The Experts below are selected from a list of 25626 Experts worldwide ranked by ideXlab platform
Ruedi Aebersold - One of the best experts on this subject based on the ideXlab platform.
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The Proteome: Analysis and utility
Peptides for the New Millennium, 2020Co-Authors: Ruedi Aebersold, Beate Rist, Steven P. GygiAbstract:In this manuscript we have shown that in the emerging post-genomic era, technologies that can quantitatively, globally, and automatically measure gene expression at the protein level are essential for the comprehensive Analysis of biological processes and systems. We have furthermore documented the limitations of the current standard method for large-scale protein Analysis with respect to the Analysis of low abundance proteins and proposed a new approach to quantitative Proteome Analysis. We anticipate that the new ICAT strategy will provide broadly applicable means for the quantitative cataloging and comparison of expressed proteins in a variety of normal, developmental, and disease states.
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Quantitative Proteome Analysis: methods and applications.
Annals of the New York Academy of Sciences, 2006Co-Authors: Ruedi Aebersold, Beate Rist, Steven P. GygiAbstract:Abstract: With the completion of a rapidly increasing number of complete genomic sequences, much attention is currently focused on how the information contained in sequence databases might be interpreted in terms of the structure, function, and control of biological systems. Quantitative Proteome Analysis, the global Analysis of protein expression, has been proposed as a method to study steady-state gene expression and perturbation-induced changes. Here, we discuss the rationale for quantitative Proteome Analysis, highlight the limitations in the current standard technology, and introduce a new experimental approach to quantitative Proteome Analysis.
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Quantitative Proteome Analysis: Methods and Applications
The Journal of Infectious Diseases, 2003Co-Authors: Ruedi AebersoldAbstract:With the completion of the genomic sequencing of a number of species, including that of humans, much attention is currently focused on how the information in these sequences might be interpreted in terms of the structure, function, and control of biologic systems and processes. Quantitative Proteome Analysis, the global Analysis of protein expression, is increasingly being used as a method to study steady-state and perturbation-induced changes in protein profiles. The rationale for quantitative Proteome Analysis is described, along with a new technology for high throughput quantitative profiling of proteins in complex mixtures and its current status with selected applications.
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Development of a Multiplexed Microcapillary Liquid Chromatography System for High-Throughput Proteome Analysis
Analytical Chemistry, 2002Co-Authors: Timothy J. Griffin, Steven P. Gygi, And Beate Rist, Ruedi AebersoldAbstract:Comprehensive Proteome Analysis requires the identification (and quantification) of the proteins in samples consisting of thousands of proteins spanning a range of abundance of several orders of magnitude. The currency of Proteome Analysis by mass spectrometry is the peptides generated by protein proteolysis. The high sample complexity of such samples requires a large separation capacity, which is commonly achieved by fractionation of the mixture followed by further serial separations of each fraction. The sample throughput of Proteome Analysis is therefore limited by the need to sequentially process large numbers of samples. We have developed a novel fourplexed microcapillary liquid chromatography system for automated, high-throughput separation of complex peptide samples. The system supports the concurrent separation of four different samples by directing identically split solvent−gradient flows into four microcapillary C18 columns. The simple design of the system achieves multiplexed separation without...
