The protein complement of an organism coded for by its genome.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
Electrophoresis in which a second perpendicular electrophoretic transport is performed on the separate components resulting from the first electrophoresis. This technique is usually performed on polyacrylamide gels.
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
Chromatographic techniques in which the mobile phase is a liquid.
A mass spectrometry technique using two (MS/MS) or more mass analyzers. With two in tandem, the precursor ions are mass-selected by a first mass analyzer, and focused into a collision region where they are then fragmented into product ions which are then characterized by a second mass analyzer. A variety of techniques are used to separate the compounds, ionize them, and introduce them to the first mass analyzer. For example, for in GC-MS/MS, GAS CHROMATOGRAPHY-MASS SPECTROMETRY is involved in separating relatively small compounds by GAS CHROMATOGRAPHY prior to injecting them into an ionization chamber for the mass selection.
A mass spectrometric technique that is used for the analysis of large biomolecules. Analyte molecules are embedded in an excess matrix of small organic molecules that show a high resonant absorption at the laser wavelength used. The matrix absorbs the laser energy, thus inducing a soft disintegration of the sample-matrix mixture into free (gas phase) matrix and analyte molecules and molecular ions. In general, only molecular ions of the analyte molecules are produced, and almost no fragmentation occurs. This makes the method well suited for molecular weight determinations and mixture analysis.
Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Methods of comparing two or more samples on the same two-dimensional gel electrophoresis gel.
Techniques for labeling a substance with a stable or radioactive isotope. It is not used for articles involving labeled substances unless the methods of labeling are substantively discussed. Tracers that may be labeled include chemical substances, cells, or microorganisms.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Separation of a mixture in successive stages, each stage removing from the mixture some proportion of one of the substances, for example by differential solubility in water-solvent mixtures. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Proteins found in any species of bacterium.
A mass spectrometry technique used for analysis of nonvolatile compounds such as proteins and macromolecules. The technique involves preparing electrically charged droplets from analyte molecules dissolved in solvent. The electrically charged droplets enter a vacuum chamber where the solvent is evaporated. Evaporation of solvent reduces the droplet size, thereby increasing the coulombic repulsion within the droplet. As the charged droplets get smaller, the excess charge within them causes them to disintegrate and release analyte molecules. The volatilized analyte molecules are then analyzed by mass spectrometry.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
Methods for determining interaction between PROTEINS.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)
An autosomal recessive disorder that causes premature aging in adults, characterized by sclerodermal skin changes, cataracts, subcutaneous calcification, muscular atrophy, a tendency to diabetes mellitus, aged appearance of the face, baldness, and a high incidence of neoplastic disease.
A family of structurally-related DNA helicases that play an essential role in the maintenance of genome integrity. RecQ helicases were originally discovered in E COLI and are highly conserved across both prokaryotic and eukaryotic organisms. Genetic mutations that result in loss of RecQ helicase activity gives rise to disorders that are associated with CANCER predisposition and premature aging.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
An autosomal recessive disorder characterized by telangiectatic ERYTHEMA of the face, photosensitivity, DWARFISM and other abnormalities, and a predisposition toward developing cancer. The Bloom syndrome gene (BLM) encodes a RecQ-like DNA helicase.
A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
A publication issued at stated, more or less regular, intervals.
"The business or profession of the commercial production and issuance of literature" (Webster's 3d). It includes the publisher, publication processes, editing and editors. Production may be by conventional printing methods or by electronic publishing.
The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).
Cyclic heptapeptides found in MICROCYSTIS and other CYANOBACTERIA. Hepatotoxic and carcinogenic effects have been noted. They are sometimes called cyanotoxins, which should not be confused with chemicals containing a cyano group (CN) which are toxic.
A species of gram-negative, aerobic, rod-shaped bacteria commonly isolated from clinical specimens (wound, burn, and urinary tract infections). It is also found widely distributed in soil and water. P. aeruginosa is a major agent of nosocomial infection.
The systematic study of the complete DNA sequences (GENOME) of organisms.
A phylum of oxygenic photosynthetic bacteria comprised of unicellular to multicellular bacteria possessing CHLOROPHYLL a and carrying out oxygenic PHOTOSYNTHESIS. Cyanobacteria are the only known organisms capable of fixing both CARBON DIOXIDE (in the presence of light) and NITROGEN. Cell morphology can include nitrogen-fixing heterocysts and/or resting cells called akinetes. Formerly called blue-green algae, cyanobacteria were traditionally treated as ALGAE.
A form-genus of CYANOBACTERIA in the order Chroococcales. Many species are planktonic and possess gas vacuoles.
A bacteriocin produced by a plasmid that can occur in several bacterial strains. It is a basic protein of molecular weight 56,000 and exists in a complex with its immunity protein which protects the host bacterium from its effects.
Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.
Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)
An optical disk storage system for computers on which data can be read or from which data can be retrieved but not entered or modified. A CD-ROM unit is almost identical to the compact disk playback device for home use.
NATIONAL LIBRARY OF MEDICINE service for health professionals and consumers. It links extensive information from the National Institutes of Health and other reviewed sources of information on specific diseases and conditions.

Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks. (1/6804)

Dictyostelium discoideum has been suggested as a eukaryotic model organism for glycobiology studies. Presently, the characteristics of acceptor sites for the N-acetylglucosaminyl-transferases in Dictyostelium discoideum, which link GlcNAc in an alpha linkage to hydroxyl residues, are largely unknown. This motivates the development of a species specific method for prediction of O-linked GlcNAc glycosylation sites in secreted and membrane proteins of D. discoideum. The method presented here employs a jury of artificial neural networks. These networks were trained to recognize the sequence context and protein surface accessibility in 39 experimentally determined O-alpha-GlcNAc sites found in D. discoideum glycoproteins expressed in vivo. Cross-validation of the data revealed a correlation in which 97% of the glycosylated and nonglycosylated sites were correctly identified. Based on the currently limited data set, an abundant periodicity of two (positions-3, -1, +1, +3, etc.) in Proline residues alternating with hydroxyl amino acids was observed upstream and downstream of the acceptor site. This was a consequence of the spacing of the glycosylated residues themselves which were peculiarly found to be situated only at even positions with respect to each other, indicating that these may be located within beta-strands. The method has been used for a rapid and ranked scan of the fraction of the Dictyostelium proteome available in public databases, remarkably 25-30% of which were predicted glycosylated. The scan revealed acceptor sites in several proteins known experimentally to be O-glycosylated at unmapped sites. The available proteome was classified into functional and cellular compartments to study any preferential patterns of glycosylation. A sequence based prediction server for GlcNAc O-glycosylations in D. discoideum proteins has been made available through the WWW at http://www.cbs.dtu.dk/services/DictyOGlyc/ and via E-mail to [email protected]  (+info)

Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties. (2/6804)

Normal human luminal and myoepithelial breast cells separately purified from a set of 10 reduction mammoplasties by using a double antibody magnetic affinity cell sorting and Dynabead immunomagnetic technique were used in two-dimensional gel proteome studies. A total of 43,302 proteins were detected across the 20 samples, and a master image for each cell type comprising a total of 1,738 unique proteins was derived. Differential analysis identified 170 proteins that were elevated 2-fold or more between the two breast cell types, and 51 of these were annotated by tandem mass spectrometry. Muscle-specific enzyme isoforms and contractile intermediate filaments including tropomyosin and smooth muscle (SM22) alpha protein were detected in the myoepithelial cells, and a large number of cytokeratin subclasses and isoforms characteristic of luminal cells were detected in this cell type. A further 134 nondifferentially regulated proteins were also annotated from the two breast cell types, making this the most extensive study to date of the protein expression map of the normal human breast and the basis for future studies of purified breast cancer cells.  (+info)

Proteome mapping, mass spectrometric sequencing and reverse transcription-PCR for characterization of the sulfate starvation-induced response in Pseudomonas aeruginosa PAO1. (3/6804)

A set of proteins induced in Pseudomonas aeruginosa PAO1 during growth in the absence of sulfate was characterized by differential two-dimensional electrophoresis and MS. Thirteen proteins were found to be induced de novo or upregulated in P. aeruginosa grown in a succinate/salts medium with sodium cyclohexylsulfamate as the sole sulfur source. Protein spots excised from the two-dimensional gels were analysed by N-terminal Edman sequencing and MS sequencing (MS/MS) of internal protein fragments. The coding sequences for 11 of these proteins were unambiguously identified in the P. aeruginosa genome sequence. Expression of these genes was investigated by reverse transcription-PCR, which confirmed that repression in the presence of sulfate was acting at a transcriptional level. Three classes of sulfur-regulated proteins were found. The first class (five proteins) were high-affinity periplasmic solute-binding proteins with apparent specificity for sulfate and sulfonates. A second class included enzymes involved in sulfonate and sulfate ester metabolism (three proteins). The remaining three proteins appeared to be part of a more general stress response, and included two antioxidant proteins and a putative lipoprotein. This study demonstrates the power of the proteomics approach for direct correlation of the responses of an organism to an environmental stimulus with the genetic structures responsible for that response, and the application of reverse transcription-PCR significantly increases the conclusions that can be drawn from the proteomic study.  (+info)

The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. (4/6804)

The Yeast Proteome Database (YPDtrade mark) has been for several years a resource for organized and accessible information about the proteins of Saccharomyces cerevisiae. We have now extended the YPD format to create a database containing complete proteome information about the model organism Caenorhabditis elegans (WormPDtrade mark). YPD and WormPD are designed for use not only by their respective research communities but also by the broader scientific community. In both databases, information gleaned from the literature is presented in a consistent, user-friendly Protein Report format: a single Web page presenting all available knowledge about a particular protein. Each Protein Report begins with a Title Line, a concise description of the function of that protein that is continually updated as curators review new literature. Properties and functions of the protein are presented in tabular form in the upper part of the Report, and free-text annotations organized by topic are presented in the lower part. Each Protein Report ends with a comprehensive reference list whose entries are linked to their MEDLINE s. YPD and WormPD are seamlessly integrated, with extensive links between the species. They are freely accessible to academic users on the WWW at http://www. proteome.com/databases/index.html, and are available by subscription to corporate users.  (+info)

MITOP, the mitochondrial proteome database: 2000 update. (5/6804)

MITOP (http://www.mips.biochem.mpg.de/proj/medgen/mitop/) is a comprehensive database for genetic and functional information on both nuclear- and mitochondrial-encoded proteins and their genes. The five species files--Saccharomyces cerevisiae, Mus musculus, Caenorhabditis elegans, Neurospora crassa and Homo sapiens--include annotated data derived from a variety of online resources and the literature. A wide spectrum of search facilities is given in the overlapping sections 'Gene catalogues', 'Protein catalogues', 'Homologies', 'Pathways and metabolism' and 'Human disease catalogue' including extensive references and hyperlinks to other databases. Central features are the results of various homology searches, which should facilitate the investigations into interspecies relationships. Precomputed FASTA searches using all the MITOP yeast protein entries and a list of the best human EST hits with graphical cluster alignments related to the yeast reference sequence are presented. The orthologue tables with cross-listings to all the protein entries for each species in MITOP have been expanded by adding the genomes of Rickettsia prowazeckii and Escherichia coli. To find new mitochondrial proteins the complete yeast genome has been analyzed using the MITOPROT program which identifies mitochondrial targeting sequences. The 'Human disease catalogue' contains tables with a total of 110 human diseases related to mitochondrial protein abnormalities, sorted by clinical criteria and age of onset. MITOP should contribute to the systematic genetic characterization of the mitochondrial proteome in relation to human disease.  (+info)

Proteome analysis using selective incorporation of isotopically labeled amino acids. (6/6804)

A method is described for identifying intact proteins from genomic databases using a combination of accurate molecular mass measurements and partial amino acid content. An initial demonstration was conducted for proteins isolated from Escherichia coli (E. coli) using a multiple auxotrophic strain of K12. Proteins extracted from the organism grown in natural isotopic abundance minimal medium and also minimal medium containing isotopically labeled leucine (Leu-D10), were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled Leu residue has no effect on the CIEF separation of the protein, therefore both versions of the protein are observed within the same FTICR spectrum. The difference in the molecular mass of the natural isotopic abundance and Leu-D10 isotopically labeled proteins is used to determine the number of Leu residues present in that particular protein. Knowledge of the molecular mass and number of Leu residues present can be used to unambiguously identify the intact protein. Preliminary results show the efficacy of this method for unambiguously identifying proteins isolated from E. coli.  (+info)

Research in the exercise sciences: where do we go from here? (7/6804)

The goal of this article is to provide a perspective on how research involving the acute and chronic effects of exercise (referred to as "exercise sciences") on the structure and function of organs systems will evolve in the next century. Within the last 30 years, exercise-related research has rapidly transitioned from an organ to a subcellular/molecular focus. Thus future research will continue to be heavily influenced by molecular biology tools, fueled by both emerging technologies (e.g., "gene-chip microarrays") designed to dissect gene function on a macro scale as well as by the completion of the human genome project in which the approximately 80,000 genes comprising humans will be completely sequenced. These successes will drive the emerging fields of functional genomics (the dissecting of a gene's identity and function) and proteomics (the study of the properties of proteins). Funding levels at the National Institutes of Health will likely increase in order to expand these emerging fields as well as provide avenues for translating fundamental knowledge into solving the complexities of a number of degenerative diseases influenced heavily by activity/inactivity factors such as cardiopulmonary disease, diabetes, obesity, and the debilitating disorders associated with aging. Thus there are many challenges facing future exercise scientists who must harness the new technologies and take an aggressive stance in bringing this important field to the forefront.  (+info)

Proteome analysis of Bacillus subtilis extracellular proteins: a two-dimensional protein electrophoretic study. (8/6804)

