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George AC, Schmitz I, Rouvière F, Alves S, Colsch B, Heinisch S, Afonso C, Fenaille F, Loutelier-Bourhis C. Interplatform comparison between three ion mobility techniques for human plasma lipid collision cross sections. Anal Chim Acta 2024; 1304:342535. [PMID: 38637036 DOI: 10.1016/j.aca.2024.342535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
The implementation of ion mobility spectrometry (IMS) in liquid chromatography-high-resolution mass spectrometry (LC-HRMS) workflows has become a valuable tool for improving compound annotation in metabolomics analyses by increasing peak capacity and by adding a new molecular descriptor, the collision cross section (CCS). Although some studies reported high repeatability and reproducibility of CCS determination and only few studies reported good interplatform agreement for small molecules, standardized protocols are still missing due to the lack of reference CCS values and reference materials. We present a comparison of CCS values of approximatively one hundred lipid species either commercially available or extracted from human plasma. We used three different commercial ion mobility technologies from different laboratories, drift tube IMS (DTIMS), travelling wave IMS (TWIMS) and trapped IMS (TIMS), to evaluate both instrument repeatability and interlaboratory reproducibility. We showed that CCS discrepancies of 0.3% (average) could occur depending on the data processing software tools. Moreover, eleven CCS calibrants were evaluated yielding mean RSD below 2% for eight calibrants, ESI Low concentration tuning mix (Tune Mix) showing the lowest RSD (< 0.5%) in both ion modes. Tune Mix calibrated CCS from the three different IMS instruments proved to be well correlated and highly reproducible (R2 > 0.995 and mean RSD ≤ 1%). More than 90% of the lipid CCS had deviations of less than 1%, demonstrating high comparability between techniques, and the possibility to use the CCS as molecular descriptor. We highlighted the need of standardized procedures for calibration, data acquisition, and data processing. This work demonstrates that using harmonized analytical conditions are required for interplatform reproducibility for CCS determination of human plasma lipids.
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Affiliation(s)
- Anaïs C George
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Isabelle Schmitz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Florent Rouvière
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Paris, France
| | - Benoit Colsch
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France
| | - Sabine Heinisch
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Carlos Afonso
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France
| | - Corinne Loutelier-Bourhis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France.
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2
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Kurilung A, Limjiasahapong S, Kaewnarin K, Wisanpitayakorn P, Jariyasopit N, Wanichthanarak K, Sartyoungkul S, Wong SCC, Sathirapongsasuti N, Kitiyakara C, Sirivatanauksorn Y, Khoomrung S. Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples. J Pharm Anal 2024; 14:100921. [PMID: 38799238 PMCID: PMC11127212 DOI: 10.1016/j.jpha.2023.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/17/2023] [Accepted: 12/13/2023] [Indexed: 05/29/2024] Open
Abstract
The collision cross-sections (CCS) measurement using ion mobility spectrometry (IMS) in combination with mass spectrometry (MS) offers a great opportunity to increase confidence in metabolite identification. However, owing to the lack of sensitivity and resolution, IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites (VLMs ≤ 250 Da). Here, we describe an analytical method using ultrahigh-performance liquid chromatography (UPLC) coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine samples. The experimental CCS values, along with mass spectral properties, were reported for the 174 metabolites. The experimental data included the mass-to-charge ratio (m/z), retention time (RT), tandem MS (MS/MS) spectra, and CCS values. Among the studied metabolites, 263 traveling wave ion mobility spectrometry (TWIMS)-derived CCS values (TWCCSN2) were reported for the first time, and more than 70% of these were CCS values of VLMs. The TWCCSN2 values were highly repeatable, with inter-day variations of <1% relative standard deviation (RSD). The developed method revealed excellent TWCCSN2 accuracy with a CCS difference (ΔCCS) within ±2% of the reported drift tube IMS (DTIMS) and TWIMS CCS values. The complexity of the urine matrix did not affect the precision of the method, as evidenced by ΔCCS within ±1.92%. According to the Metabolomics Standards Initiative, 55 urinary metabolites were identified with a confidence level of 1. Among these 55 metabolites, 53 (96%) were VLMs. The larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values, which clearly increased metabolite identification confidence.
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Affiliation(s)
- Alongkorn Kurilung
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Suphitcha Limjiasahapong
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Khwanta Kaewnarin
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- SingHealth Duke-NUS Institute of Biodiversity Medicine, National Cancer Centre Singapore, 168583, Singapore
| | - Pattipong Wisanpitayakorn
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Narumol Jariyasopit
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Kwanjeera Wanichthanarak
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sitanan Sartyoungkul
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | | | - Nuankanya Sathirapongsasuti
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, 10540, Thailand
| | - Chagriya Kitiyakara
- Department of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sakda Khoomrung
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
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3
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Wang N, Dixit SM, Lee T, DeFiglia SA, Ruotolo BT, Håkansson K. Salt-Bridged Peptide Anion Gaseous Structures Enable Efficient Negative Ion Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:784-792. [PMID: 38489759 DOI: 10.1021/jasms.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
We previously discovered that electron attachment to gaseous peptide anions can occur within a relatively narrow electron energy range. The resulting charge-increased radical ions undergo dissociation analogous to conventional cation electron capture/transfer dissociation (ECD/ETD), thus enabling a novel tandem mass spectrometry (MS/MS) technique that we termed negative ion electron capture dissociation (niECD). We proposed that gaseous zwitterionic structures are required for niECD with electron capture either occurring at or being directed by a positively charged site. Here, we further evaluate this zwitterion mechanism by performing niECD of peptides derivatized to alter their ability to form zwitterionic gaseous structures. Introduction of a fixed positive charge tag, a highly basic guanidino group, or a highly acidic sulfonate group to promote zwitterionic structures in singly charged anions, rescued the niECD ability of a peptide refractory to niECD in its unmodified form. We also performed a systematic study of five sets of synthetic peptides with decreasing zwitterion propensity and found that niECD efficiency decreased accordingly, further supporting the zwitterion mechanism. However, traveling-wave ion mobility-mass spectrometry experiments, performed to gain further insight into the gas-phase structures of peptides showing high niECD efficiency, exhibited an inverse correlation between the orientationally averaged collision cross sections and niECD efficiency. These results indicate that compact salt-bridged structures are also a requirement for effective niECD.
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Affiliation(s)
- Ning Wang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Teresa Lee
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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4
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Chung NA, May JC, Robinson RAS, McLean JA. Solvent Composition Can Have a Measurable Influence on the Ion Mobility-Derived Collision Cross Section of Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:234-243. [PMID: 38082535 DOI: 10.1021/jasms.3c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Ion mobility (IM) is an important analytical technique for increasing identification coverage of metabolites in untargeted studies, especially when integrated into traditional liquid chromatography-mass spectrometry workflows. While there has been extensive work surrounding best practices to obtain and standardize collision cross section (CCS) measurements necessary for comparing across different IM techniques and laboratories, there has been little investigation into experimental factors beyond the mobility separation region that could potentially influence CCS measurements. The first-principles derived CCS of 15 chemical standards were evaluated across 27 aqueous:organic solvent compositions using a high-precision drift tube instrument. A small but measurable dependency of the CCS on the solvent composition was observed, with the larger analytes from this study (m/z > 400) exhibiting a characteristic increase in CCS at the intermediate (40-60%) solvent compositions. Parallels to the behavior of solvent viscosity and protonation site tautomers (protomers) were noted, although the origin of these solvent-dependent CCS trends is as yet unclear. Taken together, these findings document a solvent dependency on CCS, which, while minor (<0.5%), identifies an important need for reporting the solvent system when utilizing CCS in comparative ion mobility studies.
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Affiliation(s)
- Nadjali A Chung
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jody C May
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A McLean
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
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5
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Kedia K, Harris R, Ekroos K, Moser KW, DeBord D, Tiberi P, Goracci L, Zhang NR, Wang W, Spellman DS, Bateman K. Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2176-2186. [PMID: 37703523 DOI: 10.1021/jasms.3c00157] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Lipids are structurally diverse molecules that play a pivotal role in a plethora of biological processes. However, deciphering the biological roles of the specific lipids is challenging due to the existence of numerous isomers. This high chemical complexity of the lipidome is one of the major challenges in lipidomics research, as the traditional liquid chromatography-mass spectrometry (LC-MS) based approaches are often not powerful enough to resolve these isomeric and isobaric nuances within complex samples. Thus, lipids are uniquely suited to the benefits provided by multidimensional liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) analysis. However, many forms of lipid isomerism, including double-bond positional isomers and regioisomers, are structurally similar such that their collision cross section (CCS) differences are unresolvable via conventional IM approaches. Here we evaluate the performance of a high resolution ion mobility (HRIM) system based on structures for lossless ion manipulation (SLIM) technology interfaced to a high resolution quadrupole time-of-flight (QTOF) analyzer to address the noted lipidomic isomerism challenge. SLIM implements the traveling wave ion mobility technique along an ∼13 m ion path, providing longer path lengths to enable improved separation of isomeric features. We demonstrate the power of HRIM-MS to dissect isomeric PC standards differing only in double bond (DB) and stereospecific number (SN) positions. The partial separation of protonated DB isomers is significantly enhanced when they are analyzed as metal adducts. For sodium adducts, we achieve close to baseline separation of three different PC 18:1/18:1 isomers with different cis-double bond locations. Similarly, PC 18:1/18:1 (cis-9) can be resolved from the corresponding PC 18:1/18:1 (trans-9) form. The separation capacity is further enhanced when using silver ion doping, enabling the baseline separation of regioisomers that cannot be resolved when measured as sodium adducts. The sensitivity and reproducibility of the approach were assessed, and the performance for more complex mixtures was benchmarked by identifying PC isomers in total brain and liver lipid extracts.
