Published in Curr Opin Chem Biol on July 05, 2013
Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Anal Chem (2015) 0.87
Mass spectrometry-based proteomics for pre-eclampsia and preterm birth. Int J Mol Sci (2015) 0.81
Neucode Labels for Multiplexed, Absolute Protein Quantification. Anal Chem (2016) 0.81
Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level. Proteomics (2016) 0.77
Evaluation and Application of Dimethylated Amino Acids as Isobaric Tags for Quantitative Proteomics of the TGF-β/Smad3 Signaling Pathway. J Proteome Res (2016) 0.75
Development of capillary liquid chromatography: A personal perspective. J Chromatogr A (2017) 0.75
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
Global quantification of mammalian gene expression control. Nature (2011) 22.36
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol (1999) 21.92
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics (2004) 19.05
A tissue-specific atlas of mouse protein phosphorylation and expression. Cell (2010) 8.65
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell (2011) 7.30
Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem (2003) 6.63
Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science (2011) 5.73
Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell (2008) 5.38
SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell (2008) 5.02
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics (2011) 4.40
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell (2010) 4.31
Global landscape of HIV-human protein complexes. Nature (2011) 3.70
MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods (2011) 3.40
Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem (2011) 3.19
Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods (2010) 2.95
Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. Cell Rep (2012) 2.66
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell (2012) 2.54
Global and site-specific quantitative phosphoproteomics: principles and applications. Annu Rev Pharmacol Toxicol (2009) 2.53
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol (2011) 2.44
Quantitative phosphoproteomics reveal mTORC1 activates de novo pyrimidine synthesis. Science (2013) 2.44
Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet (2012) 2.39
Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods (2011) 2.39
8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics (2007) 2.33
Mass spectrometry-based proteomics and network biology. Annu Rev Biochem (2012) 2.02
Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal Chem (2012) 1.96
Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods (2011) 1.87
A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods (2011) 1.87
Quantitative proteomics reveals a dynamic interactome and phase-specific phosphorylation in the Neurospora circadian clock. Mol Cell (2009) 1.80
High confidence determination of specific protein-protein interactions using quantitative mass spectrometry. Curr Opin Biotechnol (2008) 1.72
Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat Commun (2012) 1.72
A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res (2008) 1.60
Proteome-wide mapping of cholesterol-interacting proteins in mammalian cells. Nat Methods (2013) 1.59
Quantitative phosphoproteomics by mass spectrometry: past, present, and future. Proteomics (2008) 1.50
Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol Cell Proteomics (2011) 1.47
Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast. Sci Signal (2012) 1.42
Quantitative proteomics by metabolic labeling of model organisms. Mol Cell Proteomics (2009) 1.42
Neutron-encoded mass signatures for multiplexed proteome quantification. Nat Methods (2013) 1.39
Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat Methods (2011) 1.34
Proteomic changes resulting from gene copy number variations in cancer cells. PLoS Genet (2010) 1.32
Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles. Mol Cell Proteomics (2012) 1.29
High-resolution enabled TMT 8-plexing. Anal Chem (2012) 1.29
Accurate quantification of more than 4000 mouse tissue proteins reveals minimal proteome changes during aging. Mol Cell Proteomics (2010) 1.28
Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery. Mol Cell (2011) 1.27
Unbiased RNA-protein interaction screen by quantitative proteomics. Proc Natl Acad Sci U S A (2009) 1.26
The phosphotyrosine interactome of the insulin receptor family and its substrates IRS-1 and IRS-2. Mol Cell Proteomics (2008) 1.25
Proteome-wide systems analysis of a cellulosic biofuel-producing microbe. Mol Syst Biol (2011) 1.18
A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis. Cell Metab (2012) 1.16
Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding. PLoS Genet (2012) 1.13
Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J Proteome Res (2003) 1.10
Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc Natl Acad Sci U S A (2012) 1.08
Building protein-protein interaction networks with proteomics and informatics tools. J Biol Chem (2011) 0.92
Triple SILAC to determine stimulus specific interactions in the Wnt pathway. J Proteome Res (2011) 0.91
