@article{VillatoroWeberZuehlkeetal.2019, author = {Villatoro, Jos{\´e} Andr{\´e}s and Weber, M. and Z{\"u}hlke, Martin and Lehmann, A. and Zenichowski, Karl and Riebe, Daniel and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Kreuzer, O.}, title = {Structural characterization of synthetic peptides using electrospray ion mobility spectrometry and molecular dynamics simulations}, series = {International Journal of Mass Spectrometry}, volume = {436}, journal = {International Journal of Mass Spectrometry}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1387-3806}, doi = {10.1016/j.ijms.2018.10.036}, pages = {108 -- 117}, year = {2019}, abstract = {Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540-3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF). (C) 2018 Elsevier B.V. All rights reserved.}, language = {en} } @article{VillatoroZuehlkeRiebeetal.2016, author = {Villatoro, Jos{\´e} Andr{\´e}s and Z{\"u}hlke, Martin and Riebe, Daniel and Riedel, Jens and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {IR-MALDI ion mobility spectrometry}, series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis}, volume = {408}, journal = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-016-9739-x}, pages = {6259 -- 6268}, year = {2016}, abstract = {The novel combination of infrared matrix-assisted laser dispersion and ionization (IR-MALDI) with ion mobility (IM) spectrometry makes it possible to investigate biomolecules in their natural environment, liquid water. As an alternative to an ESI source, the IR-MALDI source was implemented in an in-house-developed ion mobility (IM) spectrometer. The release of ions directly from an aqueous solution is based on a phase explosion, induced by the absorption of an IR laser pulse (lambda = 2.94 mu m, 6 ns pulse width), which disperses the liquid as nano- and micro-droplets. The prerequisites for the application of IR-MALDI-IM spectrometry as an analytical method are narrow analyte ion signal peaks for a high spectrometer resolution. This can only be achieved by improving the desolvation of ions. One way to full desolvation is to give the cluster ions sufficient time to desolvate. Two methods for achieving this are studied: the implementation of an additional drift tube, as in ESI-IM-spectrometry, and the delayed extraction of the ions. As a result of this optimization procedure, limits of detection between 5 nM and 2.5 mu M as well as linear dynamic ranges of 2-3 orders of magnitude were obtained for a number of substances. The ability of this method to analyze simple mixtures is illustrated by the separation of two different surfactant mixtures.}, language = {en} } @article{VillatoroZuehlkeRiebeetal.2016, author = {Villatoro, Jos{\´e} Andr{\´e}s and Z{\"u}hlke, Martin and Riebe, Daniel and Beitz, Toralf and Weber, Marcus and Riedel, Jens and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector}, series = {International journal for ion mobility spectrometry : official publication of the International Society for Ion Mobility Spectrometry}, volume = {19}, journal = {International journal for ion mobility spectrometry : official publication of the International Society for Ion Mobility Spectrometry}, publisher = {Springer}, address = {Heidelberg}, issn = {1435-6163}, doi = {10.1007/s12127-016-0208-1}, pages = {197 -- 207}, year = {2016}, abstract = {Infrared matrix-assisted laser dispersion and ionization (IR-MALDI) in combination with ion mobility (IM) spectrometry enables the direct analysis of biomolecules in aqueous solution. The release of ions directly from an aqueous solution is based on a phase explosion, induced by the absorption of an IR laser pulse, which disperses the liquid as vapor, nano-and micro-droplets. The ionization process is characterized initially by a broad spatial distribution of the ions, which is a result of complex fluid dynamics and desolvation kinetics. These processes have a profound effect on the shape and width of the peaks in the IM spectra. In this work, the transport of ions by the phase explosion-induced shockwave could be studied independently from the transport by the electric field. The shockwave-induced mean velocities of the ions at different time scales were determined through IM spectrometry and shadowgraphy. The results show a deceleration of the ions from 118 m.s(-1) at a distance of 400 mu m from the liquid surface to 7.1 m.s(-1) at a distance of 10 mm, which is caused by a pile-up effect. Furthermore, the desolvation kinetics were investigated and a first-order desolvation constant of 325 +/- 50 s(-1) was obtained. In the second part, the IR-MALDI-IM spectrometer is used as an HPLC detector for the two-dimensional separation of a pesticide mixture.