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evaluation of two dimensional gel electrophoresis based Proteome Analysis technology
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Steven P. Gygi, Garry L Corthals, Yanni Zhang, Yvan Rochon, Ruedi AebersoldAbstract:he genomics revolution has changed the paradigm for the comprehensive Analysis of biological processes and systems. It is now hypothesized that biological processes and systems can be described based on the comparison of global, quantitative gene expression patterns from cells or tissues representing different states. To test this hypothesis, it is essential that methods for the precise measurement of gene expression be developed and applied. Several methods, including serial Analysis of gene expression, oligonucleotide and cDNA microarrays, and large-scale se- quencing of expressed sequence tags have been developed to globally and quantitatively measure gene expression at the mRNA level (1, 2). The discovery of posttranscriptional mech- anisms that control rate of synthesis and half-life of proteins (3) and the ensuing nonpredictive correlation between mRNA and protein levels expressed by a particular gene (4, 5) indicate that direct measurement of protein expression also is essential for the Analysis of biological processes and systems. Global Analysis of gene expression at the protein level is now also termed proteomics. The standard method for quantitative Proteome Analysis combines protein separation by high- resolution (isoelectric focusingySDS-PAGE) two-dimensional gel electrophoresis (2DE) with mass spectrometric (MS) or tandem MS (MSyMS) identification of selected protein spots. Important technical advances related to 2DE and protein MS have increased sensitivity, reproducibility, and throughput of Proteome Analysis while creating an integrated technology. By using 2DE with extended pH range and high-sensitivity protein identification by electrospray ionization and MSyMS, we have evaluated the potential of the 2DE-MS strategy to serve as the technology base for comprehensive and quantitative pro- teome Analysis.
Steven P. Gygi - One of the best experts on this subject based on the ideXlab platform.
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Strategies and Methods for Proteome Analysis
Proteome and Protein Analysis, 2020Co-Authors: David R. Goodlett, Steven P. Gygi, Daniel Figeys, A. Timperman, Julian D. Watts, G. Corthals, Reudi AebersoldAbstract:A Proteome has been defined as the protein complement expressed by the genome of an organism (Wilkins, et al. 1996). In multicellular organisms the Proteome is the protein complement expressed by a tissue or differentiated cell. The most common approach to Proteome Analysis involves separation of proteins by one- or two-dimensional gel electrophoresis (IEF/SDS-PAGE), enzymatic cleavage of selected proteins, tandem mass spectrometry (MS/MS) of peptides, and finally data interpretation by computer routines which also search databases (Fig. 1.1). In most cases the availability of protein and DNA sequences in public databases eliminates the need for complete protein sequence Analysis. Protein sequences are more rapidly identified by partial sequence Analysis using tandem mass spectrometry which allows rapid, complete gene identification. As reliable as protein identification by mass spectrometry has become there are still many obstacles that prevent Proteome Analysis from becoming as automated and routine as genome Analysis.
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The Proteome: Analysis and utility
Peptides for the New Millennium, 2020Co-Authors: Ruedi Aebersold, Beate Rist, Steven P. GygiAbstract:In this manuscript we have shown that in the emerging post-genomic era, technologies that can quantitatively, globally, and automatically measure gene expression at the protein level are essential for the comprehensive Analysis of biological processes and systems. We have furthermore documented the limitations of the current standard method for large-scale protein Analysis with respect to the Analysis of low abundance proteins and proposed a new approach to quantitative Proteome Analysis. We anticipate that the new ICAT strategy will provide broadly applicable means for the quantitative cataloging and comparison of expressed proteins in a variety of normal, developmental, and disease states.
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Quantitative Proteome Analysis: methods and applications.
Annals of the New York Academy of Sciences, 2006Co-Authors: Ruedi Aebersold, Beate Rist, Steven P. GygiAbstract:Abstract: With the completion of a rapidly increasing number of complete genomic sequences, much attention is currently focused on how the information contained in sequence databases might be interpreted in terms of the structure, function, and control of biological systems. Quantitative Proteome Analysis, the global Analysis of protein expression, has been proposed as a method to study steady-state gene expression and perturbation-induced changes. Here, we discuss the rationale for quantitative Proteome Analysis, highlight the limitations in the current standard technology, and introduce a new experimental approach to quantitative Proteome Analysis.