In-depth quantitative cardiac proteomics combining electron transfer dissociation and the metalloendopeptidase Lys-N with the SILAC mouse. Mol Cell Proteomics (2011) 0.83
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A (2004) 13.14
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A (2007) 5.09
Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nat Chem Biol (2007) 3.60
Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods (2008) 3.53
Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal Chem (2007) 3.32
Performance characteristics of electron transfer dissociation mass spectrometry. Mol Cell Proteomics (2007) 3.09
A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal Chem (2004) 3.08
Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics (2012) 3.05
The utility of ETD mass spectrometry in proteomic analysis. Biochim Biophys Acta (2006) 2.85
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell (2012) 2.54
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol (2011) 2.44
Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods (2011) 2.39
Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res (2010) 2.36
Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proc Natl Acad Sci U S A (2008) 2.29
Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem (2009) 2.20
COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Proteomics (2011) 2.19
Urinary proteomics in diabetes and CKD. J Am Soc Nephrol (2008) 2.12
The one hour yeast proteome. Mol Cell Proteomics (2013) 2.10
Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A (2009) 1.95
Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal Chem (2007) 1.92
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res (2008) 1.92
Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol Cell Proteomics (2010) 1.90
Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods (2011) 1.87
Post-acquisition ETD spectral processing for increased peptide identifications. J Am Soc Mass Spectrom (2009) 1.86
Phosphoproteomics for the masses. ACS Chem Biol (2010) 1.83
Recommendations for biomarker identification and qualification in clinical proteomics. Sci Transl Med (2010) 1.59
Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J Proteome Res (2007) 1.52
Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation. J Biol Chem (2007) 1.51
Urinary proteomic biomarkers in coronary artery disease. Mol Cell Proteomics (2007) 1.47
Identification and validation of urinary biomarkers for differential diagnosis and evaluation of therapeutic intervention in anti-neutrophil cytoplasmic antibody-associated vasculitis. Mol Cell Proteomics (2009) 1.41
A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. J Proteome Res (2013) 1.40
Neutron-encoded mass signatures for multiplexed proteome quantification. Nat Methods (2013) 1.39
Advancing proteomics with ion/ion chemistry. Biotechniques (2006) 1.29
Peptide and protein quantification using iTRAQ with electron transfer dissociation. J Am Soc Mass Spectrom (2008) 1.29
Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J Biol Chem (2012) 1.27
Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol (2009) 1.27
Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases. Electrophoresis (2007) 1.26
Higher-energy collision-activated dissociation without a dedicated collision cell. Mol Cell Proteomics (2011) 1.26
Over 10,000 peptide identifications from the HeLa proteome by using single-shot capillary zone electrophoresis combined with tandem mass spectrometry. Angew Chem Int Ed Engl (2014) 1.25
Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture. Anal Chem (2010) 1.22
Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal Chem (2010) 1.22
Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation. J Biol Chem (2013) 1.20
Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments. Mass Spectrom Rev (2009) 1.19
Phosphorylation regulates human OCT4. Proc Natl Acad Sci U S A (2012) 1.19
Infrared photoactivation reduces peptide folding and hydrogen-atom migration following ETD tandem mass spectrometry. Angew Chem Int Ed Engl (2009) 1.17
A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis. Cell Metab (2012) 1.16
A new probabilistic database search algorithm for ETD spectra. J Proteome Res (2009) 1.15
Valence parity renders z(*)-type ions chemically distinct. J Am Chem Soc (2008) 1.15
The effect of interfering ions on search algorithm performance for electron-transfer dissociation data. Proteomics (2010) 1.13
The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease. Proteomics (2009) 1.11
Implementing photodissociation in an Orbitrap mass spectrometer. J Am Soc Mass Spectrom (2011) 1.09
Peptide quantification using 8-plex isobaric tags and electron transfer dissociation tandem mass spectrometry. Anal Chem (2009) 1.08
Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc Natl Acad Sci U S A (2012) 1.08
Analysis of the acidic proteome with negative electron-transfer dissociation mass spectrometry. Anal Chem (2012) 1.05
Characterization and diagnostic value of amino acid side chain neutral losses following electron-transfer dissociation. J Am Soc Mass Spectrom (2011) 1.05
