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  1. Article ; Online: Author Correction

    Ziye Hu / Hans J. C. T. Wessels / Theo van Alen / Mike S. M. Jetten / Boran Kartal

    Nature Communications, Vol 13, Iss 1, Pp 1-

    Nitric oxide-dependent anaerobic ammonium oxidation

    2022  Volume 2

    Keywords Science ; Q
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Glycoproteomics in Cerebrospinal Fluid Reveals Brain-Specific Glycosylation Changes

    Melissa Baerenfaenger / Merel A. Post / Pieter Langerhorst / Karin Huijben / Fokje Zijlstra / Joannes F. M. Jacobs / Marcel M. Verbeek / Hans J. C. T. Wessels / Dirk J. Lefeber

    International Journal of Molecular Sciences, Vol 24, Iss 1937, p

    2023  Volume 1937

    Abstract: The glycosylation of proteins plays an important role in neurological development and disease. Glycoproteomic studies on cerebrospinal fluid (CSF) are a valuable tool to gain insight into brain glycosylation and its changes in disease. However, it is ... ...

    Abstract The glycosylation of proteins plays an important role in neurological development and disease. Glycoproteomic studies on cerebrospinal fluid (CSF) are a valuable tool to gain insight into brain glycosylation and its changes in disease. However, it is important to consider that most proteins in CSFs originate from the blood and enter the CSF across the blood–CSF barrier, thus not reflecting the glycosylation status of the brain. Here, we apply a glycoproteomics method to human CSF, focusing on differences between brain- and blood-derived proteins. To facilitate the analysis of the glycan site occupancy, we refrain from glycopeptide enrichment. In healthy individuals, we describe the presence of heterogeneous brain-type N-glycans on prostaglandin H2-D isomerase alongside the dominant plasma-type N-glycans for proteins such as transferrin or haptoglobin, showing the tissue specificity of protein glycosylation. We apply our methodology to patients diagnosed with various genetic glycosylation disorders who have neurological impairments. In patients with severe glycosylation alterations, we observe that heavily truncated glycans and a complete loss of glycans are more pronounced in brain-derived proteins. We speculate that a similar effect can be observed in other neurological diseases where a focus on brain-derived proteins in the CSF could be similarly beneficial to gain insight into disease-related changes.
    Keywords cerebrospinal fluid ; glycoproteomics ; biomarkers ; neurodegenerative disease ; brain-type glycosylation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 610 ; 616
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform

    Gad Armony / Sven Brehmer / Tharan Srikumar / Lennard Pfennig / Fokje Zijlstra / Dennis Trede / Gary Kruppa / Dirk J. Lefeber / Alain J. van Gool / Hans J. C. T. Wessels

    International Journal of Molecular Sciences, Vol 24, Iss 7869, p

    2023  Volume 7869

    Abstract: Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high-throughput experiments. Most importantly, it enables results-dependent acquisition (RDA), where search results can be used ... ...

    Abstract Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high-throughput experiments. Most importantly, it enables results-dependent acquisition (RDA), where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide and glycan moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with the literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks the future development of RDA technology to transcend data acquisition.
    Keywords glycoproteomics ; real-time search ; results-dependent acquisition (RDA) ; PaSER ; GlycoPaSER ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 006
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Nitric oxide-dependent anaerobic ammonium oxidation

    Ziye Hu / Hans J. C. T. Wessels / Theo van Alen / Mike S. M. Jetten / Boran Kartal

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 7

    Abstract: Anammox bacteria couple nitrite reduction to ammonium oxidation, with nitric oxide (NO) and hydrazine as intermediates, and produce N2 and nitrate. Here, Hu et al. show that an anammox bacterium can grow in the absence of nitrite by coupling ammonium ... ...

    Abstract Anammox bacteria couple nitrite reduction to ammonium oxidation, with nitric oxide (NO) and hydrazine as intermediates, and produce N2 and nitrate. Here, Hu et al. show that an anammox bacterium can grow in the absence of nitrite by coupling ammonium oxidation to NO reduction, producing only N2.
    Keywords Science ; Q
    Language English
    Publishing date 2019-03-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Publisher Correction

    Ziye Hu / Hans J. C. T. Wessels / Theo van Alen / Mike S. M. Jetten / Boran Kartal

    Nature Communications, Vol 10, Iss 1, Pp 1-

    Nitric oxide-dependent anaerobic ammonium oxidation

    2019  Volume 1

    Abstract: The original HTML version of this Article had an incorrect Published online date of 20 March 2019; it should have been 18 March 2019. This has been corrected in the HTML version of the Article. The PDF version was correct from the time of publication. ...