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Affiliation(s)
- Komal Kedia
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rachel Harris
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Kim Ekroos
- Lipidomics Consulting Ltd, Irisviksvägen 31D, 02230 Esbo, Finland
| | - Kelly W Moser
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Daniel DeBord
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Paolo Tiberi
- Molecular Discovery Ltd., Centennial Park, Borehamwood, Hertfordshire WD6 3FG United Kingdom
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | | | - Weixun Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Kevin Bateman
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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6
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Habibi SC, Nagy G. General Method to Obtain Collision Cross-Section Values in Multipass High-Resolution Cyclic Ion Mobility Separations. Anal Chem 2023; 95:8028-8035. [PMID: 37163363 DOI: 10.1021/acs.analchem.3c00919] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In recent years, ion mobility spectrometry-mass spectrometry (IMS-MS) has advanced the field of omics-based research, especially with the development of high-resolution platforms; however, these separations have generally been qualitative in nature. The rotationally averaged ion neutral collision cross section (CCS) is one of the only quantitative metrics available for aiding in characterizing biomolecules in IMS-MS. However, determining the CCS of an ion for multipass IMS systems, such as in cyclic ion mobility-mass spectrometry (cIMS-MS) and structures for lossless ion manipulations, has been challenging due to the lack of methods available for calculating CCS when more than a single pass is required for separation as well as the laborious nature of requiring calibrants and unknown compounds to be subjected to identical number of passes, which may not be possible in certain instances because of peak splitting, high levels of diffusion, etc. Herein, we present a general method that uses average ion velocities for calculating CCS values in cIMS-MS-based separations. Initially, we developed calibration curves using common CCS calibrants [i.e., tetra-alkylammonium salts, polyalanine, and hexakis(fluoroalkoxy)phosphazines] at different traveling wave (TW) conditions and the calculated cIMS CCS values were within ∼1% error or less compared to previously established drift tube IMS CCS measurements. Since it has been established that glycans can split into their α/β anomers, we utilized this method for two glycan species, 2α-mannobiose and melibiose. Both glycans were analyzed at the same TW conditions as the calibrants, and we observed anomer splitting at pathlengths of 20 m for 2α-mannobiose and 40 m for melibiose and thus assigned two unique CCS values for each glycan, which is the first time this has ever been done. We have demonstrated that the use of average ion velocities is a robust approach for obtaining CCS values with good agreement to CCS measurements from the previous literature and anticipate that this methodology can be applied to any IMS-MS platform that utilizes multipass separations. Our future work aims to incorporate this methodology for the development of a high-resolution CCS database to aid in the characterization of human milk oligosaccharides.
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Affiliation(s)
- Sanaz C Habibi
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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7
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Keating AR, Wesdemiotis C. Rapid and simple determination of average molecular weight and composition of synthetic polymers via electrospray ionization-mass spectrometry and a Bayesian universal charge deconvolution. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9478. [PMID: 36669764 DOI: 10.1002/rcm.9478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
RATIONALE Simple, affordable, and rapid methods for identifying the molecular weight (MW) distribution and macromolecular composition of polymeric materials are limited. Current tools require extensive solvent consumption, linear calibrations, and expensive consumables. A simple method for the determination of average MW (Mn , Mw ) and chain end groups is demonstrated for synthetic homopolymer standards using direct injection electrospray ionization-mass spectrometry (ESI-MS) and an open-sourced charge deconvolution (CDC) algorithm. METHODS Five homopolymer standards in the 1-7 kDa MW range were analyzed using direct-injection ESI-MS on a quadrupole/time-of-flight mass spectrometer. The samples investigated, viz. two poly(ethylene oxide) (PEO) and two poly(styrene sulfonic acid) (PSS) standards with narrow polydispersity and one poly(d,l-alanine) (pAla) standard with undefined polydispersity, were chosen to illustrate challenges with ESI-MS quantitation. Using the UniDec program, weight average MWs (Mw ) obtained from the charge-deconvoluted spectra were compared to the reported Mw data of the standards from size exclusion chromatography (SEC) measurements. RESULTS The MW data derived for the PSS, PEO, and pAla standards agreed well with the corresponding reported Mw or MW range values. The method was able to provide MW, degree of polymerization (DP), and polydispersity index (PDI) information for polymers with narrow (PSS, PEO) as well as broader (pAla) molecular weight distribution; this feature provides an advantage over MW analysis via matrix-assisted laser desorption/ionization (MALDI) for ESI-compatible materials. PSS standards differing in average MW by only a few repeat units could be confidently distinguished. Additionally, the oligomeric resolution observed for all samples studied unveiled chain-end information not available through chromatographic analysis. CONCLUSIONS Overall, the free and easy-to-use UniDec CDC algorithm provides a simple, alternative method to measuring MW and DP for polymeric materials without high solvent consumption, expensive ionization sources, or calibration curves. Information about the masses of individual oligomers and the possibility to further characterize these oligomers using tandem mass spectrometry and/or ion mobility techniques constitutes additional benefits of this approach vis-à-vis traditional MW and PDI elucidation through SEC.
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Affiliation(s)
- Addie R Keating
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Chrys Wesdemiotis
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio, USA
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8
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Asef CK, Rainey MA, Garcia BM, Gouveia GJ, Shaver AO, Leach FE, Morse AM, Edison AS, McIntyre LM, Fernández FM. Unknown Metabolite Identification Using Machine Learning Collision Cross-Section Prediction and Tandem Mass Spectrometry. Anal Chem 2023; 95:1047-1056. [PMID: 36595469 PMCID: PMC10440795 DOI: 10.1021/acs.analchem.2c03749] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ion mobility (IM) spectrometry provides semiorthogonal data to mass spectrometry (MS), showing promise for identifying unknown metabolites in complex non-targeted metabolomics data sets. While current literature has showcased IM-MS for identifying unknowns under near ideal circumstances, less work has been conducted to evaluate the performance of this approach in metabolomics studies involving highly complex samples with difficult matrices. Here, we present a workflow incorporating de novo molecular formula annotation and MS/MS structure elucidation using SIRIUS 4 with experimental IM collision cross-section (CCS) measurements and machine learning CCS predictions to identify differential unknown metabolites in mutant strains of Caenorhabditis elegans. For many of those ion features, this workflow enabled the successful filtering of candidate structures generated by in silico MS/MS predictions, though in some cases, annotations were challenged by significant hurdles in instrumentation performance and data analysis. While for 37% of differential features we were able to successfully collect both MS/MS and CCS data, fewer than half of these features benefited from a reduction in the number of possible candidate structures using CCS filtering due to poor matching of the machine learning training sets, limited accuracy of experimental and predicted CCS values, and lack of candidate structures resulting from the MS/MS data. When using a CCS error cutoff of ±3%, on average, 28% of candidate structures could be successfully filtered. Herein, we identify and describe the bottlenecks and limitations associated with the identification of unknowns in non-targeted metabolomics using IM-MS to focus and provide insights into areas requiring further improvement.
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Affiliation(s)
- Carter K Asef
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia30332, United States
| | - Markace A Rainey
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia30332, United States
| | - Brianna M Garcia
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia30602, United States
- Department of Chemistry, University of Georgia, Athens, Georgia30602, United States
| | - Goncalo J Gouveia
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia30602, United States
- Department of Biochemistry, University of Georgia, Athens, Georgia30602, United States
| | - Amanda O Shaver
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia30602, United States
- Department of Genetics, University of Georgia, Athens, Georgia30602, United States
| | - Franklin E Leach
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia30602, United States
- Department of Environment Health Science, University of Georgia, Athens, Georgia30602, United States
| | - Alison M Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida32611, United States
| | - Arthur S Edison
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia30602, United States
- Department of Chemistry, University of Georgia, Athens, Georgia30602, United States
- Department of Biochemistry, University of Georgia, Athens, Georgia30602, United States
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida32611, United States
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia30332, United States
- Petit Institute of Bioengineering and Biotechnology, Georgia Institute of Technology, Atlanta, Georgia30332, United States
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9
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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A re-calibration procedure for interoperable lipid collision cross section values measured by traveling wave ion mobility spectrometry. Anal Chim Acta 2022; 1226:340236. [DOI: 10.1016/j.aca.2022.340236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022]
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11
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Rose B, May JC, Reardon AR, McLean JA. Collision Cross-Section Calibration Strategy for Lipid Measurements in SLIM-Based High-Resolution Ion Mobility. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1229-1237. [PMID: 35653638 PMCID: PMC9516683 DOI: 10.1021/jasms.2c00067] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Structures for lossless ion manipulation-based high-resolution ion mobility (HRIM) interfaced with mass spectrometry has emerged as a powerful tool for the separation and analysis of many isomeric systems. IM-derived collision cross section (CCS) is increasingly used as a molecular descriptor for structural analysis and feature annotation, but there are few studies on the calibration of CCS from HRIM measurements. Here, we examine the accuracy, reproducibility, and practical applicability of CCS calibration strategies for a broad range of lipid subclasses and develop a straightforward and generalizable framework for obtaining high-resolution CCS values. We explore the utility of using structurally similar custom calibrant sets as well as lipid subclass-specific empirically derived correction factors. While the lipid calibrant sets lowered overall bias of reference CCS values from ∼2-3% to ∼0.5%, application of the subclass-specific correction to values calibrated with a broadly available general calibrant set resulted in biases <0.4%. Using this method, we generated a high-resolution CCS database containing over 90 lipid values with HRIM. To test the applicability of this method to a broader class range typical of lipidomics experiments, a standard lipid mix was analyzed. The results highlight the importance of both class and arrival time range when correcting or scaling CCS values and provide guidance for implementation of the method for more general applications.
