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(5FMC). 5FMC is a
LESS IS MORE: MEMBRANE PROTEIN DIGESTION BEYOND UREA The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach COMPARATIVE ANALYSIS OF THE SECRETOME FROM A MODEL Filarial nematodes (superfamily Filarioidea) are responsible for an annual global health burden of ∼6.3 million disability-adjusted life-years, which represents the greatest single component of morbidity attributable to helminths affecting humans. No vaccine exists for the major filarial diseases, lymphatic filariasis and onchocerciasis; in part because research on protective immunity LARGE-SCALE IDENTIFICATION OF TUBULIN-BINDING PROTEINS Large-scale Identification of Tubulin-binding Proteins Provides Insight on Subcellular Trafficking, Metabolic Channeling, and Signaling in Plant Cells* S Simon D. X. Chuong‡, Allen G. Good§, Gregory J. Taylor§, Michelle C. Freeman‡, A GENECENTRIC HUMAN PROTEIN ATLAS FOR EXPRESSION PROFILES An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of ACQUIRING AND ANALYZING DATA INDEPENDENT ACQUISITION Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Lindsay K. Pino1x, Seth C.Just2x, Michael J. MacCoss3x, and Brian C. Searle4,*x Data independent acquisition (DIA) is an attractive alter- INTEGRATIVE PROTEOMIC AND METABOLOMIC ANALYSIS REVEALS body (5). Moreover, metabolomic analysis provides a detailed analysis of the metabolic profile in the tissues or body fluids of living organisms to reveal changes in the metabolites and PROTEIN INTERACTIONS DURING THE FLAVIVIRUS AND HEPACIVIRUS protein and bud into the ER, thereby acquiring a lipid enve-lope embedding multiple copies of the two structural glyco-proteins. Viral particles are finally released from the cell in a HOME PAGE: MOLECULAR & CELLULAR PROTEOMICS Papers in Press Latest articles that have been fully reviewed and editorially accepted but not yet copyedited or formatted. PROTEIN IDENTIFICATION BY MASS SPECTROMETRY During the past two decades, mass spectrometry has become established as the primary method for protein identification from complex mixtures of biological origin. This is largely attributable to the fortunate coincidence of instrumental advances that allow routine analysis of minute amounts (typically femtomoles) of involatile, polar compounds such as peptides in complex mixtures, with the FIVE FRIENDS OF METHYLATED CHROMATIN TARGET OF PROTEIN54 Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop(5FMC). 5FMC is a
LESS IS MORE: MEMBRANE PROTEIN DIGESTION BEYOND UREA The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach COMPARATIVE ANALYSIS OF THE SECRETOME FROM A MODEL Filarial nematodes (superfamily Filarioidea) are responsible for an annual global health burden of ∼6.3 million disability-adjusted life-years, which represents the greatest single component of morbidity attributable to helminths affecting humans. No vaccine exists for the major filarial diseases, lymphatic filariasis and onchocerciasis; in part because research on protective immunity LARGE-SCALE IDENTIFICATION OF TUBULIN-BINDING PROTEINS Large-scale Identification of Tubulin-binding Proteins Provides Insight on Subcellular Trafficking, Metabolic Channeling, and Signaling in Plant Cells* S Simon D. X. Chuong‡, Allen G. Good§, Gregory J. Taylor§, Michelle C. Freeman‡, A GENECENTRIC HUMAN PROTEIN ATLAS FOR EXPRESSION PROFILES An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of ACQUIRING AND ANALYZING DATA INDEPENDENT ACQUISITION Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Lindsay K. Pino1x, Seth C.Just2x, Michael J. MacCoss3x, and Brian C. Searle4,*x Data independent acquisition (DIA) is an attractive alter- INTEGRATIVE PROTEOMIC AND METABOLOMIC ANALYSIS REVEALS body (5). Moreover, metabolomic analysis provides a detailed analysis of the metabolic profile in the tissues or body fluids of living organisms to reveal changes in the metabolites and PROTEIN INTERACTIONS DURING THE FLAVIVIRUS AND HEPACIVIRUS protein and bud into the ER, thereby acquiring a lipid enve-lope embedding multiple copies of the two structural glyco-proteins. Viral particles are finally released from the cell in a HOME PAGE: MOLECULAR & CELLULAR PROTEOMICS Papers in Press Latest articles that have been fully reviewed and editorially accepted but not yet copyedited or formatted. EXPONENTIALLY MODIFIED PROTEIN ABUNDANCE INDEX (EMPAI) FOR To estimate absolute protein contents in complex mixtures, we previously defined a protein abundance index (PAI) as the number of observed peptides divided by the number of observable peptides per protein (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome. Res.12, 1231–1245).