}, language = {en} } @article{VillatoroLealZuehlkeRiebeetal.2020, author = {Villatoro Leal, Jos{\´e} Andr{\´e}s and Z{\"u}hlke, Martin and Riebe, Daniel and Beitz, Toralf and Weber, Marcus and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities}, series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica}, volume = {412}, journal = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica}, number = {22}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-020-02735-0}, pages = {5247 -- 5260}, year = {2020}, abstract = {A new ion mobility (IM) spectrometer, enabling mobility measurements in the pressure range between 5 and 500 mbar and in the reduced field strength range E/N of 5-90 Td, was developed and characterized. Reduced mobility (K-0) values were studied under low E/N (constant value) as well as high E/N (deviation from low field K-0) for a series of molecular ions in nitrogen. Infrared matrix-assisted laser desorption ionization (IR-MALDI) was used in two configurations: a source working at atmospheric pressure (AP) and, for the first time, an IR-MALDI source working with a liquid (aqueous) matrix at sub-ambient/reduced pressure (RP). The influence of RP on IR-MALDI was examined and new insights into the dispersion process were gained. This enabled the optimization of the IM spectrometer for best analytical performance. While ion desolvation is less efficient at RP, the transport of ions is more efficient, leading to intensity enhancement and an increased number of oligomer ions. When deciding between AP and RP IR-MALDI, a trade-off between intensity and resolving power has to be considered. Here, the low field mobility of peptide ions was first measured and compared with reference values from ESI-IM spectrometry (at AP) as well as collision cross sections obtained from molecular dynamics simulations. The second application was the determination of the reduced mobility of various substituted ammonium ions as a function of E/N in nitrogen. The mobility is constant up to a threshold at high E/N. Beyond this threshold, mobility increases were observed. This behavior can be explained by the loss of hydrated water molecules.}, language = {en} } @article{ZuehlkeSassRiebeetal.2017, author = {Z{\"u}hlke, Martin and Sass, Stephan and Riebe, Daniel and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {Real-Time Reaction Monitoring of an Organic Multistep Reaction by Electrospray Ionization-Ion Mobility Spectrometry}, series = {ChemPlusChem}, volume = {82}, journal = {ChemPlusChem}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2192-6506}, doi = {10.1002/cplu.201700296}, pages = {1266 -- 1273}, year = {2017}, abstract = {The capability of electrospray ionization (ESI)-ion mobility (IM) spectrometry for reaction monitoring is assessed both as a stand-alone real-time technique and in combination with HPLC. A three-step chemical reaction, consisting of a Williamson ether synthesis followed by a hydrogenation and an N-alkylation step, is chosen for demonstration. Intermediates and products are determined with a drift time to mass-per-charge correlation. Addition of an HPLC column to the setup increases the separation power and allows the determination of further species. Monitoring of the intensities of the various species over the reaction time allows the detection of the end of reaction, determination of the rate-limiting step, observation of the system response in discontinuous processes, and optimization of the mass ratios of the starting materials. However, charge competition in ESI influences the quantitative detection of substances in the reaction mixture. Therefore, two different methods are investigated, which allow the quantification and investigation of reaction kinetics. The first method is based on the pre-separation of the compounds on an HPLC column and their subsequent individual detection in the ESI-IM spectrometer. The second method involves an extended calibration procedure, which considers charge competition effects and facilitates nearly real-time quantification.}, language = {en} } @article{PruefertVillatoroLealZuehlkeetal.2022, author = {Pr{\"u}fert, Christian and Villatoro Leal, Jos{\´e} Andr{\´e}s and Z{\"u}hlke, Martin and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {Liquid phase IR-MALDI and differential mobility analysis of nano- and sub-micron particles}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {24}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {4}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/d1cp04196g}, pages = {2275 -- 2286}, year = {2022}, abstract = {Infrared matrix-assisted desorption and ionization (IR-MALDI) enables the transfer of sub-micron particles (sMP) directly from suspensions into the gas phase and their characterization with differential mobility (DM) analysis. A nanosecond laser pulse at 2940 nm induces a phase explosion of the aqueous phase, dispersing the sample into nano- and microdroplets. The particles are ejected from the aqueous phase and become charged. Using IR-MALDI on sMP of up to 500 nm in diameter made it possible to surpass the 100 nm size barrier often encountered when using nano-electrospray for ionizing supramolecular structures. Thus, the charge distribution produced by IR-MALDI could be characterized systematically in the 50-500 nm size range. Well-resolved signals for up to octuply charged particles were obtained in both polarities for different particle sizes, materials, and surface modifications spanning over four orders of magnitude in concentrations. The physicochemical characterization of the IR-MALDI process was done via a detailed analysis of the charge distribution of the emerging particles, qualitatively as well as quantitatively. The Wiedensohler charge distribution, which describes the evolution of particle charging events in the gas phase, and a Poisson-derived charge distribution, which describes the evolution of charging events in the liquid phase, were compared with one another with respect to how well they describe the experimental data. Although deviations were found in both models, the IR-MALDI charging process seems to resemble a Poisson-like charge distribution mechanism, rather than a bipolar gas phase charging one.}, language = {en} } @article{ZuehlkeMeilingRoderetal.2021, author = {Z{\"u}hlke, Martin and Meiling, Till Thomas and Roder, Phillip and Riebe, Daniel and Beitz, Toralf and Bald, Ilko and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Janßen, Traute and Erhard, Marcel and Repp, Alexander}, title = {Photodynamic inactivation of E. coli bacteria via carbon nanodots}, series = {ACS omega / American Chemical Society}, volume = {6}, journal = {ACS omega / American Chemical Society}, number = {37}, publisher = {ACS Publications}, address = {Washington, DC}, issn = {2470-1343}, doi = {10.1021/acsomega.1c01700}, pages = {23742 -- 23749}, year = {2021}, abstract = {The increasing development of antibiotic resistance in bacteria has been a major problem for years, both in human and veterinary medicine. Prophylactic measures, such as the use of vaccines, are of great importance in reducing the use of antibiotics in livestock. These vaccines are mainly produced based on formaldehyde inactivation. However, the latter damages the recognition elements of the bacterial proteins and thus could reduce the immune response in the animal. An alternative inactivation method developed in this work is based on gentle photodynamic inactivation using carbon nanodots (CNDs) at excitation wavelengths λex > 290 nm. The photodynamic inactivation was characterized on the nonvirulent laboratory strain Escherichia coli K12 using synthesized CNDs. For a gentle inactivation, the CNDs must be absorbed into the cytoplasm of the E. coli cell. Thus, the inactivation through photoinduced formation of reactive oxygen species only takes place inside the bacterium, which means that the outer membrane is neither damaged nor altered. The loading of the CNDs into E. coli was examined using fluorescence microscopy. Complete loading of the bacterial cells could be achieved in less than 10 min. These studies revealed a reversible uptake process allowing the recovery and reuse of the CNDs after irradiation and before the administration of the vaccine. The success of photodynamic inactivation was verified by viability assays on agar. In a homemade flow photoreactor, the fastest successful irradiation of the bacteria could be carried out in 34 s. Therefore, the photodynamic inactivation based on CNDs is very effective. The membrane integrity of the bacteria after irradiation was verified by slide agglutination and atomic force microscopy. The method developed for the laboratory strain E. coli K12 could then be successfully applied to the important avian pathogens Bordetella avium and Ornithobacterium rhinotracheale to aid the development of novel vaccines.