    Abstract The original HTML version of this Article had an incorrect Published online date of 20 March 2019; it should have been 18 March 2019. This has been corrected in the HTML version of the Article. The PDF version was correct from the time of publication.
    Keywords Science ; Q
    Language English
    Publishing date 2019-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  6. Article ; Online: Nitric oxide-dependent anaerobic ammonium oxidation

    Ziye Hu / Hans J. C. T. Wessels / Theo van Alen / Mike S. M. Jetten / Boran Kartal

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 7

    Abstract: Anammox bacteria couple nitrite reduction to ammonium oxidation, with nitric oxide (NO) and hydrazine as intermediates, and produce N2 and nitrate. Here, Hu et al. show that an anammox bacterium can grow in the absence of nitrite by coupling ammonium ... ...

    Abstract Anammox bacteria couple nitrite reduction to ammonium oxidation, with nitric oxide (NO) and hydrazine as intermediates, and produce N2 and nitrate. Here, Hu et al. show that an anammox bacterium can grow in the absence of nitrite by coupling ammonium oxidation to NO reduction, producing only N2.
    Keywords Science ; Q
    Language English
    Publishing date 2019-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Publisher Correction

    Ziye Hu / Hans J. C. T. Wessels / Theo van Alen / Mike S. M. Jetten / Boran Kartal

    Nature Communications, Vol 10, Iss 1, Pp 1-

    Nitric oxide-dependent anaerobic ammonium oxidation

    2019  Volume 1

    Abstract: The original HTML version of this Article had an incorrect Published online date of 20 March 2019; it should have been 18 March 2019. This has been corrected in the HTML version of the Article. The PDF version was correct from the time of publication. ...

    Abstract The original HTML version of this Article had an incorrect Published online date of 20 March 2019; it should have been 18 March 2019. This has been corrected in the HTML version of the Article. The PDF version was correct from the time of publication.
    Keywords Science ; Q
    Language English
    Publishing date 2019-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  8. Article ; Online: Whole cell formaldehyde cross-linking simplifies purification of mitochondrial nucleoids and associated proteins involved in mitochondrial gene expression.

    Nina Rajala / Fenna Hensen / Hans J C T Wessels / Daniel Ives / Jolein Gloerich / Johannes N Spelbrink

    PLoS ONE, Vol 10, Iss 2, p e

    2015  Volume 0116726

    Abstract: Mitochondrial DNA/protein complexes (nucleoids) appear as discrete entities inside the mitochondrial network when observed by live-cell imaging and immunofluorescence. This somewhat trivial observation in recent years has spurred research towards ... ...

    Abstract Mitochondrial DNA/protein complexes (nucleoids) appear as discrete entities inside the mitochondrial network when observed by live-cell imaging and immunofluorescence. This somewhat trivial observation in recent years has spurred research towards isolation of these complexes and the identification of nucleoid-associated proteins. Here we show that whole cell formaldehyde crosslinking combined with affinity purification and tandem mass-spectrometry provides a simple and reproducible method to identify potential nucleoid associated proteins. The method avoids spurious mitochondrial isolation and subsequent multifarious nucleoid enrichment protocols and can be implemented to allow for label-free quantification (LFQ) by mass-spectrometry. Using expression of a Flag-tagged Twinkle helicase and appropriate controls we show that this method identifies many previously identified nucleoid associated proteins. Using LFQ to compare HEK293 cells with and without mtDNA, but both expressing Twinkle-FLAG, identifies many proteins that are reduced or absent in the absence of mtDNA. This set not only includes established mtDNA maintenance proteins but also many proteins involved in mitochondrial RNA metabolism and translation and therefore represents what can be considered an mtDNA gene expression proteome. Our data provides a very valuable resource for both basic mitochondrial researchers as well as clinical geneticists working to identify novel disease genes on the basis of exome sequence data.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Membrane-bound electron transport systems of an anammox bacterium: A complexome analysis

    de Almeida, Naomi M / Hans J.C.T. Wessels / Rob M. de Graaf / Christina Ferousi / Mike S.M. Jetten / Jan T. Keltjens / Boran Kartal

    Biochimica et biophysica acta. 2016 Oct., v. 1857, no. 10

    2016  

    Abstract: Electron transport, or oxidative phosphorylation, is one of the hallmarks of life. To this end, prokaryotes evolved a vast variety of protein complexes, only a small part of which have been discovered and studied. These protein complexes allow them to ... ...