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Development of a Multiplexed Microcapillary Liquid Chromatography System for High-Throughput Proteome Analysis
Analytical Chemistry, 2002Co-Authors: Timothy J. Griffin, Steven P. Gygi, And Beate Rist, Ruedi AebersoldAbstract:Comprehensive Proteome Analysis requires the identification (and quantification) of the proteins in samples consisting of thousands of proteins spanning a range of abundance of several orders of magnitude. The currency of Proteome Analysis by mass spectrometry is the peptides generated by protein proteolysis. The high sample complexity of such samples requires a large separation capacity, which is commonly achieved by fractionation of the mixture followed by further serial separations of each fraction. The sample throughput of Proteome Analysis is therefore limited by the need to sequentially process large numbers of samples. We have developed a novel fourplexed microcapillary liquid chromatography system for automated, high-throughput separation of complex peptide samples. The system supports the concurrent separation of four different samples by directing identically split solvent−gradient flows into four microcapillary C18 columns. The simple design of the system achieves multiplexed separation without...
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evaluation of two dimensional gel electrophoresis based Proteome Analysis technology
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Steven P. Gygi, Garry L Corthals, Yanni Zhang, Yvan Rochon, Ruedi AebersoldAbstract:he genomics revolution has changed the paradigm for the comprehensive Analysis of biological processes and systems. It is now hypothesized that biological processes and systems can be described based on the comparison of global, quantitative gene expression patterns from cells or tissues representing different states. To test this hypothesis, it is essential that methods for the precise measurement of gene expression be developed and applied. Several methods, including serial Analysis of gene expression, oligonucleotide and cDNA microarrays, and large-scale se- quencing of expressed sequence tags have been developed to globally and quantitatively measure gene expression at the mRNA level (1, 2). The discovery of posttranscriptional mech- anisms that control rate of synthesis and half-life of proteins (3) and the ensuing nonpredictive correlation between mRNA and protein levels expressed by a particular gene (4, 5) indicate that direct measurement of protein expression also is essential for the Analysis of biological processes and systems. Global Analysis of gene expression at the protein level is now also termed proteomics. The standard method for quantitative Proteome Analysis combines protein separation by high- resolution (isoelectric focusingySDS-PAGE) two-dimensional gel electrophoresis (2DE) with mass spectrometric (MS) or tandem MS (MSyMS) identification of selected protein spots. Important technical advances related to 2DE and protein MS have increased sensitivity, reproducibility, and throughput of Proteome Analysis while creating an integrated technology. By using 2DE with extended pH range and high-sensitivity protein identification by electrospray ionization and MSyMS, we have evaluated the potential of the 2DE-MS strategy to serve as the technology base for comprehensive and quantitative pro- teome Analysis.
Mingliang Ye - One of the best experts on this subject based on the ideXlab platform.
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a fully automated system with online sample loading isotope dimethyl labeling and multidimensional separation for high throughput quantitative Proteome Analysis
Analytical Chemistry, 2010Co-Authors: Fangjun Wang, Mingliang Ye, Rui Chen, Chunxia Song, Yifeng Wu, Liming WangAbstract:Multidimensional separation is often applied for large-scale qualitative and quantitative Proteome Analysis. A fully automated system with integration of a reversed phase-strong cation exchange (RP-SCX) biphasic trap column into vented sample injection system was developed to realize online sample loading, isotope dimethyl labeling and online multidimensional separation of the Proteome samples. Comparing to conventionally manual isotope labeling and off-line fractionation technologies, this system is fully automated and time-saving, which is benefit for improving the quantification reproducibility and accuracy. As phosphate SCX monolith was integrated into the biphasic trap column, high sample injection flow rate and high-resolution stepwise fractionation could be easily achieved. ∼ 1000 proteins could be quantified in ∼30 h Proteome Analysis, and the Proteome coverage of quantitative Analysis can be further greatly improved by prolong the multidimensional separation time. This system was applied to analy...
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Integration of monolithic frit into the particulate capillary (IMFPC) column in shotgun Proteome Analysis.