To analyse the proteome of Bacillus subtilis extracellular proteins, extracellular protein samples were prepared from culture media (minimal medium containing 0.4% glucose) of parental B. subtilis 168, a secA-temperature sensitive mutant and an ffh conditional mutant, and examined by two-dimensional gel electrophoresis. Approximately 100 to 110 spots were visualized in a gel of B. subtilis 168 extracellular proteins. Over 90% and 80% of these disappeared in the absence of SecA and Ffh, respectively. Thirty-eight obvious spots on the gel of the B. subtilis 168 preparation were selected and compared with spots obtained under SecA- or Ffh-deficient conditions. The appearance of 36 of these 38 spots depended on SecA and Ffh. Nineteen additional extracellular proteins were detected in cultures maintained in cellobiose, maltose and soluble starch. Among 23 proteins of which the N-terminal amino acid sequences were determined, 17 were extracellular proteins having signal peptides in their precursor form. Two membrane proteins, Yfnl and YflE, were cleaved behind 226Ala-Tyr-Ala228 and 213Ala-Leu-Ala215, respectively, and of which products seemed to be liberated into the culture medium. The production of Yfnl and YflE were also dependent on SecA and Ffh. These results indicate that most extracellular proteins target to and translocate across the cytoplasmic membrane by co-operation between the signal-recognition particle and Sec protein-secretion pathways. In contrast, a spot for Hag appeared independent from SecA and Ffh. Intracellular proteins Gap, SodA and KatA were identified in the extracellular protein samples. On the basis of these results and computer searches, it was predicted that B. subtilis produces 150 to 180 proteins extracellularly.  (+info)

