1
|
Baker ES, Uritboonthai W, Aisporna A, Hoang C, Heyman HM, Connell L, Olivier-Jimenez D, Giera M, Siuzdak G. METLIN-CCS Lipid Database: An authentic standards resource for lipid classification and identification. Nat Metab 2024; 6:981-982. [PMID: 38802544 PMCID: PMC11218851 DOI: 10.1038/s42255-024-01058-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Affiliation(s)
- Erin S Baker
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | | | - Aries Aisporna
- Scripps Center of Metabolomics and Mass Spectrometry, La Jolla, CA, USA
| | - Corey Hoang
- Scripps Center of Metabolomics and Mass Spectrometry, La Jolla, CA, USA
| | - Heino M Heyman
- Bruker Daltonics, Bruker Scientific LLC, Billerica, MA, USA
- Metabolon Inc., 617 Davis Drive. Suite 100, Morrisville, NC, USA
| | - Lisa Connell
- Avanti Polar Lipids (part of Croda International), Alabaster, AL, USA
| | - Damien Olivier-Jimenez
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Gary Siuzdak
- Scripps Center of Metabolomics and Mass Spectrometry, La Jolla, CA, USA.
- Department of Chemistry, Molecular and Computational Biology Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
2
|
Huntley AP, Hollerbach AL, Norheim RV, Hamid AM, Anderson GA, Garimella SV, Ibrahim YM. Cyclable Variable Path Length Multilevel Structures for Lossless Ion Manipulations (SLIM) Platform for Enhanced Ion Mobility Separations. Anal Chem 2024:10.1021/acs.analchem.3c05594. [PMID: 38336463 PMCID: PMC11310366 DOI: 10.1021/acs.analchem.3c05594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Ion mobility-mass spectrometry (IMS-MS) is used to analyze complex samples and provide structural information on unknown compounds. As the complexity of samples increases, there is a need to improve the resolution of IMS-MS instruments to increase the rate of molecular identification. This work evaluated a cyclable and variable path length (and hence resolving power) multilevel Structures for Lossless Ion Manipulations (SLIM) platform to achieve a higher resolving power than what was previously possible. This new multilevel SLIM platform has eight separation levels connected by ion escalators, yielding a total path length of ∼88 m (∼11 m per level). Our new multilevel SLIM can also be operated in an "ion cycling" mode by utilizing a set of return ion escalators that transport ions from the eighth level back to the first, allowing even extendable path lengths (and higher IMS resolution). The platform has been improved to enhance ion transmission and IMS separation quality by reducing the spacing between SLIM boards. The board thickness was reduced to minimize the ions' escalator residence time. Compared to the previous generation, the new multilevel SLIM demonstrated better transmission for a set of phosphazene ions, especially for the low-mobility ions. For example, the transmission of m/z 2834 ions was improved by a factor of ∼3 in the new multilevel SLIM. The new multilevel SLIM achieved 49% better resolving powers for GRGDS1+ ions in 4 levels than our previous 4-level SLIM. The collision cross-section-based resolving power of the SLIM platform was tested using a pair of reverse sequence peptides (SDGRG1+, GRGDS1+). We achieved 1100 resolving power using 88 m of path length (i.e., 8 levels) and 1400 following an additional pass through the eight levels. Further evaluation of the multilevel SLIM demonstrated enhanced separation for positively and negatively charged brain total lipid extract samples. The new multilevel SLIM enables a tunable high resolving power for a wide range of ion mobilities and improved transmission for low-mobility ions.
Collapse
Affiliation(s)
- Adam P. Huntley
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington, 99354, United States
| | - Adam L. Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington, 99354, United States
| | - Randolph V. Norheim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington, 99354, United States
| | - Ahmed M. Hamid
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington, 99354, United States
| | - Gordon A. Anderson
- Gordon A. Anderson Custom Electronics (GAACE), Kennewick, Washington, 99338
| | - Sandilya V.B. Garimella
- 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
| |
Collapse
|
3
|
Slusher GA, Kottke PA, Culberson AL, Chilmonczyk MA, Fedorov AG. Microfluidics enabled multi-omics triple-shot mass spectrometry for cell-based therapies. BIOMICROFLUIDICS 2024; 18:011302. [PMID: 38268742 PMCID: PMC10807926 DOI: 10.1063/5.0175178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/01/2024] [Indexed: 01/26/2024]
Abstract
In recent years, cell-based therapies have transformed medical treatment. These therapies present a multitude of challenges associated with identifying the mechanism of action, developing accurate safety and potency assays, and achieving low-cost product manufacturing at scale. The complexity of the problem can be attributed to the intricate composition of the therapeutic products: living cells with complex biochemical compositions. Identifying and measuring critical quality attributes (CQAs) that impact therapy success is crucial for both the therapy development and its manufacturing. Unfortunately, current analytical methods and tools for identifying and measuring CQAs are limited in both scope and speed. This Perspective explores the potential for microfluidic-enabled mass spectrometry (MS) systems to comprehensively characterize CQAs for cell-based therapies, focusing on secretome, intracellular metabolome, and surfaceome biomarkers. Powerful microfluidic sampling and processing platforms have been recently presented for the secretome and intracellular metabolome, which could be implemented with MS for fast, locally sampled screening of the cell culture. However, surfaceome analysis remains limited by the lack of rapid isolation and enrichment methods. Developing innovative microfluidic approaches for surface marker analysis and integrating them with secretome and metabolome measurements using a common analytical platform hold the promise of enhancing our understanding of CQAs across all "omes," potentially revolutionizing cell-based therapy development and manufacturing for improved efficacy and patient accessibility.
Collapse
Affiliation(s)
| | - Peter A. Kottke
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
| | | | | | | |
Collapse
|
4
|
Shi Y, Jin HF, Ma XR, Cao J. Highly sensitive determination of multiple pesticide residues in foods by supercritical fluid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry. Food Res Int 2024; 175:113769. [PMID: 38129060 DOI: 10.1016/j.foodres.2023.113769] [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: 07/31/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
This experiment aimed to establish a green, simple and highly sensitive method (supercritical fluid chromatography (SFC) coupled with ion mobility quadrupole time-of-flight mass spectrometry (IM-Q-TOF/MS)) for the detection of multiple pesticides in foods. During the experiments, several important SFC parameters, such as stationary phase, modifier, make-up solution, back-temperature and back-pressure were optimized. Here, single-field collision cross section (CCS) values and multifield CCS values of 20 pesticides were examined by IM-Q-TOF/MS as highly specific parameters with excellent experimental precision. In addition, based on accurate mass matching and fragment ion comparison, mass fragments were obtained by IM-Q-TOF/MS, which elucidated the regularities of compound structure and characteristic fragment ions. Under the optimized conditions, satisfactory linearity (R2 ≥ 0.9989) and recoveries (79.60 % to 112.97 %) were obtained. The intra- and interday precisions were favorable, with RSDs lower than 4.91 and 7.65 %, respectively. Additionally, the method showed low limits of detection (0.1-8.8 ng/mL). The proposed method has been successfully applied to the highly sensitive detection of phenylurea herbicide, triazine herbicides, organophosphorus pesticide, pyrethroid insecticide and acaricide in yam and potato.
Collapse
Affiliation(s)
- Ying Shi
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Huang-Fei Jin
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xin-Ran Ma
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Jun Cao
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China.
| |
Collapse
|
5
|
Ryan JP, Kostelic MM, Hsieh CC, Powers J, Aspinwall C, Dodds JN, Schiel JE, Marty MT, Baker ES. Characterizing Adeno-Associated Virus Capsids with Both Denaturing and Intact Analysis Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2811-2821. [PMID: 38010134 DOI: 10.1021/jasms.3c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Adeno-associated virus (AAV) capsids are among the leading gene delivery platforms used to treat a vast array of human diseases and conditions. AAVs exist in a variety of serotypes due to differences in viral protein (VP) sequences with distinct serotypes targeting specific cells and tissues. As the utility of AAVs in gene therapy increases, ensuring their specific composition is imperative for the correct targeting and gene delivery. From a quality control perspective, current analytical tools are limited in their selectivity for viral protein (VP) subunits due to their sequence similarities, instrumental difficulties in assessing the large molecular weights of intact capsids, and the uncertainty in distinguishing empty and filled capsids. To address these challenges, we combined two distinct analytical workflows that assess the intact capsids and VP subunits separately. First, a selective temporal overview of resonant ion (STORI)-based charge detection-mass spectrometry (CD-MS) was applied for characterization of the intact capsids. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations were then used for the capsid denaturing measurements. This multimethod combination was applied to three AAV serotypes (AAV2, AAV6, and AAV8) to evaluate their intact empty and filled capsid ratios and then examine the distinct VP sequences and modifications present.
