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  1. Article ; Online: Shedding light on both ends: An update on analytical approaches for N- and C-terminomics.

    Koudelka, Tomas / Winkels, Konrad / Kaleja, Patrick / Tholey, Andreas

    Biochimica et biophysica acta. Molecular cell research

    2021  Volume 1869, Issue 1, Page(s) 119137

    Abstract: Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the ... ...

    Abstract Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
    MeSH term(s) Animals ; Humans ; Proteolysis ; Proteome/chemistry ; Proteome/genetics ; Proteome/metabolism ; Proteomics/methods ; RNA Splicing
    Chemical Substances Proteome
    Language English
    Publishing date 2021-10-06
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 60-7
    ISSN 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbamcr.2021.119137
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: The intracellular proteome of the gut bacterium Bacteroides thetaiotaomicron is widely unaffected by a switch from glucose to sucrose as main carbohydrate source.

    Genth, Jerome / Kaleja, Patrick / Treitz, Christian / Schäfer, Kathrin / Graspeuntner, Simon / Rupp, Jan / Tholey, Andreas

    Proteomics

    2022  Volume 22, Issue 22, Page(s) e2200189

    Abstract: Bacteroides thetaiotaomicron is a gram negative bacterium within the human gut microbiome that metabolizes a wide range of dietary and mucosal polysaccharides. Here, we analyze the proteome response of B. thetaiotaomicron cultivated on two different ... ...

    Abstract Bacteroides thetaiotaomicron is a gram negative bacterium within the human gut microbiome that metabolizes a wide range of dietary and mucosal polysaccharides. Here, we analyze the proteome response of B. thetaiotaomicron cultivated on two different carbon sources, glucose and sucrose. Two quantitative LC-MS based proteomics approaches, encompassing label free quantification and isobaric labeling by tandem mass tags were applied. The results obtained by both workflows were compared with respect to the number of identified and quantified proteins, peptides supporting identification and quantification, sequence coverage, and reproducibility. A total of 1719 and 1696 proteins, respectively, were quantified, covering 35 % of the predicted B. thetaiotaomicron proteome. The data show that B. thetaiotaomicron widely maintains its intracellular proteome upon change of the carbohydrates and that major changes are observed solely in the machinery necessary to make use of the carbon sources provided. With respect to the central role of carbohydrates on gut health these data contribute to the understanding of how different carbohydrates contribute to shape bacterial community in the gut microbiome. All proteomics raw data have been uploaded to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD033704.
    MeSH term(s) Humans ; Bacteroides thetaiotaomicron/metabolism ; Proteome/metabolism ; Sucrose ; Glucose/metabolism ; Reproducibility of Results ; Carbon/metabolism
    Chemical Substances Proteome ; Sucrose (57-50-1) ; Glucose (IY9XDZ35W2) ; Carbon (7440-44-0)
    Language English
    Publishing date 2022-08-11
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.202200189
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  3. Article: Combination of SCX Fractionation and Charge-Reversal Derivatization Facilitates the Identification of Nontryptic Peptides in C-Terminomics

    Kaleja, Patrick / Helbig, Andreas O / Tholey, Andreas

    Journal of proteome research. 2019 June 13, v. 18, no. 7

    2019  

    Abstract: The proteome wide, mass spectrometry based identification of protein C-termini is hampered by factors such as poor ionization efficiencies, low yielding labeling strategies, or the need for enrichment procedures. We present a bottom-up proteomics ... ...

    Abstract The proteome wide, mass spectrometry based identification of protein C-termini is hampered by factors such as poor ionization efficiencies, low yielding labeling strategies, or the need for enrichment procedures. We present a bottom-up proteomics workflow to identify protein C-termini utilizing a combination of strong cation exchange chromatography, on-solid phase charge-reversal derivatization and LC–MS/MS analysis. Charge-reversal improved both MS and MS/MS spectra quality of peptides carrying nonbasic C-terminal residues, allowing the identification of a high number of noncanonical C-termini not identified in nonderivatized samples. Further, we could show that C-terminal 18O labeling introduced during proteolytic processing of the samples is not suitable to distinguish internal from C-terminal peptides. The presented workflow enables the simultaneous identification of proteins by internal peptides and additionally provides data for the C- and N-terminome. Applying the developed workflow for the analysis of a Saccharomyces cerevisiae proteome allowed the identification of 734 protein C-termini in three independent biological replicates, and additional 789 candidate C-termini identified in two or one of three biological replicates, respectively. The developed analytical workflow allowed us to chart the nature of the yeast C-terminome in unprecedented depth and provides an alternative methodology to assess C-terminal proteolytic protein processing.
    Keywords Saccharomyces cerevisiae ; cation exchange chromatography ; derivatization ; fractionation ; ionization ; isotope labeling ; peptides ; proteins ; proteolysis ; proteome ; proteomics ; stable isotopes ; tandem mass spectrometry ; yeasts
    Language English
    Dates of publication 2019-0613
    Size p. 2954-2964.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.9b00264
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Combination of SCX Fractionation and Charge-Reversal Derivatization Facilitates the Identification of Nontryptic Peptides in C-Terminomics.

    Kaleja, Patrick / Helbig, Andreas O / Tholey, Andreas

    Journal of proteome research

    2019  Volume 18, Issue 7, Page(s) 2954–2964

    Abstract: The proteome wide, mass spectrometry based identification of protein C-termini is hampered by factors such as poor ionization efficiencies, low yielding labeling strategies, or the need for enrichment procedures. We present a bottom-up proteomics ... ...

