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Journal articles on the topic 'Collision Cross Section (CCS)'

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Author: Grafiati

Published: 10 December 2022

Last updated: 29 January 2023

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1

Yang, Fan, Denice van Herwerden, Hugues Preud’homme, and Saer Samanipour. "Collision Cross Section Prediction with Molecular Fingerprint Using Machine Learning." Molecules 27, no. 19 (September 29, 2022): 6424. http://dx.doi.org/10.3390/molecules27196424.

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High-resolution mass spectrometry is a promising technique in non-target screening (NTS) to monitor contaminants of emerging concern in complex samples. Current chemical identification strategies in NTS experiments typically depend on spectral libraries, chemical databases, and in silico fragmentation tools. However, small molecule identification remains challenging due to the lack of orthogonal sources of information (e.g., unique fragments). Collision cross section (CCS) values measured by ion mobility spectrometry (IMS) offer an additional identification dimension to increase the confidence level. Thanks to the advances in analytical instrumentation, an increasing application of IMS hybrid with high-resolution mass spectrometry (HRMS) in NTS has been reported in the recent decades. Several CCS prediction tools have been developed. However, limited CCS prediction methods were based on a large scale of chemical classes and cross-platform CCS measurements. We successfully developed two prediction models using a random forest machine learning algorithm. One of the approaches was based on chemicals’ super classes; the other model was direct CCS prediction using molecular fingerprint. Over 13,324 CCS values from six different laboratories and PubChem using a variety of ion-mobility separation techniques were used for training and testing the models. The test accuracy for all the prediction models was over 0.85, and the median of relative residual was around 2.2%. The models can be applied to different IMS platforms to eliminate false positives in small molecule identification.

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2

Soper-Hopper, M. T., J. Vandegrift, E. S. Baker, and F. M. Fernández. "Metabolite collision cross section prediction without energy-minimized structures." Analyst 145, no. 16 (2020): 5414–18. http://dx.doi.org/10.1039/d0an00198h.

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3

Li, Dayu, Yang Tang, and Wei Xu. "Ion collision cross section measurements in Fourier transform-based mass analyzers." Analyst 141, no. 12 (2016): 3554–61. http://dx.doi.org/10.1039/c5an02164b.

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4

Lippens, Jennifer L., Srivathsan V. Ranganathan, Rebecca J. D'Esposito, and Daniele Fabris. "Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry." Analyst 141, no. 13 (2016): 4084–99. http://dx.doi.org/10.1039/c6an00453a.

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This study explored the use of modular nucleic acid (NA) standards to generate calibration curves capable of translating primary ion mobility readouts into corresponding collision cross section (CCS) data.

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5

Hernández-Mesa, Maykel, Bruno Le Bizec, Fabrice Monteau, Ana M. García-Campaña, and Gaud Dervilly-Pinel. "Collision Cross Section (CCS) Database: An Additional Measure to Characterize Steroids." Analytical Chemistry 90, no. 7 (March 12, 2018): 4616–25. http://dx.doi.org/10.1021/acs.analchem.7b05117.

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6

Forsythe, Jay G., Anton S. Petrov, Chelsea A. Walker, Samuel J. Allen, Jarrod S. Pellissier, Matthew F. Bush, Nicholas V. Hud, and Facundo M. Fernández. "Collision cross section calibrants for negative ion mode traveling wave ion mobility-mass spectrometry." Analyst 140, no. 20 (2015): 6853–61. http://dx.doi.org/10.1039/c5an00946d.

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7

Guntner, Armin Sebastian, Thomas Bögl, Franz Mlynek, and Wolfgang Buchberger. "Large-Scale Evaluation of Collision Cross Sections to Investigate Blood-Brain Barrier Permeation of Drugs." Pharmaceutics 13, no. 12 (December 13, 2021): 2141. http://dx.doi.org/10.3390/pharmaceutics13122141.

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Successful drug administration to the central nervous system requires accurate adjustment of the drugs’ molecular properties. Therefore, structure-derived descriptors of potential brain therapeutic agents are essential for an early evaluation of pharmacokinetics during drug development. The collision cross section (CCS) of molecules was recently introduced as a novel measurable parameter to describe blood-brain barrier (BBB) permeation. This descriptor combines molecular information about mass, structure, volume, branching and flexibility. As these chemical properties are known to influence cerebral pharmacokinetics, CCS determination of new drug candidates may provide important additional spatial information to support existing models of BBB penetration of drugs. Besides measuring CCS, calculation is also possible; but however, the reliability of computed CCS values for an evaluation of BBB permeation has not yet been fully investigated. In this work, prediction tools based on machine learning were used to compute CCS values of a large number of compounds listed in drug libraries as negative or positive with respect to brain penetration (BBB+ and BBB− compounds). Statistical evaluation of computed CCS and several other descriptors could prove the high value of CCS. Further, CCS-deduced maximum molecular size of BBB+ drugs matched the dimensions of BBB pores. A threshold for transcellular penetration and possible permeation through pore-like openings of cellular tight-junctions is suggested. In sum, CCS evaluation with modern in silico tools shows high potential for its use in the drug development process.

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8

Schroeder, Mark, Sven W. Meyer, Heino M. Heyman, Aiko Barsch, and Lloyd W. Sumner. "Generation of a Collision Cross Section Library for Multi-Dimensional Plant Metabolomics Using UHPLC-Trapped Ion Mobility-MS/MS." Metabolites 10, no. 1 (December 24, 2019): 13. http://dx.doi.org/10.3390/metabo10010013.

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The utility of metabolomics is well documented; however, its full scientific promise has not yet been realized due to multiple technical challenges. These grand challenges include accurate chemical identification of all observable metabolites and the limiting depth-of-coverage of current metabolomics methods. Here, we report a combinatorial solution to aid in both grand challenges using UHPLC-trapped ion mobility spectrometry coupled to tandem mass spectrometry (UHPLC-TIMS-TOF-MS). TIMS offers additional depth-of-coverage through increased peak capacities realized with the multi-dimensional UHPLC-TIMS separations. Metabolite identification confidence is simultaneously enhanced by incorporating orthogonal collision cross section (CCS) data matching. To facilitate metabolite identifications, we created a CCS library of 146 plant natural products. This library was generated using TIMS with N2 drift gas to record the TIMSCCSN2 of plant natural products with a high degree of reproducibility; i.e., average RSD = 0.10%. The robustness of TIMSCCSN2 data matching was tested using authentic standards spiked into complex plant extracts, and the precision of CCS measurements were determined to be independent of matrix affects. The utility of the UHPLC-TIMS-TOF-MS/MS in metabolomics was then demonstrated using extracts from the model legume Medicago truncatula and metabolites were confidently identified based on retention time, accurate mass, molecular formula, and CCS.

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9

Tejada-Casado, Carmen, Maykel Hernández-Mesa, Fabrice Monteau, Francisco J. Lara, Monsalud del Olmo-Iruela, Ana M. García-Campaña, Bruno Le Bizec, and Gaud Dervilly-Pinel. "Collision cross section (CCS) as a complementary parameter to characterize human and veterinary drugs." Analytica Chimica Acta 1043 (December 2018): 52–63. http://dx.doi.org/10.1016/j.aca.2018.09.065.

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10

Wang, Jian-Ying, Ying-Hao Yin, Jia-Yi Zheng, Li-Fang Liu, Zhong-Ping Yao, and Gui-Zhong Xin. "Least absolute shrinkage and selection operator-based prediction of collision cross section values for ion mobility mass spectrometric analysis of lipids." Analyst 147, no. 6 (2022): 1236–44. http://dx.doi.org/10.1039/d1an02161c.

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11

Steigenberger, Barbara, Henk W. P. van den Toorn, Emiel Bijl, Jean-François Greisch, Oliver Räther, Markus Lubeck, Roland J. Pieters, Albert J. R. Heck, and Richard A. Scheltema. "Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry." Molecular & Cellular Proteomics 19, no. 10 (July 21, 2020): 1677–87. http://dx.doi.org/10.1074/mcp.ra120.002094.

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Ion mobility separates molecules in the gas-phase based on their physico-chemical properties, providing information about their size as collisional cross-sections. The timsTOF Pro combines trapped ion mobility with a quadrupole, collision cell and a TOF mass analyzer, to probe ions at high speeds with on-the-fly fragmentation. Here, we show that on this platform ion mobility is beneficial for cross-linking MS (XL-MS). Cross-linking reagents covalently link amino acids in proximity, resulting in peptide pairs after proteolytic digestion. These cross-linked peptides are typically present at low abundance in the background of normal peptides, which can partially be resolved by using enrichable cross-linking reagents. Even with a very efficient enrichable cross-linking reagent, like PhoX, the analysis of cross-linked peptides is still hampered by the co-enrichment of peptides connected to a partially hydrolyzed reagent – termed mono-linked peptides. For experiments aiming to uncover protein-protein interactions these are unwanted byproducts. Here, we demonstrate that gas-phase separation by ion mobility enables the separation of mono-linked peptides from cross-linked peptide pairs. A clear partition between these two classes is observed at a CCS of 500 Å2 and a monoisotopic mass of 2 kDa, which can be used for targeted precursor selection. A total of 50-70% of the mono-linked peptides are prevented from sequencing, allowing the analysis to focus on sequencing the relevant cross-linked peptide pairs. In applications to both simple proteins and protein mixtures and a complete highly complex lysate this approach provides a substantial increase in detected cross-linked peptides.

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12

Hu, Miao, Linzhou Zhang, Shan He, Chunming Xu, and Quan Shi. "Collision cross section (CCS) measurement by ion cyclotron resonance mass spectrometry with short-time Fourier transform." Rapid Communications in Mass Spectrometry 32, no. 9 (April 14, 2018): 751–61. http://dx.doi.org/10.1002/rcm.8096.

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13

Duez, Quentin, Romain Liénard, Sébastien Moins, Vincent Lemaur, Olivier Coulembier, Jérôme Cornil, Pascal Gerbaux, and Julien De Winter. "One Step Further in the Characterization of Synthetic Polymers by Ion Mobility Mass Spectrometry: Evaluating the Contribution of End-groups." Polymers 11, no. 4 (April 16, 2019): 688. http://dx.doi.org/10.3390/polym11040688.

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Several families of polymers possessing various end-groups are characterized by ion mobility mass spectrometry (IMMS). A significant contribution of the end-groups to the ion collision cross section (CCS) is observed, although their role is neglected in current fitting models described in literature. Comparing polymers prepared from different synthetic procedures might thus, be misleading with the current theoretical treatments. We show that this issue is alleviated by comparing the CCS of various polymer ions (polyesters and polyethers) as a function of the number of atoms in the macroion instead of the usual representation involving the degree of polymerization. Finally, we extract the atom number density from the spectra which gives us the possibility to evaluate the compaction of polymer ions, and by extension to discern isomeric polymers.

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14

Xia, Jinmei, Wenhai Xiao, Xihuang Lin, Yiduo Zhou, Peng Qiu, Hongkun Si, Xiaorong Wu, Siwen Niu, Zhuhua Luo, and Xianwen Yang. "Ion Mobility-Derived Collision Cross-Sections Add Extra Capability in Distinguishing Isomers and Compounds with Similar Retention Times: The Case of Aphidicolanes." Marine Drugs 20, no. 9 (August 23, 2022): 541. http://dx.doi.org/10.3390/md20090541.

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The hyphenation of ion mobility spectrometry with high-resolution mass spectrometry has been widely used in the characterization of various metabolites. Nevertheless, such a powerful tool remains largely unexplored in natural products research, possibly mainly due to the lack of available compounds. To evaluate the ability of collision cross-sections (CCSs) in characterizing compounds, especially isomeric natural products, here we measured and compared the traveling-wave IMS-derived nitrogen CCS values for 75 marine-derived aphidicolanes. We established a CCS database for these compounds which contained 227 CCS values of different adducts. When comparing the CCS differences, 36 of 57 pairs (over 60%) of chromatographically neighboring compounds showed a ΔCCS over 2%. What is more, 64 of 104 isomeric pairs (over 60%) of aphidicolanes can be distinguished by their CCS values, and 13 of 18 pairs (over 70%) of chromatographically indistinguishable isomers can be differentiated from the mobility dimension. Our results strongly supported CCS as an important parameter with good orthogonality and complementarity with retention time. CCS is expected to play an important role in distinguishing complex and diverse marine natural products.

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15

Struwe, W. B., J. L. Benesch, D. J. Harvey, and K. Pagel. "Collision cross sections of high-mannose N-glycans in commonly observed adduct states – identification of gas-phase conformers unique to [M − H]− ions." Analyst 140, no. 20 (2015): 6799–803. http://dx.doi.org/10.1039/c5an01092f.

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We report collision cross sections (CCS) of high-mannose N-glycans as [M + Na]⁺, [M + K]⁺, [M + H]⁺, [M + Cl]⁻, [M + H₂PO₄]⁻ and [M − H]⁻ ions, measured by drift tube (DT) ion mobility-mass spectrometry (IM-MS) in helium and nitrogen gases.

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16

Comby-Zerbino, Clothilde, Martina Perić, Franck Bertorelle, Fabien Chirot, Philippe Dugourd, Vlasta Bonačić-Koutecký, and Rodolphe Antoine. "Catenane Structures of Homoleptic Thioglycolic Acid-Protected Gold Nanoclusters Evidenced by Ion Mobility-Mass Spectrometry and DFT Calculations." Nanomaterials 9, no. 3 (March 19, 2019): 457. http://dx.doi.org/10.3390/nano9030457.

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Thiolate-protected metal nanoclusters have highly size- and structure-dependent physicochemical properties and are a promising class of nanomaterials. As a consequence, for the rationalization of their synthesis and for the design of new clusters with tailored properties, a precise characterization of their composition and structure at the atomic level is required. We report a combined ion mobility-mass spectrometry approach with density functional theory (DFT) calculations for determination of the structural and optical properties of ultra-small gold nanoclusters protected by thioglycolic acid (TGA) as ligand molecules, Au10(TGA)10. Collision cross-section (CCS) measurements are reported for two charge states. DFT optimized geometrical structures are used to compute CCSs. The comparison of the experimentally- and theoretically-determined CCSs allows concluding that such nanoclusters have catenane structures.

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17

Yang, Feifei, Boxue Chen, Meiting Jiang, Huimin Wang, Ying Hu, Hongda Wang, Xiaoyan Xu, Xiumei Gao, and Wenzhi Yang. "Integrating Enhanced Profiling and Chemometrics to Unveil the Potential Markers for Differentiating among the Leaves of Panax ginseng, P. quinquefolius, and P. notoginseng by Ultra-High Performance Liquid Chromatography/Ion Mobility-Quadrupole Time-of-Flight Mass Spectrometry." Molecules 27, no. 17 (August 29, 2022): 5549. http://dx.doi.org/10.3390/molecules27175549.

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The leaves of Panax species (e.g., Panax ginseng-PGL, P. quinquefolius-PQL, and P. notoginseng-PNL) can serve as a source for healthcare products. Comprehensive characterization and unveiling of the metabolomic difference among PGL, PQL, and PNL are critical to ensure their correct use. For this purpose, enhanced profiling and chemometrics were integrated to probe into the ginsenoside markers for PGL/PQL/PNL by ultra-high performance liquid chromatography/ion mobility-quadrupole time-of-flight mass spectrometry (UHPLC/IM-QTOF-MS). A hybrid scan approach (HDMSE-HDDDA) was established achieving the dimension-enhanced metabolic profiling, with 342 saponins identified or tentatively characterized from PGL/PQL/PNL. Multivariate statistical analysis (33 batches of leaf samples) could unveil 42 marker saponins, and the characteristic ginsenosides diagnostic for differentiating among PGL/PQL/PNL were primarily established. Compared with the single DDA or DIA, the HDMSE-HDDDA hybrid scan approach could balance between the metabolome coverage and spectral reliability, leading to high-definition MS spectra and the additional collision-cross section (CCS) useful to differentiate isomers.