Collapse
Affiliation(s)
- Jack P Ryan
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
| | - Marius M Kostelic
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Joshua Powers
- Institute for Bioscience and Biotechnology Research (NIST), Gaithersburg Maryland 20899, United States
- North Carolina State University, Biomanufacturing Training and Education Center (BTEC), Raleigh, North Carolina 27695, United States
| | - Craig Aspinwall
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - James N Dodds
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
| | - John E Schiel
- Institute for Bioscience and Biotechnology Research (NIST), Gaithersburg Maryland 20899, United States
| | - Michael T Marty
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Erin S Baker
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
6
|
Krestensen KK, Heeren RMA, Balluff B. State-of-the-art mass spectrometry imaging applications in biomedical research. Analyst 2023; 148:6161-6187. [PMID: 37947390 DOI: 10.1039/d3an01495a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Mass spectrometry imaging has advanced from a niche technique to a widely applied spatial biology tool operating at the forefront of numerous fields, most notably making a significant impact in biomedical pharmacological research. The growth of the field has gone hand in hand with an increase in publications and usage of the technique by new laboratories, and consequently this has led to a shift from general MSI reviews to topic-specific reviews. Given this development, we see the need to recapitulate the strengths of MSI by providing a more holistic overview of state-of-the-art MSI studies to provide the new generation of researchers with an up-to-date reference framework. Here we review scientific advances for the six largest biomedical fields of MSI application (oncology, pharmacology, neurology, cardiovascular diseases, endocrinology, and rheumatology). These publications thereby give examples for at least one of the following categories: they provide novel mechanistic insights, use an exceptionally large cohort size, establish a workflow that has the potential to become a high-impact methodology, or are highly cited in their field. We finally have a look into new emerging fields and trends in MSI (immunology, microbiology, infectious diseases, and aging), as applied MSI is continuously broadening as a result of technological breakthroughs.
Collapse
Affiliation(s)
- Kasper K Krestensen
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Ron M A Heeren
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Benjamin Balluff
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
| |
Collapse
|
7
|
Baker ES, Hoang C, Uritboonthai W, Heyman HM, Pratt B, MacCoss M, MacLean B, Plumb R, Aisporna A, Siuzdak G. METLIN-CCS: an ion mobility spectrometry collision cross section database. Nat Methods 2023; 20:1836-1837. [PMID: 37932399 PMCID: PMC10843661 DOI: 10.1038/s41592-023-02078-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Affiliation(s)
- Erin S Baker
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Corey Hoang
- Scripps Center of Metabolomics and Mass Spectrometry, La Jolla, CA, USA
| | | | - Heino M Heyman
- Bruker Daltonics, Bruker Scientific LLC, Billerica, MA, USA
- Metabolon Inc., Morrisville, NC, USA
| | - Brian Pratt
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Robert Plumb
- Waters Corporation, Scientific Operations, IMMERSE, Cambridge, MA, USA
| | - Aries Aisporna
- Scripps Center of Metabolomics and Mass Spectrometry, La Jolla, CA, USA
| | - Gary Siuzdak
- Scripps Center of Metabolomics and Mass Spectrometry, La Jolla, CA, USA.
- Department of Chemistry, Molecular and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
8
|
Zhang H, Luo M, Wang H, Ren F, Yin Y, Zhu ZJ. AllCCS2: Curation of Ion Mobility Collision Cross-Section Atlas for Small Molecules Using Comprehensive Molecular Representations. Anal Chem 2023; 95:13913-13921. [PMID: 37664900 DOI: 10.1021/acs.analchem.3c02267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The development of ion mobility-mass spectrometry (IM-MS) has revolutionized the analysis of small molecules, such as metabolomics, lipidomics, and exposome studies. The curation of comprehensive reference collision cross-section (CCS) databases plays a pivotal role in the successful application of IM-MS for small-molecule analysis. In this study, we presented AllCCS2, an enhanced version of AllCCS, designed for the universal prediction of the ion mobility CCS values of small molecules. AllCCS2 incorporated newly available experimental CCS data, including 10,384 records and 7713 unified values, as training data. By leveraging a neural network trained on diverse molecular representations encompassing mass spectrometry features, molecular descriptors, and graph features extracted using a graph convolutional network, AllCCS2 achieved exceptional prediction accuracy. AllCCS2 achieved median relative error (MedRE) values of 0.31, 0.72, and 1.64% in the training, validation, and testing sets, respectively, surpassing existing CCS prediction tools in terms of accuracy and coverage. Furthermore, AllCCS2 exhibited excellent compatibility with different instrument platforms (DTIMS, TWIMS, and TIMS). The prediction uncertainties in AllCCS2 from the training data and the prediction model were comprehensively investigated by using representative structure similarity and model prediction variation. Notably, small molecules with high structural similarities to the training set and lower model prediction variation exhibited improved accuracy and lower relative errors. In summary, AllCCS2 serves as a valuable resource to support applications of IM-MS technologies. The AllCCS2 database and tools are freely accessible at http://allccs.zhulab.cn/.
Collapse
Affiliation(s)
- Haosong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingdu Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongmiao Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fandong Ren
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yandong Yin
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China
| |
Collapse
|
9
|
Li X, Wang H, Jiang M, Ding M, Xu X, Xu B, Zou Y, Yu Y, Yang W. Collision Cross Section Prediction Based on Machine Learning. Molecules 2023; 28:molecules28104050. [PMID: 37241791 DOI: 10.3390/molecules28104050] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Ion mobility-mass spectrometry (IM-MS) is a powerful separation technique providing an additional dimension of separation to support the enhanced separation and characterization of complex components from the tissue metabolome and medicinal herbs. The integration of machine learning (ML) with IM-MS can overcome the barrier to the lack of reference standards, promoting the creation of a large number of proprietary collision cross section (CCS) databases, which help to achieve the rapid, comprehensive, and accurate characterization of the contained chemical components. In this review, advances in CCS prediction using ML in the past 2 decades are summarized. The advantages of ion mobility-mass spectrometers and the commercially available ion mobility technologies with different principles (e.g., time dispersive, confinement and selective release, and space dispersive) are introduced and compared. The general procedures involved in CCS prediction based on ML (acquisition and optimization of the independent and dependent variables, model construction and evaluation, etc.) are highlighted. In addition, quantum chemistry, molecular dynamics, and CCS theoretical calculations are also described. Finally, the applications of CCS prediction in metabolomics, natural products, foods, and the other research fields are reflected.
Collapse
Affiliation(s)
- Xiaohang Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Hongda Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Meiting Jiang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Mengxiang Ding
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Xiaoyan Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Bei Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Yadan Zou
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Yuetong Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| | - Wenzhi Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China
| |
Collapse
|
10
|
Ross DH, Guo J, Bilbao A, Huan T, Smith RD, Zheng X. Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry-Mass Spectrometry Lipidomics Data. Molecules 2023; 28:molecules28083483. [PMID: 37110719 PMCID: PMC10142755 DOI: 10.3390/molecules28083483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.
Collapse
Affiliation(s)
- Dylan H Ross
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jian Guo
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Aivett Bilbao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| |
Collapse
|
11
|
Bilbao A, Ross DH, Lee JY, Donor MT, Williams SM, Zhu Y, Ibrahim YM, Smith RD, Zheng X. MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry. J Proteome Res 2023; 22:508-513. [PMID: 36414245 PMCID: PMC9898216 DOI: 10.1021/acs.jproteome.2c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Modern mass spectrometry-based workflows employing hybrid instrumentation and orthogonal separations collect multidimensional data, potentially allowing deeper understanding in omics studies through adoption of artificial intelligence methods. However, the large volume of these rich spectra challenges existing data storage and access technologies, therefore precluding informatics advancements. We present MZA (pronounced m-za), the mass-to-charge (m/z) generic data storage and access tool designed to facilitate software development and artificial intelligence research in multidimensional mass spectrometry measurements. Composed of a data conversion tool and a simple file structure based on the HDF5 format, MZA provides easy, cross-platform and cross-programming language access to raw MS-data, enabling fast development of new tools in data science programming languages such as Python and R. The software executable, example MS-data and example Python and R scripts are freely available at https://github.com/PNNL-m-q/mza.