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12
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Hupin S, Tognetti V, Rosu F, Renaudineau S, Proust A, Izzet G, Gabelica V, Afonso C, Lavanant H. Lennard-Jones interaction parameters of Mo and W in He and N 2 from collision cross-sections of Lindqvist and Keggin polyoxometalate anions. Phys Chem Chem Phys 2022; 24:16156-16166. [PMID: 35748666 DOI: 10.1039/d2cp00823h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Drift tube ion mobility spectrometry (DTIMS) coupled with mass spectrometry was used to determine the collision cross-sections (DTCCS) of polyoxometalate anions in helium and nitrogen. As the geometry of the ion, more than its mass, determines the collision cross-section with a given drift gas molecule, we found that both Lindqvist ions Mo6O192- and W6O192- had a DTCCSHe value of 103 ± 2 Å2, and both Keggin ions PMo12O403- and PW12O403- had a DTCCSHe value of 170 ± 2 Å2. Similarly, ion mobility experiments in N2 led to DTCCSN2 values of 223 ± 2 Å2 and 339 ± 4 Å2 for Lindqvist and Keggin anions, respectively. Using optimized structures and partial charges determined from density functional theory calculations, followed by CCS calculations via the trajectory method, we determined Lennard-Jones 6-12 potential parameters ε, σ of 5.60 meV, 3.50 Å and 3.75 meV, 4.40 Å for both Mo and W atoms interacting with He and N2, respectively. These parameters reproduced the CCS of polyoxometalates within 2% accuracy.
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Affiliation(s)
- Sébastien Hupin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Vincent Tognetti
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Frédéric Rosu
- CNRS, University of Bordeaux and INSERM, Institut Européen de Chimie et Biologie (IECB, UMS3033, US001), 2 rue Robert Escarpit, 33600 Pessac, France
| | - Séverine Renaudineau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 8232, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, F-75005 Paris, France
| | - Anna Proust
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 8232, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, F-75005 Paris, France
| | - Guillaume Izzet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 8232, Institut Parisien de Chimie Moléculaire, 4 Place Jussieu, F-75005 Paris, France
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), site IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Carlos Afonso
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Hélène Lavanant
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
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13
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Ross D, Seguin RP, Krinsky AM, Xu L. High-Throughput Measurement and Machine Learning-Based Prediction of Collision Cross Sections for Drugs and Drug Metabolites. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1061-1072. [PMID: 35548857 PMCID: PMC9165597 DOI: 10.1021/jasms.2c00111] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Drug metabolite identification is a bottleneck of drug metabolism studies due to the need for time-consuming chromatographic separation and structural confirmation. Ion mobility-mass spectrometry (IM-MS), on the other hand, separates analytes on a rapid (millisecond) time scale and enables the measurement of collision cross section (CCS), a unique physical property related to an ion's gas-phase size and shape, which can be used as an additional parameter for identification of unknowns. A current limitation to the application of IM-MS to the identification of drug metabolites is the lack of reference CCS values. In this work, we assembled a large-scale database of drug and drug metabolite CCS values using high-throughput in vitro drug metabolite generation and a rapid IM-MS analysis with automated data processing. Subsequently, we used this database to train a machine learning-based CCS prediction model, employing a combination of conventional 2D molecular descriptors and novel 3D descriptors, achieving high prediction accuracies (0.8-2.2% median relative error on test set data). The inclusion of 3D information in the prediction model enables the prediction of different CCS values for different protomers, conformers, and positional isomers, which is not possible using conventional 2D descriptors. The prediction models, dmCCS, are available at https://CCSbase.net/dmccs_predictions.
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Affiliation(s)
| | | | | | - Libin Xu
- . Tel: (206) 543-1080. Fax: (206) 685-3252
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14
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Das S, Tanemura KA, Dinpazhoh L, Keng M, Schumm C, Leahy L, Asef CK, Rainey M, Edison AS, Fernández FM, Merz KM. In Silico Collision Cross Section Calculations to Aid Metabolite Annotation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:750-759. [PMID: 35378036 PMCID: PMC9277703 DOI: 10.1021/jasms.1c00315] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The interpretation of ion mobility coupled to mass spectrometry (IM-MS) data to predict unknown structures is challenging and depends on accurate theoretical estimates of the molecular ion collision cross section (CCS) against a buffer gas in a low or atmospheric pressure drift chamber. The sensitivity and reliability of computational prediction of CCS values depend on accurately modeling the molecular state over accessible conformations. In this work, we developed an efficient CCS computational workflow using a machine learning model in conjunction with standard DFT methods and CCS calculations. Furthermore, we have performed Traveling Wave IM-MS (TWIMS) experiments to validate the extant experimental values and assess uncertainties in experimentally measured CCS values. The developed workflow yielded accurate structural predictions and provides unique insights into the likely preferred conformation analyzed using IM-MS experiments. The complete workflow makes the computation of CCS values tractable for a large number of conformationally flexible metabolites with complex molecular structures.
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Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kiyoto Aramis Tanemura
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Laleh Dinpazhoh
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Mithony Keng
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Christina Schumm
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Lydia Leahy
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Carter K Asef
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Markace Rainey
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Arthur S Edison
- Departments of Genetics and Biochemistry, Institute of Bioinformatics and Complex Carbohydrate Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
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15
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Masike K, de Villiers A, de Beer D, Joubert E, Stander MA. Application of direct injection-ion mobility spectrometry-mass spectrometry (DI-IMS-MS) for the analysis of phenolics in honeybush and rooibos tea samples. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Ion Mobility Mass Spectrometry for Structural Elucidation of Petroleum Compounds. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Haler JRN, Béchet E, Kune C, Far J, De Pauw E. Geometric Analysis of Shapes in Ion Mobility-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:273-283. [PMID: 35020377 DOI: 10.1021/jasms.1c00266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Experimental ion mobility-mass spectrometry (IM-MS) results are often correlated to three-dimensional structures based on theoretical chemistry calculations. The bottleneck of this approach is the need for accurate values, both experimentally and theoretically predicted. Here, we continue the development of the trend-based analyses to extract structural information from experimental IM-MS data sets. The experimental collision cross-sections (CCSs) of synthetic systems such as homopolymers and small ionic clusters are investigated in terms of CCS trends as a function of the number of repetitive units (e.g., degree of polymerization (DP) for homopolymers) and for each detected charge state. Then, we computed the projected areas of expanding but perfectly defined geometric objects using an in-house software called MoShade. The shapes were modeled using computer-aided design software where we considered only geometric factors: no atoms, mass, chemical potentials, or interactions were taken into consideration to make the method orthogonal to classical methods for 3D shape assessments using time-consuming computational chemistry. Our modeled shape evolutions favorably compared to experimentally obtained CCS trends, meaning that the apparent volume or envelope of homogeneously distributed mass effectively modeled the ion-drift gas interactions as sampled by IM-MS. The CCSs of convex shapes could be directly related to their surface area. More importantly, this relationship seems to hold even for moderately concave shapes, such as those obtained by geometry-optimized structures of ions from conventional computational chemistry methods. Theoretical sets of expanding beads-on-a-string shapes allowed extracting accurate bead and string dimensions for two homopolymers, without modeling any chemical interactions.
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Affiliation(s)
- Jean R N Haler
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
- Luxembourg Institute of Science and Technology - LIST, Materials Research & Technology MRT Department, L-4422 Belvaux, Luxembourg
| | - Eric Béchet
- Aerospace & Mechanical Engineering Department, Computer-aided Geometric Design, University of Liège, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
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18
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Zimnicka M, Kalenius E, Jurczak J, Danikiewicz W. Ion mobility mass spectrometry - an efficient tool for the analysis of conformational switch of macrocyclic receptors upon anion binding. Analyst 2021; 146:5337-5346. [PMID: 34323262 DOI: 10.1039/d1an00958c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interactions between anions and synthetic macrocyclic receptors belong to the extensively explored area of research due to the particularly important functions of anions in biological and environmental sciences. Structures of anion-macrocycle complexes are closely related to their function, highlighting the importance of structural analysis of the complexes. Here, we discuss the application of ion mobility mass spectrometry (IM-MS) and theoretical calculations to the structural analysis of tetralactam macrocycles (M) with varying flexibility and structural properties, and their complexes with anions [M + X]-. Collision cross section (CCS) values obtained from both direct drift tube (DT) and indirect using traveling-wave (TW) IM-MS measurements supplemented by theoretical calculations were successfully used to describe the structural properties of various macrocycle-anion complexes, proving the suitability of the IM-MS approach for sensitive, selective, and fast detection of anion complexes and characterization of their structures and conformations.
