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1. Full Text Proteogenomics connects somatic mutations to signalling in breast cancer
by Mertins, Philipp and Mani, D.R and Ruggles, Kelly V and Gillette, Michael A and Clauser, Karl R and Wang, Pei and Wang, Xianlong and Qiao, Jana W and Cao, Song and Petralia, Francesca and Kawaler, Emily and Mundt, Filip and Krug, Karsten and Tu, Zhidong and Lei, Jonathan T and Gatza, Michael L and Wilkerson, Matthew and Perou, Charles M and Yellapantula, Venkata and Huang, Kuan-Lin and Lin, Chenwei and McLellan, Michael D and Yan, Ping and Davies, Sherri R and Townsend, R. Reid and Skates, Steven J and Wang, Jing and Zhang, Bing and Kinsinger, Christopher R and Mesri, Mehdi and Rodriguez, Henry and Ding, Li and Paulovich, Amanda G and Fenyö, David and Ellis, Matthew J and Carr, Steven A and NCI CPTAC
Nature, ISSN 0028-0836, 05/2016, Volume 534, Issue 7605, pp. 55 - 62
Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly... 
PATHWAYS | HETEROGENEITY | PIK3CA MUTATIONS | PHOSPHORYLATION | MULTIDISCIPLINARY SCIENCES | GENES | BIOLOGY | RECEPTOR | EXPRESSION | SIGNATURE | REVEALS | Protein Kinases - metabolism | Focal Adhesion Kinase 1 - genetics | Receptor, Epidermal Growth Factor - genetics | Protein Kinases - genetics | Cyclin-Dependent Kinases - metabolism | Receptor, ErbB-2 - genetics | Receptors, G-Protein-Coupled - metabolism | Genomics | Humans | Gene Expression Regulation, Neoplastic | Receptor, ErbB-2 - metabolism | Phosphoproteins - metabolism | Receptor-Interacting Protein Serine-Threonine Kinase 2 - genetics | Tumor Suppressor Protein p53 - genetics | Breast Neoplasms - metabolism | Receptor-Interacting Protein Serine-Threonine Kinase 2 - metabolism | Breast Neoplasms - enzymology | Receptor, Epidermal Growth Factor - metabolism | Phosphoproteins - analysis | Mass Spectrometry | src-Family Kinases - metabolism | Female | Cyclin-Dependent Kinases - genetics | Focal Adhesion Kinase 1 - metabolism | Chromosomes, Human, Pair 5 - genetics | Breast Neoplasms - classification | Chromosome Deletion | p21-Activated Kinases - genetics | Signal Transduction | Molecular Sequence Annotation | Calcium-Binding Proteins - deficiency | Phosphoproteins - genetics | Mutation - genetics | S-Phase Kinase-Associated Proteins - metabolism | p21-Activated Kinases - metabolism | Phosphatidylinositol 3-Kinases - genetics | Breast Neoplasms - genetics | Class I Phosphatidylinositol 3-Kinases | Proteomics | S-Phase Kinase-Associated Proteins - genetics | Receptors, G-Protein-Coupled - genetics | src-Family Kinases - genetics | Calcium-Binding Proteins - genetics | Breast cancer | Genetic aspects | Research | Oncology, Experimental | Cancer | Physiological aspects | Methods | Mutation (Biology) | Proteins | Gene amplification | Peptides | Protein expression | Genomes | Mutation | Kinases | Deoxyribonucleic acid--DNA | Tumors | Index Medicus
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2. Full Text Update on New Therapies of Diabetic Foot Ulcers: A Systematic Review
by Vahid ABOLGHASEMI and Mehdi MESRI
Journal of International Translational Medicine, ISSN 2227-6394, 04/2019, Volume 7, Issue 1, pp. 61 - 64
Diabetic foot ulcers (DFUs) are as a chronic wound with a serious and rampant complication of diabetes mellitus. Treatment of DFU remains often challenging and... 