A FLUORESCENT LIVE IMAGING SCREENING ASSAY BASED ON Several cytoplasmic proteins that are involved in G protein-coupled receptor signaling cascades are known to translocate to the plasma membrane upon receptor activation, such as beta-arrestin2. Based on this example and in order to identify new cytoplasmic proteins implicated in the ON-and-OFF cycle of G protein-coupled receptor, a live-imaging screen of fluorescently labeled cytoplasmic PROTEOME ANALYSIS OF DISTINCT DEVELOPMENTAL STAGES OF The recent Natural Killer (NK) cell maturation model postulates that CD34+ hematopoietic stem cells (HSC) first develop into CD56bright NK cells, then into CD56dimCD57− and finally into terminally maturated CD56dimCD57+. The molecular mechanisms of human NK cell differentiation and maturation however are incompletely characterized. Here we present a proteome analysis of distinct MASS SPECTROMETRY: RECONNAISSANCE AT THE FRONTIERS OF The 10th International Symposium on Mass Spectrometry in the Health and Life Sciences: Molecular and Cellular Proteomics was held in San Francisco in August 2011. This biennial event has become one of the premier meetings on the proteomics agenda. As with its predecessors, this symposium was designed to showcase how mass spectrometric-based technology has developed into PLATFORM DEPENDENCIES IN BOTTOM-UP HYDROGEN/DEUTERIUM Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS QUANTITATIVE PROTEOMIC ANALYSIS REVEALS EFFECTS OF Glioblastoma multiforme is a highly invasive and aggressive brain tumor with an invariably poor prognosis. The overexpression of epidermal growth factor receptor (EGFR) is a primary influencer of invasion and proliferation in tumor cells and the constitutively active EGFRvIII mutant, found in 30–65% of Glioblastoma multiforme, confers more aggressive invasion. To better understand how EGFR MULTIPLEX N-TERMINOME ANALYSIS OF MMP-2 AND MMP-9 Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute ABSOLUTE QUANTITATION OF ISOFORMS OF POST-TRANSLATIONALLY Post-translational modification isoforms of a protein are known to play versatile biological functions in diverse cellular processes. To measure the molar amount of each post-translational modification isoform (Pisf) of a target protein present in the total protein extract using mass spectrometry, a quantitative proteomic protocol, absolute quantitation of isoforms of post-translationally THE MINIMUM INFORMATION REQUIRED FOR A GLYCOMICS The MIRAGE guidelines are being developed in response to a critical need in the glycobiology community to clarify glycoanalytic results so that they are more readily evaluated (in terms of their scope and depth) and to facilitate the reproduction of important results in the laboratory. The molecular and biological complexity of the glycosylation process makes thorough reporting of the HOME PAGE: MOLECULAR & CELLULAR PROTEOMICS Papers in Press Latest articles that have been fully reviewed and editorially accepted but not yet copyedited or formatted. REQUIRED MANUSCRIPT CONTENT AND PUBLICATION GUIDELINES The following guidelines describe the information required by the journal for all articles dealing with mass spectrometric analyses designed for protein, peptide or posttranslational modification (PTM) identification and their quantification regardless of whether the study is biological or clinical in focus.. Authors must include information in the manuscript that will allow readers and FIVE FRIENDS OF METHYLATED CHROMATIN TARGET OF PROTEIN Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop(5FMC). 5FMC is a
REVEALING THE DYNAMIC ALLOSTERIC CHANGES REQUIRED FOR CysE and CysK, the last two enzymes of the cysteine biosynthetic pathway, engage in a bienzyme complex, cysteine synthase (CS), with yet incompletely characterized three-dimensional structure and regulatory function. Being absent in mammals, the two enzymes and their complex are attractive targets for antibacterial drugs. We have used hydrogen/deuterium exchange mass spectrometry to unveil how LESS IS MORE: MEMBRANE PROTEIN DIGESTION BEYOND UREA28 The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach ANALYSIS OF HIGH THROUGHPUT PROTEIN EXPRESSION IN17 The ability to efficiently produce hundreds of proteins in parallel is the most basic