We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein identification technology (MudPIT). MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date. A total of 1,484 proteins were detected and identified. Categorization of these hits demonstrated the ability of this technology to detect and identify proteins rarely seen in proteome analysis, including low-abundance proteins like transcription factors and protein kinases. Furthermore, we identified 131 proteins with three or more predicted transmembrane domains, which allowed us to map the soluble domains of many of the integral membrane proteins. MudPIT is useful for proteome analysis and may be specifically applied to integral membrane proteins to obtain detailed biochemical ...
The Human Proteome Project (HPP) is an international project organized by the Human Proteome Organization (HUPO) that aims to revolutionize our understanding of the human proteome via a coordinated effort by many research laboratories around the world. It is designed to map the entire human proteome in a systematic effort using currently available and emerging techniques. Completion of this project will enhance understanding of human biology at the cellular level and lay a foundation for development of diagnostic, prognostic, therapeutic, and preventive medical applications. ...
Title:Global Cell Proteome Profiling, Phospho-signaling and Quantitative Proteomics for Identification of New Biomarkers in Acute Myeloid Leukemia Patients. VOLUME: 17 ISSUE: 1. Author(s):Elise Aasebø, Rakel B. Forthun, Frode Berven, Frode Selheim and Maria Hernandez-Valladares. Affiliation:Department of Biomedicine, Faculty of Medicine, Building for Basic Biology, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.. Keywords:Acute myeloid leukemia, biomarker, mass spectrometry, proteomics, phosphoproteomics, diagnosis, prognosis.. Abstract:The identification of protein biomarkers for acute myeloid leukemia (AML) that could find applications in AML diagnosis and prognosis, treatment and the selection for bone marrow transplant requires substantial comparative analyses of the proteomes from AML patients. In the past years, several studies have suggested some biomarkers for AML diagnosis or AML classification using methods for sample preparation with low proteome coverage and low ...
The word proteome was coined in 1995 to refer to the total protein complement of a genome. The human genome encodes roughly 100,000 genes, corresponding to a similar number of proteins. Not all genes are expressed in all tissues; roughly 10,000 proteins are found in any particular cell. The fraction of the proteome that is expressed by an organism varies between tissues and in response to the environment. Conventional proteome analysis is preformed by two-dimensional gel electrophoresis and requires the protein from roughly a million cells. We have improved the sensitivity of proteome analysis by six orders of magnitude. In preliminary work, we have demonstrated that we can perform a simple analysis of the proteome in a single human cancer cell. Our Preliminary work will be expanded in this R33 proposal. We will automate the manipulations of single cells, we will multiplex the instrument so that 96 cells can be analyzed simultaneously, we will expand our proteome analysis to two-dimensional ...
Plant cells are routinely exposed to various pathogens and environmental stresses that cause cell wall perturbations. Little is known of the mechanisms that plant cells use to sense these disturbances and transduce corresponding signals to regulate cellular responses to maintain cell wall integrity. Previous studies in rice have shown that removal of the cell wall leads to substantial chromatin reorganization and histone modification changes concomitant with cell wall re-synthesis. But the genes and proteins that regulate these cellular responses are still largely unknown. Here we present an examination of the nuclear proteome differential expression in response to removal of the cell wall in rice suspension cells using multiple nuclear proteome extraction methods. A total of 382 nuclear proteins were identified with two or more peptides, including 26 transcription factors. Upon removal of the cell wall, 142 nuclear proteins were up regulated and 112 were down regulated. The differentially ...
Author: Henriksen, Peter et al.; Genre: Journal Article; Published in Print: 2012-11; Open Access; Keywords: SISTER-CHROMATID COHESION; MASS-SPECTROMETRY; HISTONE ACETYLATION;|br/| SIGNALING NETWORKS; ESCHERICHIA-COLI; C-TRAP; YEAST; COMPLEXES;|br/| DEACETYLATION; PHOSPHORYLATION; Title: Proteome-wide Analysis of Lysine Acetylation Suggests its Broad|br/| Regulatory Scope in Saccharomyces cerevisiae
Fibroblasts are mesenchymal stromal cells which occur in all tissue types. While their main function is related to ECM production and physical support, they are also important players in wound healing, and have further been recognized to be able to modulate inflammatory processes and support tumor growth. Fibroblasts can display distinct phenotypes, depending on their tissue origin, as well as on their functional state. In order to contribute to the proteomic characterization of fibroblasts, we have isolated primary human fibroblasts from human skin, lung and bone marrow and generated proteome profiles of these cells by LC-MS/MS. Comparative proteome profiling revealed characteristic differences therein, which seemed to be related to the cells tissue origin. Furthermore, the cells were treated in vitro with the pro-inflammatory cytokine IL-1beta. While all fibroblasts induced the secretion of Interleukins IL-6 and IL-8 and the chemokine GRO-alpha, other inflammation-related proteins were up-regulated
MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome ...
The proteome can be larger than the genome, especially in eukaryotes, as more than one protein can be produced from one gene due to alternative splicing (e.g. human proteome consists 92,179 proteins[citation needed] out of which 71,173 are splicing variants[citation needed]).[3] On the other hand, not all genes are translated to proteins, and many known genes encode only RNA which is the final functional product. Moreover, complete proteome size vary depending the kingdom of life. For instance, eukaryotes, bacteria, archaea and viruses have on average 15,145, 3,200, 2,358 and 42 proteins respectively encoded in their genomes.[4]. The term dark proteome coined by Perdigão and colleagues, defines regions of proteins that have no detectable sequence homology to other proteins of known three-dimensional structure and therefore cannot be modeled by homology. For 546,000 Swiss-Prot proteins, 44-54% of the proteome in eukaryotes and viruses was found to be dark, compared with only ∼14% in ...
The use of dialyzed serum is essential in the application of the conventional stable isotope labeling by amino acids in cell culture (SILAC) approach to achieve complete labeling of proteins for quantitative proteomics. Here, we first evaluated the impact of dialyzed serum on the proteome and phosphoproteome
TY - JOUR. T1 - Mass-spectrometry based proteome comparison of extracellular vesicle isolation methods. T2 - Comparison of ME-kit, size-exclusion chromatography, and high-speed centrifugation. AU - Askeland, Anders. AU - Borup, Anne. AU - Østergaard, Ole. AU - Olsen, Jesper V.. AU - Lund, Sigrid M.. AU - Christiansen, Gunna. AU - Kristensen, Søren R.. AU - Heegaard, Niels H.H.. AU - Pedersen, Shona. PY - 2020. Y1 - 2020. N2 - Extracellular vesicles (EVs) are small membrane-enclosed particles released by cells under various conditions specific to cells biological states. Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. MS analysis of EVs in plasma is challenging and EV isolation is usually necessary. Therefore, we compared differences in abundance, subtypes, and contamination for EVs isolated by high-speed centrifugation, size exclusion chromatography (SEC), and peptide-affinity precipitation ...
Peptide KE exhibits immunoprotective, geroprotective, and oncostatic activities and stimulates functional activity of fibroblasts. The KE motif is present in amino acid sequences of some cytokines and peptide hormones functionally similar to KE peptide. However, the relationship between the presence of KE motif and protein functions on the scale of known human proteome has not yet received sufficient attention. The incidence of bioregulatory peptide KE in proteins of various functional groups constituting human proteome is studied. The study is carried out with the use of the available data on the human proteome (UniProt portal) comprising 20,417 proteins. The levels of KE motifs were maximum in cytoplasmic and nuclear proteins, while the presence of KE in the membrane and all other proteins was the minimum. KE peptide molecules released from nuclear proteins during limited proteolysis can bind to DNA and regulate gene expression.. ...
Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect
Background. Thoracic aortic aneurysm (TAA) is a degenerative disease of the aortic wall and is associated with an increased risk of aortic rupture. TAA is a more prevalent complication in patients with bicuspid aortic valve (BAV) compared to those with tricuspid aortic valve (TAV). Objectives. We aimed to investigate first, changes in intracellular proteins by comparing BAV and TAV patients with aneurysm, and second, regional changes in extracellular matrix (ECM) proteins by comparing the lesser (concavity) and the greater (convexity) aortic curvatures of BAV patients with and without aneurysm. The findings obtained in human patients were followed up by mechanistic studies in mice. Methods. Human and murine aortic specimens were analysed by mass spectrometry (MS) after extraction of intracellular and ECM proteins. Immunoblotting and gene expression analysis were used to validate the proteomics findings. An ECM protease knockout mouse model was used to better characterise proteolytic processing ...
The term proteome was coined by Mark Wilkins first in 1994 in the symposium: 2D Electrophoresis: from protein maps to genomes in Siena, Italy, and was subsequently published in 1995 (1), which was part of his PhD thesis. The term proteome is a blend of proteins and genome and Wilkins used it to describe the entire complement of proteins expressed by a genome, cell, tissue or organism. Subsequently this term has been specified to contain all the expressed proteins at a given time point under defined conditions. The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organisms complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term ...
The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-HPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data ...
article{c8bd2452-0966-4124-b995-eef3ae4c8ede, abstract = {The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-FIPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, ...
We used 2H2O metabolic labeling to assess large scale plasma proteome dynamics in vivo. Administration of 2H2O in a bolus injection followed by 5% supplementation in the drinking water enabled accurate measurement of the FSR of multiple plasma proteins in less than 8 h. This approach considers 2H2O as the labeling precursor and is based on the assumption that 2H from 2H2O rapidly equilibrates with the carbon-bound hydrogen atoms of proteogenic amino acids before they are incorporated into newly synthesized proteins (12, 17). This key assumption was validated based on the analysis of temporal changes in 2H labeling of body water and hepatic proteogenic amino acids. The steady state labeling of nonexchangeable hydrogen atoms in free amino acids within 1 h of 2H2O administration demonstrates that the rate-limiting step of 2H incorporation into long-lived proteins (t½ , ∼3 h) is protein synthesis from amino acids. Protein synthesis is assessed from the rate of 2H incorporation into a proteolytic ...
Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive
Additional file 13: of Integration of Ixodes ricinus genome sequencing with transcriptome and proteome annotation of the naĂŻve midgut
Jennifer E Van Eyk, Fernando Jose Corrales, Ruedi Aebersold, Ferdinando Cerciello, Eric W Deutsch, Paola Roncada, Jean-Charles Sanchez, Tadashi Yamamoto, Pengyuan Yang, Hui Zhang, Gilbert S Omenn Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. Journal or Proteome Research, DOI: 10.1021/acs.jproteome.6b00444 Publication Date (Web): August 30, 2016. 2. NIH Bio-specimens National Cancer Institute (NCI) Specimen resource locator https://specimens.cancer.gov/. 3. CPTAC publications. Zhang, H, Liu T, Zhang Z, Payne S. et al (2016) Integrated proteogenomic characterization of human high grade serous ovarian cancer. Cell. http://www.cell.com/cell/home. Mertins P, et al (2016) Proteogenomic Analysis of Human Breast Cancer Connects Genetic Alterations to Phosphorylation NetworksNature . http://www.nature.com/nature.. Zhang B, Wang J, Wang X, Zhu J, et al. (2014) Proteogenomic characterization of human colon and rectal cancer Nature 513 (7518): 382-7. ...
Agilent Technologies Inc. (NYSE: A) and Proteome Systems a leading in...Proteome Systems developed GlycomIQ to address the emerging field of g... Analysis of protein glycosylation is a demanding task that has often ...The co-marketed product is expected to be available this summer. Agile... Agilent is proud of this collaboration with Proteome Systems said T...,Integration,of,Agilents,MS,technology,,Proteome,Systems,software,to,help,scientists,in,proteomics,research,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
The role of mass spectrometry in proteome studies.: Mass spectrometry (MS) is an important tool in modern protein chemistry. In proteome analyses the expression
Human proteome analysis Since the human proteome was first revealed, scientists have been increasing their efforts to repeat the process more quickly in order to lay the groundwork for routine systems biology experiments, accelerate disease biomarker discovery and guide us towards the realm of personalised medicine. Many improvements have been...
The Human Eye Proteome Project Perspectives on an emerging proteome Proteomics , 2013, 13 , 2500-2511 Richard D. Semba, Jan J. Enghild, Vidya Venkatraman, Thomas F. Dyrlund, Jennifer E. Van Eyk Abstract There are an estimated 285 million people with visual impairment worldwide, of whom 39 million are blind. The pathogenesis of many eye diseases...
TY - JOUR. T1 - Global secretome analysis identifies novel mediators of bone metastasis. AU - Blanco, Mario Andres. AU - Leroy, Gary. AU - Khan, Zia. AU - Alečković, Maša. AU - Zee, Barry M.. AU - Garcia, Benjamin A.. AU - Kang, Yibin. PY - 2012/9. Y1 - 2012/9. N2 - Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis ...
Comprehensive, systematic characterization of the plasma proteome in healthy and diseased states greatly facilitates the development of biosignatures for early disease detection, clinical diagnosis, and therapy. Blood plasma is the most complex human-derived proteome containing other tissue proteome subsets as well as a wide dynamic range of protein concentrations. Therefore, the characterization of biosignatures in the human plasma proteome is a very complicated task. Advances in methods and technology for profiling plasma proteins now enable construction of a comprehensive pipeline from candidate discovery, qualification, verification, research assay optimization, validation to eventual commercialization.. Analysis of the proteome from samples obtained from this population is of prime importance. The plasma and serum is isolated from the blood sample collected and flash frozen on site prior to be being shipped to our central cryostorage facility. The sample is then analyzed using a 2D-gel ...
Antibodies are crucial for the study of human proteins and have been defined as one of the three pillars in the human chromosome-centric Human Proteome Project (CHPP). In this article the chromosome-centric structure has been used to analyze the availability of antibodies as judged by the presence within the portal Antibodypedia, a database designed to allow comparisons and scoring of publicly available antibodies toward human protein targets. This public database displays antibody data from more than one million antibodies toward human protein targets. A summary of the content in this knowledge resource reveals that there exist more than 10 antibodies to over 70% of all the putative human genes, evenly distributed over the 24 human chromosomes. The analysis also shows that at present, less than 10% of the putative human protein-coding genes (n = 1882) predicted from the genome sequence lack antibodies, suggesting that focused efforts from the antibody-based and mass spectrometry-based proteomic ...
Egea, J., Fabregat, I., Frapart, Y. M., Ghezzi, P., Görlach, A., Kietzmann, T., Kubaichuk, K., Knaus, U. G., Lopez, M. G., Olaso-Gonzalez, G., Petry, A., Schulz, R., Vina, J., Winyard, P., Abbas, K., Ademowo, O. S., Afonso, C. B., Andreadou, I., Antelmann, H., Antunes, F., Aslan, M., Bachschmid, M. M., Barbosa, R. M., Belousov, V., Berndt, C., Bernlohr, D., Bertrán, E., Bindoli, A., Bottari, S. P., Brito, P. M., Carrara, G., Casas, A. I., Chatzi, A., Chondrogianni, N., Conrad, M., Cooke, M. S., Costa, J. G., Cuadrado, A., My-Chan Dang, P., De Smet, B., Debelec-Butuner, B., Dias, I. H. K., Dunn, J. D., Edson, A. J., El Assar, M., El-Benna, J., Ferdinandy, P., Fernandes, A. S., Fladmark, K. E., Förstermann, U., Giniatullin, R., Giricz, Z., Görbe, A., Griffiths, H., Hampl, V., Hanf, A., Herget, J., Hernansanz-Agustín, P., Hillion, M., Huang, J., Ilikay, S., Jansen-Dürr, P., Jaquet, V., Joles, J. A., Kalyanaraman, B., Kaminskyy, D., Karbaschi, M., Kleanthous, M., Klotz, L. O., Korac, B., ...
Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures. In psychrophilic bacteria, serine, aspartic acid, threonine and alanine are overrepresented in the coil regions of secondary structures, whilst glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic and hydrophilic side chains are
Current conventions limit the size and complexity of the detectable proteome and prevent mass-spectrometry-based proteomics from providing a comprehensive characterization of biological systems. OpenProt enables improved mapping of the proteome because, in addition to currently annotated CDSs and proteins, OpenProt displays the sequence, functional annotation and expression evidence of previously hidden altORFs and their corresponding altProts. The OpenProt platform is freely available to users.. ...