Treatment | Clinicians | Diabetes mellitus | Diabetic foot ulcers
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3. Full Text Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma
by Rudnick, Paul A and Niles, Richard K and Vega-Montoto, Lorenzo J and Mani, D R and Abbatiello, Susan E and Tegeler, Tony J and Tempst, Paul and Gibson, Bradford W and Cusack, Michael P and Buck, Charles and Hall, Steven C and Neubert, Thomas A and Mesri, Mehdi and Tabb, David L and Johansen, Eric B and Ransohoff, David and Addona, Terri A and Bunk, David M and Hiltke, Tara and Zhao, Lei and Schilling, Birgit and Regnier, Fred E and Rodriguez, Henry and Liebler, Daniel C and Wahlander, Åsa and Ham, Amy-Joan L and Dodder, Nathan G and Spiegelman, Clifford H and Carr, Steven A and Li, Jing and Allen, Simon and Variyath, Asokan M and Waldemarson, Sofia and Smith, Derek and Jackson, Angela and Borchers, Christoph H and Anderson, N Leigh and Wang, Mu and Keshishian, Hasmik and Fisher, Susan J and Held, Jason M and Pulsipher, Trenton C and Blackman, Ronald K and Skates, Steven J and Whiteaker, Jeffrey R and Zimmerman, Lisa J and Cardasis, Helene L and Kinsinger, Christopher R and Paulovich, Amanda G
Nature Biotechnology, ISSN 1087-0156, 07/2009, Volume 27, Issue 7, pp. 633 - 641
Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed... 
LIMITS | LC/MS/MS | PROTEOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOMARKER DISCOVERY | MASS-SPECTROMETRIC QUANTITATION | ASSAYS | SERUM | ABSOLUTE QUANTIFICATION | PEPTIDE STANDARDS | ISOTOPE-DILUTION | Blood Chemical Analysis - methods | Blood Proteins - analysis | Mass Spectrometry - standards | Reproducibility of Results | Humans | Sensitivity and Specificity | Linear Models | Biomarkers - blood | Proteome - analysis | Mass Spectrometry - methods | Technology Assessment, Biomedical | Infants (Newborn) | Usage | Research | Diagnosis | Biological markers | Health aspects | Mass spectrometry | Blood proteins | Diseases | Proteins | Biomarkers | Plasma | Biotechnology | Innovations | Index Medicus
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4. Full Text Leukocyte Microparticles Stimulate Endothelial Cell Cytokine Release and Tissue Factor Induction in a JNK1 Signaling Pathway
by Mehdi Mesri and Dario C. Altieri
Journal of Biological Chemistry, ISSN 0021-9258, 08/1999, Volume 274, Issue 33, pp. 23111 - 23118
A role of membrane microparticles (MP) released by vascular cells in endothelial cell (EC) activation was investigated. Flow cytofluorimetric analysis of blood... 
VESICULATION | PLATELET-DERIVED MICROPARTICLES | ACTIVATED PROTEIN-KINASE | MECHANISM | BIOCHEMISTRY & MOLECULAR BIOLOGY | ATHEROSCLEROSIS | MONOCYTES | ADHESION MOLECULES | PLASMA-MEMBRANE | EXPRESSION | PROCOAGULANT ACTIVITIES | Endothelium, Vascular - cytology | Mitogen-Activated Protein Kinases | Signal Transduction | Humans | Cells, Cultured | Neutrophils - ultrastructure | DNA Primers | Inflammation - metabolism | Endothelium, Vascular - metabolism | Base Sequence | Coagulants - metabolism | JNK Mitogen-Activated Protein Kinases | Chemokine CCL2 - metabolism | Interleukin-6 - metabolism | Neutrophils - metabolism | Thromboplastin - biosynthesis | Calcium-Calmodulin-Dependent Protein Kinases - metabolism | Index Medicus
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5. Full Text Reduced graphene oxide decorated on Cu/CuO-Ag nanocomposite as a high-performance material for the construction of a non-enzymatic sensor: Application to the determination of carbaryl and fenamiphos pesticides
by Hashemi, Pegah and Karimian, Nashmil and Khoshsafar, Hosein and Arduini, Fabiana and Mesri, Mehdi and Afkhami, Abbas and Bagheri, Hasan
Materials Science & Engineering C, ISSN 0928-4931, 09/2019, Volume 102, pp. 764 - 772
A novel electrochemical sensor based on the reduced graphene oxide-Cu/CuO-Ag nanocomposite modified glassy carbon electrode (rGO/Cu/CuO-Ag/GCE) has been... 
