Published in Mol Cell Proteomics on October 04, 2005
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
Large-scale proteomics analysis of the human kinome. Mol Cell Proteomics (2009) 2.49
Discovery of TBC1D1 as an insulin-, AICAR-, and contraction-stimulated signaling nexus in mouse skeletal muscle. J Biol Chem (2008) 2.09
A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat Biotechnol (2013) 1.93
Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis. Proc Natl Acad Sci U S A (2008) 1.34
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database (Oxford) (2011) 1.32
Identification of novel protein kinase A phosphorylation sites in the M-domain of human and murine cardiac myosin binding protein-C using mass spectrometry analysis. J Proteome Res (2010) 1.28
Herpesvirus gB-induced fusion between the virion envelope and outer nuclear membrane during virus egress is regulated by the viral US3 kinase. J Virol (2009) 1.27
Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry. Mol Cell Proteomics (2009) 1.22
JNK phosphorylates beta-catenin and regulates adherens junctions. FASEB J (2009) 1.21
The geometry of multisite phosphorylation. Biophys J (2008) 1.19
Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Mol Cell Proteomics (2012) 1.15
PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity. BMC Bioinformatics (2011) 1.10
Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. Mol Cell Proteomics (2014) 1.08
Distributivity and processivity in multisite phosphorylation can be distinguished through steady-state invariants. Biophys J (2007) 1.06
Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions. Mol Syst Biol (2011) 1.03
Spatial differences in an integral membrane proteome detected in laser capture microdissected samples. J Proteome Res (2008) 1.03
Quantitative proteomics analysis of phosphorylated proteins in the hippocampus of Alzheimer's disease subjects. J Proteomics (2011) 1.01
Phosphorylation of the 12 S globulin cruciferin in wild-type and abi1-1 mutant Arabidopsis thaliana (thale cress) seeds. Biochem J (2007) 1.01
Chemical visualization of phosphoproteomes on membrane. Mol Cell Proteomics (2012) 1.01
Diphosphoinositol polyphosphates: what are the mechanisms? Adv Enzyme Regul (2010) 0.98
Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry. J Mass Spectrom (2008) 0.97
Tyrosine phosphorylation in the SH3 domain disrupts negative regulatory interactions within the c-Abl kinase core. J Mol Biol (2008) 0.95
Quantification of protein phosphorylation by liquid chromatography-mass spectrometry. Anal Chem (2008) 0.95
Introduction to computational proteomics. PLoS Comput Biol (2007) 0.94
Identifying protein phosphorylation sites with kinase substrate specificity on human viruses. PLoS One (2012) 0.93
Mass spectral characterization of organophosphate-labeled, tyrosine-containing peptides: characteristic mass fragments and a new binding motif for organophosphates. J Chromatogr B Analyt Technol Biomed Life Sci (2009) 0.92
Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea. MBio (2016) 0.91
Identification and characterization of phosphorylation sites within the pregnane X receptor protein. Biochem Pharmacol (2013) 0.89
Unambiguous determination of isobaric histone modifications by reversed-phase retention time and high-mass accuracy. Anal Biochem (2009) 0.87
A method to determine the ionization efficiency change of peptides caused by phosphorylation. J Am Soc Mass Spectrom (2007) 0.86
PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information. J Proteome Res (2008) 0.86
Deconstructing honeybee vitellogenin: novel 40 kDa fragment assigned to its N terminus. J Exp Biol (2011) 0.86
Covalent tagging of phosphorylated peptides by phosphate-specific deoxyribozymes. Chembiochem (2012) 0.85
Mesoporous zirconium oxide nanomaterials effectively enrich phosphopeptides for mass spectrometry-based phosphoproteomics. Chem Commun (Camb) (2009) 0.84
Phosphopeptide elution times in reversed-phase liquid chromatography. J Chromatogr A (2007) 0.84
Strong cation exchange chromatography in analysis of posttranslational modifications: innovations and perspectives. J Biomed Biotechnol (2011) 0.84
Phosphorylation of the proline-rich domain of Xp95 modulates Xp95 interaction with partner proteins. Biochem J (2007) 0.84
