Electrophoresis, Gel, Two-Dimensional
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
Two-Dimensional Difference Gel Electrophoresis
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.
Gene Expression Profiling
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
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
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.
Metabolic Networks and Pathways
Protein Interaction Maps
Molecular Sequence Annotation
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.
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)
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, ... 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 ...
"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 ...
Users can view and download Proteome Analyst's results or ask Proteome Analyst to explain its predictions. Proteome Analyst ... Proteome Analyst was originally developed by the Proteome Analyst Research Group at the University of Alberta, and was ... Proteome Analyst is an example of one of the better performing subcellular prediction tools. Proteome Analyst makes predictions ... The initial release of Proteome Analyst used Naïve Bayes classifier to perform its predictions. The current version of Proteome ...
Human Proteome Project
J. Proteome Res. 13:1-4 (2014). Omenn GS., et al. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome ... "Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project". Journal of Proteome ... J. Proteome Res. 12:23-27 (2013). Paik Y-K., et al. Genome-wide Proteomics, Chromosome-centric Human Proteome Project (C-HPP), ... The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization. Its stated goal is ...
Plant Proteome Database
Proteome Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ. (2008) PPDB, the Plant Proteomics Database at Cornell ... The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each ... 2 Oct PPDB Home Page: http://ppdb.tc.cornell.edu/ Plant Proteome Database home page (Plant physiology, Government databases in ...
Human Proteome Organization
"HUPO Congresses , Human Proteome Organization". www.hupo.org. Archived from the original on 2013-09-11. "HUPO - Past Award ... The Human Proteome Organization (HUPO) is an international consortium of national proteomics research associations, government ... Ultimately, it is organized to gain a better and more complete understanding of the human proteome. Since 2002, HUPO organizes ... Award in Proteomic Sciences Human Genome Organisation Human Genome Project Proteomics Standards Initiative Human Proteome ...
Journal of Proteome Research
In 2013, J. Proteome Res. had an impact factor of 5.001 as reported in the 2013 Journal Citation Reports by Thomson Reuters, ... The Journal of Proteome Research is a peer-reviewed scientific journal published since 2002 by the American Chemical Society. ...
Human Proteome Folding Project
The Human Proteome Folding Project (HPF) is a collaborative effort between New York University (Bonneau Lab), the Institute for ... home Foldit Human proteome project List of volunteer computing projects World Community Grid Post - HPF2 Update, June 2013, ... "Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology", PLOS ...
"Proteomes". www.mdpi.com. Retrieved 2022-02-21. "Proteomes". www.mdpi.com. Retrieved 2022-02-21. "Proteomes - NLM Catalog - ... Proteomes is a peer-reviewed open access scientific journal covering research in biochemistry and molecular biology, and ... focused on proteome analysis. It is published by MDPI and was established in 2013. The joint editor-in-chief are Jens R. ...
Reverse phase protein lysate microarray
Proteome Science. Ramaswamy et al.; licensee BioMed Central Ltd. 9 (3). Proteome Science , Full text , Development of reverse ...
Peptide mass fingerprinting
"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, ...
2008). "Protein profiling of the dimorphic, pathogenic fungus, Penicillium marneffei". Proteome Sci. 6 (1): 17. doi:10.1186/ ...
Proteome Science. 3 (1): 2. doi:10.1186/1477-5956-3-2. PMC 554085. PMID 15730566. Burmester T, Weich B, Reinhardt S, Hankeln T ...
Tohoku Medical Megabank Project
Proteome analysis. Transcriptome analysis. Epigenome analysis. Oral Microbiome analysis. 2013 Recruitment of TMM Community- ... 2015 A portal site of Japanese Multi Omics Reference Panel (jMorp), providing metabolome and proteome data from the cohort ... As of 2022, jMorp covers metabolome, proteome, transcriptome, methylome, as well as genome reference panel. 2016 Recruitment of ...
"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 ...