Simultaneous determination | Reduced graphene oxide-Cu/CuO-Ag nanocomposite | Modified electrodes | Pesticides | Electrochemical sensors | MATERIALS SCIENCE, BIOMATERIALS | ELECTROANALYTICAL DETERMINATION | CARBAMATE PESTICIDES | COMPOSITE | ACETYLCHOLINESTERASE | FRUIT | ELECTROCHEMICAL DETERMINATION | NATURAL-WATERS | BIOSENSOR | CARBON-PASTE | CATALYSTS | Enzymes | Electrochemical reactions | Graphene | Carbamates | Sensors | Electric properties | Analytical methods | Chemical sensors | Infrared spectroscopy | Fourier transformation | Fourier transforms | Electrochemical analysis | Fenamiphos | Construction materials | X-ray diffraction | Oxides | Voltammetry | Glassy carbon | Electrodes | Oxidation | Copper | Detection limits | Silver | Transmission electron microscopy | Nanocomposites | Carbaryl | Electrochemistry | Copper oxides
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6. Full Text Recommendations for the generation, quantification, storage, and handling of peptides used for mass spectrometry-based assays
by Hoofnagle, Andrew N and Whiteaker, Jeffrey R and Carr, Steven A and Kuhn, Eric and Liu, Tao and Massoni, Sam A and Thomas, Stefani N and Reid Townsend, R and Zimmerman, Lisa J and Boja, Emily and Chen, Jing and Crimmins, Daniel L and Davies, Sherri R and Gao, Yuqian and Hiltke, Tara R and Ketchum, Karen A and Kinsinger, Christopher R and Mesri, Mehdi and Meyer, Matthew R and Qian, Wei-Jun and Schoenherr, Regine M and Scott, Mitchell G and Shi, Tujin and Whiteley, Gordon R and Wrobel, John A and Wu, Chaochao and Ackermann, Brad L and Aebersold, Ruedi and Barnidge, David R and Bunk, David M and Clarke, Nigel and Fishman, Jordan B and Grant, Russ P and Kusebauch, Ulrike and Kushnir, Mark M and Lowenthal, Mark S and Moritz, Robert L and Neubert, Hendrik and Patterson, Scott D and Rockwood, Alan L and Rogers, John and Singh, Ravinder J and Van Eyk, Jennifer E and Wong, Steven H and Zhang, Shucha and Chan, Daniel W and Chen, Xian and Ellis, Matthew J and Liebler, Daniel C and Rodland, Karin D and Rodriguez, Henry and Smith, Richard D and Zhang, Zhen and Zhang, Hui and Paulovich, Amanda G and Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Clinical Chemistry, ISSN 0009-9147, 01/2016, Volume 62, Issue 1, pp. 48 - 69
BACKGROUND: For many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in... 
PERFORMANCE LIQUID-CHROMATOGRAPHY | INTERNAL STANDARD | LC-MS/MS | PROTEIN QUANTIFICATION | PROTEOTYPIC PEPTIDES | MEDICAL LABORATORY TECHNOLOGY | AMINO-ACID-ANALYSIS | QUANTITATIVE BIOANALYSIS | ISOTOPE-DILUTION | PROTEOMICS | PREDICTION | Specimen Handling | Guidelines as Topic | Peptides - isolation & purification | Research Personnel | Clinical Laboratory Techniques | Humans | Mass Spectrometry | Proteomics | Peptides - analysis | Proteins | Medical laboratories | Proteolysis | Mass spectrometry | Chemical properties | Analysis | Medical research | Reference materials | Peptides | Laboratories | Funding | Calibration | 21st century | Quality standards | Researchers | Scientific imaging | Methods | Cancer | Index Medicus | Environmental Molecular Sciences Laboratory | peptide | lc-ms | calibrators | ms | mass spectrometry | reference material | internal standards
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7. Full Text Accelerated rigor mortis: A case letter
by Mesri, Mehdi and Behzadnia, MohammadJavad and Dorooshi, Gholamali
Journal of Research in Medical Sciences, ISSN 1735-1995, 11/2017, Volume 22, Issue 11, pp. 126 - 126
The vital signs on admission were heart rate - 95 beats/min, blood pressure - 129/75 mmHg, respiratory rate - 20 breaths/min, oxygen saturation - 91%, and... 
