Oxidation products of alpha-pinene and their electrical mobilities

2020 ◽  
Author(s):  
Aurora Skyttä ◽  
Lauri Ahonen ◽  
Runlong Cai ◽  
Juha Kangasluoma
Keyword(s):  
Gas Flow ◽  
Structural Information ◽  
Uv Light ◽  
Protein Complexes ◽  
Measurement Techniques ◽  
Oxidation Products ◽  
Electrical Mobility ◽  
Mobility Spectrum ◽  
Negative Mode ◽  
Alpha Pinene

<p>OXIDATION PRODUCTS OF ALPHA-PINENE AND THEIR ELECTRICAL MOBILITIES<br>A. SKYTTÄ 1 , L. AHONEN 1 , R. CAI 1 and J. KANGASLUOMA 1<br>1 Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of<br>Helsinki, Helsinki, 00140, Finland</p><p>α-pinene C10H16 is a monoterpene emitted by vegetation and its low volatile oxidation products are important source for secondary organic aerosols (SOA) in the atmosphere (Ehn et al., 2014). Because of the significant amount of α-pinene in the atmosphere, we investigated the oxidation<br>products of α-pinene.</p><p>In our setup we used parallel plate DMA (SEADM; (de la Mora et al., 2006)) at mobility resolution of about 80 coupled with APITOF-MS (Tofwerk AG; (Junninen et al., 2010)) and a flow tube system. A DMA can be used to measure the electrical mobility of the molecule or cluster and mass<br>spectrometer to measure the mass of those clusters. Based on the mass the chemical composition of the cluster can be determined.</p><p><br>The electrospray solution is sprayed through a thin capillary into the chamber through which neutral<br>sample is passed through. As a solute we used NaNO3 , NaI, LiCl and CH3CO2K dissolved in<br>methanol all charged in positive and negative mode. Particles that are charged by reagent ions are<br>led into the DMA via narrow inlet slit.</p><p><br>α-pinene was evaporated into a carrier gas flow and then oxidized using ozone produced from synthetic air with UV-light. The oxidation products are detected by charging them with ions sprayed from the electrospray solution and then directed into the DMA chamber. α-pinene oxidation products of oxidation state C10H16O2−7 were detected with almost all charger ions. Also, other products with different amounts of carbon and hydrogen were detected. Measurements made in negative mode were much more clear and because of this concentrated to examine them.</p><p><br>Mobility provides information on the structure of the compound. One cluster can have multiple peaks in the mobility spectrum if it has multiple different structures. In the mobility spectrum of C10H16O3 charged with NO3− we observe two peaks clearly separate mobility peaks that likely<br>correspond to two different structural isomers of the compound. We will present analysis of the mobility-mass measurements of α-pinene oxidation products, from where structural information will be obtained when combined to chemical reaction pathways and modeling of the electrical mobilities from the calculated structures.</p><p><br>REFERENCES<br>Ehn, M. et al, (2014). A large source of low-volatility secondary organic aerosol. (Nature, 506(7489), 476-+.<br>doi:10.1038/nature13032).</p><p><br>Fernández de la Mora et al, (2006). The potential of differen-<br>tial mobility analysis coupled to MS for the study of very large singly and multiply chargedproteins and protein complexes in the gas phase.<br>doi:10.1002/biot.200600070). (Biotechnology Journal, 1(9), 988-997.</p><p><br>Junninen, H. et al, (2010). A high-resolution mass spectrometer<br>to measure atmospheric ion composition. (Atmospheric Measurement Techniques, 3(4), 1039-<br>1053. doi:10.5194/amt-3-1039-2010).</p>

scholarly journals Surface-Induced Dissociation of Anionic vs Cationic Native-like Protein Complexes

2021 ◽  
Author(s):  
Sophie Harvey ◽  
Zachary VanAernum ◽  
Vicki Wysocki
Keyword(s):  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Charge Reduction ◽  
Surface Induced Dissociation ◽  
Negative Mode ◽  
Peak Broadening ◽  
Lower Charge ◽  
Positive Mode ◽  
Charge States

<p>Characterizing protein-protein interactions, stoichiometries, and subunit connectivity is key to understanding how subunits assemble in biologically relevant multi-subunit protein complexes. Native mass spectrometry (nMS) has emerged as a powerful tool to study protein complexes due to its low sample requirements and tolerance for heterogeneity. For such nMS studies, positive mode ionization is routinely used and charge reduction, through the addition of solution additives, is often used, as the resulting lower charge states are often more compact and considered more native like. When studied with surface-induced dissociation, charge reduced complexes often give increased structural information over their “normal-charged” counter parts. A disadvantage of charge-reduction is that increased adduction, and hence peak broadening, is often observed when charge-reducing solution additives are present. Recent studies have shown that protein complexes ionized using negative mode generally form in lower charge states relative to positive mode. Here we demonstrate that the lower charged protein complex anions, activated by SID in an ultrahigh mass range Orbitrap mass spectrometer, fragment in a manner consistent with their solved structure, hence providing substructural information. Negative mode ionization in ammonium acetate offers the advantage of charge reduction without the peak broadening associated with solution phase charge reduction additives and provides direct structural information, when coupled with SID. </p>

scholarly journals Surface-Induced Dissociation of Anionic vs Cationic Native-like Protein Complexes

2021 ◽  
Author(s):  
Sophie Harvey ◽  
Zachary VanAernum ◽  
Vicki Wysocki
Keyword(s):  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Charge Reduction ◽  
Surface Induced Dissociation ◽  
Negative Mode ◽  
Peak Broadening ◽  
Lower Charge ◽  
Positive Mode ◽  
Charge States

<p>Characterizing protein-protein interactions, stoichiometries, and subunit connectivity is key to understanding how subunits assemble in biologically relevant multi-subunit protein complexes. Native mass spectrometry (nMS) has emerged as a powerful tool to study protein complexes due to its low sample requirements and tolerance for heterogeneity. For such nMS studies, positive mode ionization is routinely used and charge reduction, through the addition of solution additives, is often used, as the resulting lower charge states are often more compact and considered more native like. When studied with surface-induced dissociation, charge reduced complexes often give increased structural information over their “normal-charged” counter parts. A disadvantage of charge-reduction is that increased adduction, and hence peak broadening, is often observed when charge-reducing solution additives are present. Recent studies have shown that protein complexes ionized using negative mode generally form in lower charge states relative to positive mode. Here we demonstrate that the lower charged protein complex anions, activated by SID in an ultrahigh mass range Orbitrap mass spectrometer, fragment in a manner consistent with their solved structure, hence providing substructural information. Negative mode ionization in ammonium acetate offers the advantage of charge reduction without the peak broadening associated with solution phase charge reduction additives and provides direct structural information, when coupled with SID. </p>

scholarly journals Surface-Induced Dissociation of Anionic vs Cationic Native-like Protein Complexes

2021 ◽  
Author(s):  
Sophie Harvey ◽  
Zachary VanAernum ◽  
Vicki Wysocki
Keyword(s):  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Charge Reduction ◽  
Surface Induced Dissociation ◽  
Negative Mode ◽  
Peak Broadening ◽  
Lower Charge ◽  
Positive Mode ◽  
Charge States

<p>Characterizing protein-protein interactions, stoichiometries, and subunit connectivity is key to understanding how subunits assemble in biologically relevant multi-subunit protein complexes. Native mass spectrometry (nMS) has emerged as a powerful tool to study protein complexes due to its low sample requirements and tolerance for heterogeneity. For such nMS studies, positive mode ionization is routinely used and charge reduction, through the addition of solution additives, is often used, as the resulting lower charge states are often more compact and considered more native like. When studied with surface-induced dissociation, charge reduced complexes often give increased structural information over their “normal-charged” counter parts. A disadvantage of charge-reduction is that increased adduction, and hence peak broadening, is often observed when charge-reducing solution additives are present. Recent studies have shown that protein complexes ionized using negative mode generally form in lower charge states relative to positive mode. Here we demonstrate that the lower charged protein complex anions, activated by SID in an ultrahigh mass range Orbitrap mass spectrometer, fragment in a manner consistent with their solved structure, hence providing substructural information. Negative mode ionization in ammonium acetate offers the advantage of charge reduction without the peak broadening associated with solution phase charge reduction additives and provides direct structural information, when coupled with SID. </p>

Rapid Online Buffer Exchange: A Method for Screening of Proteins, Protein Complexes, and Cell Lysates by Native Mass Spectrometry

2019 ◽  
Author(s):  
Zachary VanAernum ◽  
Florian Busch ◽  
Benjamin J. Jones ◽  
Mengxuan Jia ◽  
Zibo Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Speed ◽  
Structural Information ◽  
Protein Complexes ◽  
High Sensitivity ◽  
Native Mass Spectrometry ◽  
Structural Features ◽  
Consumer Products ◽  
Cell Lysates ◽  
Protein Expression And Purification

It is important to assess the identity and purity of proteins and protein complexes during and after protein purification to ensure that samples are of sufficient quality for further biochemical and structural characterization, as well as for use in consumer products, chemical processes, and therapeutics. Native mass spectrometry (nMS) has become an important tool in protein analysis due to its ability to retain non-covalent interactions during measurements, making it possible to obtain protein structural information with high sensitivity and at high speed. Interferences from the presence of non-volatiles are typically alleviated by offline buffer exchange, which is timeconsuming and difficult to automate. We provide a protocol for rapid online buffer exchange (OBE) nMS to directly screen structural features of pre-purified proteins, protein complexes, or clarified cell lysates. Information obtained by OBE nMS can be used for fast (<5 min) quality control and can further guide protein expression and purification optimization.

Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

2020 ◽  
Vol 27 (37) ◽  
pp. 6306-6355 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Drug Discovery ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Structural Features ◽  
Protein Protein Interactions ◽  
Modular Architecture ◽  
Post Translational Modifications ◽  
Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

Micro-Scale Flow Simulations and Permeability Estimation of Cleat Networks in Coal

2016 ◽  
Vol 846 ◽  
pp. 42-47
Author(s):  
J. Busse ◽  
S. Galindo Torres ◽  
Alexander Scheuermann ◽  
L. Li ◽  
D. Bringemeier
Keyword(s):  
Gas Flow ◽  
Structural Information ◽  
Porous Matrix ◽  
Groundwater Levels ◽  
Micro Scale ◽  
Wide Range ◽  
Boltzmann Method ◽  
The Impact ◽  
Flow Experiments

Coal mining raises a number of environmental and operational challenges, including the impact of changing groundwater levels and flow patterns on adjacent aquifer and surface water systems. Therefore it is of paramount importance to fully understand the flow of water and gases in the geological system on all scales. Flow in coal seams takes place on a wide range of scales from large faults and fractures to the micro-structure of a porous matrix intersected by a characteristic cleat network. On the micro-scale these cleats provide the principal source of permeability for fluid and gas flow. Description of the behaviour of the flow within the network is challenging due to the variations in number, sizing, orientation, aperture and connectivity at a given site. This paper presents a methodology to simulate flow and investigate the permeability of fractured media. A profound characterization of the geometry of the cleat network in micrometer resolution can be derived by CT-scans. The structural information is fed into a Lattice Boltzmann Method (LBM) based model that allows the implementation of virtual flow experiments. With the application of suitable hydraulic boundary conditions the full permeability tensor can be calculated in 3D.

scholarly journals Univariate and multivariate DMS calibration for a single analyte

2019 ◽  
Vol 100 ◽  
pp. 00078
Author(s):  
Andrzej Szczurek ◽  
Monika Maciejewska ◽  
Żaneta Zajiczek
Keyword(s):  
Electric Fields ◽  
Gas Flow ◽  
Chemical Warfare Agents ◽  
Calibration Procedure ◽  
Quantitative Information ◽  
Multivariate Approach ◽  
Least Squares Regression ◽  
Differential Mobility ◽  
Mobility Spectrum ◽  
Warfare Agents

Differential mobility spectrometry (DMS) is a promising measurement technique. It is used in the detection of chemical warfare agents, explosives, drugs, and volatile organic compounds. The measurement principle is based on separation of gas-phase ions according to their differential mobility in alternating low and high electric fields. The DMS measurement result is a two dimensional spectrum of ion current displayed as a function of separation voltage and compensation voltage. The DMS spectral peaks, in terms of their height, location and width, are affected by gas sample composition, separation field and the gas flow rate. In this work, there is presented the calibration procedure which utilises the univariate and multivariate approach to differential ion mobility spectrum. We demonstrated the possibility of a successful retrieval of quantitative information using partial least squares regression as well as univariate linear regression. However, the multivariate approach outperformed the univariate one in terms of the quality of the model and the concentration prediction accuracy.

scholarly journals Atmospheric β-Caryophyllene-Derived Ozonolysis Products at Interfaces

2018 ◽  
Author(s):  
Ariana Gray Bé ◽  
Hilary M. Chase ◽  
Liu, Yangdongliu ◽  
Mary Alice Upshur ◽  
Zhang, Yue ◽  
...  
Keyword(s):  
Gas Phase ◽  
Structural Information ◽  
High Surface ◽  
Organic Aerosol ◽  
Oxidation Products ◽  
Laboratory Studies ◽  
Sum Frequency ◽  
Sum Frequency Generation Spectroscopy ◽  
Surface Active ◽  
Cloud Activation

<p>By integrating organic synthesis, secondary organic aerosol synthesis and collection, DFT calculations, and vibrational sum frequency generation spectroscopy, we identify close spectral matches between the surface vibrational spectra of β-caryophyllene-derived secondary organic material and those of β-caryophyllene aldehyde and β-caryophyllonic acid at various interfaces. Combined with the record high surface tension depression described previously for these same oxidation products, we discuss possibilities for an intrinsically chemical origin for cloud activation by terpene-derived surfactants. Although the present study does not unequivocally identify the synthesized and analyzed oxidation products on the β-caryophyllenederived SOM surfaces, these two compounds appear to be the most surface active out of the series, and have also been foci of previous β-caryophyllene field and laboratory studies.</p><p>An orientation analysis by phase-resolved SFG spectroscopy reveals a “pincer-like” configuration of the β-caryophyllene oxidation products, albeit on a model quartz surface, that somewhat resembles the orientation of inverse double-tailed surfactants at the surfaces biological systems. The structural information suggests that the less polar moiety of a surface-localized oxidation product, such as those studied here, may be the first site-of-contact for a gas-phase molecule approaching an SOA particle containing surface-active β-caryophyllene oxidation products.</p>

scholarly journals Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy

2021 ◽  
Author(s):  
Ingrid Guarnetti Prandi ◽  
Vladislav Sláma ◽  
Cristina Pecorilla ◽  
Lorenzo Cupellini ◽  
Benedetta Mennucci
Keyword(s):  
Structural Model ◽  
Light Harvesting ◽  
Structural Information ◽  
Protein Complexes ◽  
Complex Stress ◽  
Main Function ◽  
Light Harvesting Complexes ◽  
Light Harvesting Complex ◽  
Pigment Protein Complexes ◽  
Computational Strategy

Light-harvesting complexes (LHCs) are pigment-protein complexes whose main function is to capture sunlight and transfer the energy to reaction centers of photosystems. In response to varying light conditions, LH complexes also play photoregulation and photoprotection roles. In algae and mosses, a sub-family of LHCs, Light-Harvesting complex stress related (LHCSR), is responsible for photoprotective quenching. Despite their functional and evolutionary importance, no direct structural information on LHCSRs is available that can explain their unique properties. In this work we propose a structural model of LHCSR1 from the moss P. Patens, obtained through an integrated computational strategy that combines homology modeling, molecular dynamics, and multiscale quantum chemical calculations. The model is validated by reproducing the spectral properties of LHCSR1. Our model reveals the structural specificity of LHCSR1, as compared with the CP29 LH complex, and poses the basis for understanding photoprotective quenching in mosses.

scholarly journals Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) for on- and off-line analysis of atmospheric gas and aerosol species

2016 ◽  
Author(s):  
Jordan E. Krechmer ◽  
Michael Groessl ◽  
Xuan Zhang ◽  
Heikki Junninen ◽  
Paola Massoli ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Measurement Techniques ◽  
Molecular Ions ◽  
Molecular Structures ◽  
Water Soluble ◽  
Oxidation Products ◽  
Time Resolved ◽  
Organic Species

Abstract. Measurement techniques that provide molecular-level information are needed to elucidate the multi-phase processes that produce secondary organic aerosol (SOA) species in the atmosphere. Here we demonstrate the application of ion mobility spectrometry-mass spectrometry (IMS-MS) to the simultaneous characterization of the elemental composition and molecular structures of organic species in the gas and particulate phases. Molecular ions of gas-phase organic species are measured online with IMS-MS after ionization with a custom build nitrate chemical ionization (CI) source. This CI-IMS-MS technique is used to obtain time-resolved measurements (5 min) of highly oxidized organic molecules during the 2013 Southern Oxidant and Aerosol Study (SOAS) ambient field campaign in the forested SE US. The ambient IMS-MS signals are consistent with laboratory IMS-MS spectra obtained from single-component carboxylic acids and multicomponent mixtures of isoprene and monoterpene oxidation products. Mass-mobility correlations in the 2-dimensional IMS-MS space provide a means of identifying ions with similar molecular structures within complex mass spectra and are used to separate and identify monoterpene oxidation products in the ambient data that are produced from different chemical pathways. Water-soluble organic carbon (WSOC) constituents of fine aerosol particles that are not resolvable with standard analytical separation methods, such as liquid chromatography (LC), are shown to be separable with IMS-MS coupled to an electrospray ionization (ESI) source. The capability to use ion mobility to differentiate between isomers is demonstrated for organosulfates derived from the reactive uptake of isomers of isoprene epoxydiols (IEPOX) onto wet acidic sulfate aerosol. Controlled fragmentation of precursor ions by collisional dissociation (CID) in the transfer region between the IMS and the MS is used to validate MS peak assignments, elucidate structures of oligomers, and confirm the presence of the organosulfate functional group.

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