Analytica chimica acta, 2009Co-Authors: Fangjun Wang, Mingliang Ye, Jing Dong, Ren'an WuAbstract:Capillary column plays an important role in nano-flow liquid chromatography coupled with tandem mass spectrometry for dealing with the high dynamic range and complexity of protein samples in shotgun Proteome Analysis. In this study, the integrated monolithic frit into the particulate capillary (IMFPC) column was prepared. By comparing the prepared IMFPC column with conventionally fritless capillary column, smaller size of packing materials could be easily packed into the capillary to achieve higher average peak capacity and Proteome coverage. As the monolithic emitter was integrated onto this type of column, the void volume between packing particles and electrospray emitter was eliminated and the electrospray quality was improved. The prepared IMFPC column was applied to Proteome Analysis of mouse liver extracts, and it was observed that the number of identified proteins and peptides increased 14.9 and 12.9% as well as the peak capacity increased 11.6% by using IMFPC column over conventionally fritless capillary column.
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Improvement of performance in label-free quantitative Proteome Analysis with monolithic electrospray ionization emitter.
IEEE Journal of Solid-state Circuits, 2008Co-Authors: Fangjun Wang, Mingliang Ye, Ruijun Tian, Xinning Jiang, Jing Dong, Lianghai Hu, Ren’an WuAbstract:: The postcolumn void volume, which is introduced by the connecting tubing and void ESI emitter in the nanoflow LC coupled with MS/MS system (microLC-MS/MS), is harmful for the Analysis of peptides in shotgun Proteome Analysis. A new type of porous C12 monolithic ESI emitter was prepared to eliminate the disruption and mixing effects occurring in the connecting tubing and void emitter. It was demonstrated that the porous hydrophobic monolith inside the emitter played a key role in retaining the good peak profile, and the average peak capacity of the whole separation system increased 12.8% in contrast to commercially available void emitter. Then, the porous C12 monolithic emitter was applied in label-free quantitative Proteome Analysis of two standard protein mixtures that were spiked into the tryptic digest of mouse livers extract. Compared to commercially available void ESI emitter, the number of proteins with reliable results in quantification increased greatly. And the relative quantities of the four standard proteins were all determined with the relative error < or = 6.8%. However, quantitative information of only three standard proteins could be obtained when void emitter was used.
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Method Development of Efficient Protein Extraction in Bone Tissue for Proteome Analysis
Journal of Proteome Research, 2007Co-Authors: Xiaogang Jiang, Mingliang Ye, Xinning Jiang, Shun FengAbstract:Exploring bone Proteome is an important and challenging task for understanding the mechanisms of physiological/pathological process of bone tissue. However, classical methods of protein extraction for soft tissues and cells are not applicable for bone tissue. Therefore, method development of efficient protein extraction is critical for bone Proteome Analysis. We found in this study that the protein extraction efficiency was improved significantly when bone tissue was demineralized by hydrochloric acid (HCl). A sequential protein extraction method was developed for large-scale Proteome Analysis of bone tissue. The bone tissue was first demineralized by HCl solution and then extracted using three different lysis buffers. As large amounts of acid soluble proteins also presented in the HCl solution, besides collection of proteins in the extracted lysis buffers, the proteins in the demineralized HCl solution were also collected for Proteome Analysis. Automated 2D-LC−MS/MS Analysis of the collected protein frac...
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Advances in chromatographic techniques and methods in shotgun Proteome Analysis
Trends in Analytical Chemistry, 2006Co-Authors: Mingliang Ye, Xiaogang Jiang, Shun Feng, Ruijun TianAbstract:Shotgun proteomics is a high-throughput approach to Proteome Analysis whereby the protein mixture is digested and the peptides generated are separated by capillary liquid chromatography and sequenced by tandem mass spectrometry (MS). Due to the huge number of peptide species, separation prior to MS Analysis plays an important role in shotgun proteomics. Overall sensitivity, dynamic range, throughput and general effectiveness of shotgun proteomic Analysis largely depend on how well the peptide mixture is separated. In recent years, new separation techniques have been applied successfully to Proteome Analysis and have dramatically improved protein identification. We briefly review the recent development of chromatographic techniques and methods in shotgun Proteome Analysis, including the following three aspects: one-dimensional separation; multidimensional separation; and, automated Proteome-Analysis systems.
Harald Mischak - One of the best experts on this subject based on the ideXlab platform.
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Proteome Analysis in hematology using capillary electrophoresis coupled on-line to mass spectrometry.
Mini-reviews in Medicinal Chemistry, 2009Co-Authors: Eva M. Weissinger, Harald Mischak, Julia Kontsendorn, A. Hahn, N. Hahn, Michael A. Morgan, Arnold GanserAbstract:Proteome Analysis, the key technology for biomarker discovery, continues to gain importance in clinical diagnosis and follow-up. In this review we describe Proteome Analysis in the context of allogeneic, hematopoietic stem cell transplantation concentrating on capillary electrophoresis coupled on-line to mass spectrometry.
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advances in urinary Proteome Analysis and biomarker discovery
Journal of The American Society of Nephrology, 2007Co-Authors: Danilo Fliser, Visith Thongboonkerd, Jan Novak, Angel Argiles, Vera Jankowski, Mark Girolami, Joachim Jankowski, Harald MischakAbstract:Noninvasive diagnosis of kidney diseases and assessment of the prognosis are still challenges in clinical nephrology. Definition of biomarkers on the basis of Proteome Analysis, especially of the urine, has advanced recently and may provide new tools to solve those challenges. This article highlights the most promising technological approaches toward deciphering the human Proteome and applications of the knowledge in clinical nephrology, with emphasis on the urinary Proteome. The data in the current literature indicate that although a thorough investigation of the entire urinary Proteome is still a distant goal, clinical applications are already available. Progress in the Analysis of human Proteome in health and disease will depend more on the standardization of data and availability of suitable bioinformatics and software solutions than on new technological advances. It is predicted that proteomics will play an important role in clinical nephrology in the very near future and that this progress will require interactive dialogue and collaboration between clinicians and analytical specialists.
Beate Rist - One of the best experts on this subject based on the ideXlab platform.
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The Proteome: Analysis and utility
Peptides for the New Millennium, 2020Co-Authors: Ruedi Aebersold, Beate Rist, Steven P. GygiAbstract:In this manuscript we have shown that in the emerging post-genomic era, technologies that can quantitatively, globally, and automatically measure gene expression at the protein level are essential for the comprehensive Analysis of biological processes and systems. We have furthermore documented the limitations of the current standard method for large-scale protein Analysis with respect to the Analysis of low abundance proteins and proposed a new approach to quantitative Proteome Analysis. We anticipate that the new ICAT strategy will provide broadly applicable means for the quantitative cataloging and comparison of expressed proteins in a variety of normal, developmental, and disease states.
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Quantitative Proteome Analysis: methods and applications.
Annals of the New York Academy of Sciences, 2006Co-Authors: Ruedi Aebersold, Beate Rist, Steven P. GygiAbstract:Abstract: With the completion of a rapidly increasing number of complete genomic sequences, much attention is currently focused on how the information contained in sequence databases might be interpreted in terms of the structure, function, and control of biological systems. Quantitative Proteome Analysis, the global Analysis of protein expression, has been proposed as a method to study steady-state gene expression and perturbation-induced changes. Here, we discuss the rationale for quantitative Proteome Analysis, highlight the limitations in the current standard technology, and introduce a new experimental approach to quantitative Proteome Analysis.
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Measuring gene expression by quantitative Proteome Analysis
Current Opinion in Biotechnology, 2000Co-Authors: Stephen P. Gygi, Beate Rist, Ruedi AebersoldAbstract:Proteome Analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis for protein separation, visualization, and quantification and mass spectrometry for protein identification. Over the past year, exceptional progress has been made towards developing a new technology base for the precise quantification and identification of proteins in complex mixtures, that is, quantitative proteomics.