Oncogenic RET kinase domain mutations perturb the autophosphorylation trajectory by enhancing substrate presentation in trans. Mol Cell (2014) 0.83
Effective enrichment and mass spectrometry analysis of phosphopeptides using mesoporous metal oxide nanomaterials. Anal Chem (2010) 0.82
Sulfonium ion derivatization, isobaric stable isotope labeling and data dependent CID- and ETD-MS/MS for enhanced phosphopeptide quantitation, identification and phosphorylation site characterization. J Am Soc Mass Spectrom (2011) 0.81
Post-translational regulation of calsarcin-1 during pressure overload-induced cardiac hypertrophy. J Mol Cell Cardiol (2010) 0.81
Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis (2014) 0.81
Protein-protein interactions of tandem affinity purified protein kinases from rice. PLoS One (2009) 0.81
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. BMC Bioinformatics (2013) 0.80
Facile identification and quantitation of protein phosphorylation via beta-elimination and Michael addition with natural abundance and stable isotope labeled thiocholine. Anal Chem (2010) 0.79
Enhanced MALDI-TOF MS analysis of phosphopeptides using an optimized DHAP/DAHC matrix. J Biomed Biotechnol (2010) 0.79
New insights in osteogenic differentiation revealed by mass spectrometric assessment of phosphorylated substrates in murine skin mesenchymal cells. BMC Cell Biol (2013) 0.79
Highly efficient ionization of phosphopeptides at low pH by desorption electrospray ionization mass spectrometry. Analyst (2013) 0.78
Computational phosphoproteomics: from identification to localization. Proteomics (2015) 0.76
Proteomic analysis of phosphoproteins sensitive to a phosphatidylinositol 3-kinase inhibitor, ZSTK474, by using SELDI-TOF MS. Proteome Sci (2009) 0.76
Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes. Sci Rep (2016) 0.76
PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. J Biol Res (Thessalon) (2016) 0.76
G Protein-Coupled Receptor Kinase 2 (GRK2) and 5 (GRK5) Exhibit Selective Phosphorylation of the Neurotensin Receptor in Vitro. Biochemistry (2015) 0.76
Unblocking the sink: improved CID-based analysis of phosphorylated peptides by enzymatic removal of the basic C-terminal residue. J Am Soc Mass Spectrom (2013) 0.75
Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease. Proteomics (2016) 0.75
Internalization of the Extracellular Full-Length Tau Inside Neuro2A and Cortical Cells Is Enhanced by Phosphorylation. Biomolecules (2016) 0.75
Understanding cell signaling in cancer stem cells for targeted therapy - can phosphoproteomics help to reveal the secrets? Cell Commun Signal (2017) 0.75
High throughput profiling of serum phosphoproteins/peptides using the SELDI-TOF-MS platform. Methods Mol Biol (2012) 0.75
Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides. Int J Mass Spectrom (2014) 0.75
Sensitive measurement of total protein phosphorylation level in complex protein samples. Analyst (2015) 0.75
Single nucleoprotein residue modulates arenavirus replication complex formation. MBio (2015) 0.75
Detection of a phosphorylated glycine-serine linker in an IgG-based fusion protein. MAbs (2016) 0.75
The Impact of Phosphorylation on Electron Capture Dissociation of Proteins: A Top-Down Perspective. J Am Soc Mass Spectrom (2017) 0.75
Interrogating the hidden phosphoproteome. Proteomics (2017) 0.75
Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell (2007) 17.98
Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci U S A (2014) 14.78
A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol (2006) 12.13
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A (2003) 10.82
Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling. Nature (2009) 9.15
Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell (2011) 7.30
Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science (2012) 6.79
Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck. Nature (2002) 6.26
Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell (2009) 6.16
A PtdInsP(3)- and Rho GTPase-mediated positive feedback loop regulates neutrophil polarity. Nat Cell Biol (2002) 5.58
Signaling networks assembled by oncogenic EGFR and c-Met. Proc Natl Acad Sci U S A (2008) 5.08
The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biol (2003) 4.89
Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics (2005) 4.33
Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat Cell Biol (2006) 4.25
Toca-1 mediates Cdc42-dependent actin nucleation by activating the N-WASP-WIP complex. Cell (2004) 4.21
Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities. Nature (2007) 4.14
Cell growth and size homeostasis in proliferating animal cells. Science (2009) 3.89
Degradation of the SCF component Skp2 in cell-cycle phase G1 by the anaphase-promoting complex. Nature (2004) 3.63
Autonomous regulation of the anaphase-promoting complex couples mitosis to S-phase entry. Nature (2004) 3.62
Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol Cell Proteomics (2006) 3.56
ZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner. Nature (2012) 3.44
The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell (2009) 3.38
An actin-based wave generator organizes cell motility. PLoS Biol (2007) 3.36
Global identification of modular cullin-RING ligase substrates. Cell (2011) 3.13
Profiling of UV-induced ATM/ATR signaling pathways. Proc Natl Acad Sci U S A (2007) 3.12
Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS One (2011) 3.10
Hem-1 complexes are essential for Rac activation, actin polymerization, and myosin regulation during neutrophil chemotaxis. PLoS Biol (2006) 3.01
The processivity of multiubiquitination by the APC determines the order of substrate degradation. Cell (2006) 2.91
Using buoyant mass to measure the growth of single cells. Nat Methods (2010) 2.67
Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Sci Signal (2010) 2.64
Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell (2010) 2.59
The Chlamydomonas reinhardtii BBSome is an IFT cargo required for export of specific signaling proteins from flagella. J Cell Biol (2009) 2.55
A proteomics approach for the identification and cloning of monoclonal antibodies from serum. Nat Biotechnol (2012) 2.51
Erk/Src phosphorylation of cortactin acts as a switch on-switch off mechanism that controls its ability to activate N-WASP. Mol Cell Biol (2004) 2.36
Direct observation of mammalian cell growth and size regulation. Nat Methods (2012) 2.34
Purification and architecture of the ubiquitous Wave complex. Proc Natl Acad Sci U S A (2004) 2.25
Marine cloud brightening. Philos Trans A Math Phys Eng Sci (2012) 2.23
Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res (2009) 2.20
UBE2S drives elongation of K11-linked ubiquitin chains by the anaphase-promoting complex. Proc Natl Acad Sci U S A (2010) 2.15
Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med (2010) 2.13
Evidence that fold-change, and not absolute level, of beta-catenin dictates Wnt signaling. Mol Cell (2009) 2.11
Chemical inhibition of N-WASP by stabilization of a native autoinhibited conformation. Nat Struct Mol Biol (2004) 2.11
Targeting cell division: small-molecule inhibitors of FtsZ GTPase perturb cytokinetic ring assembly and induce bacterial lethality. Proc Natl Acad Sci U S A (2004) 2.08
Activation of the WAVE complex by coincident signals controls actin assembly. Mol Cell (2009) 2.08
Sororin, a substrate of the anaphase-promoting complex, is required for sister chromatid cohesion in vertebrates. Mol Cell (2005) 2.05
Multiple phases of chondrocyte enlargement underlie differences in skeletal proportions. Nature (2013) 2.02
The tumour suppressor RASSF1A regulates mitosis by inhibiting the APC-Cdc20 complex. Nat Cell Biol (2004) 1.99
WAVE2 deficiency reveals distinct roles in embryogenesis and Rac-mediated actin-based motility. EMBO J (2003) 1.98
System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties. Chem Biol (2008) 1.97
Regulation of Cdc25C by ERK-MAP kinases during the G2/M transition. Cell (2007) 1.97
A general lack of compensation for gene dosage in yeast. Mol Syst Biol (2010) 1.96
Self-assembly of filopodia-like structures on supported lipid bilayers. Science (2010) 1.87
Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci U S A (2005) 1.83
Mouse ribonucleotide reductase R2 protein: a new target for anaphase-promoting complex-Cdh1-mediated proteolysis. Proc Natl Acad Sci U S A (2003) 1.77
Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. Dev Cell (2011) 1.76
The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme control reversible ubiquitination at the spliceosome. Genes Dev (2010) 1.74
