with amino acids in cell culture and spectral counting for relative quantification of protein expression.

One-Year Plasma N-linked Glycome Intra-individual and Inter-individual Variability in the Chicken Model of Spontaneous Ovarian Adenocarcinoma.

N-linked global glycan profiling by nanoLC mass spectrometry.

Evaluation of normalization methods on GeLC-MS/MS label-free spectral counting data to correct for variation during proteomic workflows.

Spectral accuracy and sulfur counting capabilities of the LTQ-FT-ICR and the LTQ-Orbitrap XL for small molecule analysis.

Hydrophobic derivatization of N-linked glycans for increased ion abundance in electrospray ionization mass spectrometry.

Absolute quantification of free glutathione and cysteine in aquatic insects using isotope dilution and selected reaction monitoring.

Global optimization of the infrared matrix-assisted laser desorption electrospray ionization (IR MALDESI) source for mass spectrometry using statistical design of experiments.

The subcellular proteome of undifferentiated human embryonic stem cells.

Membrane protein complexes catalyze both 4- and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis.

High-resolution mass spectrometry.

Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry.

Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS).

Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis.

Polyubiquitin is required for growth, development and pathogenicity in the rice blast fungus Magnaporthe oryzae.

Systematic comparison of reverse phase and hydrophilic interaction liquid chromatography platforms for the analysis of N-linked glycans.

Targeted proteomics of the secretory pathway reveals the secretome of mouse embryonic fibroblasts and human embryonic stem cells.

In-depth analysis of the Magnaporthe oryzae conidial proteome.

Poly-specific trans-acyltransferase machinery revealed via engineered acyl-CoA synthetases.

Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) imaging source coupled to a FT-ICR mass spectrometer.

Direct analysis of textile fabrics and dyes using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry.

Monolignol pathway 4-coumaric acid:coenzyme A ligases in Populus trichocarpa: novel specificity, metabolic regulation, and simulation of coenzyme A ligation fluxes.

Comparative proteomic analysis and IgE binding properties of peanut seed and testa (skin).

MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

Multi-peptide nLC-PC-IDMS-SRM-based assay for the quantification of biomarkers in the chicken ovarian cancer model.

Temporal analysis of the magnaporthe oryzae proteome during conidial germination and cyclic AMP (cAMP)-mediated appressorium formation.

The use of a xylosylated plant glycoprotein as an internal standard accounting for N-linked glycan cleavage and sample preparation variability.

Mass recalibration of FT-ICR mass spectrometry imaging data using the average frequency shift of ambient ions.

Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa.

Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT): a novel glycan-relative quantification strategy.

Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole Orbitrap mass spectrometer.

Understanding the role of proteolytic digestion on discovery and targeted proteomic measurements using liquid chromatography tandem mass spectrometry and design of experiments.

Accurate identification of deamidated peptides in global proteomics using a quadrupole orbitrap mass spectrometer.

Reply to the Comment on: "Utilizing artificial neural networks in MATLAB to achieve parts-per-billion mass measurement accuracy with a Fourier transform ion cyclotron resonance mass spectrometer" by D. Keith Williams Jr., Alexander L. Kovach, David C. Muddiman, and Kenneth W. Hanck. J. Am. Soc. Mass Spectrom. 20, 1303-1310 (2009).

IR-MALDESI mass spectrometry imaging of biological tissue sections using ice as a matrix.

Are presentations at ASMS conferences publications?

Compartment proteomics analysis of white perch (Morone americana) ovary using support vector machines.

Complete proteomic-based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic flux and lignin in Populus trichocarpa.

Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid:coenzyme A ligase protein complex formation, regulation, and numerical modeling.

Mapping antiretroviral drugs in tissue by IR-MALDESI MSI coupled to the Q Exactive and comparison with LC-MS/MS SRM assay.

Analysis of trace fibers by IR-MALDESI imaging coupled with high resolving power MS.

Hierarchical self-assembly of supramolecular hydrophobic metallacycles into ordered nanostructures.

Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry.

Silver dopants for targeted and untargeted direct analysis of unsaturated lipids via infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI).

Quantitative mass spectrometry imaging of emtricitabine in cervical tissue model using infrared matrix-assisted laser desorption electrospray ionization.

Focus on advancing high performance mass spectrometry, honoring dr. Richard d. Smith, recipient of the 2013 award for a distinguished contribution in mass spectrometry.

4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa.

Evaluating nonpolar surface area and liquid chromatography/mass spectrometry response: an application for site occupancy measurements for enzyme intermediates in polyketide biosynthesis.

C/EBPα regulates CRL4(Cdt2)-mediated degradation of p21 in response to UVB-induced DNA damage to control the G1/S checkpoint.

Cellular-level mass spectrometry imaging using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) by oversampling.

Michael Gross: 25 years of dedication and leadership of JASMS (1990-2015).

4-Coumaroyl and caffeoyl shikimic acids inhibit 4-coumaric acid:coenzyme A ligases and modulate metabolic flux for 3-hydroxylation in monolignol biosynthesis of Populus trichocarpa.

Activin/nodal signaling switches the terminal fate of human embryonic stem cell-derived trophoblasts.

Mass spectrometry imaging reveals heterogeneous efavirenz distribution within putative HIV reservoirs.

Influence of Desorption Conditions on Analyte Sensitivity and Internal Energy in Discrete Tissue or Whole Body Imaging by IR-MALDESI.

Machine learning reveals sex-specific 17β-estradiol-responsive expression patterns in white perch (Morone americana) plasma proteins.

Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development.

Assessing drug and metabolite detection in liver tissue by UV-MALDI and IR-MALDESI mass spectrometry imaging coupled to FT-ICR MS.

Definitive Screening Design Optimization of Mass Spectrometry Parameters for Sensitive Comparison of Filter and Solid Phase Extraction Purified, INLIGHT Plasma N-Glycans.

Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis.

In-depth LC-MS/MS analysis of the chicken ovarian cancer proteome reveals conserved and novel differentially regulated proteins in humans.

Global Proteomic Analysis of Functional Compartments in Immature Avian Follicles Using Laser Microdissection Coupled to LC-MS/MS.

Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa.

Relative Quantification and Higher-Order Modeling of the Plasma Glycan Cancer Burden Ratio in Ovarian Cancer Case-Control Samples.

Polarity switching mass spectrometry imaging of healthy and cancerous hen ovarian tissue sections by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI).

Influence of C-Trap Ion Accumulation Time on the Detectability of Analytes in IR-MALDESI MSI.

Mechanisms of Egg Yolk Formation and Implications on Early Life History of White Perch (Morone americana).

What if you could only publish 50 papers your entire career?

Analysis of Antiretrovirals in Single Hair Strands for Evaluation of Drug Adherence with Infrared-Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry Imaging.

Wall modified photonic crystal fibre capillaries as porous layer open tubular columns for in-capillary micro-extraction and capillary chromatography.

TransOmic analysis of forebrain sections in Sp2 conditional knockout embryonic mice using IR-MALDESI imaging of lipids and LC-MS/MS label-free proteomics.

Optimizing Mass Spectrometry Analyses: A Tailored Review on the Utility of Design of Experiments.