TY - JOUR. T1 - Novel surgical approaches for sampling the ovarian surface epithelium and proximal fluid proteome. AU - Rungruang, Bunja. AU - Hood, Brian L.. AU - Sun, Mai. AU - Hoskins, Ebony. AU - Conrads, Thomas P.. AU - Zorn, Kristin K.. PY - 2010/11/5. Y1 - 2010/11/5. N2 - The pathogenesis of ovarian, fallopian tube, and peritoneal cancers has been difficult to elucidate despite intense effort. Recently, though, the care of women felt to be at high risk due to a strong family history of breast and/or ovarian cancer or a known germline BRCA1 or BRCA2 mutation has provided potential insight into the development of these malignancies. Risk-reducing surgical removal of the fallopian tubes and ovaries, called risk-reducing bilateral salpingo-oopherectomy (RRBSO), is commonly performed as a laparoscopic procedure to minimize recovery time. We describe here an optimized surgical sampling workflow for analyzing the proteomes of peritoneal, fallopian tube, and ovarian surface epithelial (OSE) ...
Whole-proteome distributions of protein isoelectric point (pI) values in different organisms are bi- or trimodal with some variations. It was suggested that the observed multimodality of the proteome-wide pI distributions is associated with subcellular localization-specific differences in the local pI distributions. However, the factors responsible for variation of the intracellular localization-specific pI profiles have not been investigated in detail. In this work, we explored proteome-wide pI distributions of 32,138 human proteins predicted to reside in 10 subcellular compartments, as well as the pI distributions of experimentally observed lysosomal and Golgi proteins. The distributions were found to differ significantly, although all of them adhered to the major recurrent bimodal pattern. Grossly, acid-biased and alkaline-biased patterns with various minor statistical features were observed at different subcellular locations. Bioinformatics analysis revealed the existence of strong statistically
The high-throughput identification and accurate quantification of proteins are essential strategies for exploring cellularfunctions and processes in quantitative proteomics. Stable isotope tagging is a key technique in quantitative proteomicresearch, accompanied by automated tandem mass spectrometry. For the differential proteome analysis of mouse neuronal celllines, we used a multiplexed isobaric tagging method, in which a four-plex set of amine-reactive isobaric tags are available forpeptide derivatization. Using the four-plex set of isobaric tag for relative and absolute quantitation (iTRAQ) reagents, we analyzedthe differential proteome in several stroke time pathways (0, 4, and 8 h) after the mouse neuronal cells have been stressed usinga glutamate oxidant. In order to obtain a list of the differentially expressed proteins, we selected those proteins which had apparentlychanged significantly during the stress test. With 95% of the peptides showing only a small variation in quantity before ...
textit{Proteome research : mass spectrometry}. Edited by Peter James. Berlin: Springer-Verlag, 2001. xxi, 274 s. ISBN~3-540-67255-9 ...
Soon after the introduction of high resolution two-dimensional electrophoresis (2-DE) in 1975 by Klose (16), OFarrell (17), and others, the technique was applied to the plasma proteins by the present authors (18) with the result that the number of resolved species increased to 300 or more. The 2-DE map of human plasma that resulted is recognizably the same as those produced later by many investigators: in contrast to cellular protein patterns, the plasma 2-DE pattern appears basically the same in everyones hands perhaps due to the very high solubility of the proteins involved and the ease with which the distinctive glycosylation trains of specific proteins can be recognized. A more comprehensive database was reported in 1991 in which 727 spots were resolved, of which 376 were identified as 49 different proteins (19). A plasma map using an immobilized pH gradient first dimension separation was presented the following year with 40 protein identifications carried out by microsequencing (20), and ...
Source: Journal of Proteome Research - October 28, 2019 Category: Biochemistry Authors: Alexander I. Archakov* †, Alexander L. Aseev‡, Victor A. Bykov§, Anatoly I. Grigoriev?, Vadim M. Govorun?, Ekaterina V. Ilgisonis†, Yuri D. Ivanov†, Vadim T. Ivanov#, Olga I. Kiseleva†, Arthur T. Kopylov†, Andrey V. Lisitsa†, Sergey N. Mazu Source Type: research. [ASAP] Brain Region-Specific nAChR and Associated Protein Abundance Alterations Following Chronic Nicotine and/or Menthol Exposure ...
Prior, M. J., Larance, M., Lawrence, R. T., Soul, J., Humphrey, S., Burchfield, J., Kistler, C., Davey, J. R., La-Borde, P. J., Buckley, M., Kanazawa, H., Parton, R. G., Guilhaus, M. & James, D. E. 4 Nov 2011 In : Journal of Proteome Research. 10, 11, p. 4970-4982 13 p.. Research output: Contribution to journal › Article ...
Changes in nuclear proteome inrinmutant reveal the potential downstream targets ofRIN. (a) Nuclear proteins were isolated from wild-type (WT)and rin mutant frui
The quantitative proteome analysis is a key technology for most of the projects within the CRC 1218. The aim of the Z02 project is to support the projects with mass spectrometric expertise. Besides the assessment of global protein expression profiles, the major focus of the facility is the identification of protein-protein interaction in order to decipher molecular networks within mitochondria. In addition, we will investigate activated signalling pathways by the enrichment of post translational modifications, including phosphorylated and ubiquitinated peptides. Moreover, the Z02 project will also support the CRC with statistical and bioinformatics data analysis.. Latest publication ...
The Korea-led Global Human ChromosomeCentric Human Proteome Project (C-HPP) (Chair: Paik Young-Ki, Underwood Distinguished Prof.) made its official launch on September 10, 2012. As the largest project since the human genome, the C-HPP is planned to be implemented over the next ten years (September 2012-September 2022). The project consortium consists of 25 international teams, which focus on each human chromosome (1-22, X, Y and mitochondria). The headquarters office is located at Yonsei Proteome Research Center, directed by Prof. Paik at Yonsei University. The launching ceremony of the C-HPP was held during the annual congress of the Human Proteome Organization (HUPO) in Boston in 2012, which was attended by officials from the U.S. National Institute of Health, the Canadian Institute of Health Research, and key figures in the fields of biomedical research and bio industries who delivered congratulatory speeches on the vision and significance of the project. Historically, the initial C-HPP team ...
Characterizing the molecular components of the basic unit of life; the cell, is crucial for a complete understanding of human biology. The cell is divided into compartments to create a suitable environment for the resident proteins to fulfill their functions. Therefore, spatial mapping of the human proteome is essential to understand protein function in health and disease.. Spatial proteomics is most commonly investigated using mass spectrometry or imaging, combined with machine learning for the data analysis. Until now, studies have been limited to high abundant proteins and relied on the purification of organelle fractions from a bulk of cells. Within the scope of this thesis, we were able to systematically localize proteins in their native cellular environment using antibody-based imaging techniques, and to investigate protein subcellular localization and dynamics on a single cell level, introducing a major advance within the field of spatial proteomics.. Paper I of this thesis presents a ...
TY - JOUR. T1 - Data detailing the platelet acetyl-lysine proteome. AU - Aslan, Joseph E.. AU - David, Larry L.. AU - McCarty, Owen J.T.. N1 - Funding Information: We thank P. Wilmarth (OHSU) for assistance with proteomics analyses. Proteomics studies were supported by a Research Core award from the OHSU School of Medicine , and NIH Grants P30EY010572, P30CA069533, and S10OD012246 . This work was supported by Grants from the National Institutes of Health ( R01HL101972 to O.J.T.M.), the American Heart Association ( 13POST13730003 to J.E.A. and 13EIA12630000 to O.J.T.M). The authors have no conflicts of interest to declare. PY - 2015/12/1. Y1 - 2015/12/1. N2 - Here we detail proteomics data that describe the acetyl-lysine proteome of blood platelets (Aslan et al., 2015 [1]). An affinity purification - mass spectrometry (AP-MS) approach was used to identify proteins modified by Nε-lysine acetylation in quiescent, washed human platelets. The data provide insights into potential regulatory ...
agilent_technologies_inc_nyse_a_and_proteome_systems_a_leading_international_proteomics_company_today_announced_they_have_signed_a_marketing_agreement_to_collaborate_on_an_integrated_solution_for_the_analysis_of_glycoproteins_molecules_that_are_important_in_the_study_of_many_diseases_including_cancer_influenza_and_arthritis_under_the_agreement_proteome_systems_will_make_its_glycomiq_
JPT Peptide Technologies is a DIN ISO 9001:2015 certified and GCLP compliant integrated provider of innovative peptide based catalog products and custom services.
The massive characterization of host-associated and environmental microbial communities has represented a real breakthrough in the life sciences in the last years. In this context, metaproteomics specifically enables the transition from assessing the genomic potential to actually measuring the functional expression of a microbiome. However, significant research efforts are still required to develop analysis pipelines optimized for metaproteome characterization. This work presents an efficient analytical pipeline for shotgun metaproteomic analysis, combining bead-beating/freeze-thawing for protein extraction, filter-aided sample preparation for cleanup and digestion, and single-run liquid chromatography-tandem mass spectrometry for peptide separation and identification. The overall procedure is more time-effective and less labor-intensive when compared to state-of-the-art metaproteomic techniques. The pipeline was first evaluated using mock microbial mixtures containing different types of bacteria and
After all the press surrounding the first human proteome drafts last year, it might be easy to forget about the chromosome centric human proteome project (C-HPP). This HUGE, multinational project represents years of work into getting a full picture of the human proteome ...
Two independent research collaborations have released highly detailed maps of the human proteome in the same publication, identifying a high proportion of the proteins encoded by the human genome. They will help efforts worldwide in the search for new biomarkers of disease. Both methods relied on mass spectrometry to deliver the results, which...
Tobacco BY-2 proteome display, protein profiling and annotation using two-dimensional electrophoresis and mass spectrometry-based cross-species identification ...
Scope and method of study: To study the plant cell wall degradation process and changes in overall physiology during the growth of A. nidulans on sorghum stover at proteomic and genomic level, A. nidulans was grown on sorghum stover under solid-state culture conditions for 1, 2, 3, 5, 7 and 14 days. Semi-quantitative extracellular proteome analysis (1-D PAGE LC-MS/MS), whole genome microarray analysis, scanning and transmission electron microscopy, along with qualitative and quantitative analysis of extracellular hydrolytic enzyme activities, and analysis of the breakdown products by enzymes was used to study sorghum cell wall degradation by A. nidulans.Findings and conclusions: Based on analysis of chitin content, A. nidulans grew to be 4-5% of the total biomass in the culture. A hyphal mat developed on the surface of the sorghum by day one and as seen by scanning electron microscopy the hyphae enmeshed the sorghum particles by day 5. A total of 294 extracellular proteins were identified with ...
TY - JOUR. T1 - Copper exposure effects on yeast mitochondrial proteome. AU - Banci, Lucia. AU - Bertini, Ivano. AU - Ciofi-Baffoni, Simone. AU - DAlessandro, Annamaria. AU - Jaiswal, Deepa. AU - Marzano, Valeria. AU - Neri, Sara. AU - Ronci, Maurizio. AU - Urbani, Andrea. PY - 2011/10/1. Y1 - 2011/10/1. N2 - Mitochondria play an important role on the entire cellular copper homeostatic mechanisms. Alteration of cellular copper levels may thus influence mitochondrial proteome and its investigation represents an important contribution to the general understanding of copper-related cellular effects. In these study we have performed an organelle targeted proteomic investigation focusing our attention on the effect of non-lethal 1 mM copper concentration on Saccharomyces cerevisiae mitochondrial proteome. Functional copper effects on yeast mitochondrial proteome were evaluated by using both 2D electrophoresis (2-DE) and liquid chromatography coupled with tandem mass spectrometry. Proteomic data have ...
The last 30 years Enterococcus faecium has become an important nosocomial pathogen in hospitals worldwide. The aim of this study was to obtain insight in the cell surface proteome of E. faecium when grown in laboratory and clinically relevant conditions. Enterococcus faecium E1162, a clinical blood stream isolate, was grown ... read more until mid-log phase in brain heart infusion medium (BHI) with, or without 0.02% bile salts, Tryptic Soy Broth with 1% glucose (TSBg) and urine, and its cell surface was shaved using immobilized trypsin. Peptides were identified using MS/MS. Mapping against the translated E1162 whole genome sequence identified 67 proteins that were differentially detected in different conditions. In urine, 14 proteins were significantly more and nine proteins less abundant relative to the other conditions. Growth in BHI-bile and TSBg, revealed four and six proteins, respectively, which were uniquely present in these conditions while two proteins were uniquely present in both ...
The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of equine recurrent uveitis, an autoimmune inflammatory disease in horses leading to breakdown of the outer blood-retinal barrier and influx of autoreactive T-cells into affected horses vitrei. Cell surface proteins of native and cultured RPE cells from eye-healthy horses were captured by biotinylation, analyzed by high resolution mass spectrometry coupled to liquid chromatography (LC MS/MS), and the most interesting candidates were validated by PCR, immunoblotting and immunocytochemistry. A total of 112 proteins were identified, of which 84% were cell surface membrane proteins. Twenty-three of these proteins were concurrently expressed by both cell states, 28 proteins exclusively by native RPE cells. Among the
Time-Course Proteome Analysis Reveals the Dynamic Response of Cryptococcus gattii Cells to Fluconazole. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Human Plasma Proteome Analysis Following Endotoxin Challenge Identifies New Proteins that Contribute to Molecular Phenotype of Innate Immunity
phdthesis{be258743-7e2f-4e1a-b45d-bbfdaaa3d645, abstract = {Proteomics is expected to generate new insights into biological processes as well as identify novel biomarkers and therapeutic targets since most biological functions are transmitted through proteins. However, due to the complexity displayed by a proteome and inherent limitations associated with current methodologies, proteomic analyses often result in incomplete coverage and inconsistent measurements. Clearly, the development of novel high-performing proteomic platforms will be essential in order to successfully decipher the human proteome(s).,br/,,br, ,br/,,br, This thesis, based on four original papers denoted I to IV, describes the development and applicability of a novel proteomic technology platform entitled Global Proteome Survey (GPS) capable of transforming affinity proteomics into a global discovery engine. The GPS methodology combines the best features of affinity proteomics and mass spectrometry, and is based on using ...
Bifidobacterium animalis subsp. lactis BB-12 is a widely used probiotic strain associated with a variety of health-promoting traits. There is, however, only limited knowledge available regarding the membrane proteome and the proteins involved in oligosaccharide transport in BB-12. We applied two enrichment strategies to improve the identification of membrane proteins from BB-12 cultures grown on glucose and on xylo-oligosaccharides, the latter being an emerging prebiotic substrate recently reported to be fermented by BB-12. Our approach encompassed consecutive steps of detergent- and carbonate-treatment in order to generate inside-out membrane vesicles and to interfere with binding of membrane-associated proteins to the membrane, respectively. Proteins in the enriched membrane fraction and membrane-associated fraction were digested by lysyl endopeptidase and trypsin followed by peptide sequencing by LC-ESI-Q-TOF MS/MS. Ninety of a total of 248 identified unique proteins were predicted to possess ...
Fingerprint Dive into the research topics of The genome and structural proteome of an ocean siphovirus: A new window into the cyanobacterial mobilome. Together they form a unique fingerprint. ...
TY - JOUR. T1 - Testing the significance of microorganism identification by mass spectrometry and proteome database search. AU - Pineda, Fernando J.. AU - Lin, Jeffrey S.. AU - Fenselau, Catherine. AU - Demirev, Plamen A.. PY - 2000/8/15. Y1 - 2000/8/15. N2 - We derive and validate a simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases. The model allows us to calculate the significance of previously reported microorganism identification results. In particular, for Δm = ±1.5 Da, we find that the computed significance levels are sufficient to demonstrate the ability to identify microorganisms, provided the number of candidate microorganisms is limited to roughly three Escherichia coli-like or roughly 10 Bacillus subtilis-like microorganisms (in the sense of having roughly the same number of proteins per unit-mass interval). We conclude that, given the ...