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Affiliation(s)
- Magdalena Zimnicka
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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19
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Auth T, Grabarics M, Schlangen M, Pagel K, Koszinowski K. Modular Ion Mobility Calibrants for Organometallic Anions Based on Tetraorganylborate Salts. Anal Chem 2021; 93:9797-9807. [PMID: 34227799 DOI: 10.1021/acs.analchem.1c01333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organometallics are widely used in catalysis and synthesis. Their analysis relies heavily on mass spectrometric methods, among which traveling-wave ion mobility spectrometry (TWIMS) has gained increasing importance. Collision cross sections (CCS) obtainable by TWIMS significantly aid the structural characterization of ions in the gas phase, but for organometallics, their accuracy has been limited by the lack of appropriate calibrants. Here, we propose tetraorganylborates and their alkali-metal bound oligomers [Mn-1(BR4)n]- (M = Li, Na, K, Rb, Cs; R = aryl, Et; n = 1-6) as calibrants for electrospray ionization (ESI) TWIMS. These species chemically resemble typical organometallics and readily form upon negative-ion mode ESI of solutions of alkali-metal tetraorganylborates. By combining different tetraorganylborate salts, we have generated a large number of anions in a modular manner and determined their CCS values by drift-tube ion mobility spectrometry (DTIMS) (DTCCSHe = 81-585, DTCCSN2 = 130-704 Å2). In proof-of-concept experiments, we then applied these DTCCS values to the calibration of a TWIMS instrument and analyzed phenylcuprate and argentate anions, [Lin-1MnPh2n]- and [MnPhn+1]- (M = Cu, Ag), as prototypical reactive organometallics. The TWCCSN2 values derived from TWIMS measurements are in excellent agreement with those determined by DTIMS (<2% relative difference), demonstrating the effectiveness of the proposed calibration scheme. Moreover, we used theoretical methods to predict the structures and CCS values of the anions considered. These predictions are in good agreement with the experimental results and give further insight into the trends governing the assembly of tetraorganylborate, cuprate, and argentate oligomers.
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Affiliation(s)
- Thomas Auth
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, Göttingen 37077, Germany
| | - Márkó Grabarics
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, Berlin 14195, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, Abteilung Molekülphysik, Faradayweg 4-6, Berlin 14195, Germany
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, Berlin 10623, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, Berlin 14195, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, Abteilung Molekülphysik, Faradayweg 4-6, Berlin 14195, Germany
| | - Konrad Koszinowski
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, Göttingen 37077, Germany
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20
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Grabarics M, Lettow M, Kirk AT, von Helden G, Causon TJ, Pagel K. Plate-height model of ion mobility-mass spectrometry: Part 2-Peak-to-peak resolution and peak capacity. J Sep Sci 2021; 44:2798-2813. [PMID: 33945207 DOI: 10.1002/jssc.202100201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/30/2022]
Abstract
In a previous work, we explored zone broadening and the achievable plate numbers in linear drift tube ion mobility-mass spectrometry through developing a plate-height model [1]. On the basis of these findings, the present theoretical study extends the model by exploring peak-to-peak resolution and peak capacity in ion mobility separations. The first part provides a critical overview of chromatography-influenced resolution equations, including refinement of existing formulae. Furthermore, we present exact resolution equations for drift tube ion mobility spectrometry based on first principles. Upon implementing simple modifications, these exact formulae could be readily extended to traveling wave ion mobility separations and to cases when ion mobility spectrometry is coupled to mass spectrometry. The second part focuses on peak capacity. The well-known assumptions of constant plate number and constant peak width form the basis of existing approximate solutions. To overcome their limitations, an exact peak capacity equation is derived for drift tube ion mobility spectrometry. This exact solution is rooted in a suitable physical model of peak broadening, accounting for the finite injection pulse and subsequent diffusional spreading. By borrowing concepts from the theoretical toolbox of chromatography, we believe that the present study will help in integrating ion mobility spectrometry into the unified language of separation science.
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Affiliation(s)
- Márkó Grabarics
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Maike Lettow
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Leibniz Universität Hannover, Hannover, Germany
| | - Gert von Helden
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Tim J Causon
- Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
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21
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Hollerbach AL, Conant CR, Nagy G, Monroe ME, Gupta K, Donor M, Giberson CM, Garimella SVB, Smith RD, Ibrahim YM. Dynamic Time-Warping Correction for Shifts in Ultrahigh Resolving Power Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:996-1007. [PMID: 33666432 PMCID: PMC8216491 DOI: 10.1021/jasms.1c00005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Detection of arrival time shifts between ion mobility spectrometry (IMS) separations can limit achievable resolving power (Rp), particularly when multiple separations are summed or averaged, as commonly practiced in IMS. Such variations can be apparent in higher Rp measurements and are particularly evident in long path length traveling wave structures for lossless ion manipulations (SLIM) IMS due to their typically much longer separation times. Here, we explore data processing approaches employing single value alignment (SVA) and nonlinear dynamic time warping (DTW) to correct for variations between IMS separations, such as due to pressure fluctuations, to enable more effective spectrum summation for improving Rp and detection of low-intensity species. For multipass SLIM IMS separations, where narrow mobility range measurements have arrival times that can extend to several seconds, the SVA approach effectively corrected for such variations and significantly improved Rp for summed separations. However, SVA was much less effective for broad mobility range separations, such as obtained with multilevel SLIM IMS. Changes in ions' arrival times were observed to be correlated with small pressure changes, with approximately 0.6% relative arrival time shifts being common, sufficient to result in a loss of Rp for summed separations. Comparison of the approaches showed that DTW alignment performed similarly to SVA when used over a narrow mobility range but was significantly better (providing narrower peaks and higher signal intensities) for wide mobility range data. We found that the DTW approach increased Rp by as much as 115% for measurements in which 50 IMS separations over 2 s were summed. We conclude that DTW is superior to SVA for ultra-high-resolution broad mobility range SLIM IMS separations and leads to a large improvement in effective Rp, correcting for ion arrival time shifts regardless of the cause, as well as improving the detectability of low-abundance species. Our tool is publicly available for use with universal ion mobility format (.UIMF) and text (.txt) files.
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Affiliation(s)
- Adam L Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Christopher R Conant
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Khushboo Gupta
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Micah Donor
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Cameron M Giberson
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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22
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An RP-LC-UV-TWIMS-HRMS and Chemometric Approach to Differentiate between Momordicabalsamina Chemotypes from Three Different Geographical Locations in Limpopo Province of South Africa. Molecules 2021; 26:molecules26071896. [PMID: 33801575 PMCID: PMC8036689 DOI: 10.3390/molecules26071896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 11/23/2022] Open
Abstract
Momordica balsamina leaf extracts originating from three different geographical locations were analyzed using reversed-phase liquid chromatography (RP-LC) coupled to travelling wave ion mobility (TWIMS) and high-resolution mass spectrometry (HRMS) in conjunction with chemometric analysis to differentiate between potential chemotypes. Furthermore, the cytotoxicity of the three individual chemotypes was evaluated using HT-29 colon cancer cells. A total of 11 molecular species including three flavonol glycosides, five cucurbitane-type triterpenoid aglycones and three glycosidic cucurbitane-type triterpenoids were identified. The cucurbitane-type triterpenoid aglycones were detected in the positive ionization mode following dehydration [M + H − H2O]+ of the parent compound, whereas the cucurbitane-type triterpenoid glycosides were primarily identified following adduct formation with ammonia [M + NH4]+. The principle component analysis (PCA) loadings plot and a variable influence on projection (VIP) analysis revealed that the isomeric pair balsaminol E and/or karavilagen E was the key molecular species contributing to the distinction between geographical samples. Ultimately, based on statistical analysis, it is hypothesized that balsaminol E and/or karavilagen E are likely responsible for the cytotoxic effects in HT-29 cells.
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23
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Naylor CN, Clowers BH. Reevaluating the Role of Polarizability in Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:618-627. [PMID: 33533630 DOI: 10.1021/jasms.0c00338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the expanding commercial availability of gas-phase separation systems that incorporate gas-phase mobility, there is a concurrent rise in efforts to cast the gas-phase mobility coefficient in terms of an ion-neutral collision cross-section (CCS). The motivating factors for this trend are varied, but many aim to complement experimental results with computationally generated CCS values from in silico structural approximations. Unfortunately, the current paradigm for relating experimental mobility results to computationally derived structures relies upon empirical approaches, including a myriad of variables that do not realistically bound the comparison. In this Critical Insight, we advocate for the development of a self-consistent experimental and computational framework that uses laboratory results to constrain the scope of the modeling effort. This paper aims to prompt discussion, challenge assumptions, and promote the development of more efficient, accurate computational techniques within the gas-phase ion measurement community. Specifically, we postulate whether experimental deviations from Langevin's polarization limit (Kpol) are suitable to estimate the relative contributions of hard-sphere collisions and long-range interactions within CCS values. Not surprisingly, different molecule classes exhibit different trends in the K/Kpol ratio when normalized for reduced mass, and the most common IMS calibrants (e.g., tune mix, polyalanine, tetraalkylammonium salts) follow different polarizability trends than many of the analytes probed in the literature. Succinctly, if gas-phase ion structure is largely invariant based upon the colliding neutral and newly developed experimental efforts can quantitatively capture ion polarizability, then modeling efforts describing a target analyte must be self-consistent as the collision neutral is changed in silico.