requirement of many aspects of proteomics. Overcoming the technical and financial barriers associated with high throughput protein production is essential for the development of an experimental platform to query and browse the protein content of a cell (e.g. protein and antibody arrays). PARALLEL REACTION MONITORING FOR HIGH RESOLUTION AND HIGH Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* S Amelia C. Peterson‡, Jason D. Russell‡, Derek J. Bailey‡, Michael S. Westphall‡, IDENTIFICATION OF CANDIDATE PLASMA PROTEIN BIOMARKERS FOR Identification of Candidate Plasma Protein Biomarkers for Cervical Cancer Using the Multiplex Proximity Extension Assay Authors Malin Berggrund, Stefan Enroth, Martin Lundberg, Erika Assarsson, Karin Stålberg, David Lindquist, INSIGHTS INTO THE PROTEOME OF GASTROINTESTINAL STROMAL Insights into the Proteome of Gastrointestinal Stromal Tumors-Derived Exosomes Reveals New Potential Diagnostic Biomarkers* S Safinur Atay‡**, Daniel W. Wilkey§, Mohammed Milhem¶, Michael Merchant§, ACQUIRING AND ANALYZING DATA INDEPENDENT ACQUISITION Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Lindsay K. Pino1x, Seth C.Just2x, Michael J. MacCoss3x, and Brian C. Searle4,*x Data independent acquisition (DIA) is an attractive alter- HOME PAGE: MOLECULAR & CELLULAR PROTEOMICS Papers in Press Latest articles that have been fully reviewed and editorially accepted but not yet copyedited or formatted. REQUIRED MANUSCRIPT CONTENT AND PUBLICATION GUIDELINES The following guidelines describe the information required by the journal for all articles dealing with mass spectrometric analyses designed for protein, peptide or posttranslational modification (PTM) identification and their quantification regardless of whether the study is biological or clinical in focus.. Authors must include information in the manuscript that will allow readers and FIVE FRIENDS OF METHYLATED CHROMATIN TARGET OF PROTEIN Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop(5FMC). 5FMC is a
REVEALING THE DYNAMIC ALLOSTERIC CHANGES REQUIRED FOR CysE and CysK, the last two enzymes of the cysteine biosynthetic pathway, engage in a bienzyme complex, cysteine synthase (CS), with yet incompletely characterized three-dimensional structure and regulatory function. Being absent in mammals, the two enzymes and their complex are attractive targets for antibacterial drugs. We have used hydrogen/deuterium exchange mass spectrometry to unveil how LESS IS MORE: MEMBRANE PROTEIN DIGESTION BEYOND UREA28 The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach ANALYSIS OF HIGH THROUGHPUT PROTEIN EXPRESSION IN17 The ability to efficiently produce hundreds of proteins in parallel is the most basic requirement of many aspects of proteomics. Overcoming the technical and financial barriers associated with high throughput protein production is essential for the development of an experimental platform to query and browse the protein content of a cell (e.g. protein and antibody arrays). PARALLEL REACTION MONITORING FOR HIGH RESOLUTION AND HIGH Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* S Amelia C. Peterson‡, Jason D. Russell‡, Derek J. Bailey‡, Michael S. Westphall‡, IDENTIFICATION OF CANDIDATE PLASMA PROTEIN BIOMARKERS FOR Identification of Candidate Plasma Protein Biomarkers for Cervical Cancer Using the Multiplex Proximity Extension Assay Authors Malin Berggrund, Stefan Enroth, Martin Lundberg, Erika Assarsson, Karin Stålberg, David Lindquist, INSIGHTS INTO THE PROTEOME OF GASTROINTESTINAL STROMAL Insights into the Proteome of Gastrointestinal Stromal Tumors-Derived Exosomes Reveals New Potential Diagnostic Biomarkers* S Safinur Atay‡**, Daniel W. Wilkey§, Mohammed Milhem¶, Michael Merchant§, ACQUIRING AND ANALYZING DATA INDEPENDENT ACQUISITION Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Lindsay K. Pino1x, Seth C.Just2x, Michael J. MacCoss3x, and Brian C. Searle4,*x Data independent acquisition (DIA) is an attractive alter- PROTEIN IDENTIFICATION BY MASS SPECTROMETRY During the past two decades, mass spectrometry has become established as the primary method for protein identification from complex mixtures of biological origin. This is largely attributable to the fortunate coincidence of instrumental advances that allow routine analysis of minute