List of mass spectrometry software
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. 6 (2): 654-61. doi:10.1021/pr0604054. PMC 2525619. PMID 17269722. "OMSSA ms/ms search engine". ... Journal of Proteome Research. 15 (1): 332-338. doi:10.1021/acs.jproteome.5b00666. ISSN 1535-3907. PMID 26616242. Titeca, Kevin ...
Proteome Science. 6: 19. doi:10.1186/1477-5956-6-19. PMC 2440369. PMID 18558005. Arasaradnam, RP; Wicaksono, A; O'Brien, H; ...
Methods to investigate protein-protein interactions
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) ( ...
Radioimmunoprecipitation assay buffer
Proteome Sci. 6 (1): 30. doi:10.1186/1477-5956-6-30. PMC 2600628. PMID 18950484. v t e (Laboratory techniques, All stub ...
Chicken or the egg
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 ...
Poly (ADP-ribose) polymerase
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 ...
60S ribosomal protein L7
Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M (January 2005). "Nucleolar proteome dynamics". Nature. 433 ( ...
Calcium-regulated heat stable protein 1
Kim JE, Tannenbaum SR, White FM (2005). "Global phosphoproteome of HT-29 human colon adenocarcinoma cells". J. Proteome Res. 4 ...
Catherine E. Costello
"HUPOST The newsletter of the Human Proteome Organisation" (PDF). Human Proteome Organization. Archived (PDF) from the original ... She participated in the Human Proteome Project, the SysteMHC Atlas project, and the Minimum Information Required for a ... Costello served as the president of the American Society for Mass Spectrometry (2002-2004), the Human Proteome Organization ( ... Spectrometry Foundation Thomson Medal 2008 Human Proteome Organization Discovery in Proteomic Sciences Award US Human Proteome ...
Proteome Res. 6 (1): 298-305. CiteSeerX 10.1.1.401.4220. doi:10.1021/pr060438j. PMID 17203973. Pezzatini S, Morbidelli L, ...
St. Jude and Scripps Research Institute scientists help launch Human Dark Proteome Initiative
... and other institutions today announced the launch of the Human Dark Proteome Initiative (HDPI). The initiative aims to ... The term "dark proteome" describes the large portion of the proteome-the complete collection of proteins in an organism-that do ... Jude and Scripps Research Institute scientists help launch Human Dark Proteome Initiative. *Download PDF Copy ... These little-studied proteins make up about one third of the human proteome and control many aspects of cellular behavior. ...
proteome-elements - Metabolomics Society
Proteomes | Free Full-Text | Regional Diversity in the Postsynaptic Proteome of the Mouse Brain
Postsynaptic proteomes were isolated from seven forebrain and hindbrain regions in mice and their composition determined using ... Diversity in synapse proteome composition is key feature of mouse and human brain structure. ... The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is ... Combining proteomic and connectomic data shows that interconnected regions have specific proteome signatures. ...
Publications - Proteome Sciences
Comprehensive listings of proteomics publications by Proteome Sciences and collaborators. ... Carbonyl-reactive tandem mass tags for the proteome-wide quantification of N-linked glycans. Product: Tandem Mass Tag Protein ... In-depth profiling of the peripheral blood mononuclear cells proteome for clinical blood proteomics. Product: TMT-MS2 Broadest ... Comparison of the nuclear proteomes of mammary epithelial cells at different stages of functional differentiation.. ...
Salivary proteome of aphthous stomatitis reveals the participation of vitamin metabolism, nutrients, and bacteria | medRxiv
Xiao, H. & Wong, D. T. Method development for proteome stabilization in human saliva. Anal Chim Acta 722, 63-69, doi:10.1016/j. ... Grassl, N. et al. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome. Genome Med 8, 44, doi: ... Bao, J. et al. Combined signatures of serum proteome and transcriptome in patients with recurrent aphthous ulcer. Oral Dis, doi ... Salivary proteome of aphthous stomatitis reveals the participation of vitamin metabolism, nutrients, and bacteria. Romina ...