Collapse
Affiliation(s)
- Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA,Corresponding authors Aivett Bilbao – Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, United States; .; Xueyun Zheng – Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States;
| | - Dylan H. Ross
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joon-Yong Lee
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Micah T. Donor
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ying Zhu
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | | | - Xueyun Zheng
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA,Corresponding authors Aivett Bilbao – Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, United States; .; Xueyun Zheng – Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States;
| |
Collapse
|
12
|
Liao Y, Ding Y, Wu Y, Du Q, Xia J, Jia J, Lin H, Benjakul S, Zhang B, Hu Y. Analysis of volatile compounds and flavor fingerprint in hairtail ( Trichiurus lepturus) during air-drying using headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). Front Nutr 2023; 9:1088128. [PMID: 36712508 PMCID: PMC9875018 DOI: 10.3389/fnut.2022.1088128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
In the present study, changes in volatile compounds during processing were analyzed using the headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), to investigate the generation of aroma in hairtails (Trichiurus lepturus) during air-drying. Physicochemical indices, such as moisture content and thiobarbituric acid reactive substances (TBARS), were also detected. Flavor fingerprints were studied and developed to distinguish the samples of fresh hairtails (0 day) from air-dried hairtails (2 and 4 days). A total of 75 volatile organic compounds (VOCs) were identified in hairtails, in which alcohols, aldehydes, ketones, and esters were the principal contributors to the formation of the overall flavor of hairtails during air-drying. Seven flavor compounds (ethanol, 3-methyl-1-butanol, 1-pentanol, hexanal, octanal, benzaldehyde, and 3-methylbutanal), two flavor compounds (acetoin and dimethyl sulfide), and eight flavor compounds (1-hexanol, 1-octen-3-ol, nonanal, heptanal, 2-heptanone, ethyl acetate, trimethylamine, and ammonia) were identified in 0, 2, and 4 air-dried hairtails as biomarkers, respectively. The results showed that HS-GC-IMS could detect VOCs in different air-dried hairtails rapidly and comprehensively.
Collapse
Affiliation(s)
- Yueqin Liao
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Yixuan Ding
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Yingru Wu
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Qi Du
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Jiangyue Xia
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Junqi Jia
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Huimin Lin
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China,Pisa Marine Graduate School, Zhejiang Ocean University, Zhoushan, China,*Correspondence: Huimin Lin ✉ ; ✉
| | - Soottawat Benjakul
- Faculty of Agro-Industry, International Center of Excellence in Seafood Science and Innovation, Prince of Songkla University, Hat Yai, Thailand
| | - Bin Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China,Pisa Marine Graduate School, Zhejiang Ocean University, Zhoushan, China,Bin Zhang ✉ ; ✉
| | - Yi Hu
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| |
Collapse
|
13
|
Characterization of the Volatile Compounds of Onion with Different Fresh-Cut Styles and Storage Temperatures. Foods 2022; 11:foods11233829. [PMID: 36496638 PMCID: PMC9736120 DOI: 10.3390/foods11233829] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/15/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The flavor of fresh onion and its processed products is an important index with which to evaluate its quality. In this study, the highly volatile compounds of onion with different fresh-cut styles (bulb, ring, and square) and different storage temperatures (4 °C, 20 °C, and 25 °C) were characterized at the molecular level, focusing in particular on the volatile sulfur compounds. Headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) were employed. A total of 14 highly volatile compounds were identified in onion samples by HS-GC-IMS, and the square sample contained more volatile components. (E,E)-2,4-heptadianal, ethyl acetate, 2-methyl-1-pentanol, 2-pentylfuran, propyl acetate, and 2,6-dimethylpyrazine were produced in the ring and square samples when stored at higher temperatures, while pentanal, 2-heptenal, hexanal were decreased after cutting. Simultaneously, 16 sulfur compounds were identified in onions by HS-SPME-GC-MS. The sulfur compounds profile of the bulbs was significantly different from that of the rings and squares at any temperature. When stored at a low temperature (4 °C), cutting onions into a ring or square shape produced more sulfur. However, at higher temperatures (20 °C and 25 °C), fresh-cutting decreased the sulfur concentration. The total content of sulfur compounds was higher in the same cut style stored at higher temperatures (20 °C or 25 °C). 2-Mercapto-3,4-dimethyl-2,3-dihydrothiophene and 2,4-dimethylthiophene were formed during storage; however, (E)-1-(prop-1-en-1-yl)-3-propyltrisulfane, 1-(1-(methylthio)propyl)-2-propyldisulfane, (Z)-1-(1-propenyldithio)propyl disulfide, dipropyl trisulfide, and methyl 1-(1-propenylthio)propyl disulfide were lost from all samples after storage.
Collapse
|
14
|
Gou MJ, Kose MC, Crommen J, Nix C, Cobraiville G, Caers J, Fillet M. Contribution of Capillary Zone Electrophoresis Hyphenated with Drift Tube Ion Mobility Mass Spectrometry as a Complementary Tool to Microfluidic Reversed Phase Liquid Chromatography for Antigen Discovery. Int J Mol Sci 2022; 23:13350. [PMID: 36362139 PMCID: PMC9659090 DOI: 10.3390/ijms232113350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 10/14/2023] Open
Abstract
The discovery of new antigens specific to multiple myeloma that could be targeted by novel immunotherapeutic approaches is currently of great interest. To this end, it is important to increase the number of proteins identified in the sample by combining different separation strategies. A capillary zone electrophoresis (CZE) method, coupled with drift tube ion mobility (DTIMS) and quadrupole time-of-flight mass spectrometry (QTOF), was developed for antigen discovery using the human myeloma cell line LP-1. This method was first optimized to obtain a maximum number of identifications. Then, its performance in terms of uniqueness of identifications was compared to data acquired by a microfluidic reverse phase liquid chromatography (RPLC) method. The orthogonality of these two approaches and the physicochemical properties of the entities identified by CZE and RPLC were evaluated. In addition, the contribution of DTIMS to CZE was investigated in terms of orthogonality as well as the ability to provide unique information. In conclusion, we believe that the combination of CZE-DTIMS-QTOF and microfluidic RPLC provides unique information in the context of antigen discovery.
Collapse
Affiliation(s)
- Marie-Jia Gou
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
| | - Murat Cem Kose
- Laboratory of Hematology, GIGA I3, University of Liège, Avenue de l’Hopital 11, B34, 4000 Liege, Belgium
| | - Jacques Crommen
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
| | - Cindy Nix
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
| | - Gael Cobraiville
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
| | - Jo Caers
- Laboratory of Hematology, GIGA I3, University of Liège, Avenue de l’Hopital 11, B34, 4000 Liege, Belgium
- Department of Hematology, Centre Hospitalier Universitaire (CHU) de Liège, Avenue de l’Hopital 1, 4000 Liege, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
| |
Collapse
|
15
|
Delvaux A, Rathahao-Paris E, Alves S. Different ion mobility-mass spectrometry coupling techniques to promote metabolomics. MASS SPECTROMETRY REVIEWS 2022; 41:695-721. [PMID: 33492707 DOI: 10.1002/mas.21685] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Metabolomics has become increasingly popular in recent years for many applications ranging from clinical diagnosis, human health to biotechnological questioning. Despite technological advances, metabolomic studies are still currently limited by the difficulty of identifying all metabolites, a class of compounds with great chemical diversity. Although lengthy chromatographic analyses are often used to obtain comprehensive data, many isobar and isomer metabolites still remain unresolved, which is a critical point for the compound identification. Currently, ion mobility spectrometry is being explored in metabolomics as a way to improve metabolome coverage, analysis throughput and isomer separation. In this review, all the steps of a typical workflow for untargeted metabolomics are discussed considering the use of an ion mobility instrument. An overview of metabolomics is first presented followed by a brief description of ion mobility instrumentation. The ion mobility potential for complex mixture analysis is discussed regarding its coupling with a mass spectrometer alone, providing gas-phase separation before mass analysis as well as its combination with different separation platforms (conventional hyphenation but also multidimensional ion mobility couplings), offering multidimensional separation. Various instrumental and analytical conditions for improving the ion mobility separation are also described. Finally, data mining, including software packages and visualization approaches, as well as the construction of ion mobility databases for the metabolite identification are examined.
Collapse
Affiliation(s)
- Aurélie Delvaux
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, 75005, France
| | - Estelle Rathahao-Paris
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, 75005, France
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, 91191, France
| | - Sandra Alves
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, 75005, France
| |
Collapse
|
16
|
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.
Collapse
|
17
|
Izquierdo-Sandoval D, Fabregat-Safont D, Lacalle-Bergeron L, Sancho JV, Hernández F, Portoles T. Benefits of Ion Mobility Separation in GC-APCI-HRMS Screening: From the Construction of a CCS Library to the Application to Real-World Samples. Anal Chem 2022; 94:9040-9047. [PMID: 35696365 PMCID: PMC9974067 DOI: 10.1021/acs.analchem.2c01118] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The performance of gas chromatography (GC) combined with the improved identification properties of ion mobility separation coupled to high-resolution mass spectrometry (IMS-HRMS) is presented as a promising approach for the monitoring of (semi)volatile compounds in complex matrices. The soft ionization promoted by an atmospheric pressure chemical ionization (APCI) source designed for GC preserves the molecular and/or quasi-molecular ion information enabling a rapid, sensitive, and efficient wide-scope screening. Additionally, ion mobility separation (IMS) separates species of interest from coeluting matrix interferences and/or resolves isomers based on their charge, shape, and size, making IMS-derived collision cross section (CCS) a robust and matrix-independent parameter comparable between instruments. In this way, GC-APCI-IMS-HRMS becomes a powerful approach for both target and suspect screening due to the improvements in (tentative) identifications. In this work, mobility data for 264 relevant multiclass organic pollutants in environmental and food-safety fields were collected by coupling GC-APCI with IMS-HRMS, generating CCS information for molecular ion and/or protonated molecules and some in-source fragments. The identification power of GC-APCI-IMS-HRMS for the studied compounds was assessed in complex-matrix samples, including fish feed extracts, surface waters, and different fruit and vegetable samples.
Collapse
|
18
|
te Brinke E, Arrizabalaga-Larrañaga A, Blokland MH. Insights of ion mobility spectrometry and its application on food safety and authenticity: A review. Anal Chim Acta 2022; 1222:340039. [DOI: 10.1016/j.aca.2022.340039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/01/2022]
|
19
|
Oluwatoba DS, Islam MF, Som B, Sindt AJ, Smith MD, Shimizu LS, Do TD. Evaluating the Effects of Metal Adduction and Charge Isomerism on Ion-Mobility Measurements using m-Xylene Macrocycles as Models. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:840-850. [PMID: 35471025 DOI: 10.1021/jasms.2c00033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gas-phase ion-mobility spectrometry provides a unique platform to study the effect of mobile charge(s) or charge location on collisional cross section and ion separation. Here, we evaluate the effects of cation/anion adduction in a series of xylene and pyridyl macrocycles that contain ureas and thioureas. We explore how zinc binding led to unexpected deprotonation of the thiourea macrocyclic host in positive polarity ionization and subsequently how charge isomerism due to cation (zinc metal) and anion (chloride counterion) adduction or proton competition among acceptors can affect the measured collisional cross sections in helium and nitrogen buffer gases. Our approach uses synthetic chemistry to design macrocycle targets and a combination of ion-mobility spectrometry mass spectrometry experiments and quantum mechanics calculations to characterize their structural properties. We demonstrate that charge isomerism significantly improves ion-mobility resolution and allows for determination of the metal binding mechanism in metal-inclusion macrocyclic complexes. Additionally, charge isomers can be populated in molecules where individual protons are shared between acceptors. In these cases, interactions via drift gas collisions magnify the conformational differences. Finally, for the macrocyclic systems we report here, charge isomers are observed in both helium and nitrogen drift gases with similar resolution. The separation factor does not simply increase with increasing drift gas polarizability. Our study sheds light on important properties of charge isomerism and offers strategies to take advantage of this phenomenon in analytical separations.
Collapse
Affiliation(s)
- Damilola S Oluwatoba
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Md Faizul Islam
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Bozumeh Som
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Chemistry, University of Ghana, P.O. Box LG 56, Legon, Accra, Ghana
| | - Ammon J Sindt
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D Smith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Linda S Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Thanh D Do
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
20
|
Development of Microchip Isotachophoresis Coupled with Ion Mobility Spectrometry and Evaluation of Its Potential for the Analysis of Food, Biological and Pharmaceutical Samples. Molecules 2021; 26:molecules26206094. [PMID: 34684674 PMCID: PMC8538814 DOI: 10.3390/molecules26206094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 01/10/2023] Open
Abstract
An online coupling of microchip isotachophoresis (µITP) with ion mobility spectrometry (IMS) using thermal evaporation interface is reported for the first time. This combination integrates preconcentration power of the µITP followed by unambiguous identification of trace compounds in complex samples by IMS. Short-chain carboxylic acids, chosen as model analytes, were first separated by the µITP in a discontinuous electrolyte system at pH 5–6, and subsequently evaporated at 130 °C during their transfer to the IMS analyzer. Various parameters, affecting the transfer of the separated sample components through the evaporation system, were optimized to minimize dispersion and loss of the analytes as well as to improve sensitivity. The following analytical attributes were obtained for carboxylic acids in the standard solutions: 0.1–0.3 mg L−1 detection limits, 0.4–0.9 mg L−1 quantitation limits, linear calibration range from the quantitation limit to 75 mg L−1, 0.2–0.3% RSD of the IMS response and 98–102% accuracy. The analytical potential of the developed µITP-IMS combination was demonstrated on the analysis of various food, pharmaceutical and biological samples, in which the studied acids are naturally present. These include: apple vinegar, wine, fish sauce, saliva and ear drops. In the real samples, 0.3–0.6% RSD of the IMS response and 93–109% accuracy were obtained.
Collapse
|
21
|
Sharma S, Joshi R, Kumar D. Metabolomics insights and bioprospection of Polygonatum verticillatum: An important dietary medicinal herb of alpine Himalaya. Food Res Int 2021; 148:110619. [DOI: 10.1016/j.foodres.2021.110619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
|
22
|
Schwaiger-Haber M, Stancliffe E, Arends V, Thyagarajan B, Sindelar M, Patti GJ. A Workflow to Perform Targeted Metabolomics at the Untargeted Scale on a Triple Quadrupole Mass Spectrometer. ACS MEASUREMENT SCIENCE AU 2021; 1:35-45. [PMID: 34476422 PMCID: PMC8377714 DOI: 10.1021/acsmeasuresciau.1c00007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Indexed: 05/25/2023]
Abstract
The thousands of features commonly observed when performing untargeted metabolomics with quadrupole time-of-flight (QTOF) and Orbitrap mass spectrometers often correspond to only a few hundred unique metabolites of biological origin, which is in the range of what can be assayed in a single targeted metabolomics experiment by using a triple quadrupole (QqQ) mass spectrometer. A major benefit of performing targeted metabolomics with QqQ mass spectrometry is the affordability of the instruments relative to high-resolution QTOF and Orbitrap platforms. Optimizing targeted methods to profile hundreds of metabolites on a QqQ mass spectrometer, however, has historically been limited by the availability of authentic standards, particularly for "unknowns" that have yet to be structurally identified. Here, we report a strategy to develop multiple reaction monitoring (MRM) methods for QqQ instruments on the basis of high-resolution spectra, thereby enabling us to use data from untargeted metabolomics to design targeted experiments without the need for authentic standards. We demonstrate that using high-resolution fragmentation data alone to design MRM methods results in the same quantitative performance as when methods are optimized by measuring authentic standards on QqQ instruments, as is conventionally done. The approach was validated by showing that Orbitrap ID-X data can be used to establish MRM methods on a Thermo TSQ Altis and two Agilent QqQs for hundreds of metabolites, including unknowns, without a dependence on standards. Finally, we highlight an application where metabolite profiling was performed on an ID-X and a QqQ by using the strategy introduced here, with both data sets yielding the same result. The described approach therefore allows us to use QqQ instruments, which are often associated with targeted metabolomics, to profile knowns and unknowns at a comprehensive scale that is typical of untargeted metabolomics.