MEDICINE, GENERAL & INTERNAL | Medicine | Toxicology | Emergency medical care | Forensic pathology | Funeral homes | Adenosine triphosphate
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8. Full Text Proteogenomic integration reveals therapeutic targets in breast cancer xenografts
by Huang, Kuan-Lin and Li, Shunqiang and Mertins, Philipp and Cao, Song and Gunawardena, Harsha P and Ruggles, Kelly V and Mani, D.R and Clauser, Karl R and Tanioka, Maki and Usary, Jerry and Kavuri, Shyam M and Xie, Ling and Yoon, Christopher and Qiao, Jana W and Wrobel, John and Wyczalkowski, Matthew A and Erdmann-Gilmore, Petra and Snider, Jacqueline E and Hoog, Jeremy and Singh, Purba and Niu, Beifung and Guo, Zhanfang and Sun, Sam Qiancheng and Sanati, Souzan and Kawaler, Emily and Wang, Xuya and Scott, Adam and Ye, Kai and McLellan, Michael D and Wendl, Michael C and Malovannaya, Anna and Held, Jason M and Gillette, Michael A and Fenyö, David and Kinsinger, Christopher R and Mesri, Mehdi and Rodriguez, Henry and Davies, Sherri R and Perou, Charles M and Ma, Cynthia and Reid Townsend, R and Chen, Xian and Carr, Steven A and Ellis, Matthew J and Ding, Li
Nature Communications, ISSN 2041-1723, 03/2017, Volume 8, Issue 1, pp. 14864 - 14864
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein... 
TUMOR XENOGRAFTS | GENOMICS | PATHWAY | QUANTIFICATION | MULTIDISCIPLINARY SCIENCES | MUTATIONS | INHIBITOR | DISCOVERY | MTOR | Index Medicus
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9. Full Text Proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction
by Wang, Jing and Ma, Zihao and Carr, Steven A and Mertins, Philipp and Zhang, Hui and Zhang, Zhen and Chan, Daniel W and Ellis, Matthew J. C and Townsend, R. Reid and Smith, Richard D and McDermott, Jason E and Chen, Xian and Paulovich, Amanda G and Boja, Emily S and Mesri, Mehdi and Kinsinger, Christopher R and Rodriguez, Henry and Rodland, Karin D and Lieblerc, Daniel C and Zhang, Bing and Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Molecular and Cellular Proteomics, ISSN 1535-9476, 01/2017, Volume 16, Issue 1, pp. 121 - 134
Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this... 
BREAST-CANCER | COMPLEMENT | RNA | PROTEOGENOMIC CHARACTERIZATION | QUANTIFICATION | BIOCHEMICAL RESEARCH METHODS | NETWORKS | EXPRESSION PROFILES | ASSOCIATION | MICROARRAY DATA | GENOME | Neoplasms - metabolism | Oligonucleotide Array Sequence Analysis | Humans | Gene Expression Regulation, Neoplastic | Gene Expression Profiling - methods | Chromosome Mapping | Gene Regulatory Networks | Protein Interaction Maps | Algorithms | Neoplasms - genetics | Mass Spectrometry | Epithelial-Mesenchymal Transition | Proteomics - methods | Web Browser | Networks | Profiling | Mesenchyme | Genes | Modules | Data processing | Mass spectroscopy | Breast cancer | Genomes | Gene expression | ErbB-2 protein | Biological activity | Consortia | Proteins | Wiring | Complement activation | Proteomics | Mass spectrometry | Cancer | Index Medicus | Environmental Molecular Sciences Laboratory | BASIC BIOLOGICAL SCIENCES | Research
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10. Full Text Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses
by Paul A. Rudnick and Karl R. Clauser and Lisa E. Kilpatrick and Dmitrii V. Tchekhovskoi and Pedatsur Neta and Nikša Blonder and Dean D. Billheimer and Ronald K. Blackman and David M. Bunk and Helene L. Cardasis and Amy-Joan L. Ham and Jacob D. Jaffe and Christopher R. Kinsinger and Mehdi Mesri and Thomas A. Neubert and Birgit Schilling and David L. Tabb and Tony J. Tegeler and Lorenzo Vega-Montoto and Asokan Mulayath Variyath and Mu Wang and Pei Wang and Jeffrey R. Whiteaker and Lisa J. Zimmerman and Steven A. Carr and Susan J. Fisher and Bradford W. Gibson and Amanda G. Paulovich and Fred E. Regnier and Henry Rodriguez and Cliff Spiegelman and Paul Tempst and Daniel C. Liebler and Stephen E. Stein
Molecular & Cellular Proteomics, ISSN 1535-9476, 02/2010, Volume 9, Issue 2, pp. 225 - 241
A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical... 
