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  1. Article: Pyoverdine Analysis - From High-resolution MS/MS Fragmentation to Ion Mobility Measurements.

    Rehm, Karoline / Vollenweider, Vera / Kümmerli, Rolf / Bigler, Laurent

    Chimia

    2023  Volume 77, Issue 4, Page(s) 250–253

    Abstract: Microorganisms produce iron chelators called siderophores that are a rich source for drug discovery or plant protective agents. Pyoverdines are a class of siderophores from fluorescent Pseudomonas members and consist of different peptide chains specific ... ...

    Abstract Microorganisms produce iron chelators called siderophores that are a rich source for drug discovery or plant protective agents. Pyoverdines are a class of siderophores from fluorescent Pseudomonas members and consist of different peptide chains specific to each bacterial species. The structural elucidation and characterization of pyoverdines require comprehensive analytical methods as bacterial extracts are complex mixtures. Here, we present a high-throughput UHPLC-MS/MS pipeline and the application of ion mobility spectrometry to facilitate research in the field of medicine and agriculture.
    MeSH term(s) Siderophores ; Tandem Mass Spectrometry ; Oligopeptides ; Agriculture
    Chemical Substances pyoverdin (8062-00-8) ; Siderophores ; Oligopeptides
    Language English
    Publishing date 2023-04-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1516-7
    ISSN 0009-4293
    ISSN 0009-4293
    DOI 10.2533/chimia.2023.250
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Screening of leaf extraction and storage conditions for eco-metabolomics studies.

    Lang, Jakob / Ramos, Sergio E / Smohunova, Marharyta / Bigler, Laurent / Schuman, Meredith C

    Plant direct

    2024  Volume 8, Issue 4, Page(s) e578

    Abstract: Mass spectrometry-based plant metabolomics is frequently used to identify novel natural products or study the effect of specific treatments on a plant's metabolism. Reliable sample handling is required to avoid artifacts, which is why most protocols ... ...

    Abstract Mass spectrometry-based plant metabolomics is frequently used to identify novel natural products or study the effect of specific treatments on a plant's metabolism. Reliable sample handling is required to avoid artifacts, which is why most protocols mandate shock freezing of plant tissue in liquid nitrogen and an uninterrupted cooling chain. However, the logistical challenges of this approach make it infeasible for many ecological studies. Especially for research in the tropics, permanent cooling poses a challenge, which is why many of those studies use dried leaf tissue instead. We screened a total of 10 extraction and storage approaches for plant metabolites extracted from maize leaf tissue across two cropping seasons to develop a methodology for agroecological studies in logistically challenging tropical locations. All methods were evaluated based on changes in the metabolite profile across a 2-month storage period at different temperatures with the goal of reproducing the metabolite profile of the living plant as closely as possible. We show that our newly developed on-site liquid-liquid extraction protocol provides a good compromise between sample replicability, extraction efficiency, material logistics, and metabolite profile stability. We further discuss alternative methods which showed promising results and feasibility of on-site sample handling for field studies.
    Language English
    Publishing date 2024-04-10
    Publishing country England
    Document type Journal Article
    ISSN 2475-4455
    ISSN (online) 2475-4455
    DOI 10.1002/pld3.578
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Quantification of glucocorticoid and progestogen metabolites in bovine plasma, skimmed milk and saliva by UHPLC-HR-MS with polarity switching.

    Rehm, Karoline / Hankele, Anna-Katharina / Ulbrich, Susanne E / Bigler, Laurent

    Analytica chimica acta

    2023  Volume 1287, Page(s) 342118

    Abstract: Steroid metabolites are increasingly in focus when searching for novel biomarkers in physiological mechanisms and their disorders. While major steroids such as progesterone and cortisol are well-researched and routinely determined to assess the health, ... ...