Diurnal Dynamics of the Arabidopsis Rosette Proteome and Phosphoproteome | bioRxiv
Diurnal Dynamics of the Arabidopsis Rosette Proteome and Phosphoproteome. View ORCID ProfileR. Glen Uhrig, Sira Echevarría- ... Diurnal Dynamics of the Arabidopsis Rosette Proteome and Phosphoproteome Message Subject (Your Name) has forwarded a page to ... Here we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 h light : 12 h ... The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, ...
Volatiles from the fungal phytopathogen Penicillium aurantiogriseum modulate root metabolism and architecture through proteome...
Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells | PNNL
2018. Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells. Nature ... Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells ... illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues. ...
A chronic hypoxic response in photoreceptors alters the vitreous proteome in mice - Zurich Open Repository and Archive
Only few of the regulated proteins were shared by the models indicating that the vitreous proteome is differentially affected ... Only few of the regulated proteins were shared by the models indicating that the vitreous proteome is differentially affected ... A chronic hypoxic response in photoreceptors alters the vitreous proteome in mice ... we also evaluated the vitreous proteome of wild type mice after exposure to acute hypoxia. 1043 of the identified proteins ...
High-throughput and Deep-proteome Profiling by 16-plex Tandem Mass Tag Labeling Coupled with Two-dimensional Chromatography and...
Ow, S. Y., et al. iTRAQ underestimation in simple and complex mixtures: "The good, the bad and the ugly". Journal of Proteome ... Chick, J. M., et al. Defining the consequences of genetic variation on a proteome-wide scale. Nature. 534 (7608), 500-505 (2016 ... Kelstrup, C. D., et al. Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field orbitrap mass ... Bekker-Jensen, D. B., et al. An optimized shotgun strategy for the rapid generation of comprehensive human proteomes. Cell ...
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex | BMC Bioinformatics | Full Text
In the complete proteome, there are 30,550 putative proteins. However, about 10,000 of them have no known homologues. Currently ... We compared the properties of the Daphnias protein families with those of the mouse and the fruitfly proteomes. Functional ... Applying a careful inference protocol resulted in functional assignments for over 86% of the complete proteome. We conclude ... for automatic annotation of the Daphnias proteome. 98.7% (26,625) of the Daphnia full-length proteins were successfully mapped ...
Feed based on vegetable materials changes the muscle proteome of the carnivore rainbow trout<...
Jessen, F, Wulff, T, Bach Mikkelsen, J & Nielsen, HH 2011, Feed based on vegetable materials changes the muscle proteome of the ... Feed based on vegetable materials changes the muscle proteome of the carnivore rainbow trout. / Jessen, Flemming; Wulff, Tune; ... Feed based on vegetable materials changes the muscle proteome of the carnivore rainbow trout. In WEFTA 2011 - Seafood for the ... Feed based on vegetable materials changes the muscle proteome of the carnivore rainbow trout. WEFTA 2011 - Seafood for the ...
Distinguished Mycologists,British mycology,Vacancy,CME program Philadelphia,Yeast proteomes,Courses China, Superficial...
Left ventricular diastolic function in relation to the urinary proteome: a proof-of-concept study in a general population -...
Left ventricular diastolic function in relation to the urinary proteome: a proof-of-concept study in a general population ... Conclusions: In a general population, the urinary proteome correlated with diastolic LV dysfunction, proving its utility for ... Left ventricular diastolic function in relation to the urinary proteome: a proof-of-concept study in a general population. ... and the urinary proteome by capillary electrophoresis coupled with mass spectrometry. ...
'Zhu, Chun Quan' / Journal: Journal of Proteome Research / Publication Year: 2016 / Subject: acid deposition and Calvin cycle -...
You searched for: Zhu, Chun Quan Remove constraint Zhu, Chun Quan Journal Journal of Proteome Research Remove constraint ... Journal of Proteome Research 2016 v.15 no.1 pp. 216-228. ISSN:. 1535-3907. Subject:. Calvin cycle; Liquidambar formosana; ... Journal: Journal of Proteome Research Publication Year 2016 Remove constraint Publication Year: 2016 Subject acid deposition ... proteome; proteomics; quantitative polymerase chain reaction; reactive oxygen species; reverse transcriptase polymerase chain ...