Collapse
Affiliation(s)
- Michaela Schwaiger-Haber
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
- Department
of Medicine, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Ethan Stancliffe
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
- Department
of Medicine, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Valerie Arends
- Department
of Laboratory Medicine and Pathology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Bharat Thyagarajan
- Department
of Laboratory Medicine and Pathology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Miriam Sindelar
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
- Department
of Medicine, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Gary J. Patti
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
- Department
of Medicine, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
23
|
Li T, Yin Y, Zhou Z, Qiu J, Liu W, Zhang X, He K, Cai Y, Zhu ZJ. Ion mobility-based sterolomics reveals spatially and temporally distinctive sterol lipids in the mouse brain. Nat Commun 2021; 12:4343. [PMID: 34267224 PMCID: PMC8282640 DOI: 10.1038/s41467-021-24672-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
Aberrant sterol lipid metabolism is associated with physiological dysfunctions in the aging brain and aging-dependent disorders such as neurodegenerative diseases. There is an unmet demand to comprehensively profile sterol lipids spatially and temporally in different brain regions during aging. Here, we develop an ion mobility-mass spectrometry based four-dimensional sterolomics technology leveraged by a machine learning-empowered high-coverage library (>2000 sterol lipids) for accurate identification. We apply this four-dimensional technology to profile the spatially resolved landscapes of sterol lipids in ten functional regions of the mouse brain, and quantitatively uncover ~200 sterol lipids uniquely distributed in specific regions with concentrations spanning up to 8 orders of magnitude. Further spatial analysis pinpoints age-associated differences in region-specific sterol lipid metabolism, revealing changes in the numbers of altered sterol lipids, concentration variations, and age-dependent coregulation networks. These findings will contribute to our understanding of abnormal sterol lipid metabolism and its role in brain diseases.
Collapse
Affiliation(s)
- Tongzhou Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yandong Yin
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Zhiwei Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqian Qiu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenbin Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Xueting Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kaiwen He
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yuping Cai
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
24
|
Bi J, Lin Z, Li Y, Chen F, Liu S, Li C. Effects of different cooking methods on volatile flavor compounds of chicken breast. J Food Biochem 2021; 45:e13770. [PMID: 34254338 DOI: 10.1111/jfbc.13770] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/26/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Chicken is one of the highest selling meats worldwide. Different cooking methods produce various flavor compounds in cooked chicken, which affect consumers' food choices. In this study, the volatile flavor components of Gushi chicken breast after stewing and air frying were detected using gas chromatography-ion mobility chromatography (GC-IMS) and principal component analysis (PCA), and the relative odor activity value (ROAV) was determined using PCA. A total of 43 volatile substances were identified. 3-(methylthio)propionaldehyde-M and benzene acetaldehyde can be used as characteristic flavor markers in the air-fried chicken breast.ethyl acetate, (E)-2-octenal-D, and 2-ethyl-1-hexanol-D can be used as characteristic flavor markers in the stewed chicken breast. Because these five substances have the most obvious contrast in the fingerprint. The following part describes the specific substances that have mainly contributed to the flavor system in the volatile system obtained by different cooking methods. Finally, the main flavor compounds of the stewed chicken breast were 3-methylbutanal-D, octanal-D, (E)-2-nonenal, and other 11 types of compounds (ROAV ≥1). Nine types of compounds (ROAV ≥1), including 3-methylbutanal-D, (E)-2-nonenal-M octanal-M, and hexanal-M, were the main compounds to characterize the air-fried chicken breast. PRACTICAL APPLICATIONS: GC-IMS technology combined with the principal component analysis of ROAV can be used to rapidly identify the main flavor substances and the flavor substances having an important role in modifying the overall taste of the sample. It plays a considerably important role in the aroma recombination of substances and can play a role in food processing.
Collapse
Affiliation(s)
- Jicai Bi
- Post-doctoral Research Base & School of Food Science, Henan Institute of Science and Technology, Xinxiang, P.R. China
- College of Food Science and Engineering, Hainan University, Haikou, P.R. China
- Food Science and Engineering Post-doctoral Research Station, Henan University of Technology, Zhengzhou, P.R. China
| | - Zeyuan Lin
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Yang Li
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Fusheng Chen
- Food Science and Engineering Post-doctoral Research Station, Henan University of Technology, Zhengzhou, P.R. China
| | - Sixin Liu
- College of Food Science and Engineering, Hainan University, Haikou, P.R. China
| | - Congfa Li
- College of Food Science and Engineering, Hainan University, Haikou, P.R. China
| |
Collapse
|
25
|
Zhu J, Sun Z, Xu J, Walczak RD, Dziuban JA, Lee C. Volatile organic compounds sensing based on Bennet doubler-inspired triboelectric nanogenerator and machine learning-assisted ion mobility analysis. Sci Bull (Beijing) 2021; 66:1176-1185. [PMID: 36654355 DOI: 10.1016/j.scib.2021.03.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
Ion mobility analysis is a well-known analytical technique for identifying gas-phase compounds in fast-response gas-monitoring systems. However, the conventional plasma discharge system is bulky, operates at a high temperature, and inappropriate for volatile organic compounds (VOCs) concentration detection. Therefore, we report a machine learning (ML)-enhanced ion mobility analyzer with a triboelectric-based ionizer, which offers good ion mobility selectivity and VOC recognition ability with a small-sized device and non-strict operating environment. Based on the charge accumulation mechanism, a multi-switched manipulation triboelectric nanogenerator (SM-TENG) can provide a direct current (DC) bias at the order of a few hundred, which can be further leveraged as the power source to obtain a unique and repeatable discharge characteristic of different VOCs, and their mixtures, with a special tip-plate electrode configuration. Aiming to tackle the grand challenge in the detection of multiple VOCs, the ML-enhanced ion mobility analysis method was successfully demonstrated by extracting specific features automatically from ion mobility spectrometry data with ML algorithms, which significantly enhance the detection ability of the SM-TENG based VOC analyzer, showing a portable real-time VOC monitoring solution with rapid response and low power consumption for future internet of things based environmental monitoring applications.
Collapse
Affiliation(s)
- Jianxiong Zhu
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China; Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117576, Singapore; Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117576, Singapore; NUS Suzhou Research Institute (NUSRI), Suzhou 215123, China
| | - Zhongda Sun
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117576, Singapore; Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117576, Singapore; NUS Suzhou Research Institute (NUSRI), Suzhou 215123, China
| | - Jikai Xu
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117576, Singapore; Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117576, Singapore; NUS Suzhou Research Institute (NUSRI), Suzhou 215123, China
| | - Rafal D Walczak
- Department of Mircroengineering and Photovoltaics, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Jan A Dziuban
- Department of Mircroengineering and Photovoltaics, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117576, Singapore; Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore 117576, Singapore; NUS Suzhou Research Institute (NUSRI), Suzhou 215123, China; Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore 119077, Singapore.
| |
Collapse
|
26
|
Wang F, Gao Y, Wang H, Xi B, He X, Yang X, Li W. Analysis of volatile compounds and flavor fingerprint in Jingyuan lamb of different ages using gas chromatography-ion mobility spectrometry (GC-IMS). Meat Sci 2021; 175:108449. [PMID: 33550158 DOI: 10.1016/j.meatsci.2021.108449] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022]
Abstract
In this study, gas chromatography coupled to an ion mobility spectrometry (GC-IMS) was used for analyzing some volatile components and flavor fingerprint in samples from Jingyuan lambs of different ages (2, 6, and 12 months). The data obtained from ion mobility were processed using laboratory analysis view processing software for fingerprint recognition, and the principal component analysis (PCA) was performed. GC-IMS provided information on the characteristics and strength of 66 volatile flavor compounds (monomers and dimers). The differences in flavoring substances between lambs of different ages were observed. The compounds with higher intensity peaks in the lamb meat samples were alcohols (1-octen-3-ol, ethanol, (E)-2-hexen-1-ol, 1-pentanol, and 2-propanol), ketones (2-pentanone, 2-heptanone, 3-hydroxy-2-butanone, 2-hexanone, 2-butanone, 2-propanone, and 4-methyl-2-pentanone), aldehydes (n-nonanal, octanal, heptanal, 3-methylbutanal, hexanal, pentanal, 2-methylbutanal, (E)-2-octenal, (E)-2-nonenal, methional, and phenylacetaldehyde), esters (methyl benzoate), furan (2-pentylfuran), and thiazole (trimethylthiazole). The results showed that the flavor fingerprint in samples from Jingyuan lambs of different ages (2, 6, and 12 months) can be established by GC-IMS and PCA based on the identified volatile compounds. This method might be used for the rapid and comprehensive analysis of volatile components in lamb meat.