    Abstract Steroid metabolites are increasingly in focus when searching for novel biomarkers in physiological mechanisms and their disorders. While major steroids such as progesterone and cortisol are well-researched and routinely determined to assess the health, particularly the reproductive status of mammals, the function of potentially biologically active progestogen and glucocorticoid metabolites is widely unexplored. One of the main reasons for this is the lack of comprehensive, sensitive, and specific analytical methods. This is particularly the case when analyzing matrices like milk or saliva obtained by non-invasive sampling with steroid concentrations often below those present in plasma. Therefore, a new UHPLC-HR-MS method based on an Ultimate UHPLC system equipped with an Acquity HSS T3 reversed-phase column and a Q Exactive™ mass spectrometer was developed, enabling the simultaneous chromatographic separation, detection and quantification of eleven isobaric glucocorticoids (11-dehydrocorticosterone (A), corticosterone (B), cortisol (F), cortisone (E), the tetrahydrocortisols (THF): 3α,5α-THF, 3α,5β-THF, 3β,5α-THF, 3β,5β-THF, and the tetrahydrocortisones (THE): 3α,5α-THE, 3α,5β-THE, 3β,5α-THE) and twelve progestogens (progesterone (P4), pregnenolone (P5), the dihydroprogesterones (DHP): 20α-DHP, 20β-DHP, 3α-DHP, 3β-DHP, 5α-DHP, 5β-DHP, and the tetrahydroprogesterones (THP): 3α,5α-THP, 3α,5β-THP, 3β,5α-THP, 3β,5β-THP) in bovine plasma, skimmed milk, and saliva. A simple liquid-liquid extraction (LLE) with MTBE (methyl tert-butyl ether) was used for sample preparation of 500 μL plasma, skimmed milk, and saliva. Heated electrospray ionization (HESI) with polarity switching was applied to analyze steroids in high-resolution full scan mode (HR-FS). The method validation covered the investigation of sensitivity, selectivity, curve fitting, carry-over, accuracy, precision, recovery, matrix effects and applicability. A high sensitivity in the range of pg mL
    MeSH term(s) Cattle ; Animals ; Progestins ; Glucocorticoids ; Progesterone ; Hydrocortisone ; Milk ; Saliva ; Chromatography, High Pressure Liquid ; Mammals
    Chemical Substances Progestins ; Glucocorticoids ; Progesterone (4G7DS2Q64Y) ; Hydrocortisone (WI4X0X7BPJ)
    Language English
    Publishing date 2023-12-08
    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.2023.342118
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  4. Article ; Online: Rapid identification of pyoverdines of fluorescent Pseudomonas spp. by UHPLC-IM-MS.

    Rehm, Karoline / Vollenweider, Vera / Kümmerli, Rolf / Bigler, Laurent

    Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine

    2022  Volume 36, Issue 1, Page(s) 19–34

    Abstract: Siderophores are iron-chelating molecules produced by bacteria and other microbes. They are involved with virulence in infections and play key roles in bacterial community assembly and as plant protectants due to their pathogen control properties. ... ...

    Abstract Siderophores are iron-chelating molecules produced by bacteria and other microbes. They are involved with virulence in infections and play key roles in bacterial community assembly and as plant protectants due to their pathogen control properties. Although assays exist to screen whether newly isolated bacteria can produce siderophores, the chemical structures of many of these bio-active molecules remain unidentified due to the lack of rapid analytical procedures. An important group of siderophores are pyoverdines. They consist of a structurally diverse group of chromopeptides, whose amino acid sequence is characteristic for the fluorescent Pseudomonas species that secrets them. Although over 60 pyoverdine structures have been described so far, their characterization is cumbersome and several methods (isoelectrofocusing, iron uptake measurement, mass determination) are typically combined as ambiguous results are often achieved by a single method. Those additional experiments consume valuable time and resources and prevent high-throughput analysis. In this work, we present a new pyoverdine characterisation option by recording their collision cross sections (CCS) using trapped ion mobility spectrometry. This can be done simultaneously in combination with UHPLC and high-resolution MS resulting in a rapid identification of pyoverdines. The high specificity of CCS values is presented for 17 pyoverdines secreted by different Pseudomonas strains. The pyoverdine mass determination by full scan MS was supported by fragments obtained from broadband collision induced dissociation (bbCID). As iron contaminations in laboratories are not uncommon, CCS values of ferripyoverdines were also evaluated. Thereby, unusual and highly characteristic ion mobility patterns were obtained that are suitable as an alternative identification marker.
    MeSH term(s) Pseudomonas/metabolism ; Siderophores/chemistry ; Chromatography, High Pressure Liquid ; Iron/metabolism ; Coloring Agents
    Chemical Substances Siderophores ; pyoverdin (8062-00-8) ; Iron (E1UOL152H7) ; Coloring Agents
    Language English
    Publishing date 2022-10-20
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1112688-7
    ISSN 1572-8773 ; 0966-0844
    ISSN (online) 1572-8773
    ISSN 0966-0844
    DOI 10.1007/s10534-022-00454-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A comprehensive method to elucidate pyoverdines produced by fluorescent Pseudomonas spp. by UHPLC-HR-MS/MS.

