Article
Engineering, Environmental
Xue-Chao Song, Nicola Dreolin, Elena Canellas, Jeff Goshawk, Cristina Nerin
Summary: This study reports a method for predicting the collision cross-section (CCS) values, a structural descriptor, of extractables and leachables from plastic products using machine learning techniques. The model was developed by collecting experimental CCS values and assessing the performance of different molecular descriptors and machine learning algorithms. The results showed that a support vector machine (SVM) model based on Chemistry Development Kit (CDK) descriptors provided the most accurate prediction, which was successfully applied to the identification of plastic-related chemicals in river water.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Xiaohang Li, Hongda Wang, Meiting Jiang, Mengxiang Ding, Xiaoyan Xu, Bei Xu, Yadan Zou, Yuetong Yu, Wenzhi Yang
Summary: Ion mobility-mass spectrometry (IM-MS) is a powerful separation technique that enhances the separation and characterization of complex components. The integration of machine learning (ML) with IM-MS overcomes the lack of reference standards and helps in rapid, comprehensive, and accurate characterization of chemical components.
Article
Biochemical Research Methods
S. M. Bargeen Alam Turzo, Justin T. Seffernick, Sergey Lyskov, Steffen Lindert
Summary: This article introduces a method for predicting collision cross section (CCSIM) based on protein structures using the projection approximation with PARCS on the Rosetta Online Server that Includes Everyone (ROSIE) webserver. The user only needs to provide one or more PDB files as input. Results show that CCSIM predictions with ROSIE-PARCS are highly accurate, with an average error of 6.12%. Furthermore, the absolute difference between CCSIM and CCSPARCS can help distinguish accurate and inaccurate AlphaFold2 protein structure predictions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Joon-Yong Lee, Aivett Bilbao, Christopher R. Conant, Kent J. Bloodsworth, Daniel J. Orton, Mowei Zhou, Jesse W. Wilson, Xueyun Zheng, Ian K. Webb, Ailin Li, Kim K. Hixson, John C. Fjeldsted, Yehia M. Ibrahim, Samuel H. Payne, Christer Jansson, Richard D. Smith, Thomas O. Metz
Summary: AutoCCS is an open-source software for rapid determination of CCS values from IMS-MS measurements, demonstrating accuracy and reproducibility for standard and unknown analyte ions under various conditions.
Review
Chemistry, Multidisciplinary
Nicolas M. Morato, R. Graham Cooks
Summary: Mass spectrometry (MS) is widely used in the chemical sciences for various applications such as monitoring reaction products, identifying disease biomarkers, and measuring thermodynamic parameters. Electrospray ionization (ESI) is a commonly used method to ionize polar compounds from solution. Desorption electrospray ionization (DESI) is a technique that directly generates ions from objects in the ambient environment. The simplicity and wide applicability of DESI revolutionized the analysis of complex materials for their organic components, particularly for in situ applications.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Optics
Ruti Ben-shlomi, Meirav Pinkas, Ziv Meir, Tomas Sikorsky, Or Katz, Nitzan Akerman, Roee Ozeri
Summary: A method for directly measuring atom-ion collisional cross section has been reported, with energy range of 0.2-12 mK x k(B) using ultracold atoms trapped in an optical-lattice and radio-frequency trapped ions to achieve high energy resolution. The energy resolution is estimated to be below 200 mu K x k(B) and the method allows for studying inelastic processes and searching for quantum signatures such as shape resonances.
Article
Biochemistry & Molecular Biology
Fan Yang, Denice van Herwerden, Hugues Preud'homme, Saer Samanipour
Summary: High-resolution mass spectrometry combined with ion mobility spectrometry has been widely used in non-target screening, improving the accuracy of small molecule identification. Two CCS prediction models were developed using machine learning algorithm, successfully applied on different IMS platforms to eliminate false positives in small molecule identification.
