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  • 1
    Language: English
    In: Science (New York, N.Y.), 26 April 2013, Vol.340(6131), pp.475-8
    Description: Protein secretion allows communication of distant cells in an organism and controls a broad range of physiological functions. We describe a quantitative, high-resolution mass spectrometric workflow to detect and quantify proteins that are released from immune cells upon receptor ligation. We quantified the time-resolved release of 775 proteins, including 52 annotated cytokines from only 150,000 primary Toll-like receptor 4-activated macrophages per condition. Achieving low picogram sensitivity, we detected secreted proteins whose abundance increased by a factor of more than 10,000 upon stimulation. Secretome to transcriptome comparisons revealed the transcriptionally decoupled release of lysosomal proteins. From genetic models, we defined secretory profiles that depended on distinct intracellular signaling adaptors and showed that secretion of many proinflammatory proteins is safeguarded by redundant mechanisms, whereas signaling adaptor synergy promoted the release of anti-inflammatory proteins.
    Keywords: Macrophage Activation ; Macrophages -- Immunology ; Mass Spectrometry -- Methods ; Proteins -- Metabolism ; Proteome -- Metabolism ; Toll-Like Receptor 4 -- Agonists
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 2
    In: Nature, 2016, Vol.537(7620), p.347
    Description: Numerous biological processes are concurrently and coordinately active in every living cell. Each of them encompasses synthetic, catalytic and regulatory functions that are, almost always, carried out by proteins organized further into higher order structures and networks. For decades, the structures and functions of selected proteins have been studied using biochemical and biophysical methods. However, the properties and behaviour of the proteome as an integrated system have largely remained elusive. Powerful mass-spectrometry-based technologies now provide unprecedented insights into the composition, structure, function and control of the proteome, shedding light on complex biological processes and phenotypes. proteome data. This Review highlights the achievements of mass-spectrometry-based proteomics and the challenges that remain. Efforts to catalogue systematically the proteomes of an array of species and to transform these catalogues into highly specific assays that can quantify any component are described. The analysis of post-translational modifications is discussed, especially with regard to completeness of measurement and how the research community might assign functions to the tens of thousands of modified sites that have been discovered in the past decade. The state of mass spectrometry is reviewed in the context of the study of functional modules in which components of the proteome come together stably or temporarily in complexes to carry out a biochemical function. Last, mass spectrometry-based techniques that are capable of quantifying thousands of proteins across collections of large numbers of samples with a high degree of reproducibility are described; these generate large datasets that can be mined by statistical machine-learning tools to determine the state of the proteome and its response to perturbations. Such datasets start to uncover systemic malfunctions at the cellular and organismal levels in diseases that have been difficult to reach through classic protein-based or nucleic-acid-based research.
    Keywords: Biologischer Prozess ; Protein ; Exploration ; Proteom ; Integriertes System ; Proteomik ; Nukleinsäure ; Spektrometrie ; Maschinelles Lernen ; Betriebsstörung ; Sciences (General) ; Physics;
    ISSN: 0028-0836
    E-ISSN: 1476-4687
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  • 3
    Article
    Article
    Language: English
    In: Nature, Nov 7, 2002, Vol.420(6911), p.21(1)
    Description: The new journal "Molecular and Cellular Proteomics," a spin-off from the "Journal of Biological Chemistry," is the official outlet for the American Society for Biochemistry and Molecular Biology.
    Keywords: Journals ; Biochemistry ; Molecular Biology ; Molecular & Cellular Proteomics;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 4
    Article
    Article
    In: Nature, 2002, Vol.418(6899), p.731
    Description: Efficient and sensitive methods to determine whether, and to what extent, a person is infected with malaria should help to improve treatment. A high-tech approach, using mass spectrometry, may be the answer.