    Rehm, Karoline / Vollenweider, Vera / Kümmerli, Rolf / Bigler, Laurent

    Analytical and bioanalytical chemistry

    2022  Volume 414, Issue 8, Page(s) 2671–2685

    Abstract: Microbial secondary metabolites represent a rich source for drug discovery, plant protective agents, and biotechnologically relevant compounds. Among them are siderophores, iron-chelating molecules, that show a great influence on bacterial community ... ...

    Abstract Microbial secondary metabolites represent a rich source for drug discovery, plant protective agents, and biotechnologically relevant compounds. Among them are siderophores, iron-chelating molecules, that show a great influence on bacterial community assembly and the potential to control pathogen invasions. One of such a siderophore is pyoverdine that is produced by fluorescent Pseudomonas members and consists of different peptide chains specific to each bacterial species. The identification and structural elucidation of such suites of siderophores remain widely underexplored as general high-throughput analytical protocols are missing. Therefore, a dedicated method was established allowing a rapid localization and structural elucidation of pyoverdines. Liquid bacterial culture samples were purified by an easy small-scale solid-phase extraction (SPE). Ultra-high-performance liquid chromatography high-resolution tandem mass spectrometry (UHPLC-HR-MS/MS) separated highly polar pyoverdines and their derivatives. All ion fragmentation (AIF) generated mass spectra containing the characteristic fragments of the biological precursor of pyoverdine, ferribactin. This led to the revelation of the mass of secreted pyoverdines. Targeted MS/MS experiments at multiple collision energies accomplished the full structure elucidation of the pyoverdine peptide chain. A mass calculator and a fragmentation predictor facilitated greatly the interpretation of MS/MS spectra by providing accurate masses for a straightforward comparison of measured and theoretical values. The method was successfully validated using four well-known pyoverdines with various peptide chains. Finally, the applicability was proven by the analysis of 13 unknown pyoverdines secreted by sampled bacterial cultures. Among these, 4 novel pyoverdine peptide chains were discovered and are herein reported for the first time.
    MeSH term(s) Chromatography, High Pressure Liquid ; Oligopeptides ; Pseudomonas/metabolism ; Siderophores ; Tandem Mass Spectrometry
    Chemical Substances Oligopeptides ; Siderophores ; pyoverdin (8062-00-8)
    Language English
    Publishing date 2022-01-27
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 201093-8
    ISSN 1618-2650 ; 0016-1152 ; 0372-7920
    ISSN (online) 1618-2650
    ISSN 0016-1152 ; 0372-7920
    DOI 10.1007/s00216-022-03907-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: A comprehensive method to elucidate pyoverdines produced by fluorescent Pseudomonas spp. by UHPLC-HR-MS/MS

    Rehm, Karoline / Vollenweider, Vera / Kümmerli, Rolf / Bigler, Laurent

    Analytical and bioanalytical chemistry. 2022 Mar., v. 414, no. 8

    2022  

    Abstract: Microbial secondary metabolites represent a rich source for drug discovery, plant protective agents, and biotechnologically relevant compounds. Among them are siderophores, iron-chelating molecules, that show a great influence on bacterial community ... ...