Collapse
Affiliation(s)
- Fang Wang
- Lanzhou Institute of Animal Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Quality Safety Risk Assessment of Animal Products (Lanzhou), Ministry of Agriculture, Lanzhou 730050, China
| | - Yaqin Gao
- Lanzhou Institute of Animal Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Quality Safety Risk Assessment of Animal Products (Lanzhou), Ministry of Agriculture, Lanzhou 730050, China.
| | - Hongbo Wang
- Lanzhou Institute of Animal Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Quality Safety Risk Assessment of Animal Products (Lanzhou), Ministry of Agriculture, Lanzhou 730050, China
| | - Bin Xi
- Lanzhou Institute of Animal Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Quality Safety Risk Assessment of Animal Products (Lanzhou), Ministry of Agriculture, Lanzhou 730050, China
| | - Xiaona He
- Lanzhou Institute of Animal Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Quality Safety Risk Assessment of Animal Products (Lanzhou), Ministry of Agriculture, Lanzhou 730050, China
| | - Xiaoling Yang
- Lanzhou Institute of Animal Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Quality Safety Risk Assessment of Animal Products (Lanzhou), Ministry of Agriculture, Lanzhou 730050, China
| | - Weihong Li
- Lanzhou Institute of Animal Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Quality Safety Risk Assessment of Animal Products (Lanzhou), Ministry of Agriculture, Lanzhou 730050, China
| |
Collapse
|
27
|
Alikord M, Mohammadi A, Kamankesh M, Shariatifar N. Food safety and quality assessment: comprehensive review and recent trends in the applications of ion mobility spectrometry (IMS). Crit Rev Food Sci Nutr 2021; 62:4833-4866. [PMID: 33554631 DOI: 10.1080/10408398.2021.1879003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ion mobility spectrometry (IMS) is an analytical separation and diagnostic technique that is simple and sensitive and a rapid response and low-priced technique for detecting trace levels of chemical compounds in different matrices. Chemical agents and environmental contaminants are successfully detected by IMS and have been recently considered to employ in food safety. In addition, IMS uses stand-alone or coupled analytical diagnostic tools with chromatographic and spectroscopic methods. Scientific publications show that IMS has been applied 21% in the pharmaceutical industry, 9% in environmental studies and 13% in quality control and food safety. Nevertheless, applications of IMS in food safety and quality analysis have not been adequately explored. This review presents the IMS-related analysis and focuses on the application of IMS in food safety and quality. This review presents the important topics including detection of traces of chemicals, rate of food spoilage and freshness, food adulteration and authenticity as well as natural toxins, pesticides, herbicides, fungicides, veterinary, and growth promoter drug residues. Further, persistent organic pollutants (POPs), acrylamide, polycyclic aromatic hydrocarbon (PAH), biogenic amines, nitrosamine, furfural, phenolic compounds, heavy metals, food packaging materials, melamine, and food additives were also examined for the first time. Therefore, it is logical to predict that the application of the IMS technique in food safety, food quality, and contaminant analysis will be impressively increased in the future. HighlightsCurrent status of IMS for residues and contaminant detection in food safety.To assess all the detected contaminants in food safety, for the first time.Identified IMS-related parameters and chemical compounds in food safety control.
Collapse
Affiliation(s)
- Mahsa Alikord
- Department of Environmental Health, Food Safety Division, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdorreza Mohammadi
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Kamankesh
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Nabi Shariatifar
- Department of Environmental Health, Food Safety Division, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Halal Research Center of the Islamic Republic of Iran, Tehran, Iran
| |
Collapse
|
28
|
Abdrakhimov DA, Bubis JA, Gorshkov V, Kjeldsen F, Gorshkov MV, Ivanov MV. Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021:e9045. [PMID: 33450063 DOI: 10.1002/rcm.9045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/20/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE One of the important steps in initial data processing of peptide mass spectra is the detection of peptide features in full-range mass spectra. Ion mobility offers advantages over previous methods performing this detection by providing an additional structure-specific separation dimension. However, there is a lack of open-source software that utilizes these advantages and detects peptide features in mass spectra acquired along with ion mobility data using new instruments such as timsTOF and/or FAIMS-Orbitrap. METHODS Recently, a utility called Dinosaur was presented, which provides an efficient way for feature detection in peptide ion mass spectra. In this work we extended its functionality by developing Biosaur software to fully employ the additional information provided by ion mobility data. Biosaur was developed using the Python 3.8 programming language. RESULTS Biosaur supports the processing of data acquired using mass spectrometers with ion mobility capabilities, specifically timsTOF and FAIMS. In addition, it processes mass spectra obtained in negative ion mode and reports cosine correlation table for peptide features which is useful for differentiation between in-source fragments and semi-tryptic peptides. CONCLUSIONS Biosaur is a utility for detecting peptide features in liquid chromatography-mass spectra with ion mobility and negative ion supports. The software is distributed with an open-source APACHE 2.0 license and is freely available on Github: https://github.com/abdrakhimov1/Biosaur.
Collapse
Affiliation(s)
- Daniil A Abdrakhimov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology, National Research University, G. Dolgoprudny, Institutsky Lane 9, Dolgoprudnyj, RU, 141701, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow, 119334, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow, 119334, Russia
| | - Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow, 119334, Russia
| |
Collapse
|
29
|
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.
Collapse
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.
| |
Collapse
|
30
|
Addepalli RV, Mullangi R. A concise review on lipidomics analysis in biological samples. ADMET AND DMPK 2020; 9:1-22. [PMID: 35299875 PMCID: PMC8923307 DOI: 10.5599/admet.913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Lipids are a complex and critical heterogeneous molecular entity, playing an intricate and key role in understanding biological activities and disease processes. Lipidomics aims to quantitatively define the lipid classes, including their molecular species. The analysis of the biological tissues and fluids are challenging due to the extreme sample complexity and occurrence of the molecular species as isomers or isobars. This review documents the overview of lipidomics workflow, beginning from the approaches of sample preparation, various analytical techniques and emphasizing the state-of-the-art mass spectrometry either by shotgun or coupled with liquid chromatography. We have considered the latest ion mobility spectroscopy technologies to deal with the vast number of structural isomers, different imaging techniques. All these techniques have their pitfalls and we have discussed how to circumvent them after reviewing the power of each technique with examples..
Collapse
Affiliation(s)
| | - Ramesh Mullangi
- Laxai Life Sciences Pvt Ltd, MN Park, Genome Valley, Shamirpet, Hyderabad-500 078, India
| |
Collapse
|
31
|
Mesa Sanchez D, Creger S, Singla V, Kurulugama RT, Fjeldsted J, Laskin J. Ion Mobility-Mass Spectrometry Imaging Workflow. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2437-2442. [PMID: 32841564 DOI: 10.1021/jasms.0c00142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique for the label-free spatially resolved analysis of biological tissues. Coupling ion mobility (IM) separation with MSI allows for separation of isobars in the mobility dimension and increases confidence of peak assignments. Recently, imaging experiments have been implemented on several commercially available and custom-designed ion mobility instruments, making IM-MSI experiments more broadly accessible to the MS community. However, the absence of open access data analysis software for IM-MSI systems presents a bottleneck. Herein, we present an imaging workflow to visualize IM-MSI data produced on the Agilent 6560 ion mobility quadrupole time-of-flight system. Specifically, we have developed a Python script, the ion mobility-mass spectrometry image creation script (IM-MSIC), which interfaces Agilent's Mass Hunter Mass Profiler software with the MacCoss lab's Skyline software and generates drift time and mass-to-charge-selected ion images. In the workflow, Mass Profiler is used for an untargeted feature detection. The IM-MSIC script mediates user input of data, extracts ion chronograms utilizing Skyline's command-line interface, and then proceeds toward ion image generation within a single user interface. Ion image postprocessing is subsequently performed using different tools implemented in accompanying scripts. Though the current work only showcases Agilent IM-MSI data, this workflow can be readily adapted for use with most major instrument vendors.