Statistical analysis of electron transfer dissociation pairwise fragmentation patterns. Anal Chem (2011) 1.02
Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal Chem (2007) 1.01
Infrared multiphoton dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer. Anal Chem (2009) 1.01
Rapid phosphoproteomic and transcriptomic changes in the rhizobia-legume symbiosis. Mol Cell Proteomics (2012) 1.00
Discovery and validation of urinary biomarkers for prostate cancer. Proteomics Clin Appl (2008) 1.00
Comprehensive mass spectrometric mapping of the hydroxylated amino acid residues of the α1(V) collagen chain. J Biol Chem (2012) 0.99
Neutron encoded labeling for peptide identification. Anal Chem (2013) 0.96
Toward defining the phosphoproteome of Xenopus laevis embryos. Dev Dyn (2009) 0.94
Characterization of molecules binding to the 70K N-terminal region of fibronectin by IFAST purification coupled with mass spectrometry. J Proteome Res (2013) 0.93
Sub-part-per-million precursor and product mass accuracy for high-throughput proteomics on an electron transfer dissociation-enabled orbitrap mass spectrometer. Mol Cell Proteomics (2010) 0.92
Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation. Mol Cell Proteomics (2013) 0.92
Cascade dissociations of peptide cation-radicals. Part 1. Scope and effects of amino acid residues in penta-, nona-, and decapeptides. J Am Soc Mass Spectrom (2012) 0.91
Intelligent data acquisition blends targeted and discovery methods. J Proteome Res (2014) 0.90
Development of a GC/Quadrupole-Orbitrap mass spectrometer, part II: new approaches for discovery metabolomics. Anal Chem (2014) 0.89
Activated ion ETD performed in a modified collision cell on a hybrid QLT-Oribtrap mass spectrometer. J Am Soc Mass Spectrom (2013) 0.88
Segmentation of precursor mass range using "tiling" approach increases peptide identifications for MS1-based label-free quantification. Anal Chem (2013) 0.88
Development and characterization of a GC-enabled QLT-Orbitrap for high-resolution and high-mass accuracy GC/MS. Anal Chem (2010) 0.88
Neutron-encoded signatures enable product ion annotation from tandem mass spectra. Mol Cell Proteomics (2013) 0.88
Multipurpose dissociation cell for enhanced ETD of intact protein species. J Am Soc Mass Spectrom (2013) 0.87
A proteogenomic survey of the Medicago truncatula genome. Mol Cell Proteomics (2012) 0.87
Neutron-encoded mass signatures for quantitative top-down proteomics. Anal Chem (2014) 0.87
Top-down protein fragmentation by infrared multiphoton dissociation in a dual pressure linear ion trap. Anal Chem (2009) 0.86
Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry. PLoS One (2013) 0.86
Phosphorylation sites of Epstein-Barr virus EBNA1 regulate its function. J Gen Virol (2009) 0.86
Unraveling the histone's potential: a proteomics perspective. Epigenetics (2008) 0.86
Medicago PhosphoProtein Database: a repository for Medicago truncatula phosphoprotein data. Front Plant Sci (2012) 0.85
Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization. Anal Chem (2014) 0.85
Automated gas-phase purification for accurate, multiplexed quantification on a stand-alone ion-trap mass spectrometer. Anal Chem (2012) 0.85
Chemical derivatization of peptide carboxyl groups for highly efficient electron transfer dissociation. J Am Soc Mass Spectrom (2013) 0.84
Characterizing peptide neutral losses induced by negative electron-transfer dissociation (NETD). J Am Soc Mass Spectrom (2012) 0.84
Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides. J Am Soc Mass Spectrom (2012) 0.84
Multiplexed quantification for data-independent acquisition. Anal Chem (2015) 0.83
Neutron-encoded protein quantification by peptide carbamylation. J Am Soc Mass Spectrom (2013) 0.83
In vacuo formation of peptide-metal coordination complexes. Int J Mass Spectrom (2008) 0.81
Ion-Ion Reactions with Fixed-Charge Modified Proteins to Produce Ions in a Single, Very High Charge State. Int J Mass Spectrom (2008) 0.80
Organic acid quantitation by NeuCode methylamidation. Anal Chem (2014) 0.79
Mass spectrometric analysis of body fluids for biomarker discovery. Methods Mol Biol (2009) 0.78
Proteomics and pluripotency. Crit Rev Biochem Mol Biol (2011) 0.77
Infrared multiphoton dissociation for quantitative shotgun proteomics. Anal Chem (2012) 0.77
Protein digestion and phosphopeptide enrichment on a glass microchip. Anal Chim Acta (2005) 0.76
Identifying post-translational modifications of NEMO by tandem mass spectrometry after high affinity purification. Protein Expr Purif (2013) 0.76
F-box protein FBXL16 binds PP2A-B55α and regulates differentiation of embryonic stem cells along the FLK1+ lineage. Mol Cell Proteomics (2014) 0.76
Parallel detection of intrinsic fluorescence from peptides and proteins for quantification during mass spectrometric analysis. Anal Chem (2011) 0.76
Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLoS Genet (2016) 0.75
Intellinsity: a tool for visualization and analysis of liquid chromatography/tandem mass spectrometry sampling events. Rapid Commun Mass Spectrom (2010) 0.75