    Abstract Microbial secondary metabolites represent a rich source for drug discovery, plant protective agents, and biotechnologically relevant compounds. Among them are siderophores, iron-chelating molecules, that show a great influence on bacterial community assembly and the potential to control pathogen invasions. One of such a siderophore is pyoverdine that is produced by fluorescent Pseudomonas members and consists of different peptide chains specific to each bacterial species. The identification and structural elucidation of such suites of siderophores remain widely underexplored as general high-throughput analytical protocols are missing. Therefore, a dedicated method was established allowing a rapid localization and structural elucidation of pyoverdines. Liquid bacterial culture samples were purified by an easy small-scale solid-phase extraction (SPE). Ultra-high-performance liquid chromatography high-resolution tandem mass spectrometry (UHPLC-HR-MS/MS) separated highly polar pyoverdines and their derivatives. All ion fragmentation (AIF) generated mass spectra containing the characteristic fragments of the biological precursor of pyoverdine, ferribactin. This led to the revelation of the mass of secreted pyoverdines. Targeted MS/MS experiments at multiple collision energies accomplished the full structure elucidation of the pyoverdine peptide chain. A mass calculator and a fragmentation predictor facilitated greatly the interpretation of MS/MS spectra by providing accurate masses for a straightforward comparison of measured and theoretical values. The method was successfully validated using four well-known pyoverdines with various peptide chains. Finally, the applicability was proven by the analysis of 13 unknown pyoverdines secreted by sampled bacterial cultures. Among these, 4 novel pyoverdine peptide chains were discovered and are herein reported for the first time.
    Keywords Pseudomonas ; analytical chemistry ; bacterial communities ; bacterial culture ; drugs ; fluorescence ; liquids ; pathogens ; peptides ; pyoverdines ; secondary metabolites ; solid phase extraction ; tandem mass spectrometry ; ultra-performance liquid chromatography
    Language English
    Dates of publication 2022-03
    Size p. 2671-2685.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ISSN 1618-2642
    DOI 10.1007/s00216-022-03907-w
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Bioactive Nitrosylated and Nitrated

    Girel, Sergey / Schütz, Vadim / Bigler, Laurent / Dörmann, Peter / Schulz, Margot

    Molecules (Basel, Switzerland)

    2022  Volume 27, Issue 15

    Abstract: Incubation ... ...

    Abstract Incubation of
    MeSH term(s) Acetamides ; Acetanilides ; Arabidopsis/metabolism ; Glucosides/metabolism ; Nitrates ; Pantoea ; Tandem Mass Spectrometry
    Chemical Substances Acetamides ; Acetanilides ; Glucosides ; Nitrates ; 2-hydroxyacetanilide (4AS8989RNI)
    Language English
    Publishing date 2022-07-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules27154786
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Chryseochelins-structural characterization of novel citrate-based siderophores produced by plant protecting Chryseobacterium spp.

    Rehm, Karoline / Vollenweider, Vera / Gu, Shaohua / Friman, Ville-Petri / Kümmerli, Rolf / Wei, Zhong / Bigler, Laurent

    Metallomics : integrated biometal science

    2023  Volume 15, Issue 3

    Abstract: Bacteria secrete siderophores whose function is to acquire iron. In recent years, the siderophores of several Chryseobacterium species were shown to promote the health and growth of various plants such as tomato or rice. However, the chemical nature of ... ...

    Abstract Bacteria secrete siderophores whose function is to acquire iron. In recent years, the siderophores of several Chryseobacterium species were shown to promote the health and growth of various plants such as tomato or rice. However, the chemical nature of Chryseobacterium siderophores remained unexplored despite great interest. In this work, we present the purification and structure elucidation by nuclear magnetic resonance (NMR) spectroscopy and tandem mass spectrometry (MS/MS) of chryseochelin A, a novel citrate-based siderophore secreted by three Chryseobacterium strains involved in plant protection. It contains the unusual building blocks 3-hydroxycadaverine and fumaric acid. Furthermore, the unstable structural isomer chryseochelin B and its stable derivative containing fatty acid chains, named chryseochelin C, were identified by mass spectrometric methods. The latter two incorporate an unusual ester connectivity to the citrate moiety showing similarities to achromobactin from the plant pathogen Dickeya dadantii. Finally, we show that chryseochelin A acts in a concentration-dependent manner against the plant-pathogenic Ralstonia solanacearum strain by reducing its access to iron. Thus, our study provides valuable knowledge about the siderophores of Chryseobacterium strains, which have great potential in various applications.
    MeSH term(s) Siderophores/chemistry ; Citric Acid ; Chryseobacterium ; Tandem Mass Spectrometry ; Iron ; Citrates
    Chemical Substances Siderophores ; Citric Acid (2968PHW8QP) ; Iron (E1UOL152H7) ; Citrates
    Language English
    Publishing date 2023-02-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2474317-3
    ISSN 1756-591X ; 1756-5901
    ISSN (online) 1756-591X
    ISSN 1756-5901
    DOI 10.1093/mtomcs/mfad008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Conference proceedings: Short Lecture “Unravel the variation of metabolites of maidong medicine (Ophiopogon japonicus and Liriope spicata): A feature-based molecular network approach”