A Complete Mass-spectrometric Map of a Eukaryotic Proteome - Research Collection
Plasma Proteome Database
Hypoxia-induced inhibin promotes tumor growth and vascular permeability in ovarian cancers | Communications Biology
Angiogenesis proteome array. Angiogenesis proteome array was performed according to manufacturers instruction (R&D Systems, ... We hence sought to determine the effect of shINHA on the angiogenic cytokine profile of the tumors using a proteome array of 55 ... 7bi). To complement the human tumor array, we analyzed changes in the mouse angiogenic proteome as well to delineate any host ... 7d). Interestingly, in our analysis of the angiogenic proteome of HEY tumors, permeability promoting cytokines, EGF, IL-8, and ...
Proteome Science | Articles
Proteome Science considers manuscripts based on all aspects of functional and structural proteomics, ... ... Proteome Science is affiliated with the Korean Human Proteome Organization (KHUPO). KHUPO is a global leader in both domestic ... The extracellular proteome of Rhizobium etli CE3 in exponential and stationary growth phase The extracellular proteome or ... Characterization of proteome alterations in Phanerochaete chrysosporium in response to lead exposure Total soluble proteome ...
Impact of exosomal HIV-1 Tat expression on the human cellular proteome | Oncotarget
Proteomics for Precision Medicine: A High-Throughput Platform for Proteome and Phospho-Proteome
PAREXEL Enhances Early Phase Biomarker Capabilities Through Alliance With Proteome Sciences - Pharmaceutical Processing World
"Our alliance with Proteome Sciences reinforces our commitment to provide customers with significant expertise to help them ... PAREXEL is using Proteome Sciences PS Biomarker Services(TM) protein and peptide biomarker capabilities to support ... Proteome Sciences will assist PAREXEL early phase experts in helping biopharmaceutical companies advance biomarker discovery ... Christopher Pearce, Chief Executive of Proteome Sciences said: "We are very pleased to have PS Biomarker Services selected by ...
PubMed:16381885 - Human Salivary Proteome Wiki
The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both ...
First draft of the human proteome
... researchers report the first draft of the human proteome blueprint. ... Ten years on from the launch of the Human Proteome Project, ... The Human Proteome Project (HPP). A decade after the release of ... Ten years on from the launch of the Human Proteome Project, researchers report the first draft of the proteome blueprint. ... "In COVID-19, for instance, there are two proteomes involved, that of the SARS-CoV-2 virus and that of the infected cells, both ...
Research Labs and Institutes | Johns Hopkins Medicine
Proteome-pI 2.0 - Proteome Isoelectric Point Database
Proteome wide database of protein isoelectric point for model organisms. ... Proteome-pI 2.0: Proteome Isoelectric Point Database Update. Nucleic Acids Res. 2021, doi: 10.1093/nar/gkab944. Contact: Lukasz ... Summary statistics related to proteome-wise predictions. Protein with the lowest isoelectric point:. >sp,Q9QU31,ORF2_TTVB1 ... Below you can find in silico digests of the whole proteome with Trypsin, Chymotrypsin, Trypsin+LysC, LysN, ArgC proteases ...
Med Grade Xylene Thinners 5 Litres | Proteome
Proteome-pI - Proteome Isoelectric Point Database statistics
Proteome wide database of protein isoelectric point for model organisms. ... Proteome-pI: proteome isoelectric point database. Nucleic Acids Res. 2016. doi: 10.1093/nar/gkw978 Contact: Lukasz P. Kozlowski ... Proteome-pI is available under Creative Commons Attribution-NoDerivs license, for more details see here ...