Article
Chemistry, Analytical
Anais C. George, Isabelle Schmitz-Afonso, Vincent Marie, Benoit Colsch, Francois Fenaille, Carlos Afonso, Corinne Loutelier-Bourhis
Summary: Collision cross sections (CCS) are important molecular descriptors in metabolomics and lipidomics analyses. Ion mobility spectrometry (IMS) can determine CCS, but different techniques require calibration and lead to varying results. This study evaluates 11 different CCS calibrants and proposes a method to recalibrate CCS values using Tune Mix solution for more accurate and comparable results.
ANALYTICA CHIMICA ACTA
(2022)
Article
Agriculture, Multidisciplinary
Xue-Chao Song, Elena Canellas, Nicola Dreolin, Jeff Goshawk, Cristina Nerin
Summary: In this study, a database of traveling wave collision cross section in nitrogen values for extractables and leachables from food contact materials was developed. The comparison of different values and prediction tools provides insights for the identification and differentiation of chemicals in these materials.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Chemistry, Analytical
Claudia Bressan, Alberto Celma, Elida Alechaga, Nuria Monfort, Rosa Ventura, Juan Vicente Sancho
Summary: The collision cross section (CCS) value of 103 steroids was determined by LC-TWIMS. High reproducibility was observed in urine and standard solutions. CCS determination in matrix was in accordance with the CCS measured in standards solution. CCS values were directly correlated with the ion mass and allowed differentiating between glucuronides, sulfates, and free steroids. Specific information was obtained for phase II metabolites, which could be useful in the structural elucidation of new steroid metabolites in the anti-doping field. The potential of IMS reducing interferences from the sample matrix was also tested.
ANALYTICA CHIMICA ACTA
(2023)
Article
Multidisciplinary Sciences
Jeroen F. van Dyck, Jonathan R. Burns, Kyle I. P. Le Huray, Albert Konijnenberg, Stefan Howorka, Frank Sobott
Summary: Recent interest in oligonucleotide nanostructures has led to the use of mass spectrometry and ion mobility to study their assembly. In this study, the authors use these techniques to characterize the structure of a hexameric DNA barrel and its intermediates and byproducts. They demonstrate the ability of these methods to determine the mass, charge state, and size of noncovalent DNA assemblies and reveal the role of ionic strength in their assembly. They also identify previously undetected higher-order assemblies and assign them to larger geometric structures.
NATURE COMMUNICATIONS
(2022)
Article
Agriculture, Multidisciplinary
Maria Mar Aparicio-Muriana, Renato Bruni, Francisco J. Lara, Monsalud del Olmo-Iruela, Maykel Hernandez-Mesa, Ana M. Garcia-Campana, Chiara Dall'Asta, Laura Righetti
Summary: The increased consumption of blue-green algae (BGA)-based dietary supplements has raised concerns about food safety due to cyanotoxin presence. A study employed ultrahigh-performance liquid chromatography coupled to traveling wave ion mobility spectrometry/quadrupole time-of-flight mass spectrometry (UHPLC-TWIMS-QTOF) to establish a comprehensive database for phycotoxins. Cyanotoxins were confidently identified in commercial BGA dietary supplements based on retention time, m/z, and collision cross section values.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Materials Science, Multidisciplinary
Christian Ieritano, W. Scott Hopkins
Summary: This study validated the performance of MobCal-MPI across 25 different model chemistries and found that the calculated collision cross sections (CCSs) correlated well with experimental values for almost all model chemistries, with only a few exceptions where the deviation was slightly larger.
