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Journal ArticleDOI

Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals.

01 Jan 1975-Human Genetics (Humangenetik)-Vol. 26, Iss: 3, pp 231-243
TL;DR: The fact that a high number of protein spots can be evaluated by a single and comparatively simple experiment suggests that this method may be useful as an assay system for induced point mutations.
Abstract: The protein-mapping method which combines isoelectric focusing in acrylamide gel and gel electrophoresis was previously used mainly for the separation of plant proteins and human serum proteins. We investigated with this technique soluble proteins of mouse tissues (whole embryos, the liver of fetal and adult mice, kidneys) and the proteins of mouse serum. The technique was tested under a number of different conditions to find those best for our purpose; they may represent some general improvements in the method. The protein patterns show high resolution and excellent reproducibility. About 275 spots were found for fetal liver, about 230 for whole embryos (day 14 p.c.) and about 100 for serum. The fact that a high number of protein spots can be evaluated by a single and comparatively simple experiment suggests that this method may be useful as an assay system for induced point mutations. The protein patterns demonstrated are compared and discgs of dominant lethal examinations after acute and subacute application of these three substances.
Citations
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Journal ArticleDOI
TL;DR: This work speculates on the reasons behind this large discrepancy between the expectations arising from proteomics and the realities of clinical diagnostics and suggests approaches by which protein-disease associations may be more effectively translated into diagnostic tools in the future.

4,062 citations

Journal ArticleDOI
TL;DR: The current 2‐DE/MS workflow is described including the following topics: sample preparation, protein solubilization, and prefractionation; protein separation by 1‐DE with IPGs; protein detection and quantitation; computer assisted analysis of 2-DE patterns; protein identification and characterization by MS; two‐dimensional protein databases.
Abstract: Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry (MS) is currently the workhorse for proteomics. In spite of promising alternative or complementary technologies (e.g. multidimensional protein identification technology, stable isotope labelling, protein or antibody arrays) that have emerged recently, 2-DE is currently the only technique that can be routinely applied for parallel quantitative expression profiling of large sets of complex protein mixtures such as whole cell lysates. 2-DE enables the separation of complex mixtures of proteins according to isoelectric point (pI), molecular mass (Mr), solubility, and relative abundance. Furthermore, it delivers a map of intact proteins, which reflects changes in protein expression level, isoforms or post-translational modifications. This is in contrast to liquid chromatography-tandem mass spectrometry based methods, which perform analysis on peptides, where Mr and pI information is lost, and where stable isotope labelling is required for quantitative analysis. Today's 2-DE technology with IPGs (Gorg et al., Electrophoresis 2000, 21, 1037-1053), has overcome the former limitations of carrier ampholyte based 2-DE (O'Farrell, J. Biol. Chem. 1975, 250, 4007-4021) with respect to reproducibility, handling, resolution, and separation of very acidic and/or basic proteins. The development of IPGs between pH 2.5-12 has enabled the analysis of very alkaline proteins and the construction of the corresponding databases. Narrow-overlapping IPGs provide increased resolution (delta pI = 0.001) and, in combination with prefractionation methods, the detection of low abundance proteins. Depending on the gel size and pH gradient used, 2-DE can resolve more than 5000 proteins simultaneously (approximately 2000 proteins routinely), and detect and quantify < 1 ng of protein per spot. In this article we describe the current 2-DE/MS workflow including the following topics: sample preparation, protein solubilization, and prefractionation; protein separation by 2-DE with IPGs; protein detection and quantitation; computer assisted analysis of 2-DE patterns; protein identification and characterization by MS; two-dimensional protein databases.

1,840 citations

Journal ArticleDOI
TL;DR: This work merges many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories.
Abstract: Attempts to correlate protein abundance with mRNA expression levels have had variable success. We review the results of these comparisons, focusing on yeast. In the process, we survey experimental techniques for determining protein abundance, principally two-dimensional gel electrophoresis and mass-spectrometry. We also merge many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories.