BREAST-CANCER | DATABASE | PEPTIDE IDENTIFICATION | SHOTGUN PROTEOMICS | PROTEIN-ABUNDANCE | BIOCHEMICAL RESEARCH METHODS | Reproducibility of Results | Tandem Mass Spectrometry - standards | Egg Proteins - analysis | Chromatography, Liquid - standards | Laboratories | Proteome - analysis | Saccharomyces cerevisiae - metabolism | Animals | Proteomics - standards | Chickens | Software | Proteomics - methods | Chromatography, Liquid - methods | Saccharomyces cerevisiae Proteins - analysis | Tandem Mass Spectrometry - methods | Index Medicus | Research
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11. Full Text CPTAC Assay Portal: A repository of targeted proteomic assays
by Whiteaker, Jeffrey R and Halusa, Goran N and Hoofnagle, Andrew N and Sharma, Vagisha and MacLean, Brendan and Yan, Ping and Wrobel, John A and Kennedy, Jacob and Mani, D.R and Zimmerman, Lisa J and Meyer, Matthew R and Mesri, Mehdi and Rodriguez, Henry and Paulovich, Amanda G and Abbatiello, Susan E and Boja, Emily and Carr, Steven A and Chan, Daniel W and Chen, Xian and Chen, Jing and Davies, Sherri R and Ellis, Matthew J. C and Fenyö, David and Hiltke, Tara and Ketchum, Karen A and Kinsinger, Chris and Kuhn, Eric and Liebler, Daniel C and Lin, De and Liu, Tao and Loss, Michael and MacCoss, Michael J and Qian, Wei-Jun and Rivers, Robert and Rodland, Karin D and Ruggles, Kelly V and Scott, Mitchell G and Smith, Richard D and Thomas, Stefani and Townsend, R. Reid and Whiteley, Gordon and Wu, Chaochao and Zhang, Hui and Zhang, Zhen and Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC)
Nature Methods, ISSN 1548-7091, 2014, Volume 11, Issue 7, pp. 703 - 704
Neoplasm Proteins - analysis | Neoplasm Proteins - chemistry | Proteomics - methods | Databases, Protein | Humans | Mass Spectrometry | Usage | Assaying | Mass spectrometry | Analysis | Methods | Proteomics | Index Medicus
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12. Full Text Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance
by Amanda G. Paulovich and Dean Billheimer and Amy-Joan L. Ham and Lorenzo Vega-Montoto and Paul A. Rudnick and David L. Tabb and Pei Wang and Ronald K. Blackman and David M. Bunk and Helene L. Cardasis and Karl R. Clauser and Christopher R. Kinsinger and Birgit Schilling and Tony J. Tegeler and Asokan Mulayath Variyath and Mu Wang and Jeffrey R. Whiteaker and Lisa J. Zimmerman and David Fenyo and Steven A. Carr and Susan J. Fisher and Bradford W. Gibson and Mehdi Mesri and Thomas A. Neubert and Fred E. Regnier and Henry Rodriguez and Cliff Spiegelman and Stephen E. Stein and Paul Tempst and Daniel C. Liebler
Molecular & Cellular Proteomics, ISSN 1535-9476, 02/2010, Volume 9, Issue 2, pp. 242 - 254
Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality... 
PLASMA | MESSENGER-RNA | PEPTIDE IDENTIFICATION | BIOMARKER DISCOVERY | PROTEIN EXPRESSION | BIOCHEMICAL RESEARCH METHODS | GLOBAL ANALYSIS | TANDEM MASS-SPECTROMETRY | SACCHAROMYCES-CEREVISIAE | PROTEOMICS | TOOLS | Biomarkers - metabolism | Saccharomyces cerevisiae - metabolism | Mass Spectrometry - standards | Chromatography, Liquid - standards | Proteomics - standards | Humans | Clinical Laboratory Techniques - standards | Chromatography, Liquid - methods | Saccharomyces cerevisiae Proteins - analysis | Mass Spectrometry - methods | Index Medicus | Research
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13. Full Text Linking cancer genome to proteome: NCI's investment into proteogenomics
by Rivers, Robert C and Kinsinger, Christopher and Boja, Emily S and Hiltke, Tara and Mesri, Mehdi and Rodriguez, Henry
PROTEOMICS, ISSN 1615-9853, 12/2014, Volume 14, Issue 23-24, pp. 2633 - 2636
Advances in both targeted and unbiased MS‐based proteomics are now at a mature stage for comprehensively and reproducibly characterizing a large part of the... 
Proteogenomics | Bioinformatics | Cancer | PERFORMANCE | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | TANDEM MASS-SPECTROMETRY | REPRODUCIBILITY | Neoplasms - metabolism | Proteome - genetics | Animals | Neoplasms - genetics | Humans | Proteomics - methods | Genomics - methods | Proteome - metabolism | Genetic aspects | Analysis | Genomics | Consortia | Genomes | Index Medicus
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