amounts (typically femtomoles) of involatile, polar compounds such as peptides in complex mixtures, with the REQUIRED MANUSCRIPT CONTENT AND PUBLICATION GUIDELINES The following guidelines describe the information required by the journal for all articles dealing with mass spectrometric analyses designed for protein, peptide or posttranslational modification (PTM) identification and their quantification regardless of whether the study is biological or clinical in focus.. Authors must include information in the manuscript that will allow readers and SEPARATION AND IDENTIFICATION OF PERMETHYLATED GLYCAN In BriefStructural analysis of glycoprotein N-linked and O-linked glycans is greatly enhanced by permethylation following release from the protein backbone. HPLC of permethylated glycans resolves isomeric glycans that are difficult to discern by direct infusion methodologies. An approach is described that utilizes standard peptide separation columns and accessible instrumentation. METABOLIC REGULATION BY LYSINE MALONYLATION, SUCCINYLATION Protein acetylation is a well-studied regulatory mechanism for several cellular processes, ranging from gene expression to metabolism. Recent discoveries of new post-translational modifications, including malonylation, succinylation, and glutarylation, have expanded our understanding of the types of modifications found on proteins. These three acidic lysine modifications are structurally DIFFERENTIAL PROTEOME ANALYSIS OF REPLICATIVE SENESCENCE Normal somatic cells undergo a finite number of divisions and then cease dividing whereas cancer cells are able to proliferate indefinitely. To identify the underlying mechanisms that limit the mitotic potential, a two-dimensional differential proteome analysis of replicative senescence in serially passaged rat embryo fibroblasts was undertaken. Triplicate independent two-dimensional gels A TANDEM AFFINITY TAG FOR TWO-STEP PURIFICATION UNDER Tandem affinity strategies reach exceptional protein purification grades and have considerably improved the outcome of mass spectrometry-based proteomic experiments. However, current tandem affinity tags are incompatible with two-step purification under fully denaturing conditions. Such stringent purification conditions are desirable for mass spectrometric analyses of protein modifications as ACETYLOME PROFILING REVEALS OVERLAP IN THE REGULATION OF Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone PLATFORM DEPENDENCIES IN BOTTOM-UP HYDROGEN/DEUTERIUM Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS THE MINIMUM INFORMATION REQUIRED FOR A GLYCOMICS The MIRAGE guidelines are being developed in response to a critical need in the glycobiology community to clarify glycoanalytic results so that they are more readily evaluated (in terms of their scope and depth) and to facilitate the reproduction of important results in the laboratory. The molecular and biological complexity of the glycosylation process makes thorough reporting of the FULL SUBUNIT COVERAGE LIQUID CHROMATOGRAPHY ELECTROSPRAY Highly active cytochrome b6f complexes from spinach and the cyanobacterium Mastigocladus laminosus have been analyzed by liquid chromatography with electrospray ionization mass spectrometry (LCMS+). Both size-exclusion and reverse-phase separations were used to separate protein subunits allowing measurement of their molecular masses to an accuracy exceeding 0.01% (±3 Da at 30,000 Da). HOME PAGE: MOLECULAR & CELLULAR PROTEOMICS Papers in Press Latest articles that have been fully reviewed and editorially accepted but not yet copyedited or formatted. PROTEIN IDENTIFICATION BY MASS SPECTROMETRY During the past two decades, mass spectrometry has become established as the primary method for protein identification from complex mixtures of biological origin. This is largely attributable to the fortunate coincidence of instrumental advances that allow routine analysis of minute amounts (typically femtomoles) of involatile, polar compounds such as peptides in complex mixtures, with the LESS IS MORE: MEMBRANE PROTEIN DIGESTION BEYOND UREA The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach FIVE FRIENDS OF METHYLATED CHROMATIN TARGET OF PROTEIN Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop(5FMC). 5FMC is a