Collapse
Affiliation(s)
- Daniela Mesa Sanchez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Steve Creger
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Veerupaksh Singla
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | | | - John Fjeldsted
- Agilent Technologies Inc., Santa Clara, California 95051, United States
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| |
Collapse
|
32
|
Hartner NT, Raddatz CR, Thoben C, Piendl SK, Zimmermann S, Belder D. On-Line Coupling of Chip-Electrochromatography and Ion Mobility Spectrometry. Anal Chem 2020; 92:15129-15136. [PMID: 33143411 DOI: 10.1021/acs.analchem.0c03446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the first hyphenation of chip-electrochromatography (ChEC) with ion mobility spectrometry (IMS). This approach combines the separation power of two electrokinetically driven separation techniques, the first in liquid phase and the second in gas phase, with a label-free detection of the analytes. For achieving this, a microfluidic glass chip incorporating a monolithic separation column, a nanofluidic liquid junction for providing post-column electrical contact, and a monolithically integrated electrospray emitter was developed. This device was successfully coupled to a custom-built high-resolution drift tube IMS with shifted potentials. After proof-of-concept studies in which a mixture of five model compounds was analyzed in less than 80 s, this first ChEC-IMS system was applied to a more complex sample, the analysis of herbicides spiked in the wine matrix. The use of ChEC before IMS detection not only facilitated the peak allocation and increased the peak capacity but also enabled analyte quantification. As both, ChEC and IMS work at ambient conditions and are driven by high voltages, no bulky pumping systems are needed, neither for the hydrodynamic pumping of the mobile phase as in high-performance liquid chromatography nor for generating a vacuum system as in mass spectrometry. Accordingly, the approach has great potential as a portable analytical system for field analysis of complex mixtures.
Collapse
Affiliation(s)
- Nora T Hartner
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Christian-Robert Raddatz
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Christian Thoben
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Sebastian K Piendl
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| |
Collapse
|
33
|
Causon TJ, Hann S. Uncertainty Estimations for Collision Cross Section Determination via Uniform Field Drift Tube-Ion Mobility-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2102-2110. [PMID: 32812758 DOI: 10.1021/jasms.0c00233] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Uniform field drift tube ion mobility-mass spectrometry (DTIM-MS) has emerged as a valuable tool for a range of analytical applications. In focus here are standardized collisional cross section values from DTIM-MS (DTCCS) as a candidate identification point for various analytical workflows. Of critical importance in establishing this parameter as a valid identification point is a rugged estimation of uncertainties according to the procedures used for their derivation. Relying on the assumption of the zero-field limit, the primary method of measurement for DTCCS values involves experimental determination of arrival times of an ion measured at several different field strengths transiting a drift tube filled with high purity drift gas, while a method using measurements of external calibrants at a single field strength is employed to allow for online measurements of transient signals (e.g., chromatographic peaks). Both approaches are here considered with respect to the uncertainty of input experimental variables (temperature, pressure, voltages, physical constants) and the steps of the calibration function employed. Estimations of uncertainty were performed according to EURACHEM with Monte Carlo simulations and reveal that existing consensus calibration standards from experimental stepped-field IM-MS determinations have estimated expanded uncertainties in the range of 2.7 to 4.6% (k = 2). Application of these standards for calibration considering these input uncertainties reveals uncertainty estimates of 4.7-9.1% (k = 2) for measured values using an established single-field calibration approach. Finally, directions for improving this situation via new experimental efforts toward standard reference and calibration materials are presented.
Collapse
Affiliation(s)
- Tim J Causon
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, Vienna 1190, Austria
| | - Stephan Hann
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, Vienna 1190, Austria
| |
Collapse
|
34
|
Drouin N, Mielcarek A, Wenz C, Rudaz S. Evaluation of ion mobility in capillary electrophoresis coupled to mass spectrometry for the identification in metabolomics. Electrophoresis 2020; 42:342-349. [PMID: 32744343 DOI: 10.1002/elps.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 01/21/2023]
Abstract
Currently, feature annotation remains one of the main challenges in untargeted metabolomics. In this context, the information provided by high-resolution mass spectrometry (HRMS) in addition to accurate mass can improve the quality of metabolite annotation, and MS/MS fragmentation patterns are widely used. Accurate mass and a separation index, such as retention time or effective mobility (μeff ), in chromatographic and electrophoretic approaches, respectively, must be used for unequivocal metabolite identification. The possibility of measuring collision cross-section (CCS) values by using ion mobility (IM) is becoming increasingly popular in metabolomic studies thanks to the new generation of IM mass spectrometers. Based on their similar separation mechanisms involving electric field and the size of the compounds, the complementarity of DT CCSN2 and μeff needs to be evaluated. In this study, a comparison of DT CCSN2 and μeff was achieved in the context of feature identification ability in untargeted metabolomics by capillary zone electrophoresis (CZE) coupled with HRMS. This study confirms the high correlation of DT CCSN2 with the mass of the studied metabolites as well as the orthogonality between accurate mass and μeff , making this combination particularly interesting for the identification of several endogenous metabolites. The use of IM-MS remains of great interest for facilitating the annotation of neutral metabolites present in the electroosmotic flow (EOF) that are poorly or not separated by CZE.
Collapse
Affiliation(s)
- Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, The Netherlands.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | | | - Christian Wenz
- Agilent Technologies, Hewlett-Packard, Waldbronn, Germany
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| |
Collapse
|
35
|
Luo MD, Zhou ZW, Zhu ZJ. The Application of Ion Mobility-Mass Spectrometry in Untargeted Metabolomics: from Separation to Identification. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00133-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
36
|
Sharma S, Joshi R, Kumar D. Quantitative analysis of flavonols, flavonol glycoside and homoisoflavonoids in Polygonatum verticillatum using UHPLC-DAD-QTOF-IMS and evaluation of their antioxidant potential. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:333-339. [PMID: 31898384 DOI: 10.1002/pca.2899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Polygonatum is widely used as a part of food in different regions of the world which covers five main categories such as drinks, vegetables, snacks, staple and seasoning foods. Presently, no analytical method is available for the quality control of Polygonatum. OBJECTIVE Development and validation of a method using ultrahigh-performance liquid chromatography diode array detector quadrupole time-of-flight (UHPLC-DAD/QTOF) technique for the estimation of six compounds including a flavonol glycoside [rutin (1)], two flavonols [quercetin (2) and kaempherol (3)] and three homoisoflavonoids [5,7-dihydroxy-3-(2-hydroxy-4-methoxybenzyl)-chroman-4-one (4), 5,7-dihydroxy-3-(2-hydroxy-4-methoxybenzyl)-8-methylchroman-4-one (5) and 5,7-dihydroxy-3-(4-methoxybenzyl)-8-methylchroman-4-one (6)]. In addition, screening of extract, fractions and compounds of P. verticillatum for antioxidant activity was also determined. METHODOLOGY The separation was achieved on C-18 column using acetonitrile and water containing 0.1% formic acid. The method was validated as per ICH (International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use) guidelines. The validated method was applied for the simultaneous identification and quantification of compounds 1-6 in extract (E) and fractions (F1-F4) of P. verticillatum. Furthermore, antioxidant potential of E, F1 and F2 and compounds was evaluated using DPPH (2,2-diphenyl-1-picrylhydrazyl) assay. RESULTS The method was within the linear range (r2 ) of 0.982 to 0.999, precise (intra- and inter-day percentage relative standard deviations < 2.72 and 2.26) and accurate with recoveries (89.1-98.3%). The limit of detection and limit of quantification were in the ranges 0.02-0.16 and 0.06-0.48 ng/mL, respectively. Compounds 1-6 were quantified in all the samples. Compounds 1, 2 and 5 showed higher activity with half maximal inhibitory concentration (IC50 ) values 0.41, 0.39, 0.72 at 10, 20 and 30 μg/mL, respectively. CONCLUSION Developed method will be helpful to assess the quality of P. verticillatum raw material and their derived products.
Collapse
Affiliation(s)
- Shruti Sharma
- Academy of Scientific and Innovative Research, CSIR-Institute of Himalayan Bioresource Technology, Palampur176 061 (HP), India
- Natural Product Chemistry and Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176 061 (HP), India
| | - Robin Joshi
- Academy of Scientific and Innovative Research, CSIR-Institute of Himalayan Bioresource Technology, Palampur176 061 (HP), India
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176 061 (HP), India
| | - Dinesh Kumar
- Academy of Scientific and Innovative Research, CSIR-Institute of Himalayan Bioresource Technology, Palampur176 061 (HP), India
- Natural Product Chemistry and Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176 061 (HP), India
| |
Collapse
|
37
|
Yang B, Li R, Liu PN, Geng X, Mooney BP, Chen C, Cheng J, Fritsche KL, Beversdorf DQ, Lee JC, Sun GY, Greenlief CM. Quantitative Proteomics Reveals Docosahexaenoic Acid-Mediated Neuroprotective Effects in Lipopolysaccharide-Stimulated Microglial Cells. J Proteome Res 2020; 19:2236-2246. [PMID: 32302149 PMCID: PMC7282485 DOI: 10.1021/acs.jproteome.9b00792] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The high levels of docosahexaenoic
acid (DHA) in cell membranes
within the brain have led to a number of studies exploring its function.