    Keywords: Mass Spectrometry ; Copyrights ; Tools ; Malaria ; Diagnosis ; General and Nonclassified (MD) ; General and Nonclassified (EC) ; General and Nonclassified (Ed) ; General and Nonclassified (Ep) ; Surveying, Theory, and Analysis (CE) ; Design Principles, Theory, and Analysis (Mt) ; Computing Milieux (General) (Ci) ; Electronics and Communications Milieux (General) (Ea) ; Solid State Milieux (General) (So) ; Article;
    ISSN: 0028-0836
    E-ISSN: 1476-4687
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  • 5
    Language: English
    In: European Journal of Operational Research, 16 September 2013, Vol.229(3), pp.718-731
    Description: This paper presents a novel solution heuristic to the General Lotsizing and Scheduling Problem for Parallel production Lines (GLSPPL). The GLSPPL addresses the problem of simultaneously deciding about the sizes and schedules of production lots on parallel, heterogeneous production lines with respect to scarce capacity, sequence-dependent setup times and deterministic, dynamic demand of multiple products. Its objective is to minimize inventory holding, sequence-dependent setup and production costs. The new heuristic iteratively decomposes the multi-line problem into a series of single-line problems, which are easier to solve. Different approaches for decomposition and for the iteration between a modified multi-line master problem and the single-line subproblems are proposed. They are compared with an existing solution method for the GLSPPL by means of medium-sized and large practical problem instances from different types of industries. The new methods prove to be superior with respect to both solution quality and computation time.
    Keywords: Scheduling ; Heuristics ; Simultaneous Lotsizing and Scheduling ; Production ; Engineering ; Business ; Computer Science
    ISSN: 0377-2217
    E-ISSN: 1872-6860
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  • 6
    Language: English
    In: Clinical chemistry, January 2016, Vol.62(1), pp.293-4
    Description: Featured Article: Shevchenko A, Wilm M, Vorm O, Mann M. Mass spectrometric sequencing of proteins from silver stained polyacrylamide gels. Anal Chem 1996;68:850–8.2 Many of today's key proteins in biology and biomedicine were originally identified by protein chemical methods. Frederick Sanger obtained his first Nobel Prize for determining the sequence of insulin in the 1950s, and the Edman degradation, in which one amino acid after another is cleaved off the end of a protein or peptide and identified by HPLC, reigned supreme into the 1990s. My background is in mass spectrometry (MS),3 in particular electrospray ionization (1), for which my advisor John Fenn won a Nobel Prize. On coming to the European Molecular Biology Laboratory (EMBL) in Heidelberg as a young group leader, I was determined to challenge what I saw as the old-fashioned chemical methods with high-tech and cool MS technology. Little did I know what I was up against, because this would require not only highly sensitive peptide sequencing by MS …
    Keywords: Mass Spectrometry ; Proteins -- Analysis ; Proteomics -- Methods
    ISSN: 00099147
    E-ISSN: 1530-8561
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  • 7
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 13 September 2011, Vol.108(37), pp.15213-8
    Description: β1 integrin tyrosine phosphorylation by oncogenic kinases, such as Src, has been predicted to induce tumorigenesis by disrupting adhesion and modifying integrin signaling. We directly tested this hypothesis by subjecting mice with "nonphosphorylatable" tyrosine-to-phenylalanine substitutions in the conserved β1 cytoplasmic tail NPxY motifs to a model of cutaneous carcinogenesis in the presence or absence of elevated Src activity. We found that hydrophobic phenylalanine substitutions of both tyrosines diminished the binding of tail-interacting proteins, including talins and kindlins, resulting in reduced β1-mediated adhesion, focal adhesion kinase (FAK) signaling, and epidermal progenitor cell-derived skin tumors. However, increased Src activity drove tumor formation independent of the phenylalanine substitutions by enhancing FAK activity, which in turn maintained the epidermal progenitor state and blocked keratinocyte differentiation. We conclude that a Src/FAK signaling unit inhibits differentiation to promote tumorigenesis downstream of β1 integrin and independent of β1 integrin tyrosine phosphorylation.