    Lei, Feiyi / Saldanha, Luiz Leonardo / Bigler, Laurent / Nyffeler, Reto / Weckerle, Caroline

    Planta Medica

    2023  Volume 89, Issue 14

    Event/congress 71st International Congress and Annual Meeting of the Society for Medicinal Plant and Natural Product Research (GA), Trinity College Dublin Ireland, 2023-07-02
    Language English
    Publishing date 2023-11-01
    Publisher Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article ; Conference proceedings
    ZDB-ID 123545-x
    ISSN 1439-0221 ; 0032-0943
    ISSN (online) 1439-0221
    ISSN 0032-0943
    DOI 10.1055/s-0043-1773819
    Database Thieme publisher's database

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  10. Article ; Online: Selective and Fast Analysis of Chlorinated Paraffins in the Presence of Chlorinated Mono-, Di-, and Tri-Olefins with the R-Based Automated Spectra Evaluation Routine (RASER).

    Knobloch, Marco C / Mathis, Flurin / Diaz, Oscar Mendo / Stalder, Urs / Bigler, Laurent / Kern, Susanne / Bleiner, Davide / Heeb, Norbert V

    Analytical chemistry

    2022  Volume 94, Issue 40, Page(s) 13777–13784

    Abstract: Chlorinated paraffins (CPs) are complex mixtures consisting of various C homologues ( ... n ... C ... ≈ 10-30) and Cl homologues ( ... n ... Cl ... ≈ 2-20). Technical CP mixtures are produced on a large scale (>10 ... 6 ... t/y) and are widely ... ...

    Abstract Chlorinated paraffins (CPs) are complex mixtures consisting of various C homologues (n<sub>C</sub> ≈ 10-30) and Cl homologues (n<sub>Cl</sub> ≈ 2-20). Technical CP mixtures are produced on a large scale (>10<sup>6</sup> t/y) and are widely used such as plasticizers in plastic and coolants in metalwork. Since 2017, short-chain CPs (C<sub>10</sub>-C<sub>13</sub>) are classified as persistent organic pollutants (POPs) by the Stockholm Convention but longer-chain CPs are not regulated. Analysis of technical CP mixtures is challenging because they consist of hundreds of homologues and millions of constitutional isomers and stereoisomers. Furthermore, such mixtures can also contain byproducts and transformation products such as chlorinated olefins (COs). We applied a liquid-chromatography method coupled to an atmospheric pressure chemical ionization technique with a high-resolution mass detector (LC-APCI-Orbitrap-MS) to study CP and CO homologues in two plastic materials. Respective mass spectra can contain up to 23,000 signals from 1320 different C-Cl homologue classes. The R-based automated spectra evaluation routine (RASER) was developed to efficiently search for characteristic ions in these complex mass spectra. With it, the time needed to evaluate such spectra was reduced from weeks to hours, compared to manual data evaluation. Unique sets of homologue distributions could be obtained from the two plastic materials. CPs were found together with their transformation products, the chlorinated mono-olefins (COs), di-olefins (CdiOs), and tri-olefins (CtriOs) in both plastic materials. Based on these examples, it can be shown that RASER is an efficient and selective tool for evaluating high-resolution mass spectra of CP mixtures containing hundreds of homologues.
    MeSH term(s) Alkenes/analysis ; China ; Complex Mixtures/analysis ; Environmental Monitoring/methods ; Hydrocarbons, Chlorinated/analysis ; Paraffin/analysis ; Paraffin/chemistry ; Persistent Organic Pollutants ; Plasticizers/analysis ; Plastics
    Chemical Substances Alkenes ; Complex Mixtures ; Hydrocarbons, Chlorinated ; Plasticizers ; Plastics ; Paraffin (8002-74-2)
    Language English
    Publishing date 2022-09-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.2c02240
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