}, language = {en} } @misc{ZuehlkeMeilingRoderetal.2021, author = {Z{\"u}hlke, Martin and Meiling, Till Thomas and Roder, Phillip and Riebe, Daniel and Beitz, Toralf and Bald, Ilko and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Janßen, Traute and Erhard, Marcel and Repp, Alexander}, title = {Photodynamic Inactivation of E. coli Bacteria via Carbon Nanodots}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, publisher = {Universit{\"a}t Potsdam}, address = {Potsdam}, issn = {1866-8372}, doi = {10.25932/publishup-53842}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-538425}, pages = {23742 -- 23749}, year = {2021}, abstract = {The increasing development of antibiotic resistance in bacteria has been a major problem for years, both in human and veterinary medicine. Prophylactic measures, such as the use of vaccines, are of great importance in reducing the use of antibiotics in livestock. These vaccines are mainly produced based on formaldehyde inactivation. However, the latter damages the recognition elements of the bacterial proteins and thus could reduce the immune response in the animal. An alternative inactivation method developed in this work is based on gentle photodynamic inactivation using carbon nanodots (CNDs) at excitation wavelengths λex > 290 nm. The photodynamic inactivation was characterized on the nonvirulent laboratory strain Escherichia coli K12 using synthesized CNDs. For a gentle inactivation, the CNDs must be absorbed into the cytoplasm of the E. coli cell. Thus, the inactivation through photoinduced formation of reactive oxygen species only takes place inside the bacterium, which means that the outer membrane is neither damaged nor altered. The loading of the CNDs into E. coli was examined using fluorescence microscopy. Complete loading of the bacterial cells could be achieved in less than 10 min. These studies revealed a reversible uptake process allowing the recovery and reuse of the CNDs after irradiation and before the administration of the vaccine. The success of photodynamic inactivation was verified by viability assays on agar. In a homemade flow photoreactor, the fastest successful irradiation of the bacteria could be carried out in 34 s. Therefore, the photodynamic inactivation based on CNDs is very effective. The membrane integrity of the bacteria after irradiation was verified by slide agglutination and atomic force microscopy. The method developed for the laboratory strain E. coli K12 could then be successfully applied to the important avian pathogens Bordetella avium and Ornithobacterium rhinotracheale to aid the development of novel vaccines.}, language = {en} } @article{ZuehlkeRiebeBeitzetal.2016, author = {Z{\"u}hlke, Martin and Riebe, Daniel and Beitz, Toralf and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Andreotti, Sandro and Reinert, Knut and Zenichowski, Karl and Diener, Marc}, title = {High-performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization, data management, and applications}, series = {Journal of separation science}, volume = {39}, journal = {Journal of separation science}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1615-9306}, doi = {10.1002/jssc.201600749}, pages = {4756 -- 4764}, year = {2016}, abstract = {The combination of high-performance liquid chromatography and electrospray ionization ion mobility spectrometry facilitates the two-dimensional separation of complex mixtures in the retention and drift time plane. The ion mobility spectrometer presented here was optimized for flow rates customarily used in high-performance liquid chromatography between 100 and 1500 mu L/min. The characterization of the system with respect to such parameters as the peak capacity of each time dimension and of the 2D spectrum was carried out based on a separation of a pesticide mixture containing 24 substances. While the total ion current chromatogram is coarsely resolved, exhibiting coelutions for a number of compounds, all substances can be separately detected in the 2D plane due to the orthogonality of the separations in retention and drift dimensions. Another major advantage of the ion mobility detector is the identification of substances based on their characteristic mobilities. Electrospray ionization allows the detection of substances lacking a chromophore. As an example, the separation of a mixture of 18 amino acids is presented. A software built upon the free mass spectrometry package OpenMS was developed for processing the extensive 2D data. The different processing steps are implemented as separate modules which can be arranged in a graphic workflow facilitating automated processing of data.