Proteomics

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  Subject Areas on Research

  • A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels. 
  • A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation. 
  • A Comparative Study of Serum Exosome Isolation Using Differential Ultracentrifugation and Three Commercial Reagents. 
  • A Genoproteomic Approach to Detect Peptide Markers of Bacterial Respiratory Pathogens. 
  • A biotin switch-based proteomics approach identifies 14-3-3ζ as a target of Sirt1 in the metabolic regulation of caspase-2. 
  • A diagnostic algorithm combining clinical and molecular data distinguishes Kawasaki disease from other febrile illnesses. 
  • A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information. 
  • A functional proteomics approach to signal transduction. 
  • A genomic- and proteomic-based hypothesis on the eclectic effects of systemic interleukin-2 administration in the context of melanoma-specific immunization. 
  • A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression. 
  • A protein microarray-based analysis of S-nitrosylation. 
  • A serum proteomic approach to gauging the state of remission in Wegener's granulomatosis. 
  • A statistical model to identify differentially expressed proteins in 2D PAGE gels. 
  • A tale of two sites: How ubiquitination of a G protein-coupled receptor is coupled to its lysosomal trafficking from distinct receptor domains. 
  • Accentuation of differentially expressed proteins using phage technology. 
  • Acetylation goes global: the emergence of acetylation biology. 
  • Alpha-2 macroglobulin in Alzheimer's disease: a marker of neuronal injury through the RCAN1 pathway. 
  • Alterations in cerebrospinal fluid proteins in a presymptomatic primary glioma model. 
  • An inducible heat shock protein 70 small molecule inhibitor demonstrates anti-dengue virus activity, validating Hsp70 as a host antiviral target. 
  • An integrated clinico-metabolomic model improves prediction of death in sepsis. 
  • An unbiased evaluation of CK2 inhibitors by chemoproteomics: characterization of inhibitor effects on CK2 and identification of novel inhibitor targets. 
  • Analysis of changes in SUMO-2/3 modification during breast cancer progression and metastasis. 
  • Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics. 
  • Application of a label-free, gel-free quantitative proteomics method for ecotoxicological studies of small fish species. 
  • Aspirin exposure reveals novel genes associated with platelet function and cardiovascular events. 
  • Association of calcineurin with the COPI protein Sec28 and the COPII protein Sec13 revealed by quantitative proteomics. 
  • Autoantibody biomarkers identified by proteomics methods distinguish ovarian cancer from non-ovarian cancer with various CA-125 levels. 
  • Automated, reproducible, titania-based phosphopeptide enrichment strategy for label-free quantitative phosphoproteomics. 
  • Autotaxin-lysophosphatidic acid axis is a novel molecular target for lowering intraocular pressure. 
  • Beta2-adrenergic receptor lysosomal trafficking is regulated by ubiquitination of lysyl residues in two distinct receptor domains. 
  • BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics. 
  • Biomarker clustering to address correlations in proteomic data. 
  • Biomarkers and proteomic analysis of osteoarthritis 
  • Biomarkers and proteomic analysis of osteoarthritis. 
  • Biomarkers for amyotrophic lateral sclerosis. 
  • Biomarkers of Diabetic Retinopathy. 
  • Calcineurin Targets Involved in Stress Survival and Fungal Virulence. 
  • Can binimetinib, encorafenib and masitinib be more efficacious than currently available mutation-based targeted therapies for melanoma treatment? 
  • Cerebrospinal fluid proteomics in children during induction for acute lymphoblastic leukemia: A pilot study. 
  • Changes in the Adult GluN2B Associated Proteome following Adolescent Intermittent Ethanol Exposure. 
  • Characterization of serum proteins associated with IL28B genotype among patients with chronic hepatitis C. 
  • Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique. 
  • Characterization of the ubiquitin-modified proteome regulated by transient forebrain ischemia. 
  • Chlamydia trachomatis Infection Leads to Defined Alterations to the Lipid Droplet Proteome in Epithelial Cells. 
  • Clinical Decision Making: Integrating Advances in the Molecular Understanding of Spine Tumors. 
  • Cloud-based solution to identify statistically significant MS peaks differentiating sample categories. 
  • Comparative genome-wide screening identifies a conserved doxorubicin repair network that is diploid specific in Saccharomyces cerevisiae. 
  • Comparative proteomic analysis of differentially expressed proteins in β-aminobutyric acid enhanced Arabidopsis thaliana tolerance to simulated acid rain. 
  • Comparative proteomic characterization of articular cartilage tissue from normal donors and patients with osteoarthritis. 