PARALLEL REACTION MONITORING FOR HIGH RESOLUTION AND HIGH Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* S Amelia C. Peterson‡, Jason D. Russell‡, Derek J. Bailey‡, Michael S. Westphall‡, COMPARATIVE ANALYSIS OF THE SECRETOME FROM A MODEL Filarial nematodes (superfamily Filarioidea) are responsible for an annual global health burden of ∼6.3 million disability-adjusted life-years, which represents the greatest single component of morbidity attributable to helminths affecting humans. No vaccine exists for the major filarial diseases, lymphatic filariasis and onchocerciasis; in part because research on protective immunity A GENECENTRIC HUMAN PROTEIN ATLAS FOR EXPRESSION PROFILES An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of INTEGRATIVE PROTEOMIC AND METABOLOMIC ANALYSIS REVEALS body (5). Moreover, metabolomic analysis provides a detailed analysis of the metabolic profile in the tissues or body fluids of living organisms to reveal changes in the metabolites and PROTEIN INTERACTIONS DURING THE FLAVIVIRUS AND HEPACIVIRUS protein and bud into the ER, thereby acquiring a lipid enve-lope embedding multiple copies of the two structural glyco-proteins. Viral particles are finally released from the cell in a ACQUIRING AND ANALYZING DATA INDEPENDENT ACQUISITION Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Lindsay K. Pino1x, Seth C.Just2x, Michael J. MacCoss3x, and Brian C. Searle4,*x Data independent acquisition (DIA) is an attractive alter- HOME PAGE: MOLECULAR & CELLULAR PROTEOMICS Papers in Press Latest articles that have been fully reviewed and editorially accepted but not yet copyedited or formatted. PROTEIN IDENTIFICATION BY MASS SPECTROMETRY During the past two decades, mass spectrometry has become established as the primary method for protein identification from complex mixtures of biological origin. This is largely attributable to the fortunate coincidence of instrumental advances that allow routine analysis of minute amounts (typically femtomoles) of involatile, polar compounds such as peptides in complex mixtures, with the LESS IS MORE: MEMBRANE PROTEIN DIGESTION BEYOND UREA The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach FIVE FRIENDS OF METHYLATED CHROMATIN TARGET OF PROTEIN Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop(5FMC). 5FMC is a
PARALLEL REACTION MONITORING FOR HIGH RESOLUTION AND HIGH Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* S Amelia C. Peterson‡, Jason D. Russell‡, Derek J. Bailey‡, Michael S. Westphall‡, COMPARATIVE ANALYSIS OF THE SECRETOME FROM A MODEL Filarial nematodes (superfamily Filarioidea) are responsible for an annual global health burden of ∼6.3 million disability-adjusted life-years, which represents the greatest single component of morbidity attributable to helminths affecting humans. No vaccine exists for the major filarial diseases, lymphatic filariasis and onchocerciasis; in part because research on protective immunity A GENECENTRIC HUMAN PROTEIN ATLAS FOR EXPRESSION PROFILES An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of INTEGRATIVE PROTEOMIC AND METABOLOMIC ANALYSIS REVEALS body (5). Moreover, metabolomic analysis provides a detailed analysis of the metabolic profile in the tissues or body fluids of living organisms to reveal changes in the metabolites and PROTEIN INTERACTIONS DURING THE FLAVIVIRUS AND HEPACIVIRUS protein and bud into the ER, thereby acquiring a lipid enve-lope embedding multiple copies of the two structural glyco-proteins. Viral particles are finally released from the cell in a ACQUIRING AND ANALYZING DATA INDEPENDENT ACQUISITION Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Lindsay K. Pino1x, Seth C.Just2x, Michael J. MacCoss3x, and Brian C. Searle4,*x Data independent acquisition (DIA) is an attractive alter- HOME PAGE: MOLECULAR & CELLULAR PROTEOMICS Papers in Press Latest articles that have been fully reviewed and editorially accepted but not yet copyedited or formatted. EXPONENTIALLY MODIFIED PROTEIN ABUNDANCE INDEX (EMPAI) FOR To estimate absolute protein contents in complex mixtures, we previously defined a protein abundance index (PAI) as the number of observed peptides divided by the number of observable peptides per protein (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome. Res.12, 1231–1245).