    Keywords: Cytoplasm -- Metabolism ; Integrin Beta1 -- Metabolism ; Precancerous Conditions -- Metabolism ; Skin Neoplasms -- Metabolism ; Tyrosine -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 8
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 2008, Vol.105(47), pp.18132-18138
    Description: Proteomics has progressed radically in the last 5 years and is now on par with most genomic technologies in throughput and comprehensiveness. Analyzing peptide mixtures by liquid chromatography coupled to high-resolution mass spectrometry (LC-MS) has emerged as the main technology for in-depth proteome analysis whereas two-dimensional gel electrophoresis, low-resolution MALDI, and protein arrays are playing niche roles. MS-based proteomics is rapidly becoming quantitative through both label-free and stable isotope labeling technologies. The latest generation of mass spectrometers combines extremely high resolving power, mass accuracy, and very high sequencing speed in routine proteomic applications. Peptide fragmentation is mostly performed in low-resolution but very sensitive and fast linear ion traps. However, alternative fragmentation methods and high-resolution fragment analysis are becoming much more practical. Recent advances in computational proteomics are removing the data analysis bottleneck. Thus, in a few specialized laboratories, "precision proteomics" can now identify and quantify almost all fragmented peptide peaks. Huge challenges and opportunities remain in technology development for proteomics; thus, this is not "the beginning of the end" but surely "the end of the beginning." ; Includes references ; p. 18132-18138.
    Keywords: Proteomics -- Research ; Mass Spectrometry -- Methods;
    ISSN: 0027-8424
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  • 9
    Language: English
    In: Proteome Science, Feb 7, 2011, Vol.9, p.7
    Description: Background Hen's egg white has been the subject of intensive chemical, biochemical and food technological research for many decades, because of its importance in human nutrition, its importance as a source of easily accessible model proteins, and its potential use in biotechnological processes. Recently the arsenal of tools used to study the protein components of egg white has been complemented by mass spectrometry-based proteomic technologies. Application of these fast and sensitive methods has already enabled the identification of a large number of new egg white proteins. Recent technological advances may be expected to further expand the egg white protein inventory. Results Using a dual pressure linear ion trap Orbitrap instrument, the LTQ Orbitrap Velos, in conjunction with data analysis in the MaxQuant software package, we identified 158 proteins in chicken egg white with two or more sequence unique peptides. This group of proteins identified with very high confidence included 79 proteins identified in egg white for the first time. In addition, 44 proteins were identified tentatively. Conclusions Our results, apart from identifying many new egg white components, indicate that current mass spectrometry technology is sufficiently advanced to permit direct identification of minor components of proteomes dominated by a few major proteins without resorting to indirect techniques, such as chromatographic depletion or peptide library binding, which change the composition of the proteome.
    Keywords: Mass Spectrometry -- Usage ; Proteins -- Physiological Aspects ; Proteins -- Research ; Bird Eggs -- Physiological Aspects ; Bird Eggs -- Research
    ISSN: 1477-5956
    Source: Cengage Learning, Inc.
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  • 10
    Language: English
    In: Proteome Science, Feb 7, 2011, Vol.9, p.7
    Description: Background Hen's egg white has been the subject of intensive chemical, biochemical and food technological research for many decades, because of its importance in human nutrition, its importance as a source of easily accessible model proteins, and its potential use in biotechnological processes. Recently the arsenal of tools used to study the protein components of egg white has been complemented by mass spectrometry-based proteomic technologies. Application of these fast and sensitive methods has already enabled the identification of a large number of new egg white proteins. Recent technological advances may be expected to further expand the egg white protein inventory. Results Using a dual pressure linear ion trap Orbitrap instrument, the LTQ Orbitrap Velos, in conjunction with data analysis in the MaxQuant software package, we identified 158 proteins in chicken egg white with two or more sequence unique peptides. This group of proteins identified with very high confidence included 79 proteins identified in egg white for the first time. In addition, 44 proteins were identified tentatively. Conclusions Our results, apart from identifying many new egg white components, indicate that current mass spectrometry technology is sufficiently advanced to permit direct identification of minor components of proteomes dominated by a few major proteins without resorting to indirect techniques, such as chromatographic depletion or peptide library binding, which change the composition of the proteome.
    Keywords: Mass Spectrometry -- Usage ; Proteins -- Physiological Aspects ; Proteins -- Research ; Bird Eggs -- Physiological Aspects ; Bird Eggs -- Research
    ISSN: 1477-5956
    Source: Cengage Learning, Inc.
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