These studies have shown that DHA can reduce inflammatory responses
in microglial cells. However, the method of action is poorly understood.
Here, we report the effects of DHA on microglial cells stimulated
with lipopolysaccharides (LPSs). Data were acquired using the parallel
accumulation serial fragmentation method in a hybrid trapped ion mobility-quadrupole
time-of-flight mass spectrometer. Over 2800 proteins are identified
using label-free quantitative proteomics. Cells exposed to LPSs and/or
DHA resulted in changes in cell morphology and expression of 49 proteins
with differential abundance (greater than 1.5-fold change). The data
provide details about pathways that are influenced in this system
including the nuclear factor κ-light-chain-enhancer of the activated
B cells (NF-κB) pathway. Western blots and enzyme-linked immunosorbent
assay studies are used to help confirm the proteomic results. The
MS data are available at ProteomeXchange.
Collapse
Affiliation(s)
- Bo Yang
- Department of Chemistry, University of Missouri, Columbia 65211, Missouri, United States.,Charles W. Gehrke Proteomics Center, University of Missouri, Columbia 65211, Missouri, United States
| | - Runting Li
- Biochemistry Department, University of Missouri, Columbia 65211, Missouri, United States
| | - Pei N Liu
- Charles W. Gehrke Proteomics Center, University of Missouri, Columbia 65211, Missouri, United States
| | - Xue Geng
- Department of Bioengineering, University of Illinois at Chicago, Chicago 60612, Illinois, United States
| | - Brian P Mooney
- Biochemistry Department, University of Missouri, Columbia 65211, Missouri, United States.,Charles W. Gehrke Proteomics Center, University of Missouri, Columbia 65211, Missouri, United States
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia 65211, Missouri, United States
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia 65211, Missouri, United States
| | - Kevin L Fritsche
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia 65211, Missouri, United States
| | - David Q Beversdorf
- Departments of Radiology, Neurology and Psychological Sciences, and the Thompson Center, University of Missouri, Columbia 65211, Missouri, United States
| | - James C Lee
- Department of Bioengineering, University of Illinois at Chicago, Chicago 60612, Illinois, United States
| | - Grace Y Sun
- Biochemistry Department, University of Missouri, Columbia 65211, Missouri, United States
| | - C Michael Greenlief
- Department of Chemistry, University of Missouri, Columbia 65211, Missouri, United States.,Charles W. Gehrke Proteomics Center, University of Missouri, Columbia 65211, Missouri, United States
| |
Collapse
|
38
|
Vimer S, Ben-Nissan G, Morgenstern D, Kumar-Deshmukh F, Polkinghorn C, Quintyn RS, Vasil’ev YV, Beckman JS, Elad N, Wysocki VH, Sharon M. Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry. ACS CENTRAL SCIENCE 2020; 6:573-588. [PMID: 32342007 PMCID: PMC7181328 DOI: 10.1021/acscentsci.0c00080] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Indexed: 05/06/2023]
Abstract
Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the Thermoplasma acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast (Saccharomyces cerevisiae) and mammals (rat - Rattus norvegicus, rabbit - Oryctolagus cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.
Collapse
Affiliation(s)
- Shay Vimer
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - David Morgenstern
- Israel
Structural Proteomics Center, Weizmann Institute
of Science, Rehovot, Israel
| | | | - Caley Polkinghorn
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Royston S. Quintyn
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Yury V. Vasil’ev
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
| | - Joseph S. Beckman
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
- Linus
Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nadav Elad
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot, Israel
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Michal Sharon
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| |
Collapse
|
39
|
Fresnais M, Muck A, Majewsky M, Statz B, Krausert S, Benzel J, Castel D, Le Dret L, Pfister S, Haefeli WE, Burhenne J, Longuespée R. Rapid and Sensitive Drug Quantification in Tissue Sections Using Matrix Assisted Laser Desorption Ionization-Ion Mobility-Mass Spectrometry Profiling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:742-751. [PMID: 31971791 DOI: 10.1021/jasms.0c00005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ion mobility spectrometry (IMS) represents a considerable asset for analytics of complex samples as it allows for rapid mass spectrometric separation of compounds. IMS is even more useful for the separation of isobaric compounds when classical separation methods such as liquid chromatography or electrophoresis cannot be used, e.g., during matrix-assisted laser desorption/ionization (MALDI) analyses of biological surfaces. In the present study, we proved the usefulness of IMS for pharmacological applications of MALDI analyses on tissue sections. To illustrate our proof-of-concept, we used the anthelmintic drug mebendazole (MBZ) as a model. Using this exemplary drug, we demonstrated the possibility of using ion mobility to discriminate a drug in tissues from the biological background that masked its signal at low concentrations. In this proof-of-concept, the IMS mode together with the use of a profiling approach for sample preparation enabled quantification of the model drug MBZ from tissue sections in the concentration range 5 to 5,000 ng/g and with a limit of detection of 1 ng/g of tissue, within 2 h. This study highlights the importance of IMS as a separation method for on-surface quantification of drugs in tissue sections.
Collapse
Affiliation(s)
- Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK)-German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | | | - Marius Majewsky
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Britta Statz
- Hopp Children's Cancer Center, NCT Heidelberg (KiTZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Sonja Krausert
- Hopp Children's Cancer Center, NCT Heidelberg (KiTZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Julia Benzel
- Hopp Children's Cancer Center, NCT Heidelberg (KiTZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - David Castel
- Biomarqueurs prédictifs et nouvelles stratégies thérapeutiques en oncologie, Inserm, Gustave Roussy, Université Paris-Saclay, 114 Rue Edouard Vaillant, 94800 Villejuif, France
| | - Ludivine Le Dret
- Biomarqueurs prédictifs et nouvelles stratégies thérapeutiques en oncologie, Inserm, Gustave Roussy, Université Paris-Saclay, 114 Rue Edouard Vaillant, 94800 Villejuif, France
| | - Stefan Pfister
- Hopp Children's Cancer Center, NCT Heidelberg (KiTZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Walter E Haefeli
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Jürgen Burhenne
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| |
Collapse
|
40
|
Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
41
|
Odenkirk MT, Baker ES. Utilizing Drift Tube Ion Mobility Spectrometry for the Evaluation of Metabolites and Xenobiotics. Methods Mol Biol 2020; 2084:35-54. [PMID: 31729652 DOI: 10.1007/978-1-0716-0030-6_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Metabolites and xenobiotics are small molecules with a molecular weight that often falls below 600 Da. Over the last few decades, multiple small molecule databases have been curated listing structures, masses, and fragmentation spectra possible in metabolomic and exposomic measurements. To date only a small portion of the spectra in these databases are experimentally derived due to the high expense of obtaining, synthesizing, and analyzing standards. A vast majority of spectra have thus been created using theoretical programs to fit the available experimental data. The errors associated with theoretical data have however caused problems with current small molecule identifications, and accurate quantitation as searching the databases using just one or two analysis dimensions (i.e., chromatography retention times and mass spectrometry (MS) m/z values) results in numerous annotations for each experimental feature. Additional analysis dimensions are therefore needed to better annotate and identify small molecules. Drift tube ion mobility spectrometry coupled with MS (DTIMS-MS) is a promising technique to address this challenge as it is able to perform rapid structural evaluations of small molecules in complex matrices by assessing the collision cross section values for each in addition to their m/z values. The use of IMS in conjunction with other separation techniques such as gas or liquid chromatography and MS has therefore enabled more accurate identifications for the small molecules present in complex biological and environmental samples. Here, we present a review of relevant parameter considerations for DTIMS application with emphasis on xenobiotics and metabolomics isomer separations.
Collapse
Affiliation(s)
- Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
42
|
Grabarics M, Lettow M, Kirk AT, von Helden G, Causon TJ, Pagel K. Plate-height model of ion mobility-mass spectrometry. Analyst 2020; 145:6313-6333. [DOI: 10.1039/d0an00433b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In analogy to chromatography, a plate-height model of drift tube ion mobility-mass spectrometry is presented that describes zone broadening and resolving power in ion mobility separations.
Collapse
Affiliation(s)
- Márkