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  1. Article ; Online: Quantification of Proteins in Blood by Absorptive Microtiter Plate-Based Affinity Purification Coupled to Liquid Chromatography-Mass Spectrometry.

    Klont, Frank / Olaleye, Oladapo / Bischoff, Rainer

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2628, Page(s) 221–233

    Abstract: Liquid chromatography (LC) coupled to mass spectrometry (MS) is increasingly used for quantification of proteins in blood. This development is prompted by ongoing improvements in detection sensitivities of LC-MS instruments and corresponding sample ... ...

    Abstract Liquid chromatography (LC) coupled to mass spectrometry (MS) is increasingly used for quantification of proteins in blood. This development is prompted by ongoing improvements in detection sensitivities of LC-MS instruments and corresponding sample preparation workflows. The combination of immunoaffinity enrichment and targeted LC-MS detection is a notable analytical platform in this regard as it allows for the quantification of low abundance proteins in biological matrices like plasma and serum. Here, we describe such hybrid methods which are based on the enrichment of proteins with antibodies or affimers coupled to adsorptive microtiter plates, the proteolytic digestion of enriched proteins to release protein-specific peptides, and the detection of these peptides by microflow LC coupled to selected reaction monitoring MS.
    MeSH term(s) Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Proteins ; Chromatography, Affinity/methods ; Peptides
    Chemical Substances Proteins ; Peptides
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2978-9_15
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  2. Article ; Online: Pre- and Post-analytical Factors in Biomarker Discovery.

    Klont, Frank / Horvatovich, Peter / Govorukhina, Natalia / Bischoff, Rainer

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 1959, Page(s) 1–22

    Abstract: The translation of promising biomarkers, which were identified in biomarker discovery experiments, to clinical assays is one of the key challenges in present-day proteomics research. Many so-called "biomarker candidates" fail to progress beyond the ... ...

    Abstract The translation of promising biomarkers, which were identified in biomarker discovery experiments, to clinical assays is one of the key challenges in present-day proteomics research. Many so-called "biomarker candidates" fail to progress beyond the discovery phase, and much emphasis is placed on pre- and post-analytical variability in an attempt to provide explanations for this bottleneck in the biomarker development pipeline. With respect to such variability, there is a large number of pre- and post-analytical factors which may impact the outcomes of proteomics experiments and thus necessitate tight control. This chapter highlights some of these factors and provides guidance for addressing them on the basis of examples from previously published proteomics studies.
    MeSH term(s) Biomarkers ; Blood Proteins ; Body Fluids/metabolism ; Chromatography, Liquid ; Factor Analysis, Statistical ; Humans ; Mass Spectrometry ; Proteome ; Proteomics/methods ; Proteomics/standards ; Quality Control ; Workflow
    Chemical Substances Biomarkers ; Blood Proteins ; Proteome
    Language English
    Publishing date 2019-03-09
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9164-8_1
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  3. Article ; Online: Translating near-infrared spectroscopy from laboratory to commercial slaughterhouse

    Mishra, Puneet / Klont, Ronald / Verkleij, Theo / Wisse, Sjaak

    Infrared Physics and Technology

    Existing challenges and solutions

    2021  Volume 119

    Abstract: In recent decades, applications of near-infrared (NIR) spectroscopy for fresh meat and meat products analysis have increased exponentially in the scientific literature. The practical applications of NIR spectroscopy in slaughterhouse conditions are, ... ...

    Abstract In recent decades, applications of near-infrared (NIR) spectroscopy for fresh meat and meat products analysis have increased exponentially in the scientific literature. The practical applications of NIR spectroscopy in slaughterhouse conditions are, however, still limited. Reasons for that are several challenges associated with the translation of NIR technology. The challenges range from reaching the best NIR calibration models for predictive analysis for predictive carcass composition analysis to combining NIR information with background information of cattle to support decision making for purposes such as pricing. This study supplies a comprehensive highlight of several existing challenges related to the translation of NIR technology from the research lab to commercial slaughterhouse conditions. The challenges covered were both related to the NIR data analysis of meat measurements, as well as the key challenges in technology transfer. Furthermore, some existing solutions are highlighted concerning each challenge. The major challenges were related to both the data analysis and proper sensor implementation in the slaughterhouse lines. Although several challenges exist, the recent innovations in data analysis techniques and innovations in sensing probe technology would defiantly ease the implementation of NIR technology in practical slaughterhouse conditions. However, all slaughterhouse lines are different and the implementation of NIR technology (from the sensor implementation point of view) for a particular slaughterhouse will be unique. However, data and models between different slaughter lines should play a complementary role.
    Keywords In-line ; Meat analysis ; Model maintenance ; Non-destructive ; Quality analysis
    Subject code 330
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2019084-0
    ISSN 1350-4495
    ISSN 1350-4495
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  4. Article ; Online: Improved prediction of minced pork meat chemical properties with near-infrared spectroscopy by a fusion of scatter-correction techniques

    Mishra, P. / Verkleij, T.J. / Klont, Ronald

    Infrared Physics and Technology

    2021  Volume 113

    Abstract: The modelling near-infrared (NIR) spectroscopy data requires removal of scattering effects from the data before applying advanced chemometrics methods. Often different scatter-correction techniques are explored, and the scatter-correction technique with ... ...

    Abstract The modelling near-infrared (NIR) spectroscopy data requires removal of scattering effects from the data before applying advanced chemometrics methods. Often different scatter-correction techniques are explored, and the scatter-correction technique with the best performance is selected. However, the information highlighted by different scatter-correction techniques may be complementary and their fusion may result in better models for predicting characteristics, such as meat quality. To test this, sequential and parallel preprocessing fusion approaches will be used in this work to fuse information from different scatter-correction techniques to try to improve the predictive performance of NIR models. Three different chemical properties, i.e., moisture, fat and protein content, were predicted. For comparison, partial least-squares regression (PLSR) was performed on standard normal variate (SNV) corrected data, as this is a widely used scatter-correction technique. Compared to this commonly used procedure, the scattering fusion approaches reduced the error and bias by up to 52% and 84%, respectively. The results suggest that fusion of scatter-correction techniques is essential to achieve optimal NIR prediction models for predicting meat characteristics such as moisture, fat and protein content.
    Keywords Fusion ; Multiblock ; Multivariate ; Preprocessing ; Spectroscopy
    Subject code 310
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2019084-0
    ISSN 1350-4495
    ISSN 1350-4495
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  5. Article ; Online: Cigarette smoking prior to blood sampling acutely affects serum levels of the chronic obstructive pulmonary disease biomarker surfactant protein D.

    Klont, Frank / Horvatovich, Péter / Ten Hacken, Nick H T / Bischoff, Rainer

    Clinical chemistry and laboratory medicine

    2020  Volume 58, Issue 8, Page(s) e138–e141

    MeSH term(s) Adult ; Aged ; Artifacts ; Biomarkers/blood ; Cigarette Smoking/blood ; Female ; Humans ; Male ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/blood ; Pulmonary Surfactant-Associated Protein D/blood ; Young Adult
    Chemical Substances Biomarkers ; Pulmonary Surfactant-Associated Protein D
    Language English
    Publishing date 2020-03-06
    Publishing country Germany
    Document type Letter
    ZDB-ID 1418007-8
    ISSN 1437-4331 ; 1434-6621 ; 1437-8523
    ISSN (online) 1437-4331
    ISSN 1434-6621 ; 1437-8523
    DOI 10.1515/cclm-2019-1246
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 121: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Untargeted 'SWATH' mass spectrometry-based metabolomics for studying chronic and intermittent exposure to xenobiotics in cohort studies.

    Klont, Frank / Stepanović, Stepan / Kremer, Daan / Bonner, Ron / Touw, Daan J / Hak, Eelko / Bakker, Stephan J L / Hopfgartner, Gérard

    Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association

    2022  Volume 165, Page(s) 113188

    Abstract: Humans are exposed to numerous chemicals daily, for example through nutrition, therapies, and lifestyle choices, which may exert beneficial or toxicological responses. In cohort studies, exposures are frequently assessed using questionnaires, although ... ...

    Abstract Humans are exposed to numerous chemicals daily, for example through nutrition, therapies, and lifestyle choices, which may exert beneficial or toxicological responses. In cohort studies, exposures are frequently assessed using questionnaires, although mass spectrometry-based metabolomics has recently emerged as complementary technique capable of yielding molecular evidence of exposures. Corresponding data processing workflows, however, have been mostly developed for detecting (omnipresent) endogenous metabolites, whereas detection of exogenous chemicals would benefit from fit-for-purpose strategies. In this work, we describe novel strategies for improved exposure detection and their application to data from an untargeted metabolomics study on urine samples from the TransplantLines Food and Nutrition Biobank and Cohort Study (NCT identifier 'NCT02811835'), which includes kidney transplant recipients, potential living kidney donors, and living kidney donors (post-donation). Specifically, we describe a reference spectra generation workflow using exposure-positive samples to detect more and also previously-undetected chronic exposures, and we present a novel approach to establish detection limits based on targeted signal extraction for more reliable and lower-level detection of intermittent exposures. These approaches can contribute to unlocking additional exposure-related information from small-molecule profiling datasets thus increasing data usefulness in metabolomics research and in environmental, food, clinical, and forensic toxicology.
    MeSH term(s) Cohort Studies ; Humans ; Mass Spectrometry/methods ; Metabolomics/methods ; Xenobiotics/toxicity
    Chemical Substances Xenobiotics
    Language English
    Publishing date 2022-05-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 782617-5
    ISSN 1873-6351 ; 0278-6915
    ISSN (online) 1873-6351
    ISSN 0278-6915
    DOI 10.1016/j.fct.2022.113188
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 529: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Book ; Online: Progress towards inline spectral sensing of lactate in pig blood at exsanguination

    Verkleij, T.J. / Mishra, P. / Kurt, Esra / van de Ven, Rick / Wisse, Sjaak / Klont, Ronald

    2023  

    Keywords Life Science
    Language English
    Publishing country nl
    Document type Book ; Online
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  8. Article ; Conference proceedings ; Online: Progress towards inline spectral sensing of lactate in pig blood at exsanguination

    Verkleij, T.J. / Mishra, P. / Kurt, Esra / van de Ven, Rick / Wisse, Sjaak / Klont, Ronald

    Proceedings of the 69th International Congress of Meat Science and Technology

    2023  

    Keywords Life Science
    Language English
    Publisher International Congress of Meat Science and Technoly
    Publishing country nl
    Document type Article ; Conference proceedings ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: SWATH data independent acquisition mass spectrometry for screening of xenobiotics in biological fluids: Opportunities and challenges for data processing.