- The term "dark proteome" describes the large portion of the proteome-the complete collection of proteins in an organism-that do not adopt defined 3D structures. (news-medical.net)
- These little-studied proteins make up about one third of the human proteome and control many aspects of cellular behavior. (news-medical.net)
- Many of the members of the new Human Dark Proteome Initiative were in Memphis last week for the Intrinsically Disordered Proteins session at the Southeastern/Southwestern Regional Meeting of the American Chemical Society. (news-medical.net)
- The proteome of the postsynaptic terminal of excitatory synapses comprises over one thousand proteins in vertebrate species and plays a central role in behavior and brain disease. (mdpi.com)
- The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. (biorxiv.org)
- Furthermore, we demonstrate robust quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues. (pnnl.gov)
- Only few of the regulated proteins were shared by the models indicating that the vitreous proteome is differentially affected by systemic hypoxia and the rod or cone-specific hypoxic response. (uzh.ch)
- In the complete proteome, there are 30,550 putative proteins. (biomedcentral.com)
- Low-abundance proteins are difficultly observed on the two-dimensional gel electrophoresis (2-DE) maps of urine proteome, because they are usually obscured by high-abundance proteins such as albumin and immuno. (biomedcentral.com)
- To determine whether the human salivary proteome is responsive to ionizing radiation exposure, we characterized the abundances of salivary proteins in humans before and after total body irradiation . (bvsalud.org)
- Because the proteome is a continuously changing set of proteins that differs from cell to cell, it is challenging for scientists to capture and study it. (cdc.gov)
- In 2014, scientists developed a draft map of the human proteome , which catalogued proteins encoded by over 17,000 human genes, or about 84% of all protein-coding genes in the human genome. (cdc.gov)
- Proteomic techniques can show the proteome profile of cells and biological fluids and can also provide more information on protein functions and post-translational modifications of proteins (5). (who.int)
- To discriminate between the consequences of a local response in photoreceptors and systemic hypoxic effects, we also evaluated the vitreous proteome of wild type mice after exposure to acute hypoxia. (uzh.ch)
- Isobaric tandem mass tag (TMT) labeling is widely used in proteomics because of its high multiplexing capacity and deep proteome coverage. (jove.com)
- Rapid developments in mass spectrometry technology have enabled to achieve high sensitivity and deep proteome coverage in proteomics applications 1 , 2 . (jove.com)
- In the laboratory, the team comprehensively and systematically profiled the make-up, activation state (as measured by protein phosphorylation), and other post-translational modifications (including acetylation) of the lung cancer proteome, matching the data to mutations and other features of each tumor's genome and comparing the data against normal lung tissue from each patient. (broadinstitute.org)
- The effects of PQ on cellular processes and biological pathways were investigated by analyzing proteome in the lung tissues in comparison with the control. (cdc.gov)
- 51.3% women), we measured early and late diastolic peak velocities of mitral inflow (E and A) and mitral annular velocities (e' and a') by conventional and tissue Doppler echocardiography, and the urinary proteome by capillary electrophoresis coupled with mass spectrometry. (gla.ac.uk)
- Conclusions: In a general population, the urinary proteome correlated with diastolic LV dysfunction, proving its utility for early diagnosis of this condition. (gla.ac.uk)
- The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is poorly understood. (mdpi.com)
- The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant. (biorxiv.org)
- Thus, the value of a comparative genomics research from its related proteomes (i.e., insects) might be somewhat limited. (biomedcentral.com)
- Comparative analysis of whole saliva proteomes for the screening of biomarkers for oral lichenplanus. (bvsalud.org)
- Quantification of pancreatic cancer proteome and phosphorylome: indicates molecular events likely contributing to cancer and activity of drug targets. (proteomics.com)
- In this manuscript, we present an optimized protocol for 16-plex TMT-based deep-proteome profiling, including protein sample preparation, enzymatic digestion, TMT labeling reaction, two-dimensional reverse-phase liquid chromatography (LC/LC) fractionation, tandem mass spectrometry (MS/MS), and computational data processing. (jove.com)