ANALYSIS OF BCL6-INTERACTING PROTEINS BY TANDEM MASS B-cell lymphoma 6 (BCL6) is a 95-kDa nuclear phosphoprotein and member of the Pox virus zinc finger/bric-a-brac, tramtrack, broad complex (POZ/BTB) family of transcription factors. BCL6 is a transcriptional repressor required for germinal center formation, and the gene encoding it is frequently altered in diffuse large B-cell and follicular lymphomas. The dysregulation of BCL6 has therefore A GENECENTRIC HUMAN PROTEIN ATLAS FOR EXPRESSION PROFILES An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of IDENTIFICATION OF SUMOYLATED PROTEINS BY SYSTEMATIC The identification of post-translational modifications to proteins is critical for understanding many important aspects of biology. Utilizing a collection of epitope-tagged yeast strains, we developed a novel approach to determine which proteins are modified by the small ubiquitin-related modifier (SUMO). We crossed traits useful for the detection of SUMO conjugation into 4246 tandem affinity SERUM MICROARRAYS FOR LARGE SCALE SCREENING OF PROTEIN There is a great need for comprehensive proteomic analysis of large patient cohorts of plasma and serum samples to identify biomarkers of human diseases. Here we describe a new antibody-based proteomic approach involving a reverse array format where serum samples are spotted on a microarray. This enables all samples to be screened for their content of a certain serum protein in a PLATFORM DEPENDENCIES IN BOTTOM-UP HYDROGEN/DEUTERIUM Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS ACETYLOME PROFILING REVEALS OVERLAP IN THE REGULATION OF Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone THE MINIMUM INFORMATION REQUIRED FOR A GLYCOMICS The MIRAGE guidelines are being developed in response to a critical need in the glycobiology community to clarify glycoanalytic results so that they are more readily evaluated (in terms of their scope and depth) and to facilitate the reproduction of important results in the laboratory. The molecular and biological complexity of the glycosylation process makes thorough reporting of the FULL SUBUNIT COVERAGE LIQUID CHROMATOGRAPHY ELECTROSPRAY Highly active cytochrome b6f complexes from spinach and the cyanobacterium Mastigocladus laminosus have been analyzed by liquid chromatography with electrospray ionization mass spectrometry (LCMS+). Both size-exclusion and reverse-phase separations were used to separate protein subunits allowing measurement of their molecular masses to an accuracy exceeding 0.01% (±3 Da at 30,000 Da). Skip to main content* __Main menu
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AS THE COMMUNITY CONTINUES TO CLOSELY MONITOR THE EMERGENCE OF #COVID19 , MCP WOULD LIKE TO AFFIRM ITS COMMITMENT TO OUR AUTHORS AND THEIR SCIENCE. PLEASE DO NOT HESITATE TO CONTACT US TO DISCUSS PUBLICATION-RELATED SITUATIONS AND POSSIBLE EXTENSIONS. BEGINNING APRIL 1, 2020, THE EDITORS OF MCP WILL NO LONGER REQUIRE AUTHORS TO COMPLETE THE APPROPRIATE CHECKLISTS WHEN SUBMITTING A NEWMANUSCRIPT.
READ OUR EDITORIAL HERE TO FIND OUT MORE ABOUT THIS CHANGE.*
Graphical Abstract, Highlights and In Brief Beginning August 1, 2018, all resubmissions must include these new elements to enhance readibility*
Virtual Issue: Technological Innovations This virtual issue celebrates some of the excellent experimental and computational technology manuscripts published in MCP since 2018.*
Special Issue: Multi-Omics Data Integration This special issue brings together a series of articles describing novel computational methods and tools, biological applications, and perspectives on multi-omics integration.*
Special Issue: Reproductive Proteomics In this MCP special issue, explore a collection of articles highlighting recent discoveries in sperm and egg biology.*
Graphical Abstract, Highlights and In Brief Beginning August 1, 2018, all resubmissions must include these new elements to enhance readibility*
Virtual Issue: Technological Innovations This virtual issue celebrates some of the excellent experimental and computational technology manuscripts published in MCP since 2018.* __1
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PAPERS IN PRESS
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PERSPECTIVE
__You have access Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries Lindsay K Pino, Seth C Just, Michael J. MacCoss and Brian C Searle Molecular & Cellular Proteomics April 20, 2020, mcp.P119.001913; https://doi.org/10.1074/mcp.P119.001913*
RESEARCH
__You have access Seminal Plasma Proteome as an Indicator of Sperm Dysfunction and Low Sperm Motility Yunlei Li, Yanyan Sun, Aixin Ni, Lei Shi, Panlin Wang, Adamu Mani Isa, Pingzhuang Ge, Linlin Jiang, Jing Fan, Hui Ma, Gongshe Yang and JilanChen
Molecular & Cellular Proteomics April 20, 2020, mcp.RA120.002017; https://doi.org/10.1074/mcp.RA120.002017*
REVIEW
__You have access Developments and Applications of Functional ProteinMicroarrays
Guan-Da Syu, Jessica Dunn and Heng Zhu Molecular & Cellular Proteomics April 17, 2020, mcp.R120.001936; https://doi.org/10.1074/mcp.R120.001936*
RESEARCH
__You have access Proteaphagy in mammalian cells can function independent of ATG5/ATG7 Tatjana Goebel, Simone Mausbach, Andreas Tuermer, Heba Eltahir, Dominic Winter, Volkmar Gieselmann and Melanie Thelen Molecular & Cellular Proteomics April 16, 2020, mcp.RA120.001983; https://doi.org/10.1074/mcp.RA120.001983*
RESEARCH
__You have access Dysregulation of Exosome Cargo by Mutant Tau Expressed in Human-Induced Pluripotent Stem Cell (iPSC) Neurons Revealed by Proteomics Analyses Sonia Podvin, Alexander Jones, Qing Liu, Brent Aulston, Linnea S Ransom, Janneca Ames, Gloria Shen, Christopher B Lietz, Zhenze Jiang, Anthony J. O'Donoghue, Charisse Winston, Tsuneya Ikezu, Robert Rissman, Shauna Yuan and Vivian Hook Molecular & Cellular Proteomics April 15, 2020, mcp.RA120.002079; https://doi.org/10.1074/mcp.RA120.002079*
RESEARCH
__You have access Quantitative proteomics of human heart samples collected in vivo reveal the remodeled protein landscape of dilated left atrium without atrial fibrillation Nora Linscheid, Pi Camilla Poulsen, Ida Dalgaard Pedersen, Emilie Gregers, Jesper Hastrup Svendsen, Morten Salling Olesen, Jesper V. Olsen, Mario Delmar and Alicia Lundby Molecular & Cellular Proteomics April 14, 2020, mcp.RA119.001878; https://doi.org/10.1074/mcp.RA119.001878 View more published ahead of print articles__ ABOUT MOLECULAR & CELLULAR PROTEOMICS _Molecular & Cellular Proteomics_ (MCP) is a monthly journal established in 2002 and published by the American Society for Biochemistry and Molecular Biology. The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. Read our Mission Statement and Scope.
ALTMETRIC DATA
Altmetrics are data that can explain both the volume and nature of attention that research receives online. Please visit the Altmetricweb site
to
learn more. For more information on how other publishers are using altmetrics to gauge influence and impact, please visit the Altmetriccase studies page .
These articles received the most attention via news outlets, blogs, social media, etc. in the last three months.*
A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients Last mentioned on Sun Apr 19 2020*
MaxQuant software for ion mobility enhanced shotgun proteomics Last mentioned on Thu Apr 09 2020*
Proximity dependent biotinylation: key enzymes and adaptation to proteomics approaches Last mentioned on Mon Apr 20 2020* See more
CURRENT ISSUE
Molecular & Cellular ProteomicsVol. 19, Issue 4
1 Apr 2020
* Table of Contents
* Table of Contents (PDF)* Cover (PDF)
* About the Cover
* Index by author
* Ed Board (PDF)
ISSUE HIGHLIGHTS
*
Integrative Metabolic Pathway Analysis Reveals Novel Therapeutic Targets in Osteoarthritis*
Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics*
Improving Identification of _In-organello_ Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker*
A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients* Most Read
* Most Cited
*
The Orbitrap Exploris 480 MS with FAIMS for Proteomics*
Proximity dependent biotinylation enzymes for proteomics*
Species-unique Peptide Biomarkers of Bacterial Pathogens*
iBASIL for precise quantitative single-cell proteomics*
MaxQuant for ion mobility MSMore...
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