TY - JOUR. T1 - Comparative proteome and peptidome analysis of the cephalic fluid secreted by Arapaima gigas (Teleostei Osteoglossidae) during and outside parental care. AU - Torati, Lucas S.. AU - Migaud, Hervé. AU - Doherty, Mary K.. AU - Siwy, Justyna. AU - Mullen, Willian. AU - Mesquita, Pedro E.C.. AU - Albalat, Amaya. N1 - ©2017 The Authors. PY - 2017/10/24. Y1 - 2017/10/24. N2 - Parental investment in Arapaima gigas includes nest building and guarding, followed by a care provision when a cephalic fluid is released from the parents head to the offspring. This fluid has presumably important functions for the offspring but so far its composition has not been characterised. In this study the proteome and peptidome of the cephalic secretion was studied in parental and non-parental fish using capillary electrophoresis coupled to mass spectrometry (CE-MS) and GeLC-MS/MS analyses. Multiple comparisons revealed 28 peptides were significantly different between males and parental males ...
Title: Amino Acid Sequence Database Suitable for the Protein and Proteome Analysis. VOLUME: 5 ISSUE: 4. Author(s):Takao Kawakami, Junko Ozaki, Kazuhiro Kondo, Shinji Sato and Harunobu Yunokawa. Affiliation:Clinical Proteome Center, Tokyo Medical University, Shinjuku Sumitomo Building 17th Floor, 2-6-1 Nishi Shinjuku, Shinjuku, Tokyo 163-0217, Japan.. Keywords:Alternative splicing, database search program, peptide identification, posttranslational processing, sequence annotation, sequence database, tandem mass spectrometry. Abstract: Amino acid sequence database is one of the essential components in the current proteomics with mass spectrometry. Protein identification routine as well as posttranslational modification analysis is based on correlation between the mass spectrometry data of peptides obtained from proteome and the entry sequences in the database. While different sequence databases are available from public resources for the correlation search, these primary sequence data can be ...
Like other DNA viruses, herpes simplex virus type 1 (HSV-1) replicates and proliferates in host cells continuously modulating the host molecular environment. Following a sophisticated temporal expression pattern, HSV-1 encodes at least 89 multifunctional proteins that interplay with and modify the host cell proteome. During the last decade, advances in mass spectrometry applications coupled to the development of proteomic separation methods have allowed to partially monitor the impact of HSV-1 infection in human cells. In this review, we discuss the current use of different proteome fractionation strategies to define HSV-1 targets in two major application areas: (i) viral-protein interactomics to decipher viral-protein interactions in host cells and (ii) differential quantitative proteomics to analyze the virally induced changes in the cellular proteome. Moreover, we will also discuss the potential application of high-throughput proteomic approaches to study global proteome dynamics and also post
2017 The Author(s). Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds largest food crops including wheat, rice, maize and soybean. Despite impacting global food security, little is known about the pathogenicity mechanisms employed by R. solani. To enable prediction of effectors possessing either broad efficacy or host specificity, a combined secretome was constructed from a monocot specific isolate, a dicot specific isolate and broad host range isolate infecting both monocot and dicot hosts. Secretome analysis suggested R. solani employs largely different virulence mechanisms to well-studied pathogens, despite in many instances infecting the same host plants. Furthermore, the secretome of the broad host range AG8 isolate may be shaped by maintaining functions for saprophytic life stages while minimising opportunities for host plant recognition. Analysis of possible co-evolution with host plants and in-planta up-regulation in particular, aided ...
TY - JOUR. T1 - Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.. AU - Jeong, Jun Seop. AU - Jiang, Lizhi. AU - Albino, Edisa. AU - Marrero, Josean. AU - Rho, Hee Sool. AU - Hu, Jianfei. AU - Hu, Shaohui. AU - Vera, Carlos. AU - Bayron-Poueymiroy, Diane. AU - Rivera-Pacheco, Zully Ann. AU - Ramos, Leonardo. AU - Torres-Castro, Cecil. AU - Qian, Jiang. AU - Bonaventura, Joseph. AU - Boeke, Jef D.. AU - Yap, Wendy Y.. AU - Pino, Ignacio. AU - Eichinger, Daniel J.. AU - Zhu, Heng. AU - Blackshaw, Seth. PY - 2012/6. Y1 - 2012/6. N2 - To broaden the range of tools available for proteomic research, we generated a library of 16,368 unique full-length human ORFs that are expressible as N-terminal GST-His(6) fusion proteins. Following expression in yeast, these proteins were then individually purified and used to construct a human proteome microarray. To demonstrate the usefulness of this reagent, we developed a streamlined strategy for the production of ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
The Human Cell chapters provide a knowledge-based analysis of the human cellular proteomes and an entry into the Human Protein Atlas from different perspectives. The Cell Atlas can be explored on the basis of the transcriptomes of a large panel of human cell lines. This includes the classification of genes with variable and stable expression across the panel. Furthermore, various spatiotemporal aspects of the human proteome can be explored, such as the organelle proteomes, the multilocalizing proteome and the proteome showing single-cell variation. The human proteome can further be explored based on the expression in different organelles and cellular structures. This enables the definition of organelle proteomes that indicates the distinct organelle structures and functions. Each separate chapter includes a description of a particular proteome and explorations of protein expression patterns, a complete list of proteins that build a proteome, as well as examples of detailed images ...
Carboxylate efflux from roots is a crucial and differential response of soybean genotypes to low phosphorus (P) stress. Exudation of carboxylic acids including oxalate, citrate, succinate and fumarate was induced under low P stress, particularly in P-efficient soybean genotypes. Enhancement of root length, surface area and volume further improved P acquisition under low P stress. To understand the molecular basis of carboxylate efflux under low P stress, the root proteome of contrasting genotypes (P-efficient: EC-232019 and P-inefficient: EC-113396) was compared. Among a total of 325 spots, 105 (32%) were differentially abundant proteins (DAPs) between sufficient (250 µM) and low P (4 µM) levels. Abundance of 44 (14%) proteins decreased by more than two-fold under low P stress, while 61 (19%) proteins increased by more than two-fold. Protein identification and annotation revealed that the DAPs were involved in a myriad of functions including carboxylic acid synthesis, carbohydrate, protein and lipid
In line with the aims of the Chromosome-centric Human Proteome Project (C-HPP) to completely annotate proteins of each chromosome and biology/disease driven HPP (B/D-HPP) to decipher their relation to diseases, we have generated a nonredundant catalogue of protein-coding genes for Chromosome 12 (Chr …
Our study showed for the first time the effect of the long term consumption of four dietary models, providing different quantity and quality of dietary lipids, on the whole proteome of peripheral blood mononuclear cells (PBMC) from patients with MetS. In this study, we analyzed separately the changes induced in the nuclear and cytoplasmic proteome after the long-term consumption of a high saturated fatty acid diet (HSFA), a high monounsaturated fatty acids-rich diet (HMUFA), a low-fat high carbohydrates diet (LFHCC) and a low-fat high carbohydrates diet supplemented with n-3 fatty acids (LFHCC n-3).. The proteins responding to the quantity and quality of dietary lipids identified in our study showed that dietary lipids regulate different biomechanisms directly involved in the etiology of MetS. This idea is supported by the relationship found between MetS parameters, mainly in changes in the TAG and glucose levels and several changes in the proteome. Long-term consumption of an HSFA diet leads to ...
The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease
Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the
A bottom-up label-free mass spectrometric proteomic strategy was used to analyse the protein profiles of the human embryonic secretome. Culture media samples used for embryonic culture of patients undergoing intracytoplasmic sperm injection cycles were selected as a test case for this exploratory proof-of-principle study. The media were stored after embryo transfer and then pooled into positive (n = 8) and negative (n = 8) implantation groups. The absolute quantitative bottom-up technique employed a multidimensional protein identification technology based on separation by nano-ultra-high pressure chromatography and identification via tandem nano-electrospray ionization mass spectrometry with data-independent scanning in a hydrid QqTOF mass spectrometer. By applying quantitative bottom-up proteomics, unique proteins were found exclusively in both the positive- and negative-implantation groups, which suggest that competent embryos express and secrete unique biomarker proteins into the surrounding ...
Enhanced qualitative and quantitative proteomic analysis using pSMART combines data dependent and data independent acquisition for improved results.
The small intestine is an important human organ that plays a central role in many physiological functions including digestion, absorption, secretion and defense. Duodenal pathologies include, for instance, the ulcer associated to Helicobacter Pylori infection, adenoma and, in genetically predisposed individuals, celiac disease. Alterations in the bowel reduce its capability to absorb nutrients, minerals and fat-soluble vitamins. Anemia and osteopenia or osteoporosis may develop as a consequence of vitamins malabsorption. Adenoma is a benign tumor that has the potential to become cancerous. Adult celiac disease patients present an overall risk of cancer that is almost twice than that found in the general population. These disease processes are not completely known. To date, a two dimensional (2D) reference map of proteins expressed in human duodenal tissue is not yet available: the aim of our study was to characterize the 2D protein map, and to identify proteins of duodenal mucosa of adult individuals
The nucleolus is the cellular organelle that manufactures ribosomes and plays a part in many vital process including cell-cycle regulation and senescence. Using the latest proteomics technologies, Andersen et al. have generated a comprehensive list of nucleolar proteins. Over 690 proteins were found in the in the nucleolar preparation, including Werners syndrome helicase and various regulatory proteins. The technology also allows analysis of changes in relative levels of proteins as a result of perturbing growth conditions with drugs. This paints a picture of a dynamic proteome: in effect there may be no definitive proteome for the nucleolus or any other organelle, rather there is a series of overlapping proteomes corresponding to different cell states. The nucleolus is a key organelle that coordinates the synthesis and assembly of ribosomal subunits and forms in the nucleus around the repeated ribosomal gene clusters. Because the production of ribosomes is a major metabolic activity, the function of
Mass spectrometry (MS) - based proteomics allows the sensitive and accurate quantification of almost complete proteomes of complex biological fluids and tissues. At the moment, however, the routinely usage of MS-based proteomics is prevented and complicated by the very complex work flow comprising sample preparation, chromatography, MS measurement followed by data processing and evaluation. The new technologies, products and assays developed by Precision Proteomics could help enabling and establishing mass spectrometry (MS) - based proteomics in academic and pharmaceutical proteomics research as well as in clinical diagnostics.. ...
Fernandes, I., et al. Secretome Analysis Identifies Potential Virulence Factors of Diplodia corticola, a Fungal Pathogen Involved in Cork Oak (Quercus suber) Decline. Fungal Biotechnology. (118) 5-6, 516-523. 18/05/2014.. ...
TY - JOUR. T1 - Serological immunoreactivity against colon cancer proteome varies upon disease progression. AU - De Monte, Lucia. AU - Sanvito, Francesca. AU - Olivieri, Stefano. AU - Viganò, Fiammetta. AU - Doglioni, Claudio. AU - Frasson, Matteo. AU - Braga, Marco. AU - Bachi, Angela. AU - Dellabona, Paolo. AU - Protti, Maria Pia. AU - Alessio, Massimo. PY - 2008/2. Y1 - 2008/2. N2 - Sera from colon carcinoma patients were used to identify tumor-associated antigens (TAAs) by screening tumor proteome resolved by 2D electrophoresis. A panel of six TAAs eliciting a serological immune response in colorectal cancer was identified, showing a modification in antigen recognition by B cells in patients as a function of colon cancer progression. The expression of these proteins was either confined or increased in tumor as compared to normal mucosa.. AB - Sera from colon carcinoma patients were used to identify tumor-associated antigens (TAAs) by screening tumor proteome resolved by 2D electrophoresis. ...
Citation. Pieper, R., Gatlin, C. L., Makusky, A. J., Russo, P. S., Schatz, C. R., Miller, S. S., Su, Q., McGrath, A. M., Estock, M. A., Parmar, P. P., Zhao, M., Huang, S. T., Zhou, J., Wang, F., Esquer-Blasco, R., Anderson, N. L., Taylor, J., Steiner, S.. The Human Serum Proteome: Display of Nearly 3700 Chromatographically Separated Protein Spots on Two-dimensional Electrophoresis Gels and Identification of 325 Distinct Proteins. Proteomics. 2003 Jul 01; 3(7): 1345-64.. PubMed Citation. Abstract. Plasma, the soluble component of the human blood, is believed to harbor thousands of distinct proteins, which originate from a variety of cells and tissues through either active secretion or leakage from blood cells or tissues. The dynamic range of plasma protein concentrations comprises at least nine orders of magnitude. Proteins involved in coagulation, immune defense, small molecule transport, and protease inhibition, many of them present in high abundance in this body fluid, have been functionally ...
Adaptation, Physiological; Animals; Cattle; Electrophoresis, Gel, Two-Dimensional; Energy Metabolism; Female; Gene Expression; Genotype; Mastitis, Bovine; Plant Proteins; Protein Interaction Maps; Proteome; Proteomics; Prototheca; Signal Transduction ...
Hypothesis:. Differences in the proteome concerning cell death pathways of glaucoma patients correspond to the differences in the mRNA expression of these patients.. Specific aims:. Characterization of the cellular proteome from human leukocytes of glaucoma patients compared to healthy controls and patients with Parkinsons disease.. Background:. Glaucoma is a worldwide leading cause of blindness. The key feature of this ocular neuropathy is characterized by an excavating optic nerve head. Loss of retinal ganglion cells is the final end point in blinding diseases of the optic nerve such as glaucoma. It is known that neuronal cell death in glaucoma occurs by an apoptotic mechanism. In earlier studies we could demonstrate that this cell death is reflected in circulating leukocytes by different parameters, like differential mRNA expression, and an increased fragmentation of the DNA. The differences in mRNA expression indicate a close relationship to cellular stress conditions and apoptotic events: ...
The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human …
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets. Obstacles for comprehensive proteomic profiling include the immense size and structural heterogeneity of the proteome, and the broad range of abundance levels, as well. Proteome-wide, untargeted profiling can be performed in tissues and cells with tandem mass spectrometry. However, applications to plasma are limited by the need for complex preanalytical sample preparation stages ...
Daphnia pulex (Water flea) is the first fully sequenced crustacean genome. The crustaceans and insects have diverged from a common ancestor. It is a model organism for studying the molecular makeup for coping with the environmental challenges. In the complete proteome, there are 30,550 putative proteins. However, about 10,000 of them have no known homologues. Currently, the UniProtoKB reports on 95% of the Daphnias proteins as putative and uncharacterized proteins. We have applied ProtoNet, an unsupervised hierarchical protein clustering method that covers about 10 million sequences, for automatic annotation of the Daphnias proteome. 98.7% (26,625) of the Daphnia full-length proteins were successfully mapped to 13,880 ProtoNet stable clusters, and only 1.3% remained unmapped. We compared the properties of the Daphnias protein families with those of the mouse and the fruitfly proteomes. Functional annotations were successfully assigned for 86% of the proteins. Most proteins (61%) were mapped to only
78069 avhandlingar från svenska högskolor och universitet. Avhandling: Advancing bioinformatics methods for in-depth proteome analysis based on high-resolution mass spectrometry.
Scientists at the Center for Proteome Analysis (CPA) in Odense, Denmark, have identified a natural protein that seems to protect the bodys insulin-producing beta cells from attack. Their approach is to analyze the thousands of gene products in cells and tissues, with special interest in galectin, a small protein that is vital in insulin dependent diabetes mellitus (IDDM). Every cell, no matter what tissue its in, carries the same full set of genetic information, the species genome. Now that genomic information is pouring in at a breathtaking pace, scientists are rushing to understand which proteins a particular type of cell synthesizes, how much the cell synthesizes, how cells modify proteins after synthesis and how all those proteins interact. This is the new science of proteomics. Among the first to realize the potential of proteomics, biologists Peter Mose Larsen and Stephen Fey founded CPA in 1997. And even today, when proteome centers are sprouting up everywhere, this research compound, ...