}, language = {en} } @phdthesis{Zuehlke2017, author = {Z{\"u}hlke, Martin}, title = {Elektrosprayionisation Ionenmobilit{\"a}tsspektrometrie}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407452}, school = {Universit{\"a}t Potsdam}, pages = {viii, 113, XIV}, year = {2017}, abstract = {Die Elektrosprayionisation (ESI) ist eine der weitverbreitetsten Ionisationstechniken f{\"u}r fl{\"u}ssige Pro-ben in der Massen- und Ionenmobilit{\"a}ts(IM)-Spektrometrie. Aufgrund ihrer schonenden Ionisierung wird ESI vorwiegend f{\"u}r empfindliche, komplexe Molek{\"u}le in der Biologie und Medizin eingesetzt. {\"U}berdies ist sie allerdings f{\"u}r ein sehr breites Spektrum an Substanzklassen anwendbar. Die IM-Spektrometrie wurde urspr{\"u}nglich zur Detektion gasf{\"o}rmiger Proben entwickelt, die haupts{\"a}chlich durch radioaktive Quellen ionisiert werden. Sie ist die einzige analytische Methode, bei der Isomere in Echtzeit getrennt und {\"u}ber ihre charakteristische IM direkt identifiziert werden k{\"o}nnen. ESI wurde in den 90ger Jahren durch die Hill Gruppe in die IM-Spektrometrie eingef{\"u}hrt. Die Kombination wird bisher jedoch nur von wenigen Gruppen verwendet und hat deshalb noch ein hohes Entwick-lungspotential. Ein vielversprechendes Anwendungsfeld ist der Einsatz in der Hochleistungs-fl{\"u}ssigkeitschromatographie (HPLC) zur mehrdimensionalen Trennung. Heutzutage ist die HPLC die Standardmethode zur Trennung komplexer Proben in der Routineanalytik. HPLC-Trennungsg{\"a}nge sind jedoch h{\"a}ufig langwierig und der Einsatz verschiedener Laufmittel, hoher Flussraten, von Puffern, sowie Laufmittelgradienten stellt hohe Anforderungen an die Detektoren. Die ESI-IM-Spektrometrie wurde in einigen Studien bereits als HPLC-Detektor eingesetzt, war dort bisher jedoch auf Flussratensplitting oder geringe Flussraten des Laufmittels beschr{\"a}nkt. In dieser kumulativen Doktorarbeit konnte daher erstmals ein ESI IM-Spektrometer als HPLC-Detektor f{\"u}r den Flussratenbereich von 200-1500 μl/min entwickelt werden. Anhand von f{\"u}nf Publi-kationen wurden (1) {\"u}ber eine umfassende Charakterisierung die Eignung des Spektrometers als HPLC-Detektor festgestellt, (2) ausgew{\"a}hlte komplexe Trenng{\"a}nge pr{\"a}sentiert und (3) die Anwen-dung zum Reaktionsmonitoring und (4, 5) m{\"o}gliche Weiterentwicklungen gezeigt. Erfolgreich konnten mit dem selbst-entwickelten ESI IM-Spektrometer typische HPLC-Bedingungen wie Wassergehalte im Laufmittel von bis zu 90\%, Pufferkonzentrationen von bis zu 10 mM, sowie Nachweisgrenzen von bis zu 50 nM erreicht werden. Weiterhin wurde anhand der komplexen Trennungsg{\"a}nge (24 Pestizide/18 Aminos{\"a}uren) gezeigt, dass die HPLC und die IM-Spektrometrie eine hohe Orthogonalit{\"a}t besitzen. Eine effektive Peakkapazit{\"a}t von 240 wurde so realisiert. Auf der HPLC-S{\"a}ule koeluierende Substanzen konnten {\"u}ber die Driftzeit getrennt und {\"u}ber ihre IM identifi-ziert werden, sodass die Gesamttrennzeiten erheblich minimiert werden konnten. Die Anwend-barkeit des ESI IM-Spektrometers zur {\"U}berwachung chemischer Synthesen wurde anhand einer dreistufigen Reaktion demonstriert. Es konnten die wichtigsten Edukte, Zwischenprodukte und Produkte aller Stufen identifiziert werden. Eine quantitative Auswertung war sowohl {\"u}ber eine kurze HPLC-Vortrennung als auch durch die Entwicklung eines eigenen Kalibrierverfahrens, welches die Ladungskonkurrenz bei ESI ber{\"u}cksichtigt, ohne HPLC m{\"o}glich. Im zweiten Teil der Arbeit werden zwei Weiterentwicklungen des Spektrometers pr{\"a}sentiert. Eine M{\"o}glichkeit ist die Reduzierung des Drucks in den intermedi{\"a}ren Bereich (300 - 1000 mbar) mit dem Ziel der Verringerung der ben{\"o}tigten Spannungen. Mithilfe von Streulichtbildern und Strom-Spannungs-Kurven wurden f{\"u}r geringe Dr{\"u}cke eine verminderte Freisetzung der Analyt-Ionen aus den Tropfen festgestellt. Die Verluste konnten jedoch {\"u}ber h{\"o}here elektrische Feldst{\"a}rken ausgeglichen werden, sodass gleiche Nachweisgrenzen bei 500 mbar und bei 1 bar erreicht wurden. Die zweite Weiterentwicklung ist ein neuartiges Ionentors mit Pulsschaltung, welches eine Verdopplung der Aufl{\"o}sung auf bis zu R > 100 bei gleicher Sensitivit{\"a}t erm{\"o}glichte. Eine denkbare Anwendung im Bereich der Peptidanalytik wurde mit beachtlichen Aufl{\"o}sungen der Peptide von R = 90 gezeigt.}, language = {de} }