Published in Biochemistry on January 24, 2006
Decoding protein modifications using top-down mass spectrometry. Nat Methods (2007) 2.62
Top-down quantitative proteomics identified phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure. J Proteome Res (2011) 2.17
Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state. Proc Natl Acad Sci U S A (2009) 2.10
Top-down mass spectrometry: recent developments, applications and perspectives. Analyst (2011) 1.50
Comprehensive analysis of protein modifications by top-down mass spectrometry. Circ Cardiovasc Genet (2011) 1.34
Structure-based prediction of asparagine and aspartate degradation sites in antibody variable regions. PLoS One (2014) 1.28
Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides. Electrophoresis (2010) 1.22
An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications. J Proteome Res (2009) 1.21
Deamidation destabilizes and triggers aggregation of a lens protein, betaA3-crystallin. Protein Sci (2008) 1.20
Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation. Mol Cell Proteomics (2011) 1.18
Analysis of intact protein isoforms by mass spectrometry. J Biol Chem (2011) 1.15
Automethylation of CARM1 allows coupling of transcription and mRNA splicing. Nucleic Acids Res (2010) 1.09
Top-down proteomics in health and disease: challenges and opportunities. Proteomics (2014) 1.08
Simultaneous assessment of Asp isomerization and Asn deamidation in recombinant antibodies by LC-MS following incubation at elevated temperatures. PLoS One (2012) 0.98
Delineating Anopheles gambiae coactivator associated arginine methyltransferase 1 automethylation using top-down high resolution tandem mass spectrometry. Protein Sci (2009) 0.96
Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli. J Bacteriol (2008) 0.94
Effect of protein structure on deamidation rate in the Fc fragment of an IgG1 monoclonal antibody. Protein Sci (2009) 0.87
Enhanced detection and identification of glycopeptides in negative ion mode mass spectrometry. Anal Chem (2010) 0.83
Defining intact protein primary structures from saliva: a step toward the human proteome project. Anal Chem (2012) 0.82
Top-down study of β2-microglobulin deamidation. Anal Chem (2012) 0.82
Deamidation of alpha-synuclein. Protein Sci (2009) 0.80
Characterization of deamidation of barstar using electrospray ionization quadrupole time-of-flight mass spectrometry, which stabilizes an equilibrium unfolding intermediate. Protein Sci (2012) 0.80
Top-down tandem mass spectrometry on RNase A and B using a Qh/FT-ICR hybrid mass spectrometer. Proteomics (2014) 0.78
Assignments of RNase A by ADAPT-NMR and enhancer. Biomol NMR Assign (2014) 0.76
Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry. Nucleic Acids Res (2017) 0.75
Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J Am Soc Mass Spectrom (2000) 5.44
Electron capture dissociation for structural characterization of multiply charged protein cations. Anal Chem (2000) 4.93
Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Anal Chem (1994) 3.88
Top-down proteomics. Anal Chem (2004) 3.01
Multiple forms of cytochrome c in the rat. Precursor-product relationship between the main component Cy I and the minor components Cy II and Cy 3 in vivo. J Biol Chem (1968) 2.76
Controlled deamidation of peptides and proteins: an experimental hazard and a possible biological timer. Proc Natl Acad Sci U S A (1970) 2.72
Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc (2002) 2.72
Collisional activation of large multiply charged ions using Fourier transform mass spectrometry. Anal Chem (1994) 2.58
Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis (1994) 2.41
The burst phase in ribonuclease A folding and solvent dependence of the unfolded state. Nat Struct Biol (1998) 1.78
Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol (2002) 1.70
Techview: biochemistry. Biomolecule mass spectrometry. Science (1999) 1.39
Prediction of protein deamidation rates from primary and three-dimensional structure. Proc Natl Acad Sci U S A (2001) 1.36
Reconstitution and biochemical characterization of a new pyridoxal-5'-phosphate biosynthetic pathway. J Am Chem Soc (2005) 1.25
Deamidation: Differentiation of aspartyl from isoaspartyl products in peptides by electron capture dissociation. Protein Sci (2005) 1.23
Sequence and structure determinants of the nonenzymatic deamidation of asparagine and glutamine residues in proteins. Protein Eng (1991) 1.22
Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry (2001) 1.20
The specific nonenzymatic cleavage of bovine ribonuclease with hydroxylamine. J Biol Chem (1970) 1.17
Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry. Anal Chem (2003) 1.14
Fourier-transform electrospray instrumentation for tandem high-resolution mass spectrometry of large molecules. J Am Soc Mass Spectrom (1993) 1.13
Microheterogeneity of recombinant human phenylalanine hydroxylase as a result of nonenzymatic deamidations of labile amide containing amino acids. Effects on catalytic and stability properties. Eur J Biochem (2000) 1.08
