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matlab-based program dogex  (MathWorks Inc)


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    MathWorks Inc matlab-based program dogex
    LC-MS based strategies for elucidating substrates of human enzymes (Guengerich et al., 2010, 2011). One approach (in vivo) involves either expressing the human protein or deleting its apparent ortholog in a transgenic animal model. LC-MS metabolomic analysis can be done with body fluids from the animals or by removing tissues and using the in vitro incubations. Alternatively, a total in vitro approach can be used in which the protein is heterologously expressed and used with extracts of human tissue (with or without isotopically labeled cofactor). Data from the LC-MS analysis are used in comparisons (e.g., wild-type versus transgenic mice, in vitro enzyme incubations versus controls) made with one or more programs (e.g., PCA, <t>DoGEX,</t> MZmine, XCMS). The goal is to identify differences. In some cases, the mass spectrum (i.e., molecular formula) may be sufficient to identify possible matches of candidates, and the authentic materials may be available for comparison. However, if unknown compounds are involved, then not only the high-resolution MS spectra but also UV visible and NMR spectra may be needed. Ultimately, more experiments will be needed to assess the biological relevance of any findings.
    Matlab Based Program Dogex, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/matlab-based program dogex/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    matlab-based program dogex - by Bioz Stars, 2026-04
    90/100 stars

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    1) Product Images from "Orphans in the Human Cytochrome P450 Superfamily: Approaches to Discovering Functions and Relevance in Pharmacology"

    Article Title: Orphans in the Human Cytochrome P450 Superfamily: Approaches to Discovering Functions and Relevance in Pharmacology

    Journal: Pharmacological Reviews

    doi: 10.1124/pr.110.003525

    LC-MS based strategies for elucidating substrates of human enzymes (Guengerich et al., 2010, 2011). One approach (in vivo) involves either expressing the human protein or deleting its apparent ortholog in a transgenic animal model. LC-MS metabolomic analysis can be done with body fluids from the animals or by removing tissues and using the in vitro incubations. Alternatively, a total in vitro approach can be used in which the protein is heterologously expressed and used with extracts of human tissue (with or without isotopically labeled cofactor). Data from the LC-MS analysis are used in comparisons (e.g., wild-type versus transgenic mice, in vitro enzyme incubations versus controls) made with one or more programs (e.g., PCA, DoGEX, MZmine, XCMS). The goal is to identify differences. In some cases, the mass spectrum (i.e., molecular formula) may be sufficient to identify possible matches of candidates, and the authentic materials may be available for comparison. However, if unknown compounds are involved, then not only the high-resolution MS spectra but also UV visible and NMR spectra may be needed. Ultimately, more experiments will be needed to assess the biological relevance of any findings.
    Figure Legend Snippet: LC-MS based strategies for elucidating substrates of human enzymes (Guengerich et al., 2010, 2011). One approach (in vivo) involves either expressing the human protein or deleting its apparent ortholog in a transgenic animal model. LC-MS metabolomic analysis can be done with body fluids from the animals or by removing tissues and using the in vitro incubations. Alternatively, a total in vitro approach can be used in which the protein is heterologously expressed and used with extracts of human tissue (with or without isotopically labeled cofactor). Data from the LC-MS analysis are used in comparisons (e.g., wild-type versus transgenic mice, in vitro enzyme incubations versus controls) made with one or more programs (e.g., PCA, DoGEX, MZmine, XCMS). The goal is to identify differences. In some cases, the mass spectrum (i.e., molecular formula) may be sufficient to identify possible matches of candidates, and the authentic materials may be available for comparison. However, if unknown compounds are involved, then not only the high-resolution MS spectra but also UV visible and NMR spectra may be needed. Ultimately, more experiments will be needed to assess the biological relevance of any findings.

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, In Vivo, Expressing, Transgenic Assay, Animal Model, In Vitro, Labeling, Comparison

    Use of the program DoGEX in screening for candidate substrates. Raw LC-MS data from an incubation of a P450, NADPH-P450 reductase, NADPH, a tissue extract, and a 1:1 mixture of 6O2/18O2 is shown in A. B shows the analysis of mass-to-charge ratio versus retention time, with a green positive spot on a yellow background for a ratio of ∼1.0 and Δ atomic mass units = 2.0, with the positive zone expanded in part C. The data from C are produced as a plot of relative ion intensity versus mass-to-charge ratio in part D. In this case the P450 uses P450 7A1, and the product was (the succinate ester of) 7α-hydroxycholesterol (Guengerich et al., 2010, 2011; Tang et al., 2010).
    Figure Legend Snippet: Use of the program DoGEX in screening for candidate substrates. Raw LC-MS data from an incubation of a P450, NADPH-P450 reductase, NADPH, a tissue extract, and a 1:1 mixture of 6O2/18O2 is shown in A. B shows the analysis of mass-to-charge ratio versus retention time, with a green positive spot on a yellow background for a ratio of ∼1.0 and Δ atomic mass units = 2.0, with the positive zone expanded in part C. The data from C are produced as a plot of relative ion intensity versus mass-to-charge ratio in part D. In this case the P450 uses P450 7A1, and the product was (the succinate ester of) 7α-hydroxycholesterol (Guengerich et al., 2010, 2011; Tang et al., 2010).