  • Complexities associated with the molecular and proteomic identification of Paecilomyces species in the clinical mycology laboratory. 
  • Comprehensive Proteomic and Metabolomic Signatures of Nontypeable Haemophilus influenzae-Induced Acute Otitis Media Reveal Bacterial Aerobic Respiration in an Immunosuppressed Environment. 
  • Constrained selected reaction monitoring: quantification of selected post-translational modifications and protein isoforms. 
  • Defining the balance of risk and benefit in the era of genomics and proteomics. 
  • Delineating signal transduction pathways in smooth muscle through focused proteomics. 
  • Design and application of a data-independent precursor and product ion repository. 
  • Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. 
  • Discovery and verification of protein differences between Er positive/Her2/neu negative breast tumor tissue and matched adjacent normal breast tissue. 
  • Discovery of proteins related to coronary artery disease using industrial-scale proteomics analysis of pooled plasma. 
  • Elucidating the Molecular Composition of Cartilage by Proteomics. 
  • Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry. 
  • Ethanol metabolism modifies hepatic protein acylation in mice. 
  • Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. 
  • Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. 
  • Extracellular trafficking of myocilin in human trabecular meshwork cells. 
  • False-positive rate determination of protein target discovery using a covalent modification- and mass spectrometry-based proteomics platform. 
  • Fimbriae-mediated outer membrane vesicle production and invasion of Porphyromonas gingivalis. 
  • Finding diagnostic biomarkers in proteomic spectra. 
  • Fluorescence linked enzyme chemoproteomic strategy for discovery of a potent and selective DAPK1 and ZIPK inhibitor. 
  • Fluorescence-activated cell sorting in plant developmental biology. 
  • Functional nanostructures from surface chemistry patterning. 
  • Functional specialization of beta-arrestin interactions revealed by proteomic analysis. 
  • Fungal diagnostics in pneumonia. 
  • Generating mammalian sirtuin tools for protein-interaction analysis. 
  • Genetic markers: progress and potential for cardiovascular disease. 
  • Genomic convergence to identify candidate genes for Parkinson disease: SAGE analysis of the substantia nigra. 
  • Genomics and clinical medicine: rationale for creating and effectively evaluating animal models. 
  • Global analysis of protein folding thermodynamics for disease state characterization. 
  • Glycosylation site-specific analysis of clade C HIV-1 envelope proteins. 
  • High predictive accuracy of an unbiased proteomic profile for sustained virologic response in chronic hepatitis C patients. 
  • High spatial resolution proteomic comparison of the brain in humans and chimpanzees. 
  • High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. 
  • Identification and Quantitation of Coding Variants and Isoforms of Pulmonary Surfactant Protein A. 
  • Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics. 
  • Identification of S-nitrosylated targets of thioredoxin using a quantitative proteomic approach. 
  • Identification of candidate prostate cancer biomarkers in prostate needle biopsy specimens using proteomic analysis. 
  • Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins. 
  • Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system. 
  • Integrative systems biology: an attempt to describe a simple weed. 
  • Investigation of phosphoprotein signatures of archived prostate cancer tissue specimens via proteomic analysis. 
  • Irrational exuberance in clinical proteomics. 
  • Ischemic Human Heart Failure is Associated With Decreased Phosphorylation of Pyruvate Dehydrogenase and Triosephosphate Isomerase: Proteomic Evidence Supporting Carbohydrate Utilization Preference in the End-Stage Failing Ischemic Heart 
  • Lung cancer staging: proteomics. 
  • LungMAP: The Molecular Atlas of Lung Development Program. 
  • Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. 
  • MHC class I-presented lung cancer-associated tumor antigens identified by immunoproteomics analysis are targets for cancer-specific T cell response. 
  • MHC class I-presented tumor antigens identified in ovarian cancer by immunoproteomic analysis are targets for T-cell responses against breast and ovarian cancer. 
  • Manganese (III) meso-tetrakis N-ethylpyridinium-2-yl porphyrin acts as a pro-oxidant to inhibit electron transport chain proteins, modulate bioenergetics, and enhance the response to chemotherapy in lymphoma cells. 
  • Manganese porphyrin reduces renal injury and mitochondrial damage during ischemia/reperfusion. 
  • Mass spectrometry- and lysine amidination-based protocol for thermodynamic analysis of protein folding and ligand binding interactions. 
  • Maximum entropy reconstructions of dynamic signaling networks from quantitative proteomics data. 
  • Mechanism of immune response during immunotherapy. 
  • Metabolic reprogramming of macrophages: glucose transporter 1 (GLUT1)-mediated glucose metabolism drives a proinflammatory phenotype. 
  • Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results. 
  • Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function. 
  • Metaprotein expression modeling for label-free quantitative proteomics. 
  • Methodologies for the characterization, identification and quantification of S-nitrosylated proteins. 
  • Microproteomics: quantitative proteomic profiling of small numbers of laser-captured cells. 
  • Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics. 
  • Mitotic phosphorylation of eukaryotic initiation factor 4G1 (eIF4G1) at Ser1232 by Cdk1:cyclin B inhibits eIF4A helicase complex binding with RNA. 
  • Molecular and genetic markers in thoracic surgery. 
  • Molecular markers for incidence, prognosis, and response to therapy. 
  • Multi-marker strategies in heart failure: clinical and statistical approaches. 
  • Multiplexed protein array platforms for analysis of autoimmune diseases. 
  • Muscle-Specific Overexpression of PGC-1α Does Not Augment Metabolic Improvements in Response to Exercise and Caloric Restriction. 
  • National Heart, Lung, And Blood Institute Clinical Proteomics Working Group report. 
  • New developments in proteomics. 
  • Nitric oxide and redox regulation in the liver: part II. Redox biology in pathologic hepatocytes and implications for intervention. 
  • Optimized mixed Markov models for motif identification. 
  • Pacemaker-induced transient asynchrony suppresses heart failure progression. 
  • Parallel assay of oxygen equilibria of hemoglobin. 
  • Peptide array X-linking (PAX): a new peptide-protein identification approach. 
  • Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure. 
  • Pilot and feasibility study: prospective proteomic profiling of mammary epithelial cells from high-risk women provides evidence of activation of pro-survival pathways. 
  • Plasma proteomics of patients with non-valvular atrial fibrillation on chronic anti-coagulation with warfarin or a direct factor Xa inhibitor. 
  • Platelets from genome to proteome and beyond. 
  • Precision medicine for psychopharmacology: a general introduction. 
  • Pregnancy and Smoothelin-like Protein 1 (SMTNL1) Deletion Promote the Switching of Skeletal Muscle to a Glycolytic Phenotype in Human and Mice. 
  • Preoteomics, metabolomics and circulating endothelial progenitor cells in acute coronary syndromes. 
  • Preoteomics, metabolomics and progenitor cells in acute coronary syndromes. 
  • Protein fragment domains identified using 2D gel electrophoresis/MALDI-TOF. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Proteome analysis of the rat cornea during angiogenesis. 
  • Proteomic Profiling Reveals Adaptive Responses to Surgical Myocardial Ischemia-Reperfusion in Hibernating Arctic Ground Squirrels Compared to Rats. 
  • Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture. 
  • Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes. 
  • Proteomic analysis of calcium/calmodulin-dependent protein kinase I and IV in vitro substrates reveals distinct catalytic preferences. 
  • Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. 
  • Proteomic analysis of regenerated rabbit lenses reveal crystallin expression characteristic of adult rabbits. 
  • Proteomic analysis of stage I endometrial cancer tissue: identification of proteins associated with oxidative processes and inflammation. 
  • Proteomic analysis of the NOS2 interactome in human airway epithelial cells. 
  • Proteomic biomarker discovery in cerebrospinal fluid for cerebral vasospasm following subarachnoid hemorrhage. 
  • Proteomic biomarkers of intra-amniotic inflammation: relationship with funisitis and early-onset sepsis in the premature neonate. 
  • Proteomic identification and functional characterization of MYH9, Hsc70, and DNAJA1 as novel substrates of HDAC6 deacetylase activity. 
  • Proteomic identification of a stress protein, mortalin/mthsp70/GRP75: relevance to Parkinson disease. 
  • Proteomic identification of specific oxidized proteins in ApoE-knockout mice: relevance to Alzheimer's disease. 
  • Proteomic identification of the cerebral cavernous malformation signaling complex. 
  • Proteomic identification of unique photoreceptor disc components reveals the presence of PRCD, a protein linked to retinal degeneration. 
  • Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells. 
  • Proteomic profiling of patient-derived glioblastoma xenografts identifies a subset with activated EGFR: implications for drug development. 
  • Proteomics analysis of differentially expressed metastasis-associated proteins in adenoid cystic carcinoma cell lines of human salivary gland. 
  • Proteomics for monitoring immune responses to cancer vaccines. 
  • Proteomics in prostate cancer. 
  • Proteomnic and Metabolomic Profiling After Isehemia-Reperfusion Injury Reveals Bottlenecks That Underlie Cardioprotection in Hibernating Mammals 
  • Quantitative label-free phosphoproteomics strategy for multifaceted experimental designs. 
  • Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements. 
  • Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis. 
  • ROCK1 phosphorylates and activates zipper-interacting protein kinase. 
  • Real-time in vivo proteomic identification of novel kinase substrates in smooth muscle. 
  • Redox proteomic identification of HNE-bound mitochondrial proteins in cardiac tissues reveals a systemic effect on energy metabolism after doxorubicin treatment. 
  • Renal systems biology of patients with systemic inflammatory response syndrome. 
  • Right ventricular hypertrophy with early dysfunction: A proteomics study in a neonatal model. 
  • SH3 domain-based phototrapping in living cells reveals Rho family GAP signaling complexes. 
  • SILAC-pulse proteolysis: A mass spectrometry-based method for discovery and cross-validation in proteome-wide studies of ligand binding. 
  • SNOs Differ: Methodological and Biological Implications. 
  • SUMO proteomics to decipher the SUMO-modified proteome regulated by various diseases. 
  • Secrets of the perioptome: new tools for a new concept. 
  • Simultaneous proteomic profiling of four different growth states of human fibroblasts, using amine-reactive isobaric tagging reagents and tandem mass spectrometry. 
  • Small ubiquitin-like modifier 3-modified proteome regulated by brain ischemia in novel small ubiquitin-like modifier transgenic mice: putative protective proteins/pathways. 
  • Stain efficiency and MALDI-TOF MS compatibility of seven visible staining procedures. 
  • Surrogate markers for late cardiac allograft survival. 
  • Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures. 
  • Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection. 
  • Techniques for quantifying phytoplankton biodiversity. 
  • The Diacetyl-Exposed Human Airway Epithelial Secretome: New Insights into Flavoring-Induced Airways Disease. 
  • The Expressed Genome in Cardiovascular Diseases and Stroke: Refinement, Diagnosis, and Prediction: A Scientific Statement From the American Heart Association. 
  • The G Protein-Coupled Estrogen Receptor Agonist G-1 Inhibits Nuclear Estrogen Receptor Activity and Stimulates Novel Phosphoproteomic Signatures. 
  • The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis. 
  • The SNO-proteome: causation and classifications. 
  • The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia. 
  • The current epidemiology and clinical decisions surrounding acute respiratory infections. 
  • The discovery and early validation of novel plasma biomarkers in mild-to-moderate Alzheimer's disease patients responding to treatment with rosiglitazone. 
  • The metabolomics standards initiative. 
  • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. 
  • The protein expression landscape of the Arabidopsis root. 
  • Thermodynamic analysis of protein folding and stability using a tryptophan modification protocol. 
  • Thermodynamic analysis of protein-ligand binding interactions in complex biological mixtures using the stability of proteins from rates of oxidation. 
  • Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. 
  • Toxin-based targeted therapy for malignant brain tumors. 
  • Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. 
  • Unbiased plasma proteomics for novel diagnostic biomarkers in cardiovascular disease: identification of quiescin Q6 as a candidate biomarker of acutely decompensated heart failure. 
  • Urine peptidomics for clinical biomarker discovery. 
  • Urine proteomics in kidney transplantation. 
  • Verification of systems biology research in the age of collaborative competition. 
  • Visual annotation of the gene database. 
  • What is mzXML good for? 
  • What is mzXML good for? 
  • What was old is new again: using the host response to diagnose infectious disease. 
  • Workshop on cancer biometrics: identifying biomarkers and surrogates of cancer in patients: a meeting held at the Masur Auditorium, National Institutes of Health. 
  • XPO1/CRM1 Inhibition Causes Antitumor Effects by Mitochondrial Accumulation of eIF5A. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
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  Keywords of People

  • Berchuck, Andrew, James M. Ingram Professor of Gynecologic Oncology, Obstetrics and Gynecology, Gynecologic Oncology
  • Davis, Erica Ellen, Associate Professor of Pediatrics, Cell Biology
  • Granger, Christopher Bull, Professor of Medicine, School of Nursing
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Computer Science
  • Milano, Carmelo Alessio, Professor of Surgery, Surgery, Cardiovascular and Thoracic Surgery
  • Sampson, John Howard, Robert H., M.D. and Gloria Wilkins Professor of Neurosurgery, in the School of Medicine, Immunology
  • Soderling, Scott Haydn, Professor in Cell Biology, Cell Biology
  • Tsalik, Ephraim, Associate Professor of Medicine, Molecular Genetics and Microbiology
  • Wernegreen, Jennifer Jo, Associate Professor of Environmental and Evolutionary Genomics in the Division of Environmental Sciences and Policy, Environmental Sciences and Policy