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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24
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Masike K, Stander MA, de Villiers A. Recent applications of ion mobility spectrometry in natural product research. J Pharm Biomed Anal 2021; 195:113846. [PMID: 33422832 DOI: 10.1016/j.jpba.2020.113846] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Ion mobility spectrometry (IMS) is a rapid separation technique capable of extracting complementary structural information to chromatography and mass spectrometry (MS). IMS, especially in combination with MS, has experienced inordinate growth in recent years as an analytical technique, and elicited intense interest in many research fields. In natural product analysis, IMS shows promise as an additional tool to enhance the performance of analytical methods used to identify promising drug candidates. Potential benefits of the incorporation of IMS into analytical workflows currently used in natural product analysis include the discrimination of structurally similar secondary metabolites, improving the quality of mass spectral data, and the use of mobility-derived collision cross-section (CCS) values as an additional identification criterion in targeted and untargeted analyses. This review aims to provide an overview of the application of IMS to natural product analysis over the last six years. Instrumental aspects and the fundamental background of IMS will be briefly covered, and recent applications of the technique for natural product analysis will be discussed to demonstrate the utility of the technique in this field.
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Affiliation(s)
- Keabetswe Masike
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Maria A Stander
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa; Central Analytical Facility, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - André de Villiers
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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Li A, Conant CR, Zheng X, Bloodsworth KJ, Orton DJ, Garimella SVB, Attah IK, Nagy G, Smith RD, Ibrahim YM. Assessing Collision Cross Section Calibration Strategies for Traveling Wave-Based Ion Mobility Separations in Structures for Lossless Ion Manipulations. Anal Chem 2020; 92:14976-14982. [PMID: 33136380 DOI: 10.1021/acs.analchem.0c02829] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The collision cross section (CCS) is an important property that aids in the structural characterization of molecules. Here, we investigated the CCS calibration accuracy with traveling wave ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM) using three sets of calibrants. A series of singly negatively charged phospholipids and bile acids were calibrated in nitrogen buffer gas using two different TW waveform profiles (square and sine) and amplitudes (20, 25, and 30 V0-p). The calibration errors for the three calibrant sets (Agilent tuning mixture, polyalanine, and one assembled in-house) showed negligible differences using a sine-shaped TW waveform. Calibration errors were all within 1-2% of the drift tube ion mobility spectrometry (DTIMS) measurements, with lower errors for sine waveforms, presumably due to the lower average and maximum fields experienced by ions. Finally, ultrahigh-resolution multipass (long path length) SLIM TWIMS separations demonstrated improved CCS calibration for phospholipid and bile acid isomers.
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Affiliation(s)
- Ailin Li
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Conant
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kent J Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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26
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Calabrese V, Lavanant H, Rosu F, Gabelica V, Afonso C. Collision Cross Sections of Phosphoric Acid Cluster Anions in Helium Measured by Drift Tube Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:969-981. [PMID: 32153193 DOI: 10.1021/jasms.0c00034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the last years, ion mobility mass spectrometry (IMS-MS) has improved structural analysis and compound identification by giving access to the collision cross section (CCS). An increasingly wide and accurate database of CCS values is now available but often without assessment of the influence of different instrumental settings on CCS values. Here, we present 75 CCS values in helium (DTCCSHe) for phosphoric acid cluster anions [(H3PO4)n - zH]z- with charge state (z) up to 4-. The CCS values, noted DTCCSHe, were obtained with a commercial drift tube ion mobility mass spectrometer, in helium, by applying a classic multifield approach. Phosphoric acid clusters are fragile structures that allow to evaluate the effect of different experimental conditions on the retention of weak bonds and their effect on CCS values. We probed harsh and soft voltage gradients in the electrospray (ESI) source before the IMS and two different voltage gradients in the post-IMS region. The variations in the ion mobility and mass spectra consisted in a change in the distribution of the cluster anions aggregation numbers (n) and charge states (z), with a higher amount of multiply charged species for the soft pre-IMS voltage gradient and a lower proportion of cluster dissociation for soft post-IMS conditions. However, the CCS values did not change with experimental conditions for a given cluster, as long as it stays intact from the IMS to the mass analyzer. The DTCCSHe were found in good agreement among 3 to 10 replicated values, with a relative standard deviation between 0.1 and 1.7%.
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Affiliation(s)
- Valentina Calabrese
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
| | - Hélène Lavanant
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
| | - Frédéric Rosu
- CNRS, University of Bordeaux and INSERM, Institut Européen de Chimie et Biologie (IECB, UMS3033, US001), 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), Site IECB, 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Carlos Afonso
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
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27
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Gelb AS, Lai R, Li H, Dodds ED. Composition and charge state influence on the ion-neutral collision cross sections of protonated N-linked glycopeptides: an experimental and theoretical deconstruction of coulombic repulsion vs. charge solvation effects. Analyst 2020; 144:5738-5747. [PMID: 31453603 DOI: 10.1039/c9an00875f] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ion mobility spectrometry (IMS) is of significant interest as a platform for glycoanalysis. While much attention has been focused on the resolution of isomeric carbohydrates and glycoconjugates, another appealing aspect of IMS is the ability to sort different classes of biomolecules into distinct regions of mass vs. mobility space. This capability has potential to greatly simplify glycoproteomic analyses, as glycosylated and non-glycosylated peptides can be rapidly partitioned in the gas phase. Nevertheless, the physical and chemical characteristics of glycopeptides that dictate their mass vs. mobility loci have yet to be systematically investigated. This report presents an IMS study of model protonated glycopeptide ions with systematically varied oligosaccharide topologies, polypeptide sequences, and charge states. In all, over 110 ion-neutral collision cross sections (CCSs) were measured and analyzed in the context of the physicochemical characteristics of the analytes. Glycan size and composition emerged as a decisive factor in dictating the CCS space occupied by the glycopeptides and exerted this influence in a charge state dependent fashion. Furthermore, elongation of the glycan group was found to either increase or decrease glycopeptide CCSs depending on the ion charge state and the size of the glycan. Molecular dynamics (MD) simulations of the gas phase structures and CCSs of selected glycopeptides revealed that the experimental observations were consistent with a glycan size and charge state dependent interplay between destabilizing coulombic repulsion effects (tending to result in more extended structures) and stabilizing charge solvation effects in which the glycan plays a major role (tending to result in more compact structures). Taken together, these IMS and MD findings suggest the possibility of predicting and delineating glycopeptide-enriched regions of mass vs. mobility space for applications in glycoproteomics.
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Affiliation(s)
- Abby S Gelb
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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28
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Rister AL, Dodds ED. Steroid analysis by ion mobility spectrometry. Steroids 2020; 153:108531. [PMID: 31672629 PMCID: PMC6986338 DOI: 10.1016/j.steroids.2019.108531] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/26/2022]
Abstract
Steroids are an important biomolecule class for analysis due to their promise as biomarkers for various diseases and their abuse as performance enhancers in sports. Current analytical methods, including chromatography and nuclear magnetic resonance spectroscopy, fall short of being able to confidently analyze steroids, partly due to the large number of steroid isomers. Ion mobility spectrometry (IMS), a gas-phase ion separator, has shown potential for steroid analysis both in conjunction with liquid chromatography (LC) and as a stand-alone technique. This review will examine the current literature on IMS analysis of steroids. Analysis by LC-IMS will include examination of steroids and steroid glucuronides in human urine and serum samples for enhanced signal-to-noise ratios and higher confidence of identification. The stand-alone IMS analysis will examine the use of derivatization of steroids and formation of multimers to enhance resolution for steroid isomers analysis, where both methods have been shown to greatly increase the separation of steroid isomer species. However, these methods have not been applied to biological mixtures to assess their applicability to medical and forensic applications, which should be a future direction of this field.
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Affiliation(s)
- Alana L Rister
- Department of Chemistry and University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA
| | - Eric D Dodds
- Department of Chemistry and University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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Abstract
Lipidomics is a rapidly growing field that enables the characterization of the entire lipidome in cells, tissues, or an organism. Changes in lipid metabolism and homeostasis caused by different disease states or drug treatments can be probed by lipidomics experiments, which can aid our understanding of normal physiology and disease pathology at the molecular level. While current technologies using liquid chromatography coupled with high-resolution mass spectrometry have greatly increased coverage of the lipidome, there are still limitations in resolving the large number of lipid species with similar masses in a narrow mass window. We recently reported that two orthogonal separation techniques, hydrophilic interaction liquid chromatography (HILIC) and ion mobility (IM), enhance the resolution of lipid species based on headgroup polarity and gas-phase size and shape, respectively, of various classes of glycerolipids, glycolipids, phospholipids, and sphingolipids. Here we describe the application of our HILIC-IM-MS lipidomics protocol to the analysis of lipid extracts derived from either tissues or cells, to identify significant changes in the lipidome in response to an internal or external stimulus, such as exposure to environmental chemicals.
