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  • 1.
    Moruz, Luminita
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Staes, An
    Foster, Joseph M.
    Hatzou, Maria
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Timmerman, Evy
    Martens, Lennart
    Kall, Lukas
    Stockholm University, Faculty of Science, Department of Biosciences and Nutrition (together with KI).
    Chromatographic retention time prediction for posttranslationally modified peptides2012In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 12, no 8, p. 1151-1159Article in journal (Refereed)
    Abstract [en]

    Retention time prediction of peptides in liquid chromatography has proven to be a valuable tool for mass spectrometry-based proteomics, especially in designing more efficient procedures for state-of-the-art targeted workflows. Additionally, accurate retention time predictions can also be used to increase confidence in identifications in shotgun experiments. Despite these obvious benefits, the use of such methods has so far not been extended to (posttranslationally) modified peptides due to the absence of efficient predictors for such peptides. We here therefore describe a new retention time predictor for modified peptides, built on the foundations of our existing Elude algorithm. We evaluated our software by applying it on five types of commonly encountered modifications. Our results show that Elude now yields equally good prediction performances for modified and unmodified peptides, with correlation coefficients between predicted and observed retention times ranging from 0.93 to 0.98 for all the investigated datasets. Furthermore, we show that our predictor handles peptides carrying multiple modifications as well. This latest version of Elude is fully portable to new chromatographic conditions and can readily be applied to other types of posttranslational modifications. Elude is available under the permissive Apache2 open source License at or can be run via a web-interface at .

  • 2.
    Wincent, Emma
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Amini, Nahid
    Stockholm University, Faculty of Science, Department of Analytical Chemistry.
    Luecke, Sandra
    Institute of Environmental Medicine, Karolinska Institute.
    Glatt, Hansruedi
    Bergman, Jan
    Stockholm University, Faculty of Science, Department of Biosciences and Nutrition (together with KI).
    Crescenzi, Carlo
    Stockholm University, Faculty of Science, Department of Analytical Chemistry.
    Rannug, Agneta
    Institute of Environmental Medicine, Karolinska Institute.
    Rannug, Ulf
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    The Suggested Physiologic Aryl Hydrocarbon Receptor Activator and Cytochrome P4501 Substrate 6-Formylindolo[3,2-b]carbazole Is Present in Humans2009In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 284, no 5, p. 2690-2696Article in journal (Refereed)
    Abstract [en]

    Dioxins and other polycyclic aromatic compounds formed during the combustion of waste and fossil fuels represent a risk to human health, as well as to the well being of our environment. Compounds of this nature exert carcinogenic and endocrine disrupting effects in experimental animals by binding to the orphan aryl hydrocarbon receptor (AhR). Understanding the mechanism of action of these pollutants, as well as the physiological role(s) of the AhR, requires identification of the endogenous ligand(s) of this receptor. We reported earlier that activation of AhR by ultraviolet radiation is mediated by the chromophoric amino acid tryptophan (Trp), and we suggested that a new class of compounds derived from Trp, in particular 6-formylindolo[3,2-b]carbazole (FICZ), acts as natural high affinity ligands for this receptor. Here we describe seven new FICZ-derived indolo[3,2-b]carbazole-6-carboxylic acid metabolites and two sulfoconjugates, and we demonstrate the following. (i) FICZ is formed efficiently by photolysis of Trp upon exposure to visible light. (ii) FICZ is an exceptionally good substrate for cytochromes P450 (CYP) 1A1, 1A2, and 1B1, and its hydroxylated metabolites are remarkably good substrates for the sulfotransferases (SULTs) 1A1, 1A2, 1B1, and 1E1. Finally,(iii) sulfoconjugates of phenolic metabolites of FICZ are present in human urine. Our findings indicate that formylindolo[3,2-b]carbazols are the most potent naturally occurring activators ofthe AhR signaling pathway and may be the key substrates of the CYP1 and SULT1 families of enzymes. These conclusions contradict the wide spread view that xenobiotic compounds are the major AhR ligands and CYP1 substrates.

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