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18

Schweighuber, Andrea, Jörg Fischer, and Wolfgang Buchberger. "Differentiation of Polyamide 6, 6.6, and 12 Contaminations in Polyolefin-Recyclates Using HPLC Coupled to Drift-Tube Ion- Mobility Quadrupole Time-of-Flight Mass Spectrometry." Polymers 13, no. 12 (June 21, 2021): 2032. http://dx.doi.org/10.3390/polym13122032.

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Recycling is a current hot topic with a focus especially on plastics. The quality of such plastic recyclates is of utmost importance for further processing because impurities lead to a reduction thereof. Contaminations originating from other polymers are highly problematic due to their immiscibility with the recyclate, leading to possible product failures. Therefore, methods for the determination of polymer impurities in recyclates should be investigated. In this paper, an approach for the identification of three different polyamide grades (polyamide 6, 6.6, and 12) is presented, applicable for the analysis of polyolefin-recyclates. An HPLC equipped with a drift-tube ion-mobility QTOF-MS was used for the identification and differentiation of compounds originating from the polyamides, which were then used as markers. These marker compounds are specific for each type and can be identified by their corresponding value of the collision cross section (CCS). After a simple sample preparation, all three types of polyamides were identified within one measurement. In particular, the problematic differentiation of polyamide 6 and 6.6 was easily made possible.

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19

Dickinson, Quinn, and Jesse G. Meyer. "Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences." PLOS Computational Biology 18, no. 1 (January 28, 2022): e1009736. http://dx.doi.org/10.1371/journal.pcbi.1009736.

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Machine learning with multi-layered artificial neural networks, also known as “deep learning,” is effective for making biological predictions. However, model interpretation is challenging, especially for sequential input data used with recurrent neural network architectures. Here, we introduce a framework called “Positional SHAP” (PoSHAP) to interpret models trained from biological sequences by utilizing SHapely Additive exPlanations (SHAP) to generate positional model interpretations. We demonstrate this using three long short-term memory (LSTM) regression models that predict peptide properties, including binding affinity to major histocompatibility complexes (MHC), and collisional cross section (CCS) measured by ion mobility spectrometry. Interpretation of these models with PoSHAP reproduced MHC class I (rhesus macaque Mamu-A1*001 and human A*11:01) peptide binding motifs, reflected known properties of peptide CCS, and provided new insights into interpositional dependencies of amino acid interactions. PoSHAP should have widespread utility for interpreting a variety of models trained from biological sequences.

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20

Lacalle-Bergeron, Leticia, Tania Portolés, Francisco J. López, Juan Vicente Sancho, Carolina Ortega-Azorín, Eva M. Asensio, Oscar Coltell, and Dolores Corella. "Ultra-Performance Liquid Chromatography-Ion Mobility Separation-Quadruple Time-of-Flight MS (UHPLC-IMS-QTOF MS) Metabolomics for Short-Term Biomarker Discovery of Orange Intake: A Randomized, Controlled Crossover Study." Nutrients 12, no. 7 (June 29, 2020): 1916. http://dx.doi.org/10.3390/nu12071916.

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A major problem with dietary assessments is their subjective nature. Untargeted metabolomics and new technologies can shed light on this issue and provide a more complete picture of dietary intake by measuring the profile of metabolites in biological samples. Oranges are one of the most consumed fruits in the world, and therefore one of the most studied for their properties. The aim of this work was the application of untargeted metabolomics approach with the novel combination of ion mobility separation coupled to high resolution mass spectrometry (IMS-HRMS) and study the advantages that this technique can bring to the area of dietary biomarker discovery, with the specific case of biomarkers associated with orange consumption (Citrus reticulata) in plasma samples taken during an acute intervention study (consisting of a randomized, controlled crossover trial in healthy individuals). A total of six markers of acute orange consumption, including betonicines and conjugated flavonoids, were identified with the experimental data and previous literature, demonstrating the advantages of ion mobility in the identification of dietary biomarkers and the benefits that an additional structural descriptor, as the collision cross section value (CCS), can provide in this area.

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21

Rigaud, Sébastien, Abdouramane Dosso, David Lesur, Dominique Cailleu, David Mathiron, Serge Pilard, Christine Cézard, and Florence Djedaini-Pilard. "Mass Spectrometry, Ion Mobility Separation and Molecular Modelling: A Powerful Combination for the Structural Characterisation of Substituted Cyclodextrins Mixtures." International Journal of Molecular Sciences 23, no. 21 (November 1, 2022): 13352. http://dx.doi.org/10.3390/ijms232113352.

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When working on the synthesis of substituted cyclodextrins (CDs), the main challenge remains the analysis of the reaction media content. Our objective in this study was to fully characterise a complex isomers mixture of Lipidyl-βCDs (LipβCD) obtained with a degree of substitution 1 (DS = 1) from a one-step synthesis pathway. The benefit of tandem mass spectrometry (MS/MS) and ion mobility separation hyphenated with mass spectrometry (IM-MS) was investigated. The MS/MS fragment ion‘s relative intensities were analysed by principal component analysis (PCA) to discriminate isomers. The arrival time distribution (ATD) of each isomer was recorded using a travelling wave ion mobility (TWIM) cell allowing the determination of their respective experimental collision cross section (CCSexp). The comparison with the predicted theoretical CCS (CCSth) obtained from theoretical calculations propose a regioisomer assignment according to the βCD hydroxyl position (2, 3, or 6) involved in the reaction. These results were validated by extensive NMR structural analyses of pure isomers combined with molecular dynamics simulations. This innovative approach seems to be a promising tool to elucidate complex isomer mixtures such as substituted cyclodextrin derivatives.

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22

Boschmans, Jasper, Sam Jacobs, Jonathan P. Williams, Martin Palmer, Keith Richardson, Kevin Giles, Cris Lapthorn, Wouter A. Herrebout, Filip Lemière, and Frank Sobott. "Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers." Analyst 141, no. 13 (2016): 4044–54. http://dx.doi.org/10.1039/c5an02456k.

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23

Hernández-Mesa, Maykel, David Ropartz, Ana M. García-Campaña, Hélène Rogniaux, Gaud Dervilly-Pinel, and Bruno Le Bizec. "Ion Mobility Spectrometry in Food Analysis: Principles, Current Applications and Future Trends." Molecules 24, no. 15 (July 25, 2019): 2706. http://dx.doi.org/10.3390/molecules24152706.

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In the last decade, ion mobility spectrometry (IMS) has reemerged as an analytical separation technique, especially due to the commercialization of ion mobility mass spectrometers. Its applicability has been extended beyond classical applications such as the determination of chemical warfare agents and nowadays it is widely used for the characterization of biomolecules (e.g., proteins, glycans, lipids, etc.) and, more recently, of small molecules (e.g., metabolites, xenobiotics, etc.). Following this trend, the interest in this technique is growing among researchers from different fields including food science. Several advantages are attributed to IMS when integrated in traditional liquid chromatography (LC) and gas chromatography (GC) mass spectrometry (MS) workflows: (1) it improves method selectivity by providing an additional separation dimension that allows the separation of isobaric and isomeric compounds; (2) it increases method sensitivity by isolating the compounds of interest from background noise; (3) and it provides complementary information to mass spectra and retention time, the so-called collision cross section (CCS), so compounds can be identified with more confidence, either in targeted or non-targeted approaches. In this context, the number of applications focused on food analysis has increased exponentially in the last few years. This review provides an overview of the current status of IMS technology and its applicability in different areas of food analysis (i.e., food composition, process control, authentication, adulteration and safety).

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24

Prianichnikov, Nikita, Heiner Koch, Scarlet Koch, Markus Lubeck, Raphael Heilig, Sven Brehmer, Roman Fischer, and Jürgen Cox. "MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics." Molecular & Cellular Proteomics 19, no. 6 (March 10, 2020): 1058–69. http://dx.doi.org/10.1074/mcp.tir119.001720.

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Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides and proteins in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.

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25

Yue, Zi-Xuan, and Jun Cao. "A Rapid and Sensitive Method for the Simultaneous Determination of Multipolar Compounds in Plant Tea by Supercritical Fluid Chromatography Coupled to Ion Mobility Quadrupole Time-of-Flight Mass Spectrometry." Foods 11, no. 1 (January 1, 2022): 111. http://dx.doi.org/10.3390/foods11010111.

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In this study, matrix solid phase dispersion (MSPD) microextraction combined with supercritical fluid chromatography-ion mobility quadrupole time-of-flight mass spectrometry (SFC/IM-QTOF-MS) was used to analyze the multipolar compounds in plant tea. The parameters of stationary phase, mobile phase, make-up solution, temperature, and back pressure were optimized. The target analytes were gradient eluted in 8 min by supercritical CO2 on a Zorbax RX-SIL column. Collisional Cross Section (CCS) values for single and multiple fields were measured. A series of validation studies were carried out under the optimal conditions, and the linear relationship and reproducibility were good. The limits of detection were 1.4 (Scoparone (1))~70 (Naringenin (4)) ng/mL, and the limits of quantification were 4.7 (Scoparone (1))~241 (Naringenin (4)) ng/mL. The recoveries of most compounds ranged from 60.7% to 127%. As a consequence, the proposed method was used for the separation and quantitative analysis of active ingredients in caulis dendrobii.

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26

Khadri, F., A. Chefai, and K. Hammami. "Low-temperature rate constants and radiative transfer for rotational de-excitation of C5S by collision with He." Monthly Notices of the Royal Astronomical Society 498, no. 4 (September 10, 2020): 5159–65. http://dx.doi.org/10.1093/mnras/staa2746.

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ABSTRACT The C5S molecule is the largest member of the series of sulphur-containing carbon chains CnS observed in space. Given the lack of data concerning this molecule, we computed rate coefficients of C5S(1Σ+) induced by collision with He. These rates are obtained for thermal temperature below 100 K by mean of a new two-dimensional potential energy surface (PES) calculated with the explicit correlated coupled cluster with single, double, and pertubative triple excitation (ccsd(t)-f12) ab initio approach and the aug-cc-pVTZ basis sets. The C5S–He PES presents three minimums of −59.726, −55.355, and −36.506 cm−1 below its dissociation limit. Using this PES, the integral cross-sections are performed in the close-coupling (CC) and coupled-state (CS) quantum time independent formalisms for $E_\mathrm{ c}\le 500 \, \mathrm{ cm}^{-1}$ and J ≤ 13 (for CC) and J ≤ 50 (for CS). By averaging these cross-sections we obtained the downward rate coefficients. The new collisional data are used to simulate the excitation of C5S in the circumstellar gas. We obtain the excitation and brightness temperatures of the four lines observed towards the IRC+10216 which confirms the necessity of using radiative transfer calculations to accurately determine C5S abundance since the local thermodynamic equilibrium conditions are not fulfilled. The new collisional data should help to estimate the abundance of C5S in several interstellar regions.

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27

Santander, Carlos, Otoniel Denis-Alpizar, and Carlos Cárdenas. "Deexcitation rate coefficients of C₃ by collision with H₂ at low temperatures." Astronomy & Astrophysics 657 (January 2022): A55. http://dx.doi.org/10.1051/0004-6361/202142434.

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Context. An accurate analysis of the physical-chemical conditions in the regions of the interstellar medium in which C3 is observed requires knowing the collisional rate coefficients of this molecule with He, H2, electrons, and H. Aims. The main goals of this study are to present the first potential energy surface for the C3 +H2 complex, to study the dynamics of the system, and to report a set of rate coefficients at low temperature for the lower rotational states of C3 with para- and ortho-H2. Methods. A large grid of ab initio energies was computed at the explicitly correlated coupled-cluster with single-, double-, and perturbative triple-excitation level of theory, together with the augmented correlation-consistent quadruple zeta basis set (CCSD(T)-F12a/aug-cc-pVQZ). This grid of energies was fit to an analytical function. The potential energy surface was employed in close-coupling calculations at low collisional energies. Results. We present a high-level four-dimensional potential energy surface (PES) for studying the collision of C3 with H2. The global minimum of the surface is found in the linear HH-CCC configuration. Rotational deexcitation state-to-state cross sections of C3 by collision with para- and ortho-H2 are computed. Furthermore, a reduced two-dimensional surface is developed by averaging the surface over the orientation of H2. The cross sections for the collision with para-H2 using this approximation and those from the four-dimensional PES agree excellently. Finally, a set of rotational rate coefficients for the collision of C3 with para- and ortho-H2 at low temperatures are reported.

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France, Aidan P., Lukasz G. Migas, Eleanor Sinclair, Bruno Bellina, and Perdita E. Barran. "Using Collision Cross Section Distributions to Assess the Distribution of Collision Cross Section Values." Analytical Chemistry 92, no. 6 (February 13, 2020): 4340–48. http://dx.doi.org/10.1021/acs.analchem.9b05130.

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May, Jody C., Caleb B. Morris, and John A. McLean. "Ion Mobility Collision Cross Section Compendium." Analytical Chemistry 89, no. 2 (December 28, 2016): 1032–44. http://dx.doi.org/10.1021/acs.analchem.6b04905.

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Zanotto, Leandro, Gabriel Heerdt, Paulo C. T. Souza, Guido Araujo, and Munir S. Skaf. "High performance collision cross section calculation-HPCCS." Journal of Computational Chemistry 39, no. 21 (March 2, 2018): 1675–81. http://dx.doi.org/10.1002/jcc.25199.

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Lee, Gyeong Won, and Young-Dae Jung. "Influence of Electron Exchange and Quantum Shielding on the Elastic Collisions in Quantum Plasmas." Zeitschrift für Naturforschung A 68, no. 10-11 (November 1, 2013): 686–92. http://dx.doi.org/10.5560/zna.2013-0055.

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The influence of electron exchange and quantum shielding on the elastic electron-ion collision is investigated in degenerate quantum plasmas. The second-order eikonal method and effective screened potential are employed to obtain the scattering phase shift and collision cross section as functions of the impact parameter, collision energy, electron-exchange parameter, Fermi energy, and plasmon energy. It is found that the electron-exchange effect enhances the eikonal scattering phase shift as well as the eikonal collision cross section in quantum plasmas. The maximum position of the differential eikonal collision cross section is found to be receded from the collision center with an increase of the electron-exchange effect. It is interesting to note that the influence of the electron exchange on the eikonal collision cross section decreases with increasing collision energy. It is also found that the eikonal collision cross section decreases with an increase of the plasmon energy and, however, increases with increasing Fermi energy.

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32

Lee, Kul, and Hyungcheol Shin. "Distinguishing capture cross-section parameter between GIDL erase compact model and TCAD." Japanese Journal of Applied Physics 60, no. 12 (November 30, 2021): 124002. http://dx.doi.org/10.35848/1347-4065/ac2ff0.

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Abstract A compact model of 3D NAND enables simulation at circuit- or system-level. Although a compact model for gate-induced-drain-leakage (GIDL)-assisted erase was proposed in a previous study, it is difficult to use practically because it has not been properly validated. In particular, a capture cross-section (CCS) value that is far from the real value is used. Furthermore, it does not consider the latest device structure and its operation. In this paper, a conventional GIDL-assisted erase compact model is validated using TCAD and has been improved more practically. It is confirmed that we should distinguish between CCS in TCAD and the compact model due to their differences. Based on their physical differences, an equation that can interconvert them is proposed and the model is successfully validated with proper CCS. Finally, the advanced GIDL-assisted erase compact model considering a tapered angle, single-side injection and word-line voltage is suggested.

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33

Lee, Myoung-Jae, and Young-Dae Jung. "Characteristics of Polarisation in the Ramsauer–Townsend Minima in Strongly Coupled Semiclassic Plasmas." Zeitschrift für Naturforschung A 72, no. 11 (October 26, 2017): 995–1001. http://dx.doi.org/10.1515/zna-2017-0254.

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AbstractThe influence of quantum shielding on the Ramsauer–Townsend phenomena for the total electron–atom polarisation collision cross-section is investigated in partially ionised strongly coupled semiclassic plasmas. The result shows that the quantum shielding effect changes the position of the Ramsauer energy in partially ionised strongly coupled plasmas. It is also found that the quantum shielding effect enhances the total electron–atom collision cross-section when the collision energy is greater than the Ramsauer energy; however, it suppresses the collision cross-section when the collision energy is smaller than the Ramsauer energy. In addition, it is shown that the plasma screening effect significantly changes the position of the Ramsauer energy and the influence of plasma screening on the magnitude of the collision cross-section is more significant near the Ramsauer energy domain. The variations of the Ramsauer energy and the collision cross-section due to the quantum shielding effect are also discussed.

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34

Liu, Yong Wang, Zhi Chuan Guan, Guo Shan Zhao, and Chang Peng Hu. "An Anti-Collision Risk Assessment Method for Single-Row Wellheads in Vertical Well Section of Cluster Well." Advanced Materials Research 236-238 (May 2011): 8–13. http://dx.doi.org/10.4028/www.scientific.net/amr.236-238.8.

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Vertical Well-bore Section Anti-collision is one of the main problems to be resolved for clustering directional well during the construction process. In order to effectively reduce the Vertical Well Section collision risk of this wells, the relationship between Wellbore cross-collision probability and the Wellbore separation was studied, the relationship between Wellbore cross-collision probability and the parallel Section length of the two Wellbore was also studied, Based on the above study found the method to calculate the Vertical Wellbore Section cross-collision probability of the clustering directional well. The Vertical Well-bore Section arrangement with smallest cross-collision probability was found by analyzing the cross-collision probability in line style wellhead of cluster wells consisting of 4 wells through this method. The results show that when the Well-bore separation is less than 1.5m. Wellbore collision probability rapidly decrease with the increase of Well-bore separation, the wellbore collision probability trends to smooth when wellbore separation is more than this distance, and the tendency will increase with the increase of parallel section length of the two Wellbore. By optimizing the arrangement and design methods can effectively reduce the collision risk. This study provides a new idea to reduce the overall risk of Cluster Well development.

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35

Tanaka, Hiroshi, and Osamu Sueoka. "Electron Collision Cross Section Measurements on Plasma Discharges." IEEJ Transactions on Fundamentals and Materials 117, no. 12 (1997): 1151–56. http://dx.doi.org/10.1541/ieejfms1990.117.12_1151.

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36

Huo, W. M., and Y. K. Kim. "Electron collision cross-section data for plasma modeling." IEEE Transactions on Plasma Science 27, no. 5 (1999): 1225–40. http://dx.doi.org/10.1109/27.799798.

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37

KI, DAE-HAN, and YOUNG-DAE JUNG. "Influence of non-thermal shielding on the Ramsauer phenomena for the electron–atom-induced dipole scattering in Lorentzian plasmas." Journal of Plasma Physics 79, no. 1 (August 24, 2012): 113–17. http://dx.doi.org/10.1017/s002237781200075x.

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AbstractThe non-thermal shielding effects on the Ramsauer phenomena for the electron–atom-induced dipole scattering are investigated in Lorentzian plasmas. The phase theory and the modified Buckingham-type potential are employed to obtain phase shift and collision cross section as functions of spectral index, scattering length, polarizability, collision energy, and the Debye radius. It is found that the non-thermal effect enhances the collision cross section below the Ramsauer energy and suppresses the collision cross section above the Ramsauer energy. In addition, it is found that the non-thermal effect enhances the Ramsauer energy in Lorentzian plasmas.

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38

Leshchev, D. V. "The Dependence of the Clusters and Atoms Collision Cross‐section from Collision Energy." Fullerenes, Nanotubes and Carbon Nanostructures 16, no. 5-6 (September 2008): 546–50. http://dx.doi.org/10.1080/15363830802286277.

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39

Fukuyama, Tatsuya, and Haruo Itoh. "Consideration on the Excitation Collision Cross-section for Kr." IEEJ Transactions on Fundamentals and Materials 121, no. 5 (2001): 493–94. http://dx.doi.org/10.1541/ieejfms1990.121.5_493.

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40

Mori, I., J. Mori, and K. Ohya. "Investigation of the H0-H+elastic collision cross section." Journal of Physics B: Atomic and Molecular Physics 20, no. 6 (March 26, 1987): 1215–27. http://dx.doi.org/10.1088/0022-3700/20/6/010.

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41

Xue, Bing, Jun Han, and Hai-Lung Dai. "Collision Relaxation Cross Section of Highly Vibrationally Excited Molecules." Physical Review Letters 84, no. 12 (March 20, 2000): 2606–9. http://dx.doi.org/10.1103/physrevlett.84.2606.

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42

Rybczyński, Maciej, and Zbigniew Włodarczyk. "The nucleon–nucleon collision profile and cross section fluctuations." Journal of Physics G: Nuclear and Particle Physics 41, no. 1 (December 3, 2013): 015106. http://dx.doi.org/10.1088/0954-3899/41/1/015106.

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43

Igarashi, A., and L. Gulyás. "Vibrationally resolved capture cross section in p + H2 collision." Journal of Physics B: Atomic, Molecular and Optical Physics 52, no. 7 (March 14, 2019): 075204. http://dx.doi.org/10.1088/1361-6455/ab065c.