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Affiliation(s)
- Amy Li
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Kelly M Hines
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
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30
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McKenna KR, Li L, Krishnamurthy R, Liotta CL, Fernández FM. Organic acid shift reagents for the discrimination of carbohydrate isobars by ion mobility-mass spectrometry. Analyst 2020; 145:8008-8015. [DOI: 10.1039/d0an01546f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Traveling wave and drift tube ion mobility were utilized to separate isomeric disaccharides. Organic acid shift reagents were necessary to increase the resolution of these separations for mixture analysis.
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Affiliation(s)
- Kristin R. McKenna
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
| | - Li Li
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
| | | | - Charles L. Liotta
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
| | - Facundo M. Fernández
- NSF/NASA Center for Chemical Evolution
- USA
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
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31
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Dodds JN, Baker ES. Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2185-2195. [PMID: 31493234 PMCID: PMC6832852 DOI: 10.1007/s13361-019-02288-2] [Citation(s) in RCA: 220] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 05/07/2023]
Abstract
Ion mobility spectrometry (IMS) is a rapid separation technique that has experienced exponential growth as a field of study. Interfacing IMS with mass spectrometry (IMS-MS) provides additional analytical power as complementary separations from each technique enable multidimensional characterization of detected analytes. IMS separations occur on a millisecond timescale, and therefore can be readily nested into traditional GC and LC/MS workflows. However, the continual development of novel IMS methods has generated some level of confusion regarding the advantages and disadvantages of each. In this critical insight, we aim to clarify some common misconceptions for new users in the community pertaining to the fundamental concepts of the various IMS instrumental platforms (i.e., DTIMS, TWIMS, TIMS, FAIMS, and DMA), while addressing the strengths and shortcomings associated with each. Common IMS-MS applications are also discussed in this review, such as separating isomeric species, performing signal filtering for MS, and incorporating collision cross-section (CCS) values into both targeted and untargeted omics-based workflows as additional ion descriptors for chemical annotation. Although many challenges must be addressed by the IMS community before mobility information is collected in a routine fashion, the future is bright with possibilities.
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Affiliation(s)
- James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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32
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Ross DH, Seguin RP, Xu L. Characterization of the Impact of Drug Metabolism on the Gas-Phase Structures of Drugs Using Ion Mobility-Mass Spectrometry. Anal Chem 2019; 91:14498-14507. [PMID: 31613088 DOI: 10.1021/acs.analchem.9b03292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Conventional strategies for drug metabolite identification employ a combination of liquid chromatography-mass spectrometry (LC-MS), which offers higher throughput but provides limited structural information, and nuclear magnetic resonance spectroscopy, which can achieves the most definitive identification but lacks throughput. Ion mobility-mass spectrometry (IM-MS) is a rapid, two-dimensional analysis that separates ions on the basis of their gas-phase size and shape (reflected by collision cross section, CCS) and their mass-to-charge (m/z) ratios. The rapid nature of IM separation combined with the structural information provided by CCS make IM-MS a promising technique for obtaining more structural information on drug metabolites without sacrificing analytical throughput. Here, we present an in vitro biosynthesis coupled with IM-MS strategy for rapid generation and analysis of drug metabolites. Drug metabolites were generated in vitro using pooled subcellular fractions derived from human liver and analyzed using a rapid flow injection-IM-MS method. We measured CCS values for 19 parent drugs and their 37 metabolites generated in vitro (78 values in total), representing a wide variety of metabolic modifications. Post-IM fragmentation and computational modeling were used to support metabolite identifications and explore the structural characteristics driving behaviors observed in IM separation. Overall, we found the effects of metabolic modifications on the gas-phase structures of the metabolites to be highly dependent upon the structural characteristics of the parent compounds and the specific position of the modification. This in vitro biosynthesis coupled with rapid IM-MS analysis workflow represents a promising platform for rapid and high-confidence identification of drug metabolites, applicable at a large scale.
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Affiliation(s)
- Dylan H Ross
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Ryan P Seguin
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Libin Xu
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195 , United States
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33
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Lin YF, Yousef EN, Torres E, Truong L, Zahnow JM, Donald CB, Qin Y, Angel LA. Weak Acid-Base Interactions of Histidine and Cysteine Affect the Charge States, Tertiary Structure, and Zn(II)-Binding of Heptapeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2068-2081. [PMID: 31332742 DOI: 10.1007/s13361-019-02275-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 06/10/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Zinc fingers are proteins that are characterized by the coordination of zinc ions by an amino acid sequence that commonly contains two histidines and two cysteines (2His-2Cys motif). Investigations of oligopeptides that contain the 2His-2Cys motif, e.g., acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7, have discovered they exhibit pH-dependent Zn(II) chelation and have redox activities with Cu(I/II), forming a variety of metal complexes. To further understand how these 2His-2Cys oligopeptides bind these metal ions, we have undertaken a series of ion mobility-mass spectrometry and B3LYP/LanL2DZ computational studies of structurally related heptapeptides. Starting with the sequence above, we have modified the potential His, Cys, or C-terminus binding sites and report how these changes in primary structure affect the oligopeptides positive and negative charge states, conformational structure, collision-induced breakdown energies, and how effectively Zn(II) binds to these sequences. The results show evidence that the weak acid-base properties of Cys-His are intrinsically linked and can result in an intramolecular salt-bridged network that affects the oligopeptide properties.
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Affiliation(s)
- Yu-Fu Lin
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Enas N Yousef
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Efren Torres
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Linh Truong
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - James M Zahnow
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Cole B Donald
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Ying Qin
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Laurence A Angel
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA.
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34
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Nye LC, Williams JP, Munjoma NC, Letertre MP, Coen M, Bouwmeester R, Martens L, Swann JR, Nicholson JK, Plumb RS, McCullagh M, Gethings LA, Lai S, Langridge JI, Vissers JP, Wilson ID. A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry: Application to the characterisation of metabolites in rat urine. J Chromatogr A 2019; 1602:386-396. [DOI: 10.1016/j.chroma.2019.06.056] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 01/01/2023]
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Venter P, Causon T, Pasch H, de Villiers A. Comprehensive analysis of chestnut tannins by reversed phase and hydrophilic interaction chromatography coupled to ion mobility and high resolution mass spectrometry. Anal Chim Acta 2019; 1088:150-167. [PMID: 31623711 DOI: 10.1016/j.aca.2019.08.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/29/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022]
Abstract
In this study, we report a methodology based on reversed phase LC (RP-LC) and hydrophilic interaction chromatography (HILIC) separations coupled to ion mobility (IM) and high resolution mass spectrometry (HR-MS) for the detailed analysis of hydrolysable tannins. The application of this approach to the analysis of an industrial chestnut (Castanea sativa, wood chips) tannin extract is demonstrated. A total of 38 molecular species, including a large number or isomers, were identified in this sample based on HR-MS(E) and UV absorption spectral information as well as retention behaviour in both separation modes. In total, 128 and 90 isomeric species were resolved by RP- and HILIC-LC-IM-TOF-MS, respectively. The combination of low- and high collision energy mass spectral data with complementary chromatographic separations allowed tentative and putative identification of twenty molecular species, comprising 78 isomers, in chestnut for the first time. Ion mobility resolved six new dimeric and trimeric vescalagin conformers with unique arrival (drift) times, including new conformers of roburin A-D which were not separated using either RP-LC or HILIC. HILIC was found to be the preferred separation mode for the analysis of vescalagin derivatives, while RP-LC is preferred for the analysis of ellagitannins with a cyclic glucose core. For the complete separation of the galloyl glucose species, comprehensive HILIC × RP-LC separation would be required.
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Affiliation(s)
- Pieter Venter
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland, 7602, South Africa
| | - Tim Causon
- University of Natural Resources and Life Sciences (BOKU), Department of Chemistry, Division of Analytical Chemistry, Vienna, Austria
| | - Harald Pasch
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland, 7602, South Africa
| | - André de Villiers
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland, 7602, South Africa.
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36
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Venter P, Pasch H, de Villiers A. Comprehensive analysis of tara tannins by reversed-phase and hydrophilic interaction chromatography coupled to ion mobility and high-resolution mass spectrometry. Anal Bioanal Chem 2019; 411:6329-6341. [DOI: 10.1007/s00216-019-01931-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/15/2019] [Accepted: 05/17/2019] [Indexed: 11/29/2022]
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37
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Monge ME, Dodds JN, Baker ES, Edison AS, Fernández FM. Challenges in Identifying the Dark Molecules of Life. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:177-199. [PMID: 30883183 PMCID: PMC6716371 DOI: 10.1146/annurev-anchem-061318-114959] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Metabolomics is the study of the metabolome, the collection of small molecules in living organisms, cells, tissues, and biofluids. Technological advances in mass spectrometry, liquid- and gas-phase separations, nuclear magnetic resonance spectroscopy, and big data analytics have now made it possible to study metabolism at an omics or systems level. The significance of this burgeoning scientific field cannot be overstated: It impacts disciplines ranging from biomedicine to plant science. Despite these advances, the central bottleneck in metabolomics remains the identification of key metabolites that play a class-discriminant role. Because metabolites do not follow a molecular alphabet as proteins and nucleic acids do, their identification is much more time consuming, with a high failure rate. In this review, we critically discuss the state-of-the-art in metabolite identification with specific applications in metabolomics and how technologies such as mass spectrometry, ion mobility, chromatography, and nuclear magnetic resonance currently contribute to this challenging task.