1,812 citations

Journal ArticleDOI
TL;DR: This work states that any human protein can now be identified directly from genome databases on the basis of minimal data derived by mass spectrometry, and that increased automation of sample handling, analysis, and the interpretation of results will generate an avalanche of qualitative and quantitative proteomic data.
Abstract: ▪ Abstract A decade after the discovery of electrospray and matrix-assisted laser desorption ionization (MALDI), methods that finally allowed gentle ionization of large biomolecules, mass spectrometry has become a powerful tool in protein analysis and the key technology in the emerging field of proteomics. The success of mass spectrometry is driven both by innovative instrumentation designs, especially those operating on the time-of-flight or ion-trapping principles, and by large-scale biochemical strategies, which use mass spectrometry to detect the isolated proteins. Any human protein can now be identified directly from genome databases on the basis of minimal data derived by mass spectrometry. As has already happened in genomics, increased automation of sample handling, analysis, and the interpretation of results will generate an avalanche of qualitative and quantitative proteomic data. Protein-protein interactions can be analyzed directly by precipitation of a tagged bait followed by mass spectrometri...

1,205 citations

Journal ArticleDOI
TL;DR: 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.
Abstract: 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.

1,184 citations

References
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Journal ArticleDOI
25 Nov 1949-Science
TL;DR: The erythrocytes of certain individuals possess the capacity to undergo reversible changes in shape in response to changes in the partial pressure of oxygen, and these cells change their forms from the normal biconcave disk to crescent, holly wreath, and other forms.
Abstract: The erythrocytes of certain individuals possess the capacity to undergo reversible changes in shape in response to changes in the partial pressure of oxygen. When the oxygen pressure is lowered, these cells change their forms from the normal biconcave disk to crescent, holly wreath, and other forms. This process is known as sickling. About 8 percent of American Negroes possess this characteristic; usually they exhibit no pathological consequences ascribable to it. These people are said to have sicklemia, or sickle cell trait. However, about 1 in 40 (4) of these individuals whose cells are capable of sickling suffer from a severe chronic anemia resulting from excessive destruction of their erythrocytes; the term sickle cell anemia is applied to their condition.

1,835 citations

Journal ArticleDOI
17 Aug 1957-Nature
TL;DR: Gene Mutations in Human Haemoglobin: the Chemical Difference Between Normal and Sickle Cell Haemocytes is illustrated.
Abstract: Gene Mutations in Human Haemoglobin: the Chemical Difference Between Normal and Sickle Cell Haemoglobin

826 citations

Book
01 Jan 1978
TL;DR: The authors may not be able to make you love reading, but disc electrophoresis and related techniques of polyacrylamide gel electrophoreis will lead you to love reading starting from now.
Abstract: We may not be able to make you love reading, but disc electrophoresis and related techniques of polyacrylamide gel electrophoresis will lead you to love reading starting from now. Book is the window to open the new world. The world that you want is in the better stage and level. World will always guide you to even the prestige stage of the life. You know, this is some of how reading will give you the kindness. In this case, more books you read more knowledge you know, but it can mean also the bore is full.

546 citations

Book
01 Jan 1970

345 citations

Book ChapterDOI
TL;DR: One would expect that mutation, and especially “spontaneous” mutation, i.e., that occurring naturally and without any detectable external reasons, would attract the research activity of many biologists, especially geneticists, but this is not the case.
Abstract: Mutation is one of the basic phenomena of life. Without mutation, the gradual development of life from inorganic material would have been impossible, and the evolution of living beings from the first groups of molecules in which a primitive, information-carrying unit cooperated with an energy gaining device59 up to the present diversity of highly refined living organisms could not have occurred. Therefore, one would expect that mutation, and especially “spontaneous” mutation, i.e., that occurring naturally and without any detectable external reasons, would attract the research activity of many biologists, especially geneticists. Surprisingly, however, this is not the case. In most experimental studies—for example, on microorganisms, Drosophila or the mouse—research on spontaneous mutation is being carried out more or less as a sideline of other work, and the results are widely scattered.

340 citations


"Protein mapping by combined isoelec..." refers background in this paper

  • ...Generally, ':the material, to date, is much too small to permit any general statements" (Vogel, 1970)....

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  • ...However, according to considerations of other authors (Vogel, 1970; Sutton, 1972), the mutation rate for a protein (hemoglobin) lies between 10 -5 10 6 per generation, which is the range of mutation rate for visible phenotypes....

    [...]