Phosphotyrosine profiling identifies the KG-1 cell line as a model for the study of FGFR1 fusions in acute myeloid leukemia. Blood (2006) 1.65
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods (2013) 1.60
Tome-1, a trigger of mitotic entry, is degraded during G1 via the APC. Cell (2003) 1.56
High throughput proteome screening for biomarker detection. Mol Cell Proteomics (2005) 1.54
Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle. Nature (2013) 1.50
Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J Biol Chem (2011) 1.48
A novel set of Wnt-Frizzled fusion proteins identifies receptor components that activate beta -catenin-dependent signaling. J Biol Chem (2002) 1.40
Optimizing optical flow cytometry for cell volume-based sorting and analysis. PLoS One (2011) 1.39
Clustering of Nck by a 12-residue Tir phosphopeptide is sufficient to trigger localized actin assembly. J Cell Biol (2004) 1.39
Dynamic regulation of the PR-Set7 histone methyltransferase is required for normal cell cycle progression. Genes Dev (2010) 1.38
The secreted Frizzled-related protein Sizzled functions as a negative feedback regulator of extreme ventral mesoderm. Development (2003) 1.35
Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat Protoc (2011) 1.34
Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis. Proc Natl Acad Sci U S A (2008) 1.34
Quantitative reconstitution of mitotic CDK1 activation in somatic cell extracts. Mol Cell (2010) 1.25
Need-based up-regulation of protein levels in response to deletion of their duplicate genes. PLoS Biol (2010) 1.24
Kinetic responses of β-catenin specify the sites of Wnt control. Science (2012) 1.23
Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. Proc Natl Acad Sci U S A (2009) 1.23
Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nat Biotechnol (2009) 1.21
Identification of anaplastic lymphoma kinase as a potential therapeutic target in ovarian cancer. Cancer Res (2012) 1.20
A microtubule-binding Rho-GEF controls cell morphology during convergent extension of Xenopus laevis. Development (2005) 1.20
Timing of events in mitosis. Curr Biol (2002) 1.20
A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R. Mol Biosyst (2008) 1.19
A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry. Proc Natl Acad Sci U S A (2009) 1.17
Linear combinations of docking affinities explain quantitative differences in RTK signaling. Mol Syst Biol (2009) 1.16
A common phosphotyrosine signature for the Bcr-Abl kinase. Blood (2006) 1.16
The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in Xenopus. Development (2009) 1.15
FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J Proteome Res (2009) 1.15
A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia. Blood (2007) 1.15
Gap 1 phase length and mouse embryonic stem cell self-renewal. Proc Natl Acad Sci U S A (2012) 1.15
The morphology and biochemistry of nanostructures provide evidence for synthesis and signaling functions in human cerebrospinal fluid. Cerebrospinal Fluid Res (2009) 1.15
The absolute quantification strategy: application to phosphorylation profiling of human separase serine 1126. Methods Mol Biol (2007) 1.13
Biochemical suppression of small-molecule inhibitors: a strategy to identify inhibitor targets and signaling pathway components. Chem Biol (2006) 1.12
Deubiquitinase FAM/USP9X interacts with the E3 ubiquitin ligase SMURF1 protein and protects it from ligase activity-dependent self-degradation. J Biol Chem (2012) 1.12
Remodeling of the metabolome during early frog development. PLoS One (2011) 1.12
Profiling of ubiquitin-like modifications reveals features of mitotic control. Cell (2013) 1.12
Cell cycle adaptations of embryonic stem cells. Proc Natl Acad Sci U S A (2011) 1.11
Induction of myeloproliferative disorder and myelofibrosis by thrombopoietin receptor W515 mutants is mediated by cytosolic tyrosine 112 of the receptor. Blood (2009) 1.08
Size homeostasis in adherent cells studied by synthetic phase microscopy. Proc Natl Acad Sci U S A (2013) 1.07
Emi1 preferentially inhibits ubiquitin chain elongation by the anaphase-promoting complex. Nat Cell Biol (2013) 1.06
Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. J Proteome Res (2012) 1.06
Graded positional information: interpretation for both fate and guidance. Cell (2003) 1.05