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Affiliation(s)
- María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQD, Ciudad de Buenos Aires, Argentina
| | - James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Arthur S Edison
- Department of Genetics, Department of Biochemistry and Molecular Biology, and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology and Petit Institute for Biochemistry and Bioscience, Atlanta, Georgia 30332, USA;
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38
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Gabelica V, Shvartsburg AA, Afonso C, Barran P, Benesch JL, Bleiholder C, Bowers MT, Bilbao A, Bush MF, Campbell JL, Campuzano ID, Causon T, Clowers BH, Creaser CS, De Pauw E, Far J, Fernandez‐Lima F, Fjeldsted JC, Giles K, Groessl M, Hogan CJ, Hann S, Kim HI, Kurulugama RT, May JC, McLean JA, Pagel K, Richardson K, Ridgeway ME, Rosu F, Sobott F, Thalassinos K, Valentine SJ, Wyttenbach T. Recommendations for reporting ion mobility Mass Spectrometry measurements. MASS SPECTROMETRY REVIEWS 2019; 38:291-320. [PMID: 30707468 PMCID: PMC6618043 DOI: 10.1002/mas.21585] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 05/02/2023]
Abstract
Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0 ) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site2 rue Robert Escarpit, 33600PessacFrance
| | | | | | - Perdita Barran
- Michael Barber Centre for Collaborative Mass SpectrometryManchester Institute for Biotechnology, University of ManchesterManchesterUK
| | - Justin L.P. Benesch
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, OX1 3TAOxfordUK
| | - Christian Bleiholder
- Department of Chemistry and BiochemistryFlorida State UniversityTallahasseeFlorida32311
| | | | - Aivett Bilbao
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWashington
| | - Matthew F. Bush
- Department of ChemistryUniversity of WashingtonSeattleWashington
| | | | | | - Tim Causon
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Brian H. Clowers
- Department of ChemistryWashington State UniversityPullmanWashington
| | - Colin S. Creaser
- Centre for Analytical ScienceDepartment of Chemistry, Loughborough UniversityLoughboroughUK
| | - Edwin De Pauw
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | - Johann Far
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | | | | | | | - Michael Groessl
- Department of Nephrology and Hypertension and Department of BioMedical ResearchInselspital, Bern University Hospital, University of Bern, Switzerland and TofwerkThunSwitzerland
| | | | - Stephan Hann
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Hugh I. Kim
- Department of ChemistryKorea UniversitySeoulKorea
| | | | - Jody C. May
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - John A. McLean
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - Kevin Pagel
- Freie Universitaet BerlinInstitute for Chemistry and BiochemistryBerlinGermany
| | | | | | - Frédéric Rosu
- CNRS, INSERM and University of BordeauxInstitut Européen de Chimie et BiologiePessacFrance
| | - Frank Sobott
- Antwerp UniversityBiomolecular & Analytical Mass SpectrometryAntwerpBelgium
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonWC1E 6BTUK
- United Kingdom and Institute of Structural and Molecular BiologyDepartment of Biological Sciences, Birkbeck College, University of LondonLondonWC1E 7HXUK
| | - Stephen J. Valentine
- C. Eugene Bennett Department of ChemistryWest Virginia UniversityMorgantownWest Virginia
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Colby SM, Thomas DG, Nuñez JR, Baxter DJ, Glaesemann KR, Brown JM, Pirrung MA, Govind N, Teeguarden JG, Metz TO, Renslow RS. ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries. Anal Chem 2019; 91:4346-4356. [PMID: 30741529 PMCID: PMC6526953 DOI: 10.1021/acs.analchem.8b04567] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-throughput, comprehensive, and confident identifications of metabolites and other chemicals in biological and environmental samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent technological advances, metabolomics studies still result in the detection of a disproportionate number of features that cannot be confidently assigned to a chemical structure. This inadequacy is driven by the single most significant limitation in metabolomics, the reliance on reference libraries constructed by analysis of authentic reference materials with limited commercial availability. To this end, we have developed the in silico chemical library engine (ISiCLE), a high-performance computing-friendly cheminformatics workflow for generating libraries of chemical properties. In the instantiation described here, we predict probable three-dimensional molecular conformers (i.e., conformational isomers) using chemical identifiers as input, from which collision cross sections (CCS) are derived. The approach employs first-principles simulation, distinguished by the use of molecular dynamics, quantum chemistry, and ion mobility calculations, to generate structures and chemical property libraries, all without training data. Importantly, optimization of ISiCLE included a refactoring of the popular MOBCAL code for trajectory-based mobility calculations, improving its computational efficiency by over 2 orders of magnitude. Calculated CCS values were validated against 1983 experimentally measured CCS values and compared to previously reported CCS calculation approaches. Average calculated CCS error for the validation set is 3.2% using standard parameters, outperforming other density functional theory (DFT)-based methods and machine learning methods (e.g., MetCCS). An online database is introduced for sharing both calculated and experimental CCS values ( metabolomics.pnnl.gov ), initially including a CCS library with over 1 million entries. Finally, three successful applications of molecule characterization using calculated CCS are described, including providing evidence for the presence of an environmental degradation product, the separation of molecular isomers, and an initial characterization of complex blinded mixtures of exposure chemicals. This work represents a method to address the limitations of small molecule identification and offers an alternative to generating chemical identification libraries experimentally by analyzing authentic reference materials. All code is available at github.com/pnnl .
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Affiliation(s)
- Sean M. Colby
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Dennis G. Thomas
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nuñez
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Douglas J. Baxter
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kurt R. Glaesemann
- Communications and Information Technology Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Joseph M. Brown
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Meg A. Pirrung
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Niranjan Govind
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Justin G. Teeguarden
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Thomas O. Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ryan S. Renslow
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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40
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Rister AL, Martin TL, Dodds ED. Application of Group I Metal Adduction to the Separation of Steroids by Traveling Wave Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:248-255. [PMID: 30414066 PMCID: PMC6551524 DOI: 10.1007/s13361-018-2085-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 05/04/2023]
Abstract
Steroids represent an interesting class of small biomolecules due to their use as biomarkers and their status as scheduled drugs. Although the analysis of steroids is complicated by the potential for many isomers, ion mobility spectrometry (IMS) has previously shown promise for the rapid separation of steroid isomers. This work is aimed at the further development of IMS separation for the analysis of steroids. Here, traveling wave ion mobility spectrometry (TWIMS) was applied to the study of group I metal adducted steroids and their corresponding multimers for five sets of isomers. Each set of isomers had a minimum of one dimeric metal ion adduct that exhibited a resolution greater than one (i.e., approaching baseline resolution). Additionally, ion-neutral collision cross sections (CCSs) were measured using polyalanine as a calibrant, which may provide an additional metric contributing to analyte identification. Where possible, measured CCSs were compared to previously reported values. When measuring CCSs of steroid isomers using polyalanine as the calibrant, nitrogen CCS values were within 1.0% error for monomeric sodiated adducts and slightly higher for the dimeric sodiated adducts. Overall, TWIMS was found to successfully separate steroids as dimeric adducts of group I metals. Graphical Abstract ᅟ.
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Affiliation(s)
- Alana L Rister
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE, 68588-0304, USA
| | - Tiana L Martin
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE, 68588-0304, USA
- Department of Chemistry and Biochemistry, Spelman College, Atlanta, GA, 30314-4399, USA
| | - Eric D Dodds
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE, 68588-0304, USA.
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41
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Zandkarimi F, Brown LM. Application of Ion Mobility Mass Spectrometry in Lipidomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:317-326. [DOI: 10.1007/978-3-030-15950-4_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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McKenna KR, Li L, Baker AG, Ujma J, Krishnamurthy R, Liotta CL, Fernández FM. Carbohydrate isomer resolutionviamulti-site derivatization cyclic ion mobility-mass spectrometry. Analyst 2019; 144:7220-7226. [DOI: 10.1039/c9an01584a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cyclic ion mobility-tandem mass spectrometry enhances the separation and identification of small carbohydrate isomers.
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Affiliation(s)
- Kristin R. McKenna
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | - Li Li
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | | | | | | | - Charles L. Liotta
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | - Facundo M. Fernández
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
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Le Maître J, Hubert-Roux M, Paupy B, Marceau S, Rüger CP, Afonso C, Giusti P. Structural analysis of heavy oil fractions after hydrodenitrogenation by high-resolution tandem mass spectrometry and ion mobility spectrometry. Faraday Discuss 2019; 218:417-430. [DOI: 10.1039/c8fd00239h] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The purpose of this study was to identify and characterize compounds that are refractory to the hydrodenitrogenation process.