    Abstract Electron transport, or oxidative phosphorylation, is one of the hallmarks of life. To this end, prokaryotes evolved a vast variety of protein complexes, only a small part of which have been discovered and studied. These protein complexes allow them to occupy virtually every ecological niche on Earth. Here, we applied the method of proteomics-based complexome profiling to get a better understanding of the electron transport systems of the anaerobic ammonium-oxidizing (anammox) bacteria, the N2-producing key players of the global nitrogen cycle. By this method nearly all respiratory complexes that were previously predicted from genome analysis to be involved in energy and cell carbon fixation were validated. More importantly, new and unexpected ones were discovered. We believe that complexome profiling in concert with (meta)genomics offers great opportunities to expand our knowledge on bacterial respiratory processes at a rapid and massive pace, in particular in new and thus far poorly investigated non-model and environmentally-relevant species.
    Keywords anaerobic ammonium oxidation ; bacteria ; carbon dioxide fixation ; electron transfer ; energy ; genomics ; niches ; nitrogen cycle ; oxidative phosphorylation ; prokaryotic cells ; sequence analysis
    Language English
    Dates of publication 2016-10
    Size p. 1694-1704.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282711-6
    ISSN 0005-2728 ; 0304-4173
    ISSN 0005-2728 ; 0304-4173
    DOI 10.1016/j.bbabio.2016.07.006
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: Towards a routine application of Top-Down approaches for label-free discovery workflows

    Schmit, Pierre-Olivier / Alain Van Gool / Audrey Gabelle / Christophe Hirtz / Detlev Suckau / Gary Kruppa / Hans J.C.T. Wessels / Jason Wood / Jerome Vialaret / Marshall Bern / Rainer Paape / Sylvain Lehmann

    Journal of proteomics. 2017,

    2017  

    Abstract: Thanks to proteomics investigations, our vision of the role of different protein isoforms in the pathophysiology of diseases has largely evolved. The idea that protein biomarkers like tau, amyloid peptides, ApoE, cystatin, or neurogranin are represented ... ...

    Abstract Thanks to proteomics investigations, our vision of the role of different protein isoforms in the pathophysiology of diseases has largely evolved. The idea that protein biomarkers like tau, amyloid peptides, ApoE, cystatin, or neurogranin are represented in body fluids as single species is obviously over-simplified, as most proteins are present in different isoforms and subjected to numerous processing and post-translational modifications. Measuring the intact mass of proteins by MS has the advantage to provide information on the presence and relative amount of the different proteoforms. Such Top-Down approaches typically require a high degree of sample pre-fractionation to allow the MS system to deliver optimal performance in terms of dynamic range, mass accuracy and resolution. In clinical studies, however, the requirements for pre-analytical robustness and sample size large enough for statistical power restrict the routine use of a high degree of sample pre-fractionation. In this study, we have investigated the capacities of current-generation Ultra-High Resolution Q-Tof systems to deal with high complexity intact protein samples and have evaluated the approach on a cohort of patients suffering from neurodegenerative disease. Statistical analysis has shown that several proteoforms can be used to distinguish Alzheimer disease patients from patients suffering from other neurodegenerative disease.Top-down approaches have an extremely high biological relevance, especially when it comes to biomarker discovery, but the necessary pre-fractionation constraints are not easily compatible with the robustness requirements and the size of clinical sample cohorts. We have demonstrated that intact protein profiling studies could be run on UHR-Q-ToF with limited pre-fractionation. The proteoforms that have been identified as candidate biomarkers in the-proof-of concept study are derived from proteins known to play a role in the pathophysiology process of Alzheimer disease.
    Keywords Alzheimer disease ; amyloid ; biomarkers ; body fluids ; clinical trials ; neurodegenerative diseases ; pathophysiology ; patients ; peptides ; post-translational modification ; protein composition ; protein isoforms ; proteomics ; statistical analysis
    Language English
    Size p. .
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 2400835-7
    ISSN 1876-7737 ; 1874-3919
    ISSN (online) 1876-7737
    ISSN 1874-3919
    DOI 10.1016/j.jprot.2017.08.003
    Database NAL-Catalogue (AGRICOLA)

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