The Experts below are selected from a list of 1437588 Experts worldwide ranked by ideXlab platform
Dt Jones - One of the best experts on this subject based on the ideXlab platform.
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Scalable web services for the PSIPRED Protein Analysis Workbench.
Nucleic Acids Res, 2013Co-Authors: Dt JonesAbstract:Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available Analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.
Nikolai Slavov - One of the best experts on this subject based on the ideXlab platform.
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Single-cell Protein Analysis by mass-spectrometry.
Current opinion in chemical biology, 2020Co-Authors: Nikolai SlavovAbstract:Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such Analysis feasible for nucleic acids, but single-cell Protein Analysis remains limited. Mass-spectrometry is the most powerful method for Protein Analysis, but its application to single cells faces three major challenges: Efficiently delivering Proteins/peptides to MS detectors, identifying their sequences, and scaling the Analysis to many thousands of single cells. These challenges have motivated corresponding solutions, including SCoPE-design multiplexing and clean, automated, and miniaturized sample preparation. Synergistically applied, these solutions enable quantifying thousands of Proteins across many single cells and establish a solid foundation for further advances. Building upon this foundation, the SCoPE concept will enable analyzing subcellular organelles and post-translational modifications while increases in multiplexing capabilities will increase the throughput and decrease cost.
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Single-cells Protein Analysis by mass-spectrometry
arXiv: Quantitative Methods, 2020Co-Authors: Nikolai SlavovAbstract:Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such Analysis feasible for nucleic acids, but single-cell Protein Analysis remains limited. Mass-spectrometry is the most powerful method for Protein Analysis, but its application to single cells faces three major challenges: Efficiently delivering Proteins/peptides to MS detectors, identifying their sequences, and scaling the Analysis to many thousands of single cells. These challenges have motivated corresponding solutions, including SCoPE-design multiplexing and clean, automated, and miniaturized sample preparation. Synergistically applied, these solutions enable quantifying thousands of Proteins across many single cells and establish a solid foundation for further advances. Building upon this foundation, the SCoPE concept will enable analyzing subcellular organelles and post-translational modifications while increases in multiplexing capabilities will increase the throughput and decrease cost.
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Single cell Protein Analysis for systems biology
Essays in Biochemistry, 2018Co-Authors: Ezra Levy, Nikolai SlavovAbstract:The cellular abundance of Proteins can vary even between isogenic single cells. This variability between single-cell Protein levels can have regulatory roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review examples connecting Protein levels and their dynamics in single cells to cellular functions. Such findings were made possible by the introduction of antibodies, and subsequently fluorescent Proteins, for tracking Protein levels in single cells. However, in heterogeneous cell populations, such as tumors or differentiating stem cells, cellular decisions are controlled by hundreds, even thousands of Proteins acting in concert. Characterizing such complex systems demands measurements of thousands of Proteins across thousands of single cells. This demand has inspired the development of new methods for single-cell Protein Analysis, and we discuss their trade-offs, with an emphasis on their specificity and coverage. We finish by highlighting the potential of emerging mass-spec methods to enable systems-level measurement of single-cell proteomes with unprecedented coverage and specificity. Combining such methods with methods for quantitating the transcriptomes and metabolomes of single cells will provide essential data for advancing quantitative systems biology.
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Single cell Protein Analysis for systems biology
2018Co-Authors: Ezra Levy, Nikolai SlavovAbstract:The cellular abundance of Proteins can vary even between isogenic single cells. This variability between single-cell Protein levels can have functional roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review such examples of connecting Protein levels and their dynamics in single cells to cellular functions. Such findings were made possible by the introduction of antibodies, and subsequently fluorescent Proteins, for tracking Protein levels in single cells. However, in heterogeneous cell populations, such as tumors or differentiating stem cells, cellular decisions are controlled by hundreds, even thousands of Proteins acting in concert. Characterizing such complex systems demands measurements of thousands of Proteins across thousands of single cells. This demand has inspired the development of new methods for single cell Protein Analysis, and we discuss their trade-offs, with emphasis on their specificity and coverage. We finish by highlighting the potential of emerging mass-spec methods to enable systems-level measurement of single-cell proteomes with unprecedented coverage and specificity. Combining such methods with methods for quantifying the trasncriptomes and metabolomes of single cells will provide essential data for advancing quantitative systems biology.
David T. Jones - One of the best experts on this subject based on the ideXlab platform.
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The PSIPRED Protein Analysis Workbench: 20 years on.
Nucleic acids research, 2019Co-Authors: Daniel W. A. Buchan, David T. JonesAbstract:The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing Protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website.
Daniel W. A. Buchan - One of the best experts on this subject based on the ideXlab platform.
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The PSIPRED Protein Analysis Workbench: 20 years on.
Nucleic acids research, 2019Co-Authors: Daniel W. A. Buchan, David T. JonesAbstract:The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing Protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website.
John R Yates - One of the best experts on this subject based on the ideXlab platform.
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Protein Analysis by shotgun bottom up proteomics
Chemical Reviews, 2013Co-Authors: Yaoyang Zhang, Bryan R Fonslow, Bing Shan, Moonchang Baek, John R YatesAbstract:According to Genome Sequencing Project statistics (http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html), as of Feb 16, 2012, complete gene sequences have become available for 2816 viruses, 1117 prokaryotes, and 36 eukaryotes.1–2 The availability of full genome sequences has greatly facilitated biological research in many fields, and has greatly contributed to the growth of proteomics. Proteins are important because they are the direct bio-functional molecules in the living organisms. The term “proteomics” was coined from merging “Protein” and “genomics” in the 1990s.3–4 As a post-genomic discipline, proteomics encompasses efforts to identify and quantify all the Proteins of a proteome, including expression, cellular localization, interactions, post-translational modifications (PTMs), and turnover as a function of time, space and cell type, thus making the full investigation of a proteome more challenging than sequencing a genome. There are possibly 100,000 Protein forms encoded by the approximate 20,235 genes of the human genome,5 and determining the explicit function of each form will be a challenge. The progress of proteomics has been driven by the development of new technologies for peptide/Protein separation, mass spectrometry Analysis, isotope labeling for quantification, and bioinformatics data Analysis. Mass spectrometry has emerged as a core tool for large-scale Protein Analysis. In the past decade, there has been a rapid advance in the resolution, mass accuracy, sensitivity and scan rate of mass spectrometers used to analyze Proteins. In addition, hybrid mass analyzers have been introduced recently (e.g. Linear Ion Trap-Orbitrap series6–7) which have significantly improved proteomic Analysis. “Bottom-up” Protein Analysis refers to the characterization of Proteins by Analysis of peptides released from the Protein through proteolysis. When bottom-up is performed on a mixture of Proteins it is called shotgun proteomics,8–10 a name coined by the Yates lab because of its analogy to shotgun genomic sequencing.11 Shotgun proteomics provides an indirect measurement of Proteins through peptides derived from proteolytic digestion of intact Proteins. In a typical shotgun proteomics experiment, the peptide mixture is fractionated and subjected to LC-MS/MS Analysis. Peptide identification is achieved by comparing the tandem mass spectra derived from peptide fragmentation with theoretical tandem mass spectra generated from in silico digestion of a Protein database. Protein inference is accomplished by assigning peptide sequences to Proteins. Because peptides can be either uniquely assigned to a single Protein or shared by more than one Protein, the identified Proteins may be further scored and grouped based on their peptides. In contrast, another strategy, termed ‘top-down’ proteomics, is used to characterize intact Proteins (Figure 1). The top-down approach has some potential advantages for PTM and Protein isoform determination and has achieved notable success. Intact Proteins have been measured up to 200 kDa,12 and a large scale study has identified more than 1,000 Proteins by multi-dimensional separations from complex samples.13 However, the top-down method has significant limitations compared with shotgun proteomics due to difficulties with Protein fractionation, Protein ionization and fragmentation in the gas phase. By relying on the Analysis of peptides, which are more easily fractionated, ionized and fragmented, shotgun proteomics can be more universally adopted for Protein Analysis. In fact, a hybrid of bottom-up and top-down methodologies and instrumentation has been introduced as middle-down proteomics.14 Essentially, middle-down proteomics analyzes larger peptide fragments than bottom-up proteomics, minimizing peptide redundancy between Proteins. Additionally the large peptide fragments yield similar advantages as top-down proteomics, such as gaining further insight into post-translational modifications, without the analytical challenges of analyzing intact Proteins. Shotgun proteomics has become a workhorse for the Analysis of Proteins and their modifications and will be increasingly combined with top-down methods in the future. Figure 1 Proteomic strategies: bottom-up vs. top-down vs. middle-down. The bottom-up approach analyzes proteolytic peptides. The top-down method measures the intact Proteins. The middle-down strategy analyzes larger peptides resulted from limited digestion or ... In the past decade shotgun proteomics has been widely used by biologists for many different research experiments, advancing biological discoveries. Some applications include, but are not limited to, proteome profiling, Protein quantification, Protein modification, and Protein-Protein interaction. There have been several reviews nicely summarizing mass spectrometry history,15 Protein quantification with mass spectrometry,16 its biological applications,5,17–26 and many recent advances in methodology.27–32 In this review, we try to provide a full and updated survey of shotgun proteomics, including the fundamental techniques and applications that laid the foundation along with those developed and greatly improved in the past several years.