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Incubation, Produced



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    matlab-based program dogex  (MathWorks Inc)
    90
    MathWorks Inc matlab-based program dogex
    LC-MS based strategies for elucidating substrates of human enzymes (Guengerich et al., 2010, 2011). One approach (in vivo) involves either expressing the human protein or deleting its apparent ortholog in a transgenic animal model. LC-MS metabolomic analysis can be done with body fluids from the animals or by removing tissues and using the in vitro incubations. Alternatively, a total in vitro approach can be used in which the protein is heterologously expressed and used with extracts of human tissue (with or without isotopically labeled cofactor). Data from the LC-MS analysis are used in comparisons (e.g., wild-type versus transgenic mice, in vitro enzyme incubations versus controls) made with one or more programs (e.g., PCA, <t>DoGEX,</t> MZmine, XCMS). The goal is to identify differences. In some cases, the mass spectrum (i.e., molecular formula) may be sufficient to identify possible matches of candidates, and the authentic materials may be available for comparison. However, if unknown compounds are involved, then not only the high-resolution MS spectra but also UV visible and NMR spectra may be needed. Ultimately, more experiments will be needed to assess the biological relevance of any findings.
    Matlab Based Program Dogex, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/matlab-based program dogex/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    matlab-based program dogex - by Bioz Stars, 2026-04
    90/100 stars
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    matlab-based computer program dogex  (MathWorks Inc)
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    MathWorks Inc matlab-based computer program dogex
    Total ion chromatogram of the incubation of human P450 7A1 and liver extract (A), data analysis for identifying the oxidation product 7α-hydroxycholesterol using the program <t>DoGEX</t> (B), expansion of part B (C), and three-dimensional profile of part C (D).
    Matlab Based Computer Program Dogex, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/matlab-based computer program dogex/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    matlab-based computer program dogex - by Bioz Stars, 2026-04
    90/100 stars
    		  Buy from Supplier
    dogex program  (MathWorks Inc)
    90
    MathWorks Inc dogex program
    Total ion chromatogram of the incubation of human P450 7A1 and liver extract (A), data analysis for identifying the oxidation product 7α-hydroxycholesterol using the program <t>DoGEX</t> (B), expansion of part B (C), and three-dimensional profile of part C (D).
    Dogex Program, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dogex program/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    dogex program - by Bioz Stars, 2026-04
    90/100 stars
    		  Buy from Supplier

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    LC-MS based strategies for elucidating substrates of human enzymes (Guengerich et al., 2010, 2011). One approach (in vivo) involves either expressing the human protein or deleting its apparent ortholog in a transgenic animal model. LC-MS metabolomic analysis can be done with body fluids from the animals or by removing tissues and using the in vitro incubations. Alternatively, a total in vitro approach can be used in which the protein is heterologously expressed and used with extracts of human tissue (with or without isotopically labeled cofactor). Data from the LC-MS analysis are used in comparisons (e.g., wild-type versus transgenic mice, in vitro enzyme incubations versus controls) made with one or more programs (e.g., PCA, DoGEX, MZmine, XCMS). The goal is to identify differences. In some cases, the mass spectrum (i.e., molecular formula) may be sufficient to identify possible matches of candidates, and the authentic materials may be available for comparison. However, if unknown compounds are involved, then not only the high-resolution MS spectra but also UV visible and NMR spectra may be needed. Ultimately, more experiments will be needed to assess the biological relevance of any findings.

