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Proteomics

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Proteomics - Free Register to Access Experts & Abstracts

Carl Philipp Heisenberg - One of the best experts on this subject based on the ideXlab platform.

  • Proteomics of early zebrafish embryos
    BMC Developmental Biology, 2006
    Co-Authors: Vinzenz Link, Andrej Shevchenko, Carl Philipp Heisenberg
    Abstract:

    Background Zebrafish ( D. rerio ) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and Proteomics have yet to be developed. Results As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for Proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.

  • Proteomics of early zebrafish embryos
    BMC Developmental Biology, 2006
    Co-Authors: Vinzenz Link, Andrej Shevchenko, Carl Philipp Heisenberg
    Abstract:

    Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and Proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for Proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis. © 2006 Link et al; licensee BioMed Central Ltd.

Andrej Shevchenko - One of the best experts on this subject based on the ideXlab platform.

  • chromatin central towards the comparative proteome by accurate mapping of the yeast proteomic environment
    Genome Biology, 2008
    Co-Authors: Anna Shevchenko, Assen Roguev, Daniel Schaft, Luke Buchanan, Bianca Habermann, Cagri Sakalar, Henrik Thomas, Nevan J Krogan, Andrej Shevchenko
    Abstract:

    Background: Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative Proteomics can be fruitful. Results: The Saccharomyces cerevisiae proteome presents the highest quality proteomic data available. To evaluate the accuracy of these data, we intensively mapped a proteomic environment, termed 'Chromatin Central', which encompasses eight protein complexes, including the major histone acetyltransferases and deacetylases, interconnected by twelve proteomic hyperlinks. Using sequential tagging and a new method to eliminate background, we confirmed existing data but also uncovered new subunits and three new complexes, including ASTRA, which we suggest is a widely conserved aspect of telomeric maintenance, and two new variations of Rpd3 histone deacetylase complexes. We also examined the same environment in fission yeast and found a very similar architecture based on a scaffold of orthologues comprising about two-thirds of all proteins involved, whereas the remaining one-third is less constrained. Notably, most of the divergent hyperlinks were found to be due to gene duplications, hence providing a mechanism for the fixation of gene duplications in evolution. Conclusions: We define several prerequisites for comparative Proteomics and apply them to examine a proteomic environment in unprecedented detail. We suggest that high resolution mapping of proteomic environments will deliver the highest quality data for comparative Proteomics.

  • Proteomics of early zebrafish embryos
    BMC Developmental Biology, 2006
    Co-Authors: Vinzenz Link, Andrej Shevchenko, Carl Philipp Heisenberg
    Abstract:

    Background Zebrafish ( D. rerio ) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and Proteomics have yet to be developed. Results As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for Proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.

  • Proteomics of early zebrafish embryos
    BMC Developmental Biology, 2006
    Co-Authors: Vinzenz Link, Andrej Shevchenko, Carl Philipp Heisenberg
    Abstract:

    Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and Proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for Proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis. © 2006 Link et al; licensee BioMed Central Ltd.

Arul M. Chinnaiyan - One of the best experts on this subject based on the ideXlab platform.

  • current affairs in quantitative targeted Proteomics multiple reaction monitoring mass spectrometry
    Briefings in Functional Genomics and Proteomics, 2009
    Co-Authors: Anastasia K Yocum, Arul M. Chinnaiyan
    Abstract:

    Quantitative targeted Proteomics has recently taken front stage in the Proteomics community. Centered on multiple reaction monitoring ^ mass spectrometry (MRM^MS) methodologies, quantitative targeted Proteomics is being used in the verification of global Proteomics data, the discovery of lower abundance proteins, protein post-translational modifications, discrimination of select highly homologous protein isoforms and as the final step in biomarker discovery. An older methodology utilized with small molecule analysis, the Proteomics community is making great technological strides to develop MRM^MS as the next method to address previously challenging issues in global Proteomics experimentation, namely dynamic range, identification of post-translational modifications, sensitivity and selectivity of measurement which will undoubtedly further biomedical knowledge.This brief review will provide a general introduction of MRM^MS and highlight its novel application for targeted quantitative proteomic experimentations.

  • Current affairs in quantitative targeted Proteomics: multiple reaction monitoring–mass spectrometry
    Briefings in Functional Genomics and Proteomics, 2009
    Co-Authors: Anastasia K Yocum, Arul M. Chinnaiyan
    Abstract:

    Quantitative targeted Proteomics has recently taken front stage in the Proteomics community. Centered on multiple reaction monitoring ^ mass spectrometry (MRM^MS) methodologies, quantitative targeted Proteomics is being used in the verification of global Proteomics data, the discovery of lower abundance proteins, protein post-translational modifications, discrimination of select highly homologous protein isoforms and as the final step in biomarker discovery. An older methodology utilized with small molecule analysis, the Proteomics community is making great technological strides to develop MRM^MS as the next method to address previously challenging issues in global Proteomics experimentation, namely dynamic range, identification of post-translational modifications, sensitivity and selectivity of measurement which will undoubtedly further biomedical knowledge.This brief review will provide a general introduction of MRM^MS and highlight its novel application for targeted quantitative proteomic experimentations.

Manuel C. Peitsch - One of the best experts on this subject based on the ideXlab platform.

  • Proteomics for systems toxicology
    Computational and structural biotechnology journal, 2014
    Co-Authors: Bjoern Titz, Ashraf Elamin, Florian Martin, Sophie Dijon, Nikolai V Ivanov, Julia Hoeng, Thomas Schneider, Manuel C. Peitsch
    Abstract:

    Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of Proteomics for systems toxicology studies. With a focus on mass spectrometry-based Proteomics, we summarize the experimental methods for quantitative Proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how Proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, Proteomics will be an integral part of integrative systems toxicology approaches in the future.

Vinzenz Link - One of the best experts on this subject based on the ideXlab platform.

  • Proteomics of early zebrafish embryos
    BMC Developmental Biology, 2006
    Co-Authors: Vinzenz Link, Andrej Shevchenko, Carl Philipp Heisenberg
    Abstract:

    Background Zebrafish ( D. rerio ) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and Proteomics have yet to be developed. Results As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for Proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.

  • Proteomics of early zebrafish embryos
    BMC Developmental Biology, 2006
    Co-Authors: Vinzenz Link, Andrej Shevchenko, Carl Philipp Heisenberg
    Abstract:

    Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and Proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for Proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis. © 2006 Link et al; licensee BioMed Central Ltd.