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44

Soper-Hopper, M. T., A. S. Petrov, J. N. Howard, S. S. Yu, J. G. Forsythe, M. A. Grover, and F. M. Fernández. "Collision cross section predictions using 2-dimensional molecular descriptors." Chem. Commun. 53, no. 54 (2017): 7624–27. http://dx.doi.org/10.1039/c7cc04257d.

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45

Gartstein, Yu N., E. M. Conwell, and M. J. Rice. "Electron-hole collision cross section in discrete hopping systems." Chemical Physics Letters 249, no. 5-6 (February 1996): 451–58. http://dx.doi.org/10.1016/0009-2614(95)01435-7.

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46

Lee, Myoung-Jae, and Young-Dae Jung. "Quantum Shielding Effects on the Eikonal Collision Cross Section in Strongly Coupled Two-temperature Plasmas." Zeitschrift für Naturforschung A 72, no. 5 (May 1, 2017): 433–39. http://dx.doi.org/10.1515/zna-2017-0026.

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AbstractThe influence of nonisothermal and quantum shielding on the electron-ion collision process is investigated in strongly coupled two-temperature plasmas. The eikonal method is employed to obtain the eikonal scattering phase shift and eikonal cross section as functions of the impact parameter, collision energy, electron temperature, ion temperature, Debye length, and de Broglie wavelength. The results show that the quantum effect suppresses the eikonal scattering phase shift for the electron-ion collision in two-temperature dense plasmas. It is also found that the differential eikonal cross section decreases for small impact parameters. However, it increases for large impact parameters with increasing de Broglie wavelength. It is also found that the maximum position of the differential eikonal cross section is receded from the collision center with an increase in the nonisothermal character of the plasma. In addition, it is found that the total eikonal cross sections in isothermal plasmas are always greater than those in two-temperature plasmas. The variations of the eikonal cross section due to the two-temperature and quantum shielding effects are also discussed.

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47

Stiving, Alyssa Q., Benjamin J. Jones, Jakub Ujma, Kevin Giles, and Vicki H. Wysocki. "Collision Cross Sections of Charge-Reduced Proteins and Protein Complexes: A Database for Collision Cross Section Calibration." Analytical Chemistry 92, no. 6 (February 12, 2020): 4475–83. http://dx.doi.org/10.1021/acs.analchem.9b05519.

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48

JUNG, YOUNG-DAE, and WOO-PYO HONG. "Non-thermal renormalization shielding on the electron–atom collision in partially ionized generalized Lorentzian non-thermal plasmas." Journal of Plasma Physics 79, no. 5 (May 9, 2013): 783–88. http://dx.doi.org/10.1017/s0022377813000494.

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AbstractThe non-thermal renormalization shielding effects on the elastic electron–atom collision process are investigated in partially ionized generalized Lorentzian non-thermal plasmas. The eikonal analysis for the Hamilton–Jacobi solution and impact parameter method are employed to obtain the eikonal scattering phase shift and eikonal cross section as functions of the collision energy, Debye length, impact parameter, and spectral index of the Lorentzian plasma. It is found that the non-thermal renormalization shielding effect enhances the eikonal scattering phase shift as well as the eikonal collision cross section, especially for small impact parameter domains. It is also found that the non-thermal renormalization shielding effect on the eikonal scattering phase shift decreases with an increase of the impact parameter. In addition, it is found that the maximum position of the eikonal collision cross section has receded from the collision center with an increase of the non-thermal character of the plasma.

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49

Kima, Hwa-Min, and Young-Dae Jung. "Nonthermal and Plasmon Effects on Elastic Electron-Ion Collisions in Hot Quantum Lorentzian Plasmas." Zeitschrift für Naturforschung A 64, no. 1-2 (February 1, 2009): 44–48. http://dx.doi.org/10.1515/zna-2009-1-207.

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The nonthermal and plasmon effects on elastic electron-ion collisions are investigated in hot quantum Lorentzian plasmas. The modified interaction model taking into account the nonthermal screening and plasmon effects is employed to represent the electron-ion interaction potential in hot quantum Lorentzian plasmas. The eikonal phase and differential collision cross-section are obtained as functions of the impact parameter, collision energy, spectral index, and plasma parameters by using the second-order eikonal analysis. It is shown that the plasmon effect suppresses the eikonal phase and collision cross-section for 0 < β (ћω0/kBT < 0.6) and, however, enhances it for 0.6 < β < 1, where ω0 is the plasma frequency and T is the plasma temperature. It is also shown that the nonthermal character of the quantum Lorentzian plasma suppresses the elastic electron-ion collision cross-section.

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50

Na, Sang-Chul, and Young-Dae Jung. "Screened Collision-Induced Quantum Interference in Collisional Plasmas." Zeitschrift für Naturforschung A 64, no. 3-4 (April 1, 2009): 233–36. http://dx.doi.org/10.1515/zna-2009-3-410.

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Abstract The effects of neutral particle collisions on the quantum interference in electron-electron collisions are investigated in collisional plasmas. The effective potential model taking into account the electronneutral particle collision effects is employed in order to obtain the electron-electron collision cross section including the total spin states of the collision system. It is found that the collision effects significantly enhance the cross section. In addition, the collision-induced quantum interference effects are found to be significant in the singlet spin state. It is shown that the quantum interference effects decrease with increasing the thermal energy of the plasma. It is also shown that the quantum interference effects increase with an increase of the collision energy

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