    Abstract The proteome wide, mass spectrometry based identification of protein C-termini is hampered by factors such as poor ionization efficiencies, low yielding labeling strategies, or the need for enrichment procedures. We present a bottom-up proteomics workflow to identify protein C-termini utilizing a combination of strong cation exchange chromatography, on-solid phase charge-reversal derivatization and LC-MS/MS analysis. Charge-reversal improved both MS and MS/MS spectra quality of peptides carrying nonbasic C-terminal residues, allowing the identification of a high number of noncanonical C-termini not identified in nonderivatized samples. Further, we could show that C-terminal
    MeSH term(s) Carboxypeptidases ; Chromatography, Liquid ; Isotope Labeling ; Peptides/analysis ; Proteolysis ; Proteome/analysis ; Proteomics/methods ; Saccharomyces cerevisiae/chemistry ; Tandem Mass Spectrometry/methods
    Chemical Substances Peptides ; Proteome ; Carboxypeptidases (EC 3.4.-)
    Language English
    Publishing date 2019-06-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.9b00264
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  5. Article ; Online: Evaluation and improvement of protein extraction methods for analysis of skin proteome by noninvasive tape stripping.

    Kaleja, Patrick / Emmert, Hila / Gerstel, Ulrich / Weidinger, Stephan / Tholey, Andreas

    Journal of proteomics

    2020  Volume 217, Page(s) 103678

    Abstract: Analysis of the human skin proteome is key to understand molecular mechanisms maintaining health or leading to diseases of this important organ. For minimal invasive sampling of skin proteomes, the use of self-adhesive tape strips has been successfully ... ...

    Abstract Analysis of the human skin proteome is key to understand molecular mechanisms maintaining health or leading to diseases of this important organ. For minimal invasive sampling of skin proteomes, the use of self-adhesive tape strips has been successfully applied. However, the methods previously presented were evaluated on different types of skin samples (e.g. healthy, diseased) and used a variety of cell lysis/protein extraction methods, which renders a systematic comparison and thus the identification of the most efficient protocols difficult. Here, we present a study comparing five different approaches for cell lysis and protein extraction from single tape strip biopsies. Extraction using a detergent mix or 1% SDS proved to be most efficient. Further, we replaced protein precipitation by single-pot, solid-phase-enhanced sample preparation (SP3), which strongly enhanced the number of identified proteins. This fully LC-MS compatible methodology provides a fast and reproducible approach for minimal invasive sampling of human skin proteomes. BIOLOGICAL SIGNIFICANCE: Fast and reproducible minimal invasive sampling of human skin proteomes is a major prerequisite for clinical proteomics studies aiming to decipher molecular mechanisms involved in the homeostasis as well as in the development of diseases. By optimization of tape strip sampling, e.g. the introduction of SP3 sample cleanup prior to LC-MS analysis, the presented protocol leads to yet not reported numbers of protein identifications from healthy human skin. Further, due to its efficiency it allows analysis from minimal sample amounts, e.g. from single tape strips, while established protocols relied on pooling of multiple tape strips. This provides the opportunity to perform spatially (lateral) resolved proteome analyses from different depths of the skin by analysis of consecutive strips.
    MeSH term(s) Chromatography, Liquid ; Humans ; Mass Spectrometry ; Proteome ; Proteomics ; Skin
    Chemical Substances Proteome
    Language English
    Publishing date 2020-02-06
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2400835-7
    ISSN 1876-7737 ; 1874-3919
    ISSN (online) 1876-7737
    ISSN 1874-3919
    DOI 10.1016/j.jprot.2020.103678
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  6. Article ; Online: Alveolar-Capillary Barrier Protection In Vitro: Lung Cell Type-Specific Effects and Molecular Mechanisms Induced by 1α, 25-Dihydroxyvitamin D3.

    Xiong, Junyu / Kaleja, Patrick / Ückert, Larissa / Nezaratizadeh, Niloufar / Krantz, Stefanie / Krause, Martin Friedrich / Fitschen-Oestern, Stefanie / Seekamp, Andreas / Cassidy, Liam / Tholey, Andreas / Fuchs, Sabine

    International journal of molecular sciences

    2023  Volume 24, Issue 8

    Abstract: Low serum levels of 1α, 25-dihydroxyvitamin D3 (VD3) are associated with a higher mortality in trauma patients with sepsis or ARDS. However, the molecular mechanisms behind this observation are not yet understood. ... ...

    Abstract Low serum levels of 1α, 25-dihydroxyvitamin D3 (VD3) are associated with a higher mortality in trauma patients with sepsis or ARDS. However, the molecular mechanisms behind this observation are not yet understood. VD
    MeSH term(s) Humans ; Endothelial Cells ; Interleukin-6 ; Lipopolysaccharides/pharmacology ; Pulmonary Surfactant-Associated Proteins ; Alveolar Epithelial Cells ; Surface-Active Agents ; Doublecortin-Like Kinases
    Chemical Substances Interleukin-6 ; Lipopolysaccharides ; Pulmonary Surfactant-Associated Proteins ; Surface-Active Agents ; DCLK1 protein, human (EC 2.7.1.11) ; Doublecortin-Like Kinases (EC 2.7.1.11)
    Language English
    Publishing date 2023-04-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24087298
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