Published in Anal Chem on February 01, 2004
Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. J Am Soc Mass Spectrom (2008) 1.36
Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res (2006) 1.33
Structural glycobiology: a game of snakes and ladders. Glycobiology (2008) 1.25
Future directions of structural mass spectrometry using hydroxyl radical footprinting. J Mass Spectrom (2010) 1.16
Structural mass spectrometry of proteins using hydroxyl radical based protein footprinting. Anal Chem (2011) 1.03
Analysis of the oxidative damage-induced conformational changes of apo- and holocalmodulin by dose-dependent protein oxidative surface mapping. Biophys J (2006) 1.02
Fast photochemical oxidation of proteins for comparing structures of protein-ligand complexes: the calmodulin-peptide model system. Anal Chem (2010) 1.01
Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry. Anal Chem (2009) 1.00
Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. J Mass Spectrom (2010) 1.00
Fast photochemical oxidation of proteins (FPOP) maps the epitope of EGFR binding to adnectin. J Am Soc Mass Spectrom (2014) 0.98
Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data. Proc Natl Acad Sci U S A (2007) 0.98
Pulsed electron beam water radiolysis for submicrosecond hydroxyl radical protein footprinting. Anal Chem (2009) 0.95
Cross-talk between the catalytic core and the regulatory domain in cystathionine β-synthase: study by differential covalent labeling and computational modeling. Biochemistry (2010) 0.94
Visualizing water molecules in transmembrane proteins using radiolytic labeling methods. Biochemistry (2010) 0.92
Fast photochemical oxidation of proteins for comparing solvent-accessibility changes accompanying protein folding: data processing and application to barstar. Biochim Biophys Acta (2013) 0.90
High structural resolution hydroxyl radical protein footprinting reveals an extended Robo1-heparin binding interface. J Biol Chem (2015) 0.89
Computing H/D-exchange rates of single residues from data of proteolytic fragments. BMC Bioinformatics (2010) 0.87
Complementing global measures of RNA folding with local reports of backbone solvent accessibility by time resolved hydroxyl radical footprinting. Methods (2009) 0.85
Development of indole chemistry to label tryptophan residues in protein for determination of tryptophan surface accessibility. Protein Sci (2007) 0.84
Myosin binding surface on actin probed by hydroxyl radical footprinting and site-directed labels. J Mol Biol (2011) 0.84
Quantitative mapping of protein structure by hydroxyl radical footprinting-mediated structural mass spectrometry: a protection factor analysis. Biophys J (2015) 0.83
Dosimetry determines the initial OH radical concentration in fast photochemical oxidation of proteins (FPOP). J Am Soc Mass Spectrom (2015) 0.82
Cold chemical oxidation of proteins. Anal Chem (2009) 0.81
The effect of histidine oxidation on the dissociation patterns of peptide ions. J Am Soc Mass Spectrom (2006) 0.80
Antioxidant capacity of hydrolyzed animal by-products and relation to amino acid composition and peptide size distribution. J Food Sci Technol (2015) 0.79
Oxidative protein labeling in mass-spectrometry-based proteomics. Anal Bioanal Chem (2010) 0.79
Structural characterization of semen coagulum-derived SEM1(86-107) amyloid fibrils that enhance HIV-1 infection. Biochemistry (2014) 0.79
Supercharging by m-NBA Improves ETD-Based Quantification of Hydroxyl Radical Protein Footprinting. J Am Soc Mass Spectrom (2015) 0.78
In vitro oxidative footprinting provides insight into apolipoprotein B-100 structure in low-density lipoprotein. Proteomics (2014) 0.78
Chemical reactivity of brome mosaic virus capsid protein. J Mol Biol (2012) 0.78
Modeling of the DNA-binding site of yeast Pms1 by mass spectrometry. DNA Repair (Amst) (2011) 0.76
Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking. J Struct Biol (2016) 0.75
Relative Quantification of Sites of Peptide and Protein Modification Using Size Exclusion Chromatography Coupled with Electron Transfer Dissociation. J Am Soc Mass Spectrom (2016) 0.75
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Community proteomics of a natural microbial biofilm. Science (2005) 3.97
Detecting differential and correlated protein expression in label-free shotgun proteomics. J Proteome Res (2006) 3.51
Shotgun metaproteomics of the human distal gut microbiota. ISME J (2008) 3.43
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science (2012) 3.39
Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J Proteome Res (2006) 3.32
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature (2007) 2.53
Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J Bacteriol (2004) 2.23
Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A (2010) 2.12
Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol (2009) 1.86
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One (2012) 1.84
Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol (2009) 1.81
Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J (2008) 1.60
Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A (2010) 1.58
Candida albicans septin mutants are defective for invasive growth and virulence. Infect Immun (2003) 1.58
Deletion of the Cel48S cellulase from Clostridium thermocellum. Proc Natl Acad Sci U S A (2010) 1.54
Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J Proteome Res (2012) 1.50
Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol (2009) 1.45
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol (2013) 1.45
Harnessing natural diversity to probe metabolic pathways. PLoS Genet (2005) 1.39
Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach. J Proteome Res (2004) 1.38
Molecular dynamics of the Shewanella oneidensis response to chromate stress. Mol Cell Proteomics (2006) 1.35
Differential regulation and substrate preferences in two peptide transporters of Saccharomyces cerevisiae. Eukaryot Cell (2007) 1.34
MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence. Anal Chem (2005) 1.34
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J Bacteriol (2012) 1.32
Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res (2010) 1.31
DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal Chem (2005) 1.30
Genomewide screen reveals a wide regulatory network for di/tripeptide utilization in Saccharomyces cerevisiae. Genetics (2005) 1.28
An oligopeptide transporter gene family in Arabidopsis. Plant Physiol (2002) 1.25
Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS (2004) 1.25
Peptide transport in plants. Trends Plant Sci (2002) 1.20
Wangiella (Exophiala) dermatitidis WdChs5p, a class V chitin synthase, is essential for sustained cell growth at temperature of infection. Eukaryot Cell (2004) 1.18
Protein surface mapping by chemical oxidation: structural analysis by mass spectrometry. Anal Biochem (2003) 1.17
Identification of phosphorylation sites on the yeast ribonucleotide reductase inhibitor Sml1. J Biol Chem (2003) 1.17
The alpha-factor mating pheromone of Saccharomyces cerevisiae: a model for studying the interaction of peptide hormones and G protein-coupled receptors. Peptides (2004) 1.17
ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Anal Chem (2006) 1.16
Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship. PLoS One (2011) 1.14
Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics. Mol Cell Proteomics (2007) 1.13
Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics (2012) 1.13
Integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensis. J Proteome Res (2003) 1.12
Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. PLoS One (2011) 1.09
A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics (2004) 1.08
Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics. Anal Chem (2006) 1.08
Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J (2008) 1.07
Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One (2012) 1.07
Cultivation and quantitative proteomic analyses of acidophilic microbial communities. ISME J (2009) 1.07
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res (2011) 1.06
Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol (2008) 1.05
Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ Microbiol (2011) 1.04
Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles. Environ Sci Technol (2010) 1.04
Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1. Appl Environ Microbiol (2006) 1.04
Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J (2012) 1.03
Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Appl Environ Microbiol (2011) 1.03
Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial community. Appl Environ Microbiol (2008) 1.03
A fluorescent alpha-factor analogue exhibits multiple steps on binding to its G protein coupled receptor in yeast. Biochemistry (2004) 1.03
Photochemical surface mapping of C14S-Sml1p for constrained computational modeling of protein structure. Anal Biochem (2005) 1.00
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. BMC Bioinformatics (2010) 0.99
Experimental approach for deep proteome measurements from small-scale microbial biomass samples. Anal Chem (2008) 0.99
Dosage-dependent proteome response of Shewanella oneidensis MR-1 to acute chromate challenge. J Proteome Res (2007) 0.99
Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol Syst Biol (2010) 0.99
The first extracellular loop of the Saccharomyces cerevisiae G protein-coupled receptor Ste2p undergoes a conformational change upon ligand binding. J Biol Chem (2007) 0.99
Identification of ligand binding regions of the Saccharomyces cerevisiae alpha-factor pheromone receptor by photoaffinity cross-linking. Biochemistry (2004) 0.98
Unnatural amino acid replacement in a yeast G protein-coupled receptor in its native environment. Biochemistry (2008) 0.98
Identification of a contact region between the tridecapeptide alpha-factor mating pheromone of Saccharomyces cerevisiae and its G protein-coupled receptor by photoaffinity labeling. Biochemistry (2002) 0.97
Role of the CipA scaffoldin protein in cellulose solubilization, as determined by targeted gene deletion and complementation in Clostridium thermocellum. J Bacteriol (2012) 0.97
Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass. J Proteome Res (2011) 0.96
Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis. J Proteome Res (2007) 0.96
Metabolome-proteome differentiation coupled to microbial divergence. MBio (2010) 0.95
Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS (2005) 0.94
Microbes in thawing permafrost: the unknown variable in the climate change equation. ISME J (2011) 0.94
Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra. J Am Soc Mass Spectrom (2006) 0.94
Residues in the first extracellular loop of a G protein-coupled receptor play a role in signal transduction. J Biol Chem (2002) 0.93
Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteomics (2011) 0.93
Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization. J Proteome Res (2012) 0.93
Development of an electrochemical oxidation method for probing higher order protein structure with mass spectrometry. Anal Chem (2008) 0.93
Tyr266 in the sixth transmembrane domain of the yeast alpha-factor receptor plays key roles in receptor activation and ligand specificity. Biochemistry (2002) 0.92
Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow"). Appl Environ Microbiol (2013) 0.92
Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J Proteome Res (2014) 0.92
Biosynthesis and NMR analysis of a 73-residue domain of a Saccharomyces cerevisiae G protein-coupled receptor. Biochemistry (2005) 0.91
Nutrient regulation of oligopeptide transport in Saccharomyces cerevisiae. Microbiology (2006) 0.91
Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformation. J Proteome Res (2009) 0.90
Interacting residues in an activated state of a G protein-coupled receptor. J Biol Chem (2005) 0.89
New technologies for nutrition research. J Nutr (2004) 0.89
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra. Bioinformatics (2004) 0.89
Substrate preference is altered by mutations in the fifth transmembrane domain of Ptr2p, the di/tri-peptide transporter of Saccharomyces cerevisiae. Mol Membr Biol (2005) 0.88
Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME J (2011) 0.88
Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge. BMC Genomics (2010) 0.87
Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site. Proteomics (2013) 0.87
Affinity purification and characterization of a G-protein coupled receptor, Saccharomyces cerevisiae Ste2p. Protein Expr Purif (2007) 0.87
New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS". Appl Environ Microbiol (2013) 0.87
Differential accumulation of form I RubisCO in Rhodopseudomonas palustris CGA010 under Photoheterotrophic growth conditions with reduced carbon sources. J Bacteriol (2009) 0.87
Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol (2011) 0.86
Cross-linking of a DOPA-containing peptide ligand into its G protein-coupled receptor. Biochemistry (2009) 0.86
Selective labeling of a membrane peptide with 15N-amino acids using cells grown in rich medium. Biopolymers (2006) 0.85
Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community. J Proteome Res (2010) 0.85
Sequences in the intracellular loops of the yeast pheromone receptor Ste2p required for G protein activation. Biochemistry (2003) 0.84
Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J Proteome Res (2011) 0.84
Identification of residue-to-residue contact between a peptide ligand and its G protein-coupled receptor using periodate-mediated dihydroxyphenylalanine cross-linking and mass spectrometry. J Biol Chem (2010) 0.84