- Our findings show that VCs from P. aurantiogriseum modify root metabolism and architecture, and improve nutrient and water use efficiencies through transcriptionally and non‐transcriptionally regulated proteome resetting mechanisms. (csic.es)
- Scientists at St. Jude Children's Research Hospital, The Scripps Research Institute (TSRI) and other institutions today announced the launch of the Human Dark Proteome Initiative (HDPI). (news-medical.net)
- Additional information about the Human Dark Proteome Initiative can found at darkproteome.org . (news-medical.net)
- We announce the "BIOBASE Knowledge Library (BKL) - YEAST Edition", a fully manually curated database which provides comprehensive information on proteomes of S. cerevisiae, S. pombe, and 18 other human fungal pathogens including C. albicans. (isham.org)
- Studies of the human proteome have enabled scientists to track protein synthesis, modification, and degradation over time and across different cell types. (cdc.gov)
- This year, scientists released a more complete map of the human proteome estimated to include more than 90% of the human proteome. (cdc.gov)
- Wright and Kriwacki emphasized that dramatically expanded investment in basic and translational research into the dark proteome is needed to achieve the full potential for understanding and developing cures for many devastating diseases. (news-medical.net)
- Applying a careful inference protocol resulted in functional assignments for over 86% of the complete proteome. (biomedcentral.com)
- Total soluble proteome alterations of white rot fungus Phanerochaete chrysosporium in response to different doses (25, 50 and 100 μM) of Pb (II) were characterized by 2DE in combination with MALDI-TOF-MS. (biomedcentral.com)
- Pulmonary proteome and protein networks in response to the herbicide paraquat in rats. (cdc.gov)
- The importance of proteome identification of protozoa side-effects and there is growing evidence of drug secretions has been highlighted (11,12) . (who.int)
- Multiplexed isobaric labeling techniques are extensively used for proteome-wide relative quantitation of large batches of samples 3 , 4 , 5 , 6 . (jove.com)
- We conclude that the scaffold of ProtoNet can be used as an alignment-free protocol for large-scale annotation task of uncharacterized proteomes. (biomedcentral.com)
- Here we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 h light : 12 h dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. (biorxiv.org)
- Having an accurate description of the cancer proteome and its post-translational modifications is pivotal for understanding what the key therapeutic innovations might be. (broadinstitute.org)
- The highly resolved time-scale of the datasets offer new proteome-level insights for future targeted studies. (biorxiv.org)
Field of proteomics1
- The generation and analysis of proteome data are becoming increasingly widespread, as the field of proteomics is moving incrementally toward high-throughput approaches. (nih.gov)
- Applications should describe an approach for improving and/or developing protein affinity reagent technologies that can be ready for proteome scale projects within three to five years. (nih.gov)
- Symposium speakers will present varying perspectives on their proteome-based research from clinical medicine to bioinformatics via application of emerging technologies in protein chips, electrophoresis and mass spectrometry. (nih.gov)
- Technologies are currently available for the comprehensive profiling of the cell surface proteome that rely on protein tagging of intact cells. (nih.gov)
- NEI has made the Ocular Proteome dataset available so that researchers can analyze protein changes related to genetic eye diseases. (nih.gov)
- NCBI provides the human proteome as the Reference Sequence (RefSeq) protein records. (nih.gov)
- Studies of the human proteome have enabled scientists to track protein synthesis, modification, and degradation over time and across different cell types. (cdc.gov)
- Cite this: Proteome Profiling in Body Fluids and in Cancer Cell Signaling - Medscape - Jun 06, 2003. (medscape.com)
- Profiling of the cell surface proteome. (nih.gov)
- The profiling of the cell surface and plasma membrane proteomes will likely provide novel insights and uncover disease related alterations. (nih.gov)
- However, scientific understanding of the proteome has lagged behind that of the genome, partly because of the proteome's complexities. (nih.gov)
- Proteomics is essential for a comprehensive approach for cataloging all salivary secretory components and, if possible, creating the "periodic table" of the salivary proteome that will help elucidate disease pathogenesis and evaluate the influence of medications on the structure, composition and secretion of all salivary secretory constituents. (nih.gov)
- p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. (uniprot.org)