    Journal: Pharmacological Reviews

    Article Title: Orphans in the Human Cytochrome P450 Superfamily: Approaches to Discovering Functions and Relevance in Pharmacology

    doi: 10.1124/pr.110.003525

    Figure Lengend Snippet: LC-MS based strategies for elucidating substrates of human enzymes (Guengerich et al., 2010, 2011). One approach (in vivo) involves either expressing the human protein or deleting its apparent ortholog in a transgenic animal model. LC-MS metabolomic analysis can be done with body fluids from the animals or by removing tissues and using the in vitro incubations. Alternatively, a total in vitro approach can be used in which the protein is heterologously expressed and used with extracts of human tissue (with or without isotopically labeled cofactor). Data from the LC-MS analysis are used in comparisons (e.g., wild-type versus transgenic mice, in vitro enzyme incubations versus controls) made with one or more programs (e.g., PCA, DoGEX, MZmine, XCMS). The goal is to identify differences. In some cases, the mass spectrum (i.e., molecular formula) may be sufficient to identify possible matches of candidates, and the authentic materials may be available for comparison. However, if unknown compounds are involved, then not only the high-resolution MS spectra but also UV visible and NMR spectra may be needed. Ultimately, more experiments will be needed to assess the biological relevance of any findings.

    Article Snippet: A MATLAB-based program (DoGEX) was developed to search for such doublets [alternatively, the program can be set to seek other isotopic products with other ratios (e.g., chlorine)] ( ) ( Sanchez-Ponce and Guengerich, 2007 ).

    Techniques: Liquid Chromatography with Mass Spectroscopy, In Vivo, Expressing, Transgenic Assay, Animal Model, In Vitro, Labeling, Comparison

    Use of the program DoGEX in screening for candidate substrates. Raw LC-MS data from an incubation of a P450, NADPH-P450 reductase, NADPH, a tissue extract, and a 1:1 mixture of 6O2/18O2 is shown in A. B shows the analysis of mass-to-charge ratio versus retention time, with a green positive spot on a yellow background for a ratio of ∼1.0 and Δ atomic mass units = 2.0, with the positive zone expanded in part C. The data from C are produced as a plot of relative ion intensity versus mass-to-charge ratio in part D. In this case the P450 uses P450 7A1, and the product was (the succinate ester of) 7α-hydroxycholesterol (Guengerich et al., 2010, 2011; Tang et al., 2010).

    Journal: Pharmacological Reviews

    Article Title: Orphans in the Human Cytochrome P450 Superfamily: Approaches to Discovering Functions and Relevance in Pharmacology

    doi: 10.1124/pr.110.003525

    Figure Lengend Snippet: Use of the program DoGEX in screening for candidate substrates. Raw LC-MS data from an incubation of a P450, NADPH-P450 reductase, NADPH, a tissue extract, and a 1:1 mixture of 6O2/18O2 is shown in A. B shows the analysis of mass-to-charge ratio versus retention time, with a green positive spot on a yellow background for a ratio of ∼1.0 and Δ atomic mass units = 2.0, with the positive zone expanded in part C. The data from C are produced as a plot of relative ion intensity versus mass-to-charge ratio in part D. In this case the P450 uses P450 7A1, and the product was (the succinate ester of) 7α-hydroxycholesterol (Guengerich et al., 2010, 2011; Tang et al., 2010).

    Article Snippet: A MATLAB-based program (DoGEX) was developed to search for such doublets [alternatively, the program can be set to seek other isotopic products with other ratios (e.g., chlorine)] ( ) ( Sanchez-Ponce and Guengerich, 2007 ).

    Techniques: Liquid Chromatography with Mass Spectroscopy, Incubation, Produced

    Total ion chromatogram of the incubation of human P450 7A1 and liver extract (A), data analysis for identifying the oxidation product 7α-hydroxycholesterol using the program DoGEX (B), expansion of part B (C), and three-dimensional profile of part C (D).

    Journal: Analytical Chemistry

    Article Title: Elucidation of functions of human cytochrome P450 enzymes: Identification of endogenous substrates in tissue extracts using metabolomic and isotopic labeling approaches

    doi: 10.1021/ac900021a

    Figure Lengend Snippet: Total ion chromatogram of the incubation of human P450 7A1 and liver extract (A), data analysis for identifying the oxidation product 7α-hydroxycholesterol using the program DoGEX (B), expansion of part B (C), and three-dimensional profile of part C (D).

    Article Snippet: The analysis of the resulting LC-MS data was automatically done with the Matlab-based computer program DoGEX.

    Techniques: Incubation

    DoGEX results of substrate searches with liver extract and human P450 1A2.

    Journal: Analytical Chemistry

    Article Title: Elucidation of functions of human cytochrome P450 enzymes: Identification of endogenous substrates in tissue extracts using metabolomic and isotopic labeling approaches

    doi: 10.1021/ac900021a

    Figure Lengend Snippet: DoGEX results of substrate searches with liver extract and human P450 1A2.

    Article Snippet: The analysis of the resulting LC-MS data was automatically done with the Matlab-based computer program DoGEX.

    Techniques: