Proteome: The protein complement of an organism coded for by its genome.Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.Electrophoresis, Gel, Two-Dimensional: 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.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Chromatography, Liquid: Chromatographic techniques in which the mobile phase is a liquid.Tandem Mass Spectrometry: 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.Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization: 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.Protein Array 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, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Two-Dimensional Difference Gel Electrophoresis: Methods of comparing two or more samples on the same two-dimensional gel electrophoresis gel.Isotope Labeling: 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.Computational Biology: 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.Proteins: 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.Chemical Fractionation: 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)Blood Proteins: Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Bacterial Proteins: Proteins found in any species of bacterium.Spectrometry, Mass, Electrospray Ionization: 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.Sequence Analysis, Protein: 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.Molecular Sequence Data: 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.Amino Acid Sequence: 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.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Peptides: 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.Peptide Mapping: 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.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Protein Interaction Maps: Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Reproducibility of Results: 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.PubMed: 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.Periodicals as Topic: A publication issued at stated, more or less regular, intervals.BooksPublishing: "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.MEDLINE: 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).Microcystins: 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.Pseudomonas aeruginosa: 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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Cyanobacteria: 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.Microcystis: A form-genus of CYANOBACTERIA in the order Chroococcales. Many species are planktonic and possess gas vacuoles.SwitzerlandCloacin: 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.Systems Biology: 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.Encyclopedias as Topic: 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)CD-ROM: 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.MedlinePlus: 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.Skates (Fish): The common name for all members of the Rajidae family. Skates and rays are members of the same order (Rajiformes). Skates have weak electric organs.Biological Science Disciplines: All of the divisions of the natural sciences dealing with the various aspects of the phenomena of life and vital processes. The concept includes anatomy and physiology, biochemistry and biophysics, and the biology of animals, plants, and microorganisms. It should be differentiated from BIOLOGY, one of its subdivisions, concerned specifically with the origin and life processes of living organisms.Gold: A yellow metallic element with the atomic symbol Au, atomic number 79, and atomic weight 197. It is used in jewelry, goldplating of other metals, as currency, and in dental restoration. Many of its clinical applications, such as ANTIRHEUMATIC AGENTS, are in the form of its salts.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Tissue Scaffolds: Cell growth support structures composed of BIOCOMPATIBLE MATERIALS. They are specially designed solid support matrices for cell attachment in TISSUE ENGINEERING and GUIDED TISSUE REGENERATION uses.

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 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., and are available by subscription to corporate users.  (+info)

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

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)

  • 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. (
  • 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 organism's complete proteome , which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. (
  • The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. (
  • For example, all of the proteins in a virus can be called a viral 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 ] ). (
  • 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 archaea and bacteria . (
  • Numerous methods are available to study proteins, sets of proteins, or the whole proteome. (
  • Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis . (
  • Depleted plasma proteins were separated by 2D SDS-PAGE (pI 4-7), and proteomes were compared using Progenesis SameSpots statistical software. (
  • Paper I of this thesis presents a subcellular map of the human proteome, where the spatial distribution of 12,003 human proteins was mapped into 30 subcellular structures, half of which were not previously localized. (
  • In Paper III , we expanded the mitochondrial proteome with 560 novel proteins. (
  • Here, we presented the first proteome-wide spatiotemporal analysis of the nucleolus with its sub-compartments, and identified 69 nucleolar proteins that relocated to the chromosomes periphery during mitosis. (
  • 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. (
  • MudPIT is useful for proteome analysis and may be specifically applied to integral membrane proteins to obtain detailed biochemical information on this unwieldy class of proteins. (
  • 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. (
  • The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell-type is transformative for understanding systems-level properties as well as specific pathways in physiology and disease. (
  • The Human SRMAtlas now provides verified MS assays based on SRM technology developed in a uniform and consistent process for essentially every protein of the human proteome. (
  • 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. (
  • Marc Wilkins coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy. (
  • Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. (
  • Therefore, spatial mapping of the human proteome is essential to understand protein function in health and disease. (
  • The word proteome was coined in 1995 to refer to the total protein complement of a genome. (
  • Conventional proteome analysis is preformed by two-dimensional gel electrophoresis and requires the protein from roughly a million cells. (
  • 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 electrophoresis, and we will evaluate the technology by monitoring the evolution of protein expression in mouse skin tumors. (
  • 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). (
  • Journal or Proteome Research, DOI: 10.1021/acs.jproteome.6b00444 Publication Date (Web): August 30, 2016. (
  • The fraction of the proteome that is expressed by an organism varies between tissues and in response to the environment. (
  • As many as 20% of the mitochondrial proteome showed variations in their expression pattern at the single cell level, most often independent of the cell cycle. (
  • In conclusion, this thesis unravels the spatiotemporal proteome organization of the human cell over the course of a cell cycle and offers a valuable starting point for a better understanding of human cell biology in health and disease. (
  • We describe here an optimized surgical sampling workflow for analyzing the proteomes of peritoneal, fallopian tube, and ovarian surface epithelial (OSE) specimens collected at the time of laparoscopic RRBSO, a technique which has not been described previously. (
  • 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. (
  • Van PT et al (2008) Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. (
  • Proteomics is the study of the proteome. (
  • Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis. (
  • 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. (
  • 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. (
  • 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. (
  • 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. (
  • 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. (
  • They investigated their theories using carbamyl-lysine immunoblotting and a proteomics mass spectrometry (MS) approach to identify rates of carbamylation in the renal proteome. (
  • 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. (
  • General schema showing the relationships of the genome , transcriptome , proteome , and metabolome ( lipidome ). (
  • Although sequencing the human genome was a huge task, trying to figure out the proteome is more complicated by far. (
  • 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 ). (
  • Moreover the proteome has at least two levels of complexity lacking in the genome. (
  • 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. (
  • These changes include developmental and physiological alterations which influence the genome, proteome, and metabolome of the plant. (
  • NEW YORK, Dec 12 - Spotfire and Proteome said Tuesday that they have finished integrating Proteome's Yeast Proteome Database with the portal. (
  • Large-scale analysis of the yeast proteome by multidimensional protein identification technology. (
  • to evaluate the strengths and weaknesses of these methods in addition to providing the community with a comprehensive reference map of the yeast proteome. (
  • Welcome to the proteome atlas of the budding yeast! (
  • 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. (
  • 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. (
  • Wisniewski JR, Rakus D (2014) Multi-enzyme digestion FASP and the 'Total protein Approach'-based absolute quantification of the Escherichia coli proteome. (
  • 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. (
  • 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. (
  • This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. (
  • 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. (
  • 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. (
  • 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. (
  • 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. (
  • Cancer HPP partners with NCI's Clinical Proteome Tumor Analysis Consortium (CPTAC) . (
  • Proteome-wide tyrosine phosphorylation analysis reveals dysregulated signaling pathways in ovarian tumors. (
  • 1999a) Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. (
  • 2000) Comparative proteome analysis of Helicobacter pylori. (
  • 2002) Comparative proteome analysis of Chlamydia trachomatis serovar A, D and L2. (
  • VanBogelen RA, Abshire KZ, Moldover B, Olson ER and Neidhardt FC (1997) Escherichia coli proteome analysis using the gene‐protein database. (
  • 2001) Proteome analysis of the Chlamydia pneumoniae elementary body. (
  • Bumann D, Meyer TF and Jungblut PR (2001) Proteome analysis of the common human pathogen Helicobacter pylori. (
  • Jungblut PR (2001) Proteome analysis of bacterial pathogens. (
  • Introducing low-abundance species in proteome analysis 2. (
  • Chromatographic and electrophoretic pre-fractionation tools in proteome analysis 3. (
  • Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples. (
  • Analysis of the proteome of an organism tells us so much more than simple DNA sequence analysis," said Dr. Wolf. (
  • 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. (
  • 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. (
  • 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. (
  • 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. (
  • The proteome datasets were submitted to Ingenuity Pathway Analysis for identifying the networks and signaling pathways that were potentially disturbed in heart failure subjects. (
  • 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. (
  • In summary, proteome analysis of muscle has helped us better describe the molecular etiology of obesity-related disease. (
  • PCC awardees will be expected to work as an interactive group and use various standardized proteomic analysis technologies for the systematic and comprehensive proteome-wide characterization of defined sets of genomically-characterized samples. (
  • Arabidopsis] SEB Cell symposium: From Proteome to Phenotype - Submit your abstract today! (
  • We hope that future studies will prove the value of this proteome dataset for development of novel therapies and biomarkers. (
  • Chandran, V. Exploring the Psoriatic Arthritis Proteome in Search of Novel Biomarkers. (
  • 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. (
  • Our alliance with Proteome Sciences reinforces our commitment to provide customers with significant expertise to help them select relevant biomarkers for their development programs, interpret results, and determine implications for their therapies. (
  • Marc Wilkins coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy. (
  • 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 program will support broad efforts focused on several cancer types to explore further the complexities of cancer proteomes and their connections to abnormalities in cancer genomes. (
  • Characterize proteomes, proteome forms, and protein networks from different cancers and the matched non-cancers through coordinated efforts of specimen collections and data acquisitions. (
  • 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. (
  • 2000) Two‐dimensional map of the proteome of Haemophilus influenzae. (
  • 2000) Towards the proteome of Mycobacterium tuberculosis. (
  • Since it was first proposed in April 2002, the Human Liver Proteome Project has attracted more than 100 laboratories from all over the world. (
  • 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. (
  • Ueberle B, Frank R and Herrmann R (2002) The proteome of the bacterium Mycoplasma pneumoniae: comparing open reading frames to identified gene products. (
  • 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. (
  • CPD statistically analyses each proteome against a group of closely related proteomes in order to determine completeness. (
  • 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. (
  • 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). (
  • 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. (
  • Proteome Sciences is headquartered in Cobham, the UK. (
  • PAREXEL is using Proteome Sciences' PS Biomarker Services™ protein and peptide biomarker capabilities to support biopharmaceutical companies in making earlier assessments of new compounds in development. (
  • Proteome Sciences will assist PAREXEL early phase experts in helping biopharmaceutical companies advance biomarker discovery and qualification within clinical trials. (
  • Christopher Pearce, Chief Executive of Proteome Sciences said: "We are very pleased to have PS Biomarker Services selected by PAREXEL as a preferred provider of protein and peptide biomarker services. (
  • Users can submit requests to the Proteome Analyst web server by selecting the organism type and then uploading a text file containing the protein sequence in a FASTA format. (
  • 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. (
  • However, the preparation of a proteome chip from any multicellular organism is a major undertaking. (
  • Liver cancer-associated changes to the proteome: what deserves clinical focus? (