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Affiliation(s)
- Johann Le Maître
- Normandie Université
- COBRA
- UMR 6014 et FR 3038
- Université de Rouen
- INSA de Rouen
| | - Marie Hubert-Roux
- Normandie Université
- COBRA
- UMR 6014 et FR 3038
- Université de Rouen
- INSA de Rouen
| | - Benoît Paupy
- TOTAL Refining & Chemicals
- Total Research & Technology Gonfreville
- 76700 Harfleur
- France
- International Joint Laboratory – iC2MC: Complex Matrices Molecular Characterization
| | - Sabrina Marceau
- TOTAL Refining & Chemicals
- Total Research & Technology Gonfreville
- 76700 Harfleur
- France
- International Joint Laboratory – iC2MC: Complex Matrices Molecular Characterization
| | | | - Carlos Afonso
- Normandie Université
- COBRA
- UMR 6014 et FR 3038
- Université de Rouen
- INSA de Rouen
| | - Pierre Giusti
- TOTAL Refining & Chemicals
- Total Research & Technology Gonfreville
- 76700 Harfleur
- France
- International Joint Laboratory – iC2MC: Complex Matrices Molecular Characterization
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Lim D, Davidson KL, Son S, Ahmed A, Bush MF, Kim S. Determining Collision Cross‐Sections of Aromatic Compounds in Crude Oil by Using Aromatic Compound Mixture as Calibration Standard. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dongwan Lim
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
| | | | - Seungwoo Son
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
| | - Arif Ahmed
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
| | - Matthew F. Bush
- Department of ChemistryUniversity of Washington Seattle WA, 98195‐1700 USA
| | - Sunghwan Kim
- Department of ChemistryKyungpook National University Daegu 41566 Republic of Korea
- Green‐Nano Materials Research Center Daegu 41566 Republic of Korea
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45
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Ouyang H, Bo T, Zhang Z, Guo X, He M, Li J, Yang S, Ma X, Feng Y. Ion mobility mass spectrometry with molecular modelling to reveal bioactive isomer conformations and underlying relationship with isomerization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1931-1940. [PMID: 30151930 DOI: 10.1002/rcm.8271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/21/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE In medicine and drug development, molecular modelling is an important tool. It is attractive to develop a platform connecting the theoretical structural modelling and the results from experimental measurement. In addition, the separation and structural analysis of bioactive constituent isomers are still challenging tasks. METHODS Drift tube ion mobility (IM) mass spectrometry (MS) provides the experimental collision cross section (CCS) which contains the structural information. The experimental CCS can be compared with the calculated CCS of the molecular modelling structures. This technique is especially useful for bioactive constituents in herbal medicine because active isomers with the same chemical formula are common in these samples. IM helps separate and identify these isomers and reveals details about their structures and conformations. RESULTS Two model bioactive constituents, caffeoylquinic acids (CQAs) and dicaffeoylquinic acids (di-CQAs), were selected to systematically investigate the influence of solution, ion source conditions and ion heating on the isomer CCS distributions. By comparing the calculated CCS with the experimental value, we identified the favorable conformations of CQAs. The most compact conformation of a CQA was less likely to isomerize than the more extended conformation. It was found that the isomerization tendency was in accord with the conformation favorability. CONCLUSIONS This study offers an effective approach to predict and demystify the conformation and isomerization of the active constituents in herbal medicines.
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Affiliation(s)
- Hui Ouyang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Tao Bo
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Zhengxiang Zhang
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Xinqiu Guo
- Ming De Tian Sheng Biotech Inc., Changping Campus of Peking University, Beijing, 102200, China
| | - Mingzhen He
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Junmao Li
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Shilin Yang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, No. 56 Yangming Road, Nanchang, 330006, China
| | - Xin Ma
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Yulin Feng
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, No. 56 Yangming Road, Nanchang, 330006, China
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46
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Yassine MM, Dabek-Zlotorzynska E. Investigation of isomeric structures in a commercial mixture of naphthenic acids using ultrahigh pressure liquid chromatography coupled to hybrid traveling wave ion mobility-time of flight mass spectrometry. J Chromatogr A 2018; 1572:90-99. [DOI: 10.1016/j.chroma.2018.08.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/13/2018] [Accepted: 08/23/2018] [Indexed: 12/23/2022]
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Lippens JL, Ranganathan SV, D'Esposito RJ, Fabris D. Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry. Analyst 2018; 141:4084-99. [PMID: 27152369 DOI: 10.1039/c6an00453a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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. Putative calibrants consisted of single- (ss) and double-stranded (ds) oligo-deoxynucleotides reaching up to ∼40 kDa in size (i.e., 64 bp) and ∼5700 Å(2) in CCS. To ensure self-consistency among reference CCS values, computational data obtained in house were preferred to any experimental or computational data from disparate sources. Such values were obtained by molecular dynamics (MD) simulations and either the exact hard sphere scattering (EHSS) or the projection superposition approximation (PSA) methods, and then plotted against the corresponding experimental values to generate separate calibration curves. Their performance was evaluated on the basis of their correlation coefficients and ability to provide values that matched the CCS of selected test samples mimicking typical unknowns. The results indicated that the predictive power benefited from the exclusion of higher charged species that were more susceptible to the destabilizing effects of Coulombic repulsion. The results revealed discrepancies between EHSS and PSA data that were ascribable to the different approximations used to describe the ion mobility process. Within the boundaries defined by these approximations and the challenges of modeling NA structure in a solvent-free environment, the calibrant sets enabled the experimental determination of CCS with excellent reproducibility (precision) and error (accuracy), which will support the analysis of progressively larger NA samples of biological significance.
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Affiliation(s)
| | | | | | - Daniele Fabris
- University at Albany, Albany, New York, USA. and SUNY, Albany, The RNA Institute, 1400 Washington Avenue, Albany, New York, USA
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48
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Baksi A, Chakraborty P, Nag A, Ghosh D, Bhat S, Pradeep T. Monolayer-Protected Noble-Metal Clusters as Potential Standards for Negative-Ion Mass Spectrometry. Anal Chem 2018; 90:11351-11357. [DOI: 10.1021/acs.analchem.8b02280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ananya Baksi
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Papri Chakraborty
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Abhijit Nag
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Debasmita Ghosh
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Shridevi Bhat
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Thalappil Pradeep
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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49
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Chalet C, Hollebrands B, Duchateau GS, Augustijns P. Intestinal phase-II metabolism of quercetin in HT29 cells, 3D human intestinal tissues and in healthy volunteers: a qualitative comparison using LC-IMS-MS and LC-HRMS. Xenobiotica 2018; 49:945-952. [PMID: 30085847 DOI: 10.1080/00498254.2018.1509246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Flavonoids are a large class of dietary molecules, among which quercetin is the most ubiquitous, which undergo an extensive intestinal phase-II metabolism. We compared the in vivo metabolism of quercetin in healthy volunteers with two in vitro models, HT29 cells and 3 D human intestinal tissues. Supernatants of the in vitro experiments and the human intestinal fluids (HIF) were analyzed by LC-IMS-MS and LC-HRMS in a qualitative way. Quercetin glucuronides, sulfates and their methyl conjugates were detected in all three systems. The metabolic profiles were found to be different, both in terms of the metabolites produced and their relative proportions. In particular, quercetin sulfates were almost absent in supernatants from HT29 cells incubations while they were a major metabolite in HIF and also found in 3 D intestinal tissues incubations. IMS provided structural information as well as a third dimension of characterization, while HRMS brought increased sensitivity and MS/MS confirmation. HT29 cells are a useful tool to generate phase-II metabolites but do not represent the in vivo situation. 3 D intestinal tissues appear as a more relevant tool to study the intestinal phase-II metabolism of flavonoids.
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Affiliation(s)
- Clément Chalet
- a Unilever R&D , Vlaardingen , The Netherlands.,b Drug Delivery and Disposition , KU Leuven , Leuven , Belgium
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50
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Forsythe JG, English SL, Simoneaux RE, Weber AL. Synthesis of β-Peptide Standards for Use in Model Prebiotic Reactions. ORIGINS LIFE EVOL B 2018; 48:201-211. [PMID: 29796877 DOI: 10.1007/s11084-018-9558-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/30/2018] [Indexed: 10/16/2022]
Abstract
A one-pot method was developed for the preparation of a series of β-alanine standards of moderate size (2 to ≥12 residues) for studies concerning the prebiotic origins of peptides. The one-pot synthesis involved two sequential reactions: (1) dry-down self-condensation of β-alanine methyl ester, yielding β-alanine peptide methyl ester oligomers, and (2) subsequent hydrolysis of β-alanine peptide methyl ester oligomers, producing a series of β-alanine peptide standards. These standards were then spiked into a model prebiotic product mixture to confirm by HPLC the formation of β-alanine peptides under plausible reaction conditions. The simplicity of this approach suggests it can be used to prepare a variety of β-peptide standards for investigating differences between α- and β-peptides in the context of prebiotic chemistry.
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Affiliation(s)
- Jay G Forsythe
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Sloane L English
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Rachel E Simoneaux
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Arthur L Weber
- Ames Research Center, SETI Institute, Mail Stop 239-4, Moffett Field, CA, 94035, USA.
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