MATERIALS TODAY COMMUNICATIONS
(2021)
Article
Agriculture, Multidisciplinary
Xue-Chao Song, Nicola Dreolin, Tito Damiani, Elena Canellas, Cristina Nerin
Summary: This study experimentally derived the traveling wave collision cross section in nitrogen values of over 400 chemicals in food contact materials and developed a prediction model for collision cross section (CCS) based on these values and molecular descriptors. The model improved the identification confidence of oligomers and discussed the challenges and opportunities of current machine-learning models on CCS prediction.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemical Research Methods
Chih-Hsiang Chang, Darien Yeung, Victor Spicer, Kosuke Ogata, Oleg Krokhin, Yasushi Ishihama
Summary: The study investigates the impact of peptide amino acid sequence on collision cross section values (CCS); ion mobility is mainly affected by the peptide's ability to solvate positively charged sites; the positioning of amino acid residues, as well as helical propensity and hydrophobicity, play important roles in the formation of extended structures.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Siavash Vahidi, Lars Konermann
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2016)
Article
Multidisciplinary Sciences
Siavash Vahidi, Yumin Bi, Stanley D. Dunn, Lars Konermann
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Multidisciplinary Sciences
Siavash Vahidi, Zev A. Ripstein, Massimiliano Bonomi, Tairan Yuwen, Mark F. Mabanglo, Jordan B. Juravsky, Kamran Rizzolo, Algirdas Velyvis, Walid A. Houry, Michele Vendruscolo, John L. Rubinstein, Lewis E. Kay
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Review
Chemistry, Analytical
Lars Konermann, Siavash Vahidi, Modupeola A. Sowole
ANALYTICAL CHEMISTRY
(2014)
Meeting Abstract
Biophysics
Lars Konermann, Siavash Vahidi, Modupeola A. Sowole
BIOPHYSICAL JOURNAL
(2014)
Article
Biochemical Research Methods
Xuanfeng Yue, Siavash Vahidi, Lars Konermann
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2014)
Article
Chemistry, Multidisciplinary
Angela Murcia Rios, Siavash Vahidi, Stanley D. Dunn, Lars Konermann
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2018)
Article
Multidisciplinary Sciences
Siavash Vahidi, Zev A. Ripstein, Jordan B. Juravsky, Enrico Rennella, Alfred L. Goldberg, Anthony K. Mittermaier, John L. Rubinstein, Lewis E. Kay
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Zev A. Ripstein, Siavash Vahidi, Walid A. Houry, John L. Rubinstein, Lewis E. Kay
Article
Chemistry, Multidisciplinary
Zev A. Ripstein, Siavash Vahidi, John L. Rubinstein, Lewis E. Kay
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Multidisciplinary Sciences
Yingke Liang, Alicia Plourde, Stephanie A. Bueler, Jun Liu, Peter Brzezinski, Siavash Vahidi, John L. Rubinstein
Summary: Oxidative phosphorylation is a promising target for treating Mycobacterium tuberculosis and other mycobacteria infections. The structure of the mycobacterial electron transport chain reveals the presence of several important components, including the orphan protein MSMEG_2064, acyl phosphati-dylinositol dimannoside, menaquinone, and a purine nucleoside triphosphate. These findings provide insights into the function and structure of the enzyme.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Justin M. Di Trani, Andreea A. Gheorghita, Madison Turner, Peter Brzezinski, Pia Aedelroth, Siavash Vahidi, P. Lynne Howell, John L. Rubinstein
Summary: Energy conversion through electron transport chains is essential for ATP synthesis and membrane transport. The structure of a respiratory supercomplex (SC) formed between cytochrome bc1 and cytochrome cbb3 in the opportunistic pathogen Pseudomonas aeruginosa has been determined, revealing the involvement of intermediate electron carriers. Different isoforms of cytochrome cbb3 can also participate in SC formation, allowing the bacterium to adapt to different environmental conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Analytical
Bradley T. V. Davis, Algirdas Velyvis, Siavash Vahidi
Summary: This study demonstrates that 2,2-difluoroethylamine (DFEA) and 2,2,2-trifluoroethylamine (TFEA) act as new ESI-compatible neutral pH buffers with buffering capacity at physiological pH. They can preserve noncovalent protein-ligand complexes in the gas phase and are suitable for studying multisubunit protein complexes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Courtney S. Fast, Siavash Vahidi, Lars Konermann
ANALYTICAL CHEMISTRY
(2017)