    Klont, Frank / Jahn, Sandra / Grivet, Chantal / König, Stefan / Bonner, Ron / Hopfgartner, Gérard

    Talanta

    2020  Volume 211, Page(s) 120747

    Abstract: SWATH data independent acquisition (DIA) mass spectrometry (MS) has become an established technique in MS-based 'omics' research and is increasingly used for the screening of xenobiotics (e.g. drugs, drug metabolites, pesticides, toxicants). Such ... ...

    Abstract SWATH data independent acquisition (DIA) mass spectrometry (MS) has become an established technique in MS-based 'omics' research and is increasingly used for the screening of xenobiotics (e.g. drugs, drug metabolites, pesticides, toxicants). Such xenobiotic screening methods are mostly applied for tentative compound identification purposes based on spectral library searching, while additional data processing techniques are scarcely used thereby leaving the full potential of these methods often unused. Here we present an analytical workflow for screening xenobiotics in human samples using SWATH/MS based on which we highlight opportunities for unlocking unused potential of these methods. The workflow was applied to urine samples from subjects who tested positive for THC and/or cocaine during roadside drug testing with the goal of confirming the positive roadside drug tests and identifying compounds that relate to illicit drug use (e.g. cutting agents, tobacco components) or associate with corresponding lifestyle choices (e.g. nasal decongestants, painkillers). These goals could only be reached by complementing spectral library search procedures with additional multivariate data analyses due to inherent incompleteness of the spectral library that was employed. Such incompleteness represents a common challenge for applications where limited or no metadata is available for study samples, for example in toxicology, doping control in sports, and workplace or roadside drug testing. It furthermore sets the stage for employing additional data processing techniques as is outlined in the presented work.
    MeSH term(s) Chromatography, Liquid/methods ; Humans ; Software ; Substance Abuse Detection/methods ; Tandem Mass Spectrometry/methods ; Xenobiotics/urine
    Chemical Substances Xenobiotics
    Language English
    Publishing date 2020-01-15
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1500969-5
    ISSN 1873-3573 ; 0039-9140
    ISSN (online) 1873-3573
    ISSN 0039-9140
    DOI 10.1016/j.talanta.2020.120747
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  10. Article ; Online: Quantification of the soluble Receptor of Advanced Glycation End-Products (sRAGE) by LC-MS after enrichment by strong cation exchange (SCX) solid-phase extraction (SPE) at the protein level.

    Klont, Frank / Joosten, Marc R / Ten Hacken, Nick H T / Horvatovich, Péter / Bischoff, Rainer

    Analytica chimica acta

    2018  Volume 1043, Page(s) 45–51

    Abstract: The study of low abundant proteins contributes to increasing our knowledge about (patho)physiological processes and may lead to the identification and clinical application of disease markers. However, studying these proteins is challenging as high- ... ...

    Abstract The study of low abundant proteins contributes to increasing our knowledge about (patho)physiological processes and may lead to the identification and clinical application of disease markers. However, studying these proteins is challenging as high-abundant proteins complicate their analysis. Antibodies are often used to enrich proteins from biological matrices prior to their analysis, though antibody-free approaches have been described for some proteins as well. Here we report an antibody-free workflow on the basis of strong cation exchange (SCX) enrichment and liquid chromatography-mass spectrometry (LC-MS) for quantification of the soluble Receptor of Advanced Glycation End-products (sRAGE), a promising biomarker in chronic obstructive pulmonary disease (COPD). sRAGE was quantified in serum at clinically relevant low to sub ng mL
    MeSH term(s) Antibodies, Immobilized/chemistry ; Antibodies, Immobilized/immunology ; Biomarkers/blood ; Cation Exchange Resins/chemistry ; Chromatography, High Pressure Liquid ; Humans ; Isoelectric Point ; Limit of Detection ; Pulmonary Disease, Chronic Obstructive/diagnosis ; Receptor for Advanced Glycation End Products/analysis ; Receptor for Advanced Glycation End Products/immunology ; Receptor for Advanced Glycation End Products/isolation & purification ; Solid Phase Extraction/methods ; Spectrometry, Mass, Electrospray Ionization
    Chemical Substances AGER protein, human ; Antibodies, Immobilized ; Biomarkers ; Cation Exchange Resins ; Receptor for Advanced Glycation End Products
    Language English
    Publishing date 2018-09-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1483436-4
    ISSN 1873-4324 ; 0003-2670
    ISSN (online) 1873-4324
    ISSN 0003-2670
    DOI 10.1016/j.aca.2018.09.050
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