Reversible blocking of half-cystine residues of proteins and an irreversible specific deamidation of asparagine-67 of S-sulforibonuclease under mild conditions. Biochemistry (1985) 1.00
Specific glutamine and asparagine residues of gamma-S crystallin are resistant to in vivo deamidation. J Biol Chem (2000) 0.98
Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues. J Mol Biol (2004) 0.96
Selective deamidation of ribonuclease A. Isolation and characterization of the resulting isoaspartyl and aspartyl derivatives. J Biol Chem (1993) 0.96
Deamidation of the asparaginyl-glycyl sequence. Int J Pept Protein Res (1986) 0.95
Extension of dynamic range in Fourier transform ion cyclotron resonance mass spectrometry via stored waveform inverse Fourier transform excitation. Anal Chem (1986) 0.94
Local and long-range interactions in the thermal unfolding transition of bovine pancreatic ribonuclease A. Biochemistry (2001) 0.93
Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry. Chem Biol (2004) 0.85
Effect of deamidation on folding of ribonuclease A. Protein Sci (2000) 0.84
Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A. Protein Sci (1997) 0.83
Simultaneous kinetic characterization of multiple protein forms by top down mass spectrometry. J Am Soc Mass Spectrom (2005) 0.83
Deamidation of labile asparagine residues in the autoregulatory sequence of human phenylalanine hydroxylase. Eur J Biochem (2003) 0.80
Isolation and characterization of monodeamidated derivatives of bovine pancreatic ribonuclease A. Int J Pept Protein Res (1984) 0.79
Influence of deamidation(s) in the 67-74 region of ribonuclease on its refolding. Int J Pept Protein Res (1985) 0.78
Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for β-Pix in negative regulation of focal adhesion maturation. Nat Cell Biol (2011) 4.59
Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science (2006) 3.93
Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One (2008) 3.41
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci U S A (2005) 2.85
Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc (2002) 2.72
Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Proc Natl Acad Sci U S A (2002) 2.62
The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res (2008) 2.53
Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell (2002) 2.48
Detailed unfolding and folding of gaseous ubiquitin ions characterized by electron capture dissociation. J Am Chem Soc (2002) 2.45
Protein profiling of plastoglobules in chloroplasts and chromoplasts. A surprising site for differential accumulation of metabolic enzymes. Plant Physiol (2006) 2.45
A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells. Cancer Cell (2011) 2.41
The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure. PLoS Genet (2008) 2.35
PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res (2008) 2.29
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci U S A (2002) 2.20
Consequences of membrane protein overexpression in Escherichia coli. Mol Cell Proteomics (2007) 2.11
Tuning Escherichia coli for membrane protein overexpression. Proc Natl Acad Sci U S A (2008) 2.11
The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Mol Cell Proteomics (2005) 2.01
Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). J Proteome Res (2009) 1.97
Lipid segregation and IgE receptor signaling: a decade of progress. Biochim Biophys Acta (2005) 1.94
Stepwise evolution of protein native structure with electrospray into the gas phase, 10(-12) to 10(2) s. Proc Natl Acad Sci U S A (2008) 1.91
RAF inhibitors activate the MAPK pathway by relieving inhibitory autophosphorylation. Cancer Cell (2013) 1.89
Secondary and tertiary structures of gaseous protein ions characterized by electron capture dissociation mass spectrometry and photofragment spectroscopy. Proc Natl Acad Sci U S A (2002) 1.85
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proc Natl Acad Sci U S A (2002) 1.76
Arginyltransferase is an ATP-independent self-regulating enzyme that forms distinct functional complexes in vivo. Chem Biol (2011) 1.76
Proline cis-trans isomerization and protein folding. Biochemistry (2002) 1.76
Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts. Curr Opin Plant Biol (2006) 1.75
Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics. Plant Cell (2005) 1.73
Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. J Phys Chem B (2005) 1.71
Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. J Biomol NMR (2006) 1.71
Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers. Proc Natl Acad Sci U S A (2014) 1.71
Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1). Biochemistry (2003) 1.70
Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics (2008) 1.70
Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems. J Phys Chem B (2005) 1.69
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci U S A (2002) 1.64
Arginylation regulates myofibrils to maintain heart function and prevent dilated cardiomyopathy. J Mol Cell Cardiol (2012) 1.64
Molecular origin of anticooperativity in hydrophobic association. J Phys Chem B (2005) 1.62
Isogenic human iPSC Parkinson's model shows nitrosative stress-induced dysfunction in MEF2-PGC1α transcription. Cell (2013) 1.61
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation. Proc Natl Acad Sci U S A (2009) 1.59
Predicting 13Calpha chemical shifts for validation of protein structures. J Biomol NMR (2007) 1.59
MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol (2010) 1.59
Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications. J Biol Chem (2003) 1.59
Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J Mol Biol (2004) 1.58
Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize. Plant Cell (2010) 1.58
Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proc Natl Acad Sci U S A (2006) 1.57
Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54
Nonergodic and conformational control of the electron capture dissociation of protein cations. Proc Natl Acad Sci U S A (2004) 1.53
Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly. Plant Physiol (2010) 1.51
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci U S A (2008) 1.50
Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering. Mol Cell Proteomics (2010) 1.50
Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves: a new conceptual framework for nucleoid functions. Plant Physiol (2011) 1.49
New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast, and versatile fractionation strategy. J Biol Chem (2004) 1.49
Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J (2007) 1.47
O-GlcNAc transferase/host cell factor C1 complex regulates gluconeogenesis by modulating PGC-1α stability. Cell Metab (2012) 1.46
Plastoglobules: versatile lipoprotein particles in plastids. Trends Plant Sci (2007) 1.44
Transnitrosylation of XIAP regulates caspase-dependent neuronal cell death. Mol Cell (2010) 1.44
The role of hydrophobic interactions in initiation and propagation of protein folding. Proc Natl Acad Sci U S A (2006) 1.42
Principal component analysis for protein folding dynamics. J Mol Biol (2008) 1.42
Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry. J Am Soc Mass Spectrom (2003) 1.41
A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis. Nucleic Acids Res (2008) 1.41
Expression of tetanus toxin Fragment C in tobacco chloroplasts. Nucleic Acids Res (2003) 1.40
Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. J Am Chem Soc (2005) 1.40
Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test. Acta Crystallogr B (2011) 1.40
Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proc Natl Acad Sci U S A (2003) 1.40
Acetylation of sox2 induces its nuclear export in embryonic stem cells. Stem Cells (2009) 1.39
Encephalopathy as an initial symptom of rhabdomyolysis. Neurol India (2011) 1.37
A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts. Plant Cell (2007) 1.34
Retracted The pathogen-inducible nitric oxide synthase (iNOS) in plants is a variant of the P protein of the glycine decarboxylase complex. Cell (2003) 1.33
RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proc Natl Acad Sci U S A (2012) 1.32
Top-down identification and characterization of biomolecules by mass spectrometry. J Am Soc Mass Spectrom (2008) 1.31
Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test. Acta Crystallogr B (2009) 1.29
Long-lived electron capture dissociation product ions experience radical migration via hydrogen abstraction. J Am Soc Mass Spectrom (2006) 1.29
Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis. Mol Cell Proteomics (2011) 1.29
Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics (2009) 1.27
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. J Chem Theory Comput (2006) 1.27
The interaction of CtIP and Nbs1 connects CDK and ATM to regulate HR-mediated double-strand break repair. PLoS Genet (2013) 1.27
Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem (2003) 1.27
Reconstitution and biochemical characterization of a new pyridoxal-5'-phosphate biosynthetic pathway. J Am Chem Soc (2005) 1.25
Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains. J Mol Biol (2005) 1.25
Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis. Plant Cell (2009) 1.24
A new approach for plant proteomics: characterization of chloroplast proteins of Arabidopsis thaliana by top-down mass spectrometry. Mol Cell Proteomics (2003) 1.24
The biosynthesis of the thiazole phosphate moiety of thiamin: the sulfur transfer mediated by the sulfur carrier protein ThiS. Chem Biol (2004) 1.24
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems. J Phys Chem B (2007) 1.23
The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis. Plant Physiol (2012) 1.23
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. J Comput Chem (2009) 1.22
Native electron capture dissociation for the structural characterization of noncovalent interactions in native cytochrome C. Angew Chem Int Ed Engl (2003) 1.21
A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics. Rapid Commun Mass Spectrom (2006) 1.20
YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics (2009) 1.20
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A (2010) 1.19
A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing. Proc Natl Acad Sci U S A (2009) 1.19
Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins. J Chem Theory Comput (2009) 1.19