A wide range of state-of-the-art proteomics experiments are possible. These include, but are not limited, to intact mass determination, post-translational modification analysis, protein identification, and targeted (e.g. co-immunoprecipitation) or comprehensive (e.g. protein expression profiling) proteome analysis. Proteome analysis may employ a number of different isotope-labeling strategies enabling quantitative measurements on our high resolution discovery platforms (Orbitrap-Elite and Q-Exactive HF mass spectrometers) for deep proteome coverage or multiplexed targeted quantification on our triple quadrupole mass spectrometer (Xevo-TQS). Unique among regional cores is our ability to quantitatively analyze proteomes, phosphoproteomes, ubiquitylomes, and lysine acetylomes at a deep level through a process of serial enrichment. Under development are refinements of statistical and bioinformatic analyses of proteomic results. It is also possible to tailor sensitive and specific methods for ...
Lung cancer is the most common cause of cancer-related death worldwide, less than 7% of patients survive 10 years following diagnosis across all stages of lung cancer. Late stage of diagnosis and lack of effective and personalized medicine reflect the need for a better understanding of the mechanisms that underlie lung cancer progression. Quantitative proteomics provides the relative different protein abundance in normal and cancer patients which offers the information for molecular interactions, signaling pathways, and biomarker identification. Here we introduce both theoretical and practical applications in the use of quantitative proteomics approaches, with principles of current technologies and methodologies including gel-based, label free, stable isotope labeling as well as targeted proteomics. Predictive markers of drug resistance, candidate biomarkers for diagnosis, and prognostic markers in lung cancer have also been discovered and analyzed by quantitative proteomic analysis. Moreover,
Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity having the initial contact with the host. Applying two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), we established a 2-D reference map of conidial proteins. By MALDI-TOF mass spectrometry, we identified a total number of 449 different proteins. We show that 57 proteins of our map are over-represented in resting conidia compared to mycelium. Enzymes involved in reactive oxygen intermediates (ROI) detoxification, pigment biosynthesis, and conidial rodlet layer formation were highly abundant in A. fumigatus spores and most probably account for their enormous stress resistance. Interestingly, pyruvate decarboxylase and alcohol dehydrogenase were detectable in dormant ...
Source: Journal of Proteome Research - August 20, 2018 Category: Biochemistry Authors: Heeyoun Hwang, Ji Eun Jeong, Hyun Kyoung Lee, Ki Na Yun, Hyun Joo An, Bonghee Lee, Young-Ki Paik, Tae Seok Jeong, Gi Taek Yee, Jin Young Kim, Jong Shin Yoo Source Type: research. [ASAP] Transcriptional and Proteomic Analysis Revealed a Synergistic Effect of Aflatoxin M1 and Ochratoxin A Mycotoxins on the Intestinal Epithelial Integrity of Differentiated Human Caco-2 Cells ...
Background: Selection of patients to receive a primary prevention ICD is solely based on LV EF. Plasma biomarkers may compliment this but most have not been evaluated in predicting arrhythmic death. We determined whether plasma proteomic profiling could afford an unbiased, discovery based approach to identify novel biomarkers to predict cause specific event rates from SCA (arrhythmic death or defibrillation for VT/VF).. Methods: Plasma samples were obtained at entry in 203 patients in the PAREPET study. Proteomic profiling was performed in a subset of 10 patients with SCA vs. 10 survivors matched for EF (26%), age (66 years) and creatinine (1.4). We used a tandem affinity depletion method (IgY14-SuperMix) to reduce high- and medium- abundance plasma proteins, followed by extensive ion current based biomarker discovery. Plasma proteins were expressed as SCA/survivors.. Results: SCA developed 1016±735 days after sampling. Stringent cutoff criteria (0.3% peptide identification FDR ; ≥2 unique ...
NEW YORK (GenomeWeb) - A group from the Spanish National Cancer Research Centre has published a critique raising questions about two recent studies in which researchers generated the first relatively comprehensive maps of the human proteome.
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Relation to proteome[edit]. Further information: Proteome. The transcriptome can be seen as a subset of the proteome, that is, ... General schema showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome). ... The complete protein complement of a cell or organism is known as the proteome. ...
Proteome[edit]. The lentiviral proteome consists of five major structural proteins and 3-4 non-structural proteins (3 in the ...
Proteome. The genome of P1 encodes 112 proteins and 5 untranslated genes and is this about twice the size of bacteriophage ...
Proteome Science. Ramaswamy et al.; licensee BioMed Central Ltd. 9 (3). Proteome Science , Full text , Development of reverse ...
"Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels". Proc ... Proteome Science. 1 (1): 6. doi:10.1186/1477-5956-1-6. PMC 317362. PMID 14653859. Henzel, William J.; Watanabe, Colin; Stults, ...
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Proteome Science. 3 (1): 2. doi:10.1186/1477-5956-3-2. PMC 554085. PMID 15730566. Burmester T, Weich B, Reinhardt S, Hankeln T ...
"Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation". Proteome ... A total of 341 protein N termini were confidently identified in the D. deserti TMPP-labeled proteome. Among these, 63 were not ... Accurate genome annotation of its 3455 genes was guided at the stage of primary annotation by an extensive proteome analysis. A ... The N termini data set corresponds to 10% of the theoretical proteome. A significant number of erroneous annotations have ...
Pedrioli, Patrick G. A. (2010). "Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis". Proteome Bioinformatics. Methods ... Journal of Proteome Research. 3 (5): 958-64. arXiv:q-bio/0406002. Bibcode:2004q.bio.....6002G. doi:10.1021/pr0499491. PMID ... Journal of Proteome Research. 4 (6): 2348-54. doi:10.1021/pr050288x. PMID 16335984. Ma, Bin (30 June 2015). "Novor: Real-Time ... Journal of Proteome Research. 10 (4): 1794-1805. doi:10.1021/pr101065j. ISSN 1535-3893. PMID 21254760. Bern, Marshall; Cai, ...
Proteome Science. 15: 14. doi:10.1186/s12953-017-0123-3. PMC 5483283. PMID 28652856. Collins SR, Kemmeren P, Zhao XC, ... "Proteome survey reveals modularity of the yeast cell machinery". Nature. 440 (7084): 631-6. Bibcode:2006Natur.440..631G. doi: ...
The reference proteome set maintained by the UniProt resource is used in this version of PANTHER and so the source of gene sets ... "reference proteome". Details in PANTHER 9 statistics can be found here (http://www.pantherdb.org/panther/summaryStats.jsp). ...
Proteome Sci. 6 (1): 30. doi:10.1186/1477-5956-6-30. PMC 2600628. PMID 18950484. v t e. ...
Mann, Karlheinz (2015). "The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata)". Proteome ... Mann, Karlheinz; Mann, Matthias (2013). "The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) ... eggshell". Proteome Sci. 11 (1): 40. doi:10.1186/1477-5956-11-40. PMC 3766105. PMID 23981693. ...
2007). "A proteome-wide protein interaction map for Campylobacter jejuni". Genome Biol. 8 (7): R130. doi:10.1186/gb-2007-8-7- ... 2011). "The proteome and interactome of Streptococcus pneumoniae phage Cp-1". J. Bacteriol. 193 (12): 3135-8. doi:10.1128/JB. ... 2016). "A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human". Cell. 164 (1-2): ... For instance, even within a proteome two proteins may interact but their paralogs may not. Each protein-protein interactome may ...
April 2010). "Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry". Proteome ...
Proteome Res. 4 (6): 2070-80. doi:10.1021/pr0502065. PMC 1850943. PMID 16335952. Kimura K, Wakamatsu A, Suzuki Y, et al. (2006 ...
Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M (Jan 2005). "Nucleolar proteome dynamics". Nature. 433 (7021 ...
Proteome Res. 4 (6): 2070-80. doi:10.1021/pr0502065. PMC 1850943. PMID 16335952. Wouters MM, Neefs JM, Kerchove d'Exaerde A, et ...
Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M (January 2005). "Nucleolar proteome dynamics". Nature. 433 ( ...
Kim JE, Tannenbaum SR, White FM (2005). "Global phosphoproteome of HT-29 human colon adenocarcinoma cells". J. Proteome Res. 4 ...
2009). "Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation". BMC Psychiatry ... Proteome Res. 5 (1): 64-75. doi:10.1021/pr0502626. PMID 16396496. Kim H (2005). "Asparagine-473 residue is important to the ...
Proteome Res. 6 (1): 298-305. CiteSeerX 10.1.1.401.4220. doi:10.1021/pr060438j. PMID 17203973. Pezzatini S, Morbidelli L, ...
J Proteome Res. 15 (2): 339-359. doi:10.1021/acs.jproteome.5b00769. PMC 4777318. PMID 26680015. v t e. ...
Proteome Res. 4 (6): 2070-80. doi:10.1021/pr0502065. PMC 1850943. PMID 16335952. Gerhard DS, Wagner L, Feingold EA, et al. ( ...
Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M (January 2005). "Nucleolar proteome dynamics". Nature. 433 ( ...
2005). "Nucleolar proteome dynamics". Nature. 433 (7021): 77-83. Bibcode:2005Natur.433...77A. doi:10.1038/nature03207. PMID ... 2005). "Characterization of phosphorylation sites on histone H1 isoforms by tandem mass spectrometry". J. Proteome Res. 3 (6): ...
Kim JE, Tannenbaum SR, White FM (2005). "Global phosphoproteome of HT-29 human colon adenocarcinoma cells". J. Proteome Res. 4 ...
Proteome Res. 5 (1): 64-75. doi:10.1021/pr0502626. PMID 16396496. Biology portal v t e. ...
Proteome Res. 5 (4): 935-43. doi:10.1021/pr050419u. PMID 16602701. Haupt A, Thamer C, Heni M, et al. (2009). "Novel Obesity ...
Proteome Res. 5 (1): 64-75. doi:10.1021/pr0502626. PMID 16396496. Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (2006). " ...
This paints a picture of a dynamic proteome: in effect there may be no definitive proteome for the nucleolus or any other ... we perform a quantitative analysis of the proteome of human nucleoli. In vivo fluorescent imaging techniques are directly ... organelle, rather there is a series of overlapping proteomes corresponding to different cell states. The nucleolus is a key ... for the temporal characterization of protein flux through cellular organelles and demonstrate that the nucleolar proteome ...
... cellular proteome) or a subcellular system, as in a viral proteome or a nuclear proteome. ... Proteome. Definition. The proteome is the entire set of proteins produced by an organism or system and encoded by the full ... The proteome landscape of the kingdoms of life An advanced proteomics workflow is used to identify 340,000 proteins from 100 ... The myosin-II-responsive focal adhesion proteome: a tour de force? The formation and maturation of focal adhesions involves ...
2009) and, subsequently, proteomes (Schmitz-Spanke and Rettenmeier 2011). Technologies... ... Proteome Databases. Most proteomic studies involve the characterization of specific proteomes in response to changes in cell ... toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res 7(9):3755-3764PubMedGoogle Scholar ... Bascos N.A.D. (2013) Protein and Proteome Resources. In: Dubitzky W., Wolkenhauer O., Cho KH., Yokota H. (eds) Encyclopedia of ...
Proteome News and Research. RSS The proteome is the entire complement of proteins expressed by a genome, cell, tissue or ... Researchers use advanced technology to identify proteomes of Th17 and iTreg cells T helper 17 (Th17) cells belong to a group of ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Dark Proteome Is Mostly Not Disordered.. Intrinsically disordered regions are believed to account for much of the dark proteome ... In this work, we used Aquaria to survey the dark proteome in unprecedented depth. We found most of the dark proteome cannot be ... In contrast, in eukaryotes and viruses, about half (44-54%) of the proteome was dark (Fig. 1B). Of the total dark proteome, ... "dark proteome"; we believe that studying the dark proteome will clarify future research directions, as studies of dark matter ...
Recently, the advent of new proteomic tools has permitted global scale assessments of lysine acetyl-proteomes [3], [4], [5], [6 ... Liver proteome studies showed a large number of acetylation sites attributed to mitochondrial processes [4], and given that ... Kruh NA, Troudt J, Izzo A, Prenni J, Dobos KM (2010) Portrait of a pathogen: the mycobacterium tuberculosis proteome in vivo. ... Comparison of our dataset to other global-scale proteome studies revealed 53 acetyl proteins unique to the guinea pig cardiac ...
Mapping proteome-wide interactions of reactive chemicals using chemoproteomic platforms From www. .sciencedirect. .com - ... In our analysis of the PDX tumor proteomes, QuantFusion increased the number of distinct peptide ratios by 65%, representing ... In our analysis of the PDX tumor proteomes, QuantFusion increased the number of distinct peptide ratios by 65%, representing ... To maximize the quantitative precision and the number of quantifiable proteins or the quantifiable coverage of tissue proteomes ...
... Nature. 2005 Jan 6;433(7021):77-83. doi: 10.1038/nature03207. ... we perform a quantitative analysis of the proteome of human nucleoli. In vivo fluorescent imaging techniques are directly ... for the temporal characterization of protein flux through cellular organelles and demonstrate that the nucleolar proteome ...
Filter byi ,p>A search result page is subdivided into a filter panel on the left, and the actual result table on the right, occupying the majority of the screen space.,p>,a href=/help/filter_options target=_top>More...,/a>,/p> ...
A bioinformatics analysis of the proteomes of microorganisms and eukaryotic cells showed that in most cases roughly 70 percent ... Ribosome surface properties may impose limits on the nature of the cytoplasmic proteome. eLife, online as accepted. ... complex and the ambient ionic strength of the cytoplasm appear to have shaped the evolution of charges in the cellular proteome ...
Quantitating the complete human proteome. Institute for Systems Biology. Journal. Cell. Funder. National Institutes of Health, ... The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell-type is transformative ... Quantitating the complete human proteome Over 160,000 protein assays released through the Human SRMAtlas to allow the ... org and will equally benefit focused, hypothesis-driven and large proteome-scale studies. We expect this resource will ...
RaftProt: mammalian lipid raft proteome database.. Shah A1, Chen D2, Boda AR1, Foster LJ3, Davis MJ4, Hill MM5. ...
Hannes Röst describes how his lab are using diaPASEF to monitor the human proteome throughout a persons lifetime, and how ... This increase in sequencing speed is really crucial for complex proteomes because it allows us to go much deeper into complex ... Hannes Röst describes how his lab are using diaPASEF to monitor the human proteome throughout a persons lifetime, and how ... Combining Improved Ion Usage Efficiency with Data Independent Acquisition to Quantify Proteomes ...
"Mass-Spectrometry-Based Draft of the Human Proteome". Nature.. *^ Kim, Min-Sik; et al. (May 2014). "A draft map of the human ... The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain ... The proteome can be larger than the genome, especially in eukaryotes, as more than one protein can be produced from one gene ... A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental ...
While proteome generally refers to the proteome of an organism, multicellular organisms may have very different proteomes in ... Human proteome. Currently, several projects aim to map the human proteome, including the Human Proteome Map, ProteomicsDB and ... Dark proteome. The term dark proteome coined by Perdigão and colleagues, defines regions of proteins that have no detectable ... The proteins in a virus can be called a viral proteome. Usually viral proteomes are predicted from the viral genome but some ...
The vast dynamic range of the human proteome-especially the human plasma proteome-has been one of the biggest challenges in ... Human Proteome Project. www.hupo.org. Massachusetts General Hospital. www.massgeneral.org. Max Planck Institute of Biochemistry ... New Products: Panning the Proteome for Biomarker Gold. CCD CAMERAS. The CoolSNAP MYO and the CoolSNAP KINO CCD cameras are ... Panning the Proteome for Biomarker Gold Targeted proteomics is homing in on promising biomarkers to help screen for cancer and ...
Indeed, a yeast proteome chip has been used to identify CaM-binding proteins (21). However, the preparation of a proteome chip ... The mRNA-displayed proteome library was generated as described in refs. 23 and 25. The resulting mRNA-displayed proteome ... Although the proteome chip approach allows high throughput studies on protein-protein interactions, preparation of a proteome ... Scanning the human proteome for calmodulin-binding proteins. Xinchun Shen, C. Alexander Valencia, Jack Szostak, Biao Dong, Rihe ...
Spotfire and Proteome said Tuesday that they have finished integrating Proteomes Yeast Proteome Database with the Spotfire.net ... NEW YORK, Dec 12 - Spotfire and Proteome said Tuesday that they have finished integrating Proteomes Yeast Proteome Database ... Under the terms of the collaboration, customers of both Spotfire and Proteome can now access and analyze data from the YPD, a ... specific volume of Proteomes BioKnowledge Library, using the web-based analytics service. ...
The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, ... Human body fluid proteome analysis Proteomics. 2006 Dec;6(23):6326-53. doi: 10.1002/pmic.200600284. ... The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, ... and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) ...
Now that the entire human genome has been sequenced, geneticists would like to move on to the proteome: a collection of all the ... Although sequencing the human genome was a huge task, trying to figure out the proteome is more complicated by far. Thats ...
Complete Proteome Detector (CPD). CPD statistically analyses each proteome against a group of closely related proteomes in ... For each proteome, CPD uses taxonomic lineage information to identify the group of proteomes taxonomically closest to it. A ... For the proteome being analyzed, the algorithm compares selected attributes of all proteomes in its group to define the ... This evaluation classifies each proteome into three possible categories (in terms of the proteomes protein count vs. the ...
"Dark Proteome Database: Studies on Dark Proteins." Dark Proteome Database: Studies on Dark Proteins, March 27, 2019. 10.20944/ ... The dark proteome is defined as proteins with no defined three-dimensional structure. It can not be detected or analyzed with ... Dark proteins are mostly composed of unknown unknowns It estimated to be about 14% of the proteome in archaea and bacteria, and ... Large portion of the dark proteome are of viral origin. Dark protein regions are dark due to originating from unusual organisms ...
FROM HUMAN GENOME PROJECT TO HUMAN PROTEOME PROJECT /HPP/: RUSSIAN PARTICIPATION ARCHAKOV A.I. INSTITUTE OF BIOMEDICAL ... Archakov A. from human genome project to human proteome project * 1. FROM HUMAN GENOME PROJECT TO HUMAN PROTEOME PROJECT /HPP ... BIOLOGISTS INITIATE PLAN TO MAP HUMAN PROTEOME. NATURE, 452, 24, 920-921, 2008. HUMAN PROTEOME PROJECT HUPO 2008, 7 th WORLD ... li,,/ul,WHAT IT MEANS PROTEOME-BASED MEDICINE? * 32. DETECTION OF HCVcoreAg AT TWO SPOTS AFM CHIP FROM HCVcoreAg SOLUTION (C=10 ...
... based absolute quantification of the Escherichia coli proteome. J Proteome 109:322-331CrossRefGoogle Scholar ... Wiśniewski J.R. (2018) Filter-Aided Sample Preparation for Proteome Analysis. In: Becher D. (eds) Microbial Proteomics. Methods ...
... ,MS/MS analysis & visualization software. See proteins identified across multiple ... Proteome Software Inc.. 1336 SW Bertha Boulevard Portland, OR 97201 USA. Customer Service: +1 503 244-6027. Fax Number: +1 503 ...
The choice of protein sequence database used for peptide spectrum matching has a major impact on the extent and significance of protein identifications obtained in a given experiment. Finding a suitable database can be a major challenge, particularly when working with non-model organisms and complex samples containing proteins from multiple species. This chapter introduces the proteomics informed by transcriptomics (PIT) methodology, in which RNA-seq transcriptomics is used to generate a sample-specific protein database against which proteomic mass spectra can be searched. This approach extends the application of proteomics to studies in which it was not previously tractable, and is well suited to the discovery of novel translated genomic elements.. ...
Yeast two-hybrid analysis has been applied for detecting the interactions in the entire proteome of several model organisms. ... Thus, in addition to allowing analysis of the network properties of a human proteome interaction network, this large-scale ... A resource for annotating the proteome. Cell 122, 957-968 (2005). [PubMed] ... analysis of the human proteome also revealed novel regulators of cell signaling. ...
The Australian Proteome Analysis Facility (APAF), operated by Macquarie University, provides academic and corporate clients ... Australian Proteome Analysis Facility. APAFs mission is to assist the scientific community address their protein analysis ...
Proteome Sciences received a European patent that lays claim to methods of diagnosing stroke by measuring the levels of heart ... Proteome Sciences Awarded European Patent for Stroke Diagnostic Methods. January 15, 2007. 0 ... blood of patients suffering from stroke was discovered by scientists at the University of Geneva in collaboration with Proteome ...
  • Here, using mass-spectrometry-based organellar proteomics and stable isotope labelling 5 , we perform a quantitative analysis of the proteome of human nucleoli. (nature.com)
  • An advanced proteomics workflow is used to identify 340,000 proteins from 100 taxonomically diverse species, providing a comparative view of proteomes across the evolutionary range. (nature.com)
  • Van PT et al (2008) Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. (springer.com)
  • Proteomics is the study of the proteome. (wikipedia.org)
  • More often, however, virus proteomics analyzes the changes of host proteins upon virus infection, so that in effect two proteomes (of virus and its host) are studied. (wikipedia.org)
  • The use of proteomics or the study of the proteome is a step forward in personalized medicine to tailor drug cocktails to the patient's specific proteomic and genomic profile. (wikipedia.org)
  • Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis . (wikipedia.org)
  • But one day, if the promise of proteomics is realized, cancer treatments could be tailored to a patient by assessing the entire proteome of a tumor cell, rather than just one or two receptors. (sciencemag.org)
  • We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. (nih.gov)
  • Our vision for HUPO2017 Congress on 'Integrated Proteomics for Healthcare Systems' is to create a meeting that will bring together world leaders with a new generation of scientists to promote HUPO's capabilities for advancing our knowledge of the Human Proteome and the impact this will have on our understanding of health, disease and ageing. (drugs.com)
  • The human plasma proteome holds the promise of a revolution in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics and related disciplines can be addressed. (mcponline.org)
  • And even today, when proteome centers are sprouting up everywhere, this research compound, situated in the green fields outside Odense (the birthplace of Hans Christian Anderson), remains at the forefront of proteomics. (genomenewsnetwork.org)
  • The aim of INTERACTION PROTEOME is to establish Europe as the international scientific leader in functional proteomics, i.e. in the analysis of protein-protein interactions. (europa.eu)
  • They investigated their theories using carbamyl-lysine immunoblotting and a proteomics mass spectrometry (MS) approach to identify rates of carbamylation in the renal proteome. (thermofisher.com)
  • To better understand the differences between human and bovine milk, the qualitative and quantitative differences in the milk proteome as well as their changes over lactation were compared using both label-free and labelled proteomics techniques. (wur.nl)
  • The Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) performed a collaborative data analysis study focusing on the evaluation of proteomics laboratories in identifying phosphopeptides and localizing the phosphorylation sites. (abrf.org)
  • The proteome is the entire set of proteins produced by an organism or system and encoded by the full genome. (nature.com)
  • The proteome is the entire complement of proteins expressed by a genome, cell, tissue or organism. (news-medical.net)
  • The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. (wikipedia.org)
  • Usually viral proteomes are predicted from the viral genome but some attempts have been made to determine all the proteins expressed from a virus genome, i.e. the viral proteome. (wikipedia.org)
  • General schema showing the relationships of the genome , transcriptome , proteome , and metabolome ( lipidome ). (wikipedia.org)
  • The proteome can be larger than the genome , especially in eukaryotes , as more than one protein can be produced from one gene due to alternative splicing (e.g. human proteome consists 92,179 proteins [ citation needed ] out of which 71,173 are splicing variants [ citation needed ] ). (wikipedia.org)
  • Now that the entire human genome has been sequenced, geneticists would like to move on to the proteome: a collection of all the proteins coded in our genes. (sciencenetlinks.com)
  • Although sequencing the human genome was a huge task, trying to figure out the proteome is more complicated by far. (sciencenetlinks.com)
  • Molecular biology, including the genome and proteome projects, is revolutionizing the biological and medical sciences, holding out the promise of both fully understanding and effectively treating all human diseases ( 1 ). (mcponline.org)
  • Thus, the human genome is directly related to the "human proteome," the collection of all human proteins. (worldcommunitygrid.org)
  • The term proteome is a blend of proteins and genome and Wilkins used it to describe the entire complement of proteins expressed by a genome, cell, tissue or organism. (wikidoc.org)
  • The proteome is larger than the genome , especially in eukaryotes , in the sense that there are more proteins than genes . (wikidoc.org)
  • Moreover the proteome has at least two levels of complexity lacking in the genome. (wikidoc.org)
  • When the genome is defined by the sequence of nucleotides , the proteome cannot be limited to the sum of the sequences of the proteins present. (wikidoc.org)
  • The study provides the first comprehensive and unbiased identification of the long-lived proteome, the entire set of proteins expressed by a genome under a given set of environmental conditions. (phys.org)
  • A mapped human proteome will extend the value of the genome sequence and large-scale efforts aiming at elucidating protein localization, abundance and function are invaluable for biomarker and drug discovery. (diva-portal.org)
  • These changes include developmental and physiological alterations which influence the genome, proteome, and metabolome of the plant. (frontiersin.org)
  • The Human SRMAtlas is a compendium of highly specific mass spectrometry assays for the targeted identification and reproducible quantification of any protein in the predicted human proteome, including assays for many spliced variants, non-synonymous mutations and post-translational modifications. (eurekalert.org)
  • The epub proteome research mass spectrometry God has is this: Will you start Me? (vikingsword.com)
  • white capabilities will not make easy in your epub proteome research mass spectrometry of the papers you use allowed. (vikingsword.com)
  • Though it was the pronounced epub proteome research mass spectrometry, the collection submitted more than what I want. (vikingsword.com)
  • Proteome analysis is a new diagnostic method in which the concentration of several biomarkers in the urine is determined by means of mass spectrometry. (medindia.net)
  • We have analyzed proteome dynamics during light-induced development of rice ( Oryza sativa ) chloroplasts from etioplasts using quantitative two-dimensional gel electrophoresis and tandem mass spectrometry protein identification. (plantphysiol.org)
  • Proteome Science 15 (2017). (wur.nl)
  • Wisniewski JR, Rakus D (2014) Multi-enzyme digestion FASP and the 'Total protein Approach'-based absolute quantification of the Escherichia coli proteome. (springer.com)
  • By application of an isobaric tagging for relative and absolute quantification (iTRAQ)-based approach, the proteomes of bovine embryos at the zygote and 2-cell and 4-cell stage with MII oocytes as a reference were quantitatively analyzed. (uni-muenchen.de)
  • VANCOUVER, BC and LADENBURG, GERMANY --(Marketwired - January 08, 2018) - Advanced Proteome Therapeutics Corporation (APC), a therapeutics discovery and development company, and Heidelberg Pharma announced today advances in their collaborative activities. (marketwired.com)
  • A key remaining frontier in our understanding of biological systems is the "dark proteome"-that is, the regions of proteins where molecular conformation is completely unknown. (pnas.org)
  • We also found that the dark proteome has unexpected features, including an association with secretory tissues, disulfide bonding, low evolutionary conservation, and very few known interactions with other proteins. (pnas.org)
  • This work will help future research shed light on the remaining dark proteome, thus revealing molecular processes of life that are currently unknown. (pnas.org)
  • We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. (pnas.org)
  • Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. (pnas.org)
  • The dark proteome is defined as proteins with no defined three-dimensional structure. (wikipedia.org)
  • Large portion of the dark proteome are of viral origin. (wikipedia.org)
  • Dark Proteome Database: Studies on Dark Proteins. (wikipedia.org)
  • Finding Our Way in the Dark Proteome. (wikipedia.org)
  • The term "dark proteome" coined by Perdigão and colleagues, defines regions of proteins that have no detectable sequence homology to other proteins of known three-dimensional structure and therefore cannot be modeled by homology . (wikipedia.org)
  • The data establish a quantitative proteomic approach for the temporal characterization of protein flux through cellular organelles and demonstrate that the nucleolar proteome changes significantly over time in response to changes in cellular growth conditions. (nature.com)
  • Most proteomic studies involve the characterization of specific proteomes in response to changes in cell type, metabolic state, or exposure to a given agent. (springer.com)
  • Definition of liver proteome by characterization of all specific liver cell types and their interaction in health and disease. (hupo.org)
  • A key component of CPTAC, the Proteome Characterization Centers (PCCs), performed this characterization for TCGA through a 2-step pipeline. (nih.gov)
  • Proteome profiling refers to the large-scale, high-throughput analysis of biological samples for the detection, identification, and functional characterization of resident proteins. (marketresearch.com)
  • A bioinformatics analysis of the proteomes of microorganisms and eukaryotic cells showed that in most cases roughly 70 percent of the proteins are negatively charged. (eurekalert.org)
  • A quality metric is also determined based on the taxonomical closeness of the group of proteomes used for the analysis of the proteome in question. (uniprot.org)
  • Yeast two-hybrid analysis has been applied for detecting the interactions in the entire proteome of several model organisms. (sciencemag.org)
  • Thus, in addition to allowing analysis of the network properties of a human proteome interaction network, this large-scale analysis of the human proteome also revealed novel regulators of cell signaling. (sciencemag.org)
  • When comprehensive proteome analysis with deep coverage is needed, relatively long columns (lengths up to 75 cm) are typically operated with long and shallow solvent gradients, delivering the highest chromatographic performance. (genengnews.com)
  • However, routine daily proteome analysis often deals with simpler samples or demands increased sample throughput, making total analysis times above 120 min undesirable or even impossible. (genengnews.com)
  • Those human liver transcriptomes provide considerable resources not only for the integration (data-based) of transcriptome data with corresponding proteome data but also for scaling protein identification (data-based) and protein linkage map (cDNA-based) during liver proteome analysis. (mcponline.org)
  • Cancer HPP partners with NCI's Clinical Proteome Tumor Analysis Consortium (CPTAC) . (hupo.org)
  • Proteome-wide tyrosine phosphorylation analysis reveals dysregulated signaling pathways in ovarian tumors. (hupo.org)
  • 1999a) Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. (els.net)
  • 2000) Comparative proteome analysis of Helicobacter pylori. (els.net)
  • 2002) Comparative proteome analysis of Chlamydia trachomatis serovar A, D and L2. (els.net)
  • VanBogelen RA, Abshire KZ, Moldover B, Olson ER and Neidhardt FC (1997) Escherichia coli proteome analysis using the gene‐protein database. (els.net)
  • 2001) Proteome analysis of the Chlamydia pneumoniae elementary body. (els.net)
  • Bumann D, Meyer TF and Jungblut PR (2001) Proteome analysis of the common human pathogen Helicobacter pylori. (els.net)
  • Jungblut PR (2001) Proteome analysis of bacterial pathogens. (els.net)
  • Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. (jci.org)
  • Introducing low-abundance species in proteome analysis 2. (bookdepository.com)
  • Chromatographic and electrophoretic pre-fractionation tools in proteome analysis 3. (bookdepository.com)
  • Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples. (gu.se)
  • Analysis of the proteome of an organism tells us so much more than simple DNA sequence analysis," said Dr. Wolf. (newswise.com)
  • Proteome analysis gives us a snapshot of what proteins are being expressed in the cell at any given point in time. (newswise.com)
  • The analysis indicated that a high fraction of the proteome is expressed in most cell types and tissues and very few proteins are expressed in a single cell type. (sigmaaldrich.com)
  • Scientists at the Center for Proteome Analysis (CPA) in Odense, Denmark, have identified a natural protein that seems to protect the body's insulin-producing beta cells from attack. (genomenewsnetwork.org)
  • Proteome analysis comes in both as a means to get at the function and as a powerful shortcut to identifying genes that interact and are involved in disease development. (genomenewsnetwork.org)
  • For the treatment of the future, an alternative to gene therapy is drugs that stimulate the natural galectin production inside beta cells, and the CPA researchers plan to use proteome analysis to look at interesting candidates. (genomenewsnetwork.org)
  • The innovations generated in INTERACTION PROTEOME thus will provide the basis for an efficient analysis and systems modeling of fundamental biological processes in health and disease. (europa.eu)
  • The proteome datasets were submitted to Ingenuity Pathway Analysis for identifying the networks and signaling pathways that were potentially disturbed in heart failure subjects. (hindawi.com)
  • Conclusions: This study represents the first system-wide quantitative analysis of proteome changes associated to localized prostate cancer and as such constitutes a valuable resource for understanding the complex metabolic changes occurring in this disease. (diva-portal.org)
  • The German Institute for Quality and Efficiency in Health Care (IQWiG) examined the benefit of a diagnostic-therapeutic strategy using urinary proteome analysis for detection of DN versus a conventional diagnostic strategy in patients with diabetes mellitus and arterial hypertension. (medindia.net)
  • The commission awarded to IQWiG by the Federal Joint Committee specifies two aims: Firstly, the Institute was to assess the patient-relevant benefit or harm of a diagnostic-therapeutic strategy using proteome analysis versus a conventional strategy in patients with diabetes mellitus and arterial hypertension. (medindia.net)
  • Secondly, the diagnostic and prognostic accuracy of proteome analysis for the detection of DN was to be assessed. (medindia.net)
  • Results of proteome analysis are supposed to allow earlier and more precise clinical conclusions on DN than conventional diagnostic methods. (medindia.net)
  • This was commented on by Stefan Sauerland, Head of IQWiG's Department of Non-Drug Interventions, as follows, "One cannot just postulate a `monumental breakthrough`, which proteome analysis is supposed to represent. (medindia.net)
  • Thus both the patient-relevant benefit or harm of a diagnostic-prognostic strategy using proteome analysis for detection of DN, as well as the diagnostic and prognostic accuracy of this type of analysis, remain unclear. (medindia.net)
  • In summary, proteome analysis of muscle has helped us better describe the molecular etiology of obesity-related disease. (diabetesjournals.org)
  • A competitiveness analysis of proteome profiling service providers, taking into consideration the supplier strength (based on company size and its experience in this field), service strength (based on number of pre-proteome profiling service(s) offered, number of proteome profiling service(s) offered, number of other service(s) offered, number of product types profiled and number of applications) and number of samples profiled (which is depicted by size of the bubble). (marketresearch.com)
  • Here we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins in human proteomes and cells. (ovid.com)
  • By means of transcriptome, proteome and metabolome analyses we aimed to provide insight into the one step lipid production performed by partner WU. (wur.nl)
  • The Human Liver Proteome Project (HLPP) 1 is one of the initiatives launched by the Human Proteome Organization (HUPO) ( 1 - 6 ). (mcponline.org)
  • As the first initiative on human tissues/organs, HLPP aims to 1) generate an integrative approach leading to a comprehensive protein atlas of the liver, 2) expand the liver proteome to its physiome and pathome to dramatically accelerate the development of diagnostics and therapeutics toward liver diseases, and 3) develop standard operating procedures (SOPs) for other HUPO initiatives. (mcponline.org)
  • The first HUPO Liver Proteome Workshop was therefore held in Beijing (October 22-24, 2002) with the participation of more than 100 scientists from 13 countries ( Fig. 1 ). (mcponline.org)
  • The Human Cancer Proteome Project (Cancer-HPP) is an international initiative whose key objective is to decipher the human cancer proteome through a coordinated effort by cancer proteome researchers around the world. (hupo.org)
  • The goal is to map the entire human cancer proteome to disclose tumour biology leading to improved diagnostics and treatment of cancer. (hupo.org)
  • Arabidopsis] SEB Cell symposium: From Proteome to Phenotype - Submit your abstract today! (bio.net)
  • Indeed, a yeast proteome chip has been used to identify CaM-binding proteins ( 21 ). (pnas.org)
  • NEW YORK, Dec 12 - Spotfire and Proteome said Tuesday that they have finished integrating Proteome's Yeast Proteome Database with the Spotfire.net portal. (genomeweb.com)
  • to evaluate the strengths and weaknesses of these methods in addition to providing the community with a comprehensive reference map of the yeast proteome. (yeastgenome.org)
  • Newswise - Investigators at Burnham Institute for Medical Research (Burnham) have deciphered a large percentage of the total protein complement (proteome) in Schizosaccharomyces pombe ( S. pombe ) fission yeast. (newswise.com)
  • Forces were firstly concentrated on the creation of the human islet proteome, which was published in 2015, and which will be updated in 2016. (hupo.org)
  • Journal or Proteome Research, DOI: 10.1021/acs.jproteome.6b00444 Publication Date (Web): August 30, 2016. (hupo.org)
  • 2016) recently completed a deep proteome cha. (thermofisher.com)
  • 2001 [2] Extent of modifications in Human Proteome Samples…, Nielsen et al. (slideshare.net)
  • CPD statistically analyses each proteome against a group of closely related proteomes in order to determine completeness. (uniprot.org)
  • Peptides eluted after digestion on the filter were pure, allowing single-run analyses of organelles and an unprecedented depth of proteome coverage. (nih.gov)
  • This seems astonishing in view of the promising PR messages disseminated in the past months - in part specifically in reference to the current benefit assessment - by a provider of screening tests based on proteome analyses. (medindia.net)
  • Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases and lignin peroxidases in the A. mellea proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. (inra.fr)
  • We hope that future studies will prove the value of this proteome dataset for development of novel therapies and biomarkers. (diva-portal.org)
  • Chandran, V. Exploring the Psoriatic Arthritis Proteome in Search of Novel Biomarkers. (mdpi.com)
  • Proteome Sciences Plc (Proteome Sciences) is a life sciences company that delivers content for personalized medicine in various areas such as biomarker assays, isobaric and isotopic reagents, biomarker services and proprietary biomarkers. (marketpublishers.com)
  • The term proteome has also been used to refer to the collection of proteins in certain sub-cellular systems, such as organelles. (wikipedia.org)
  • Marc Wilkins coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy. (wikipedia.org)
  • The term proteome was coined by Mark Wilkins first in 1994 in the symposium: "2D Electrophoresis: from protein maps to genomes" in Siena, Italy, and was subsequently published in 1995 (1) , which was part of his PhD thesis. (wikidoc.org)
  • In fact, one study reported the potential implications of the urinary proteome in understanding the pathophysiology of the disease. (marketresearch.com)
  • It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. (wikipedia.org)
  • These assays can be rapidly deployed in systems biology and biomedical studies to identify and quantify any human protein with high sensitivity and high selectivity, and to navigate complete proteome maps to understand their biological functions. (eurekalert.org)
  • Moreover, complete proteome size vary depending the kingdom of life. (wikipedia.org)
  • This increase in sequencing speed is really crucial for complex proteomes because it allows us to go much deeper into complex proteomes and get quantitative answers for very complex samples in a short amount of time. (news-medical.net)
  • a quantitative systemic overview of the proteome changes occurring during prostate cancer (PCa) initiation and progression can result in clinically relevant discoveries. (diva-portal.org)
  • At a quantitative level, the human and bovine milk proteome differed not only between species but also over lactation within species. (wur.nl)
  • Based on the quantitative etioplast proteome map, we examined early light-induced changes during chloroplast development. (plantphysiol.org)
  • Quantitative information about all identified proteins and their regulation by light is available in plprot, the plastid proteome database ( http://www.plprot.ethz.ch ). (plantphysiol.org)
  • To complement its innovative 200-cm-long column, which is designed to perform comprehensive and sometimes time-consuming proteome research, PharmaFluidics has introduced a 50-cm-long µPAC column. (genengnews.com)
  • The HPA project is an international 10-year research effort that aims to map the full human proteome and present the data on a public web portal to researchers all over the world. (sigmaaldrich.com)
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  • Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. (diva-portal.org)
  • A significant portion of the research articles included in this Research Topic investigated proteome level alterations in diverse organ parts of the plant body upon exposure to abiotic stress factors such as drought, salinity, and submergence. (frontiersin.org)
  • Proteome Research is an important approach to this study and is the first book to comprehensively cover the application of two-dimensional electrophoresis, the central methodology in proteome research. (buecher.de)
  • FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. (jci.org)
  • Proteome dynamics in rat gastrocnemius muscle. (jci.org)
  • 2000) Two‐dimensional map of the proteome of Haemophilus influenzae. (els.net)
  • 2000) Towards the proteome of Mycobacterium tuberculosis. (els.net)
  • In fact, since 2000, more than 85 players offering proteome profiling services have been incorporated. (marketresearch.com)
  • An international group of researchers has characterized the proteome of the human cornea. (innovations-report.com)
  • TCGA analyzed gene expression, but the proteome provides an additional layer of data for researchers. (nih.gov)
  • Donate your unused processing power to World Community Grid and the Human Proteome Folding project to help researchers discover the function of human proteins that might end up being useful as therapeutic drugs. (worldcommunitygrid.org)
  • While researchers have learned a great deal about the human proteome, the functions of most of the proteins remain a mystery. (worldcommunitygrid.org)
  • Prosit", as the researchers call the AI software, is "applicable to all organisms in the world, even if their proteomes have never been examined before," explains Mathias Wilhelm. (brightsurf.com)
  • For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. (pnas.org)
  • Dark proteins are mostly composed of unknown unknowns It estimated to be about 14% of the proteome in archaea and bacteria, and as much as 44-54% of the proteome in eukaryotes and viruses, is dark. (wikipedia.org)
  • For 546,000 Swiss-Prot proteins, 44-54% of the proteome in eukaryotes and viruses was found to be "dark", compared with only ∼14% in archaea and bacteria . (wikipedia.org)
  • For eukaryotic and bacterial proteomes, we also provide the BUSCO score , which was developed to quantify genomic data completeness in terms of expected gene content. (uniprot.org)
  • A global view of bacterial proteomes will illuminate basic biological principles such as the functioning of a cell and the elucidation of pathological important proteins for vaccine development, diagnosis and therapy of infectious diseases. (els.net)
  • Characterize proteomes, proteome forms, and protein networks from different cancers and the matched non-cancers through coordinated efforts of specimen collections and data acquisitions. (hupo.org)
  • Results: The human and bovine milk proteome show similarities with regard to the distribution over biological functions, especially the dominant presence of enzymes, transport and immune-related proteins. (wur.nl)
  • While proteome generally refers to the proteome of an organism, multicellular organisms may have very different proteomes in different cells, hence it is important to distinguish proteomes in cells and organisms. (wikipedia.org)
  • However, the preparation of a proteome chip from any multicellular organism is a major undertaking. (pnas.org)
  • Proteomes represent the composition of the functional information‐containing macromolecules (proteins) of an organism or a defined part of it. (els.net)
  • The large variety of post-translational modifications (PTMs) and their concurrent appearance in proteins dramatically increase the proteome size from mere thousands to the order of millions of possible protein forms. (bio.net)
  • Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems. (ovid.com)
  • Plasma is not only the primary clinical specimen but also represents the largest and deepest version of the human proteome present in any sample: in addition to the classical "plasma proteins," it contains all tissue proteins (as leakage markers) plus very numerous distinct immunoglobulin sequences, and it has an extraordinary dynamic range in that more than 10 orders of magnitude in concentration separate albumin and the rarest proteins now measured clinically. (mcponline.org)
  • Liver cancer-associated changes to the proteome: what deserves clinical focus? (hupo.org)
  • Since it was first proposed in April 2002, the Human Liver Proteome Project has attracted more than 100 laboratories from all over the world. (mcponline.org)
  • In the postgenomic era, the Human Liver Initiative started in 2002 as a large-scale international collaborative initiative aiming to define a comprehensive and dynamic map of the human liver proteome. (hupo.org)
  • Ueberle B, Frank R and Herrmann R (2002) The proteome of the bacterium Mycoplasma pneumoniae: comparing open reading frames to identified gene products. (els.net)
  • 1 By examining the tumor proteome in comparison with normal surrounding tissue, they hoped to pinpoint differences in protein expression that could reveal altered gene expression and transcription. (thermofisher.com)
  • Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. (jci.org)
  • 10. WHY GENE CENTRIC PROTEOME PROJECT IS REALISTIC? (slideshare.net)
  • The Human Liver Proteome Project is the first initiative of the human proteome project for human organs/tissues and aims at writing a modern Prometheus myth. (mcponline.org)
  • The aim of the present project is to show changes in nasal mucus proteome between allergic rhinitis patients and healthy controls over the pollen and non pollen season and to further determine whether and if so how the proteome changes under immunotherapy. (clinicaltrials.gov)
  • The Human Proteome Folding Project will combine the power of millions of computers in a grid to help scientists understand how human proteins fold. (worldcommunitygrid.org)
  • Information about this project is provided on the web pages below and by the project scientists on the Human Proteome Folding - Phase 2 website . (worldcommunitygrid.org)
  • To comment or ask questions about this project, please submit a post in the Human Proteome Folding - Phase 2 Forum . (worldcommunitygrid.org)
  • Proteome Systems will also benefit from DCN s expertise and experience in diagnostic test development and manufacturing in other ways, as DCN will provide assistance and consulting to Proteome Systems for its TB point of care diagnostics project and to third parties interested in developing products on Proteome Systems DiagnostIQ platform. (webwire.com)
  • A proteome may refer to the complement of proteins of a specific cell type (cellular proteome) or a subcellular system, as in a viral proteome or a nuclear proteome. (nature.com)
  • The proteins in a virus can be called a viral proteome. (wikipedia.org)
  • For each proteome, CPD uses taxonomic lineage information to identify the group of proteomes taxonomically closest to it. (uniprot.org)
  • The presence of FABP's in the blood of patients suffering from stroke was discovered by scientists at the University of Geneva in collaboration with Proteome Sciences. (genengnews.com)
  • Numerous methods are available to study proteins, sets of proteins, or the whole proteome. (wikipedia.org)
  • A key obstacle to studies on Ca 2+ -sensor proteins is the difficulty in identifying their downstream targets because of the technical limitations of various methods that have been used, especially on a proteome-wide scale. (pnas.org)
  • Proteome Sciences received a European patent that lays claim to methods of diagnosing stroke by measuring the levels of heart fatty acid binding protein and/or brain fatty acid binding protein (FABP's). (genengnews.com)
  • In parallel, HDPP intend to produce extended proteomes of diabetes-related cells/tissues/fluids, which will be the starting point for the discovery of "missing proteins" not previously described at the protein level. (hupo.org)
  • To create extended proteome databases on diabetes-related cells/fluids/tissues. (hupo.org)
  • The 'Proteome Profiling Services Market, 2020-2030' report features an extensive study of the current market landscape and future opportunities associated with proteome profiling service providers. (marketresearch.com)
  • Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. (ovid.com)
  • Its global scientific objectives are to reveal the "solar system" of the human liver proteome, expression profiles, modification profiles, a protein linkage (protein-protein interaction) map, and a proteome localization map, and to define an ORFeome, physiome, and pathome. (mcponline.org)
  • Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins. (wikidoc.org)
  • INTERACTION PROTEOME will develop novel technology, including a high-end mass spectrometer with extremely large dynamic range, high density peptide arrays, and improved visualisation technology for light and electron microscopy. (europa.eu)
  • Citation Query Towards a proteome-scale map of the human protein-protein interaction network. (psu.edu)
  • Exploring the human plasma proteome. (nih.gov)
  • In exploring the proteome of epithelioid sarcoma tumors, however, Mukaihara et al. (thermofisher.com)
  • Proteome profiling of embryo chick retina. (highbeam.com)
  • a href="https://www.highbeam.com/doc/1G1-176677058.html" title="Proteome profiling of embryo chick retina. (highbeam.com)
  • Here, we performed proteome profiling of chick retina to identify proteins that are differentially expressed between ED7 and ED11 in chick retina. (highbeam.com)
  • The peptides were analyzed by LC-MS/MS on a high resolution Fourier transform mass spectrometer.RESULTS: This effort was the first total profiling of the synovial fluid proteome in RA that led to identification of 956 proteins. (amrita.edu)
  • As a result, proteome profiling has become an indispensable part of modern drug discovery and development process and disease diagnosis. (marketresearch.com)
  • Currently, the demand for proteome profiling is high, given the growing pipeline of peptide therapeutics. (marketresearch.com)
  • Amidst growing competition in the proteome profiling services market, availability of cutting-edge tools and the latest analytical serves to differentiate the offerings of stakeholders in this upcoming industry. (marketresearch.com)
  • In addition to this, the profile includes information on the proteome profiling services offered by the company, along with information on the proteome profiling technologies used. (marketresearch.com)