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Protein Analysis by Shotgun/Bottom-up Proteomics
Chemical reviews, 2013Co-Authors: Yaoyang Zhang, Bryan R Fonslow, Bing Shan, Moonchang Baek, John R YatesAbstract:According to Genome Sequencing Project statistics (http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html), as of Feb 16, 2012, complete gene sequences have become available for 2816 viruses, 1117 prokaryotes, and 36 eukaryotes.1–2 The availability of full genome sequences has greatly facilitated biological research in many fields, and has greatly contributed to the growth of proteomics. Proteins are important because they are the direct bio-functional molecules in the living organisms. The term “proteomics” was coined from merging “Protein” and “genomics” in the 1990s.3–4 As a post-genomic discipline, proteomics encompasses efforts to identify and quantify all the Proteins of a proteome, including expression, cellular localization, interactions, post-translational modifications (PTMs), and turnover as a function of time, space and cell type, thus making the full investigation of a proteome more challenging than sequencing a genome. There are possibly 100,000 Protein forms encoded by the approximate 20,235 genes of the human genome,5 and determining the explicit function of each form will be a challenge. The progress of proteomics has been driven by the development of new technologies for peptide/Protein separation, mass spectrometry Analysis, isotope labeling for quantification, and bioinformatics data Analysis. Mass spectrometry has emerged as a core tool for large-scale Protein Analysis. In the past decade, there has been a rapid advance in the resolution, mass accuracy, sensitivity and scan rate of mass spectrometers used to analyze Proteins. In addition, hybrid mass analyzers have been introduced recently (e.g. Linear Ion Trap-Orbitrap series6–7) which have significantly improved proteomic Analysis. “Bottom-up” Protein Analysis refers to the characterization of Proteins by Analysis of peptides released from the Protein through proteolysis. When bottom-up is performed on a mixture of Proteins it is called shotgun proteomics,8–10 a name coined by the Yates lab because of its analogy to shotgun genomic sequencing.11 Shotgun proteomics provides an indirect measurement of Proteins through peptides derived from proteolytic digestion of intact Proteins. In a typical shotgun proteomics experiment, the peptide mixture is fractionated and subjected to LC-MS/MS Analysis. Peptide identification is achieved by comparing the tandem mass spectra derived from peptide fragmentation with theoretical tandem mass spectra generated from in silico digestion of a Protein database. Protein inference is accomplished by assigning peptide sequences to Proteins. Because peptides can be either uniquely assigned to a single Protein or shared by more than one Protein, the identified Proteins may be further scored and grouped based on their peptides. In contrast, another strategy, termed ‘top-down’ proteomics, is used to characterize intact Proteins (Figure 1). The top-down approach has some potential advantages for PTM and Protein isoform determination and has achieved notable success. Intact Proteins have been measured up to 200 kDa,12 and a large scale study has identified more than 1,000 Proteins by multi-dimensional separations from complex samples.13 However, the top-down method has significant limitations compared with shotgun proteomics due to difficulties with Protein fractionation, Protein ionization and fragmentation in the gas phase. By relying on the Analysis of peptides, which are more easily fractionated, ionized and fragmented, shotgun proteomics can be more universally adopted for Protein Analysis. In fact, a hybrid of bottom-up and top-down methodologies and instrumentation has been introduced as middle-down proteomics.14 Essentially, middle-down proteomics analyzes larger peptide fragments than bottom-up proteomics, minimizing peptide redundancy between Proteins. Additionally the large peptide fragments yield similar advantages as top-down proteomics, such as gaining further insight into post-translational modifications, without the analytical challenges of analyzing intact Proteins. Shotgun proteomics has become a workhorse for the Analysis of Proteins and their modifications and will be increasingly combined with top-down methods in the future. Figure 1 Proteomic strategies: bottom-up vs. top-down vs. middle-down. The bottom-up approach analyzes proteolytic peptides. The top-down method measures the intact Proteins. The middle-down strategy analyzes larger peptides resulted from limited digestion or ... In the past decade shotgun proteomics has been widely used by biologists for many different research experiments, advancing biological discoveries. Some applications include, but are not limited to, proteome profiling, Protein quantification, Protein modification, and Protein-Protein interaction. There have been several reviews nicely summarizing mass spectrometry history,15 Protein quantification with mass spectrometry,16 its biological applications,5,17–26 and many recent advances in methodology.27–32 In this review, we try to provide a full and updated survey of shotgun proteomics, including the fundamental techniques and applications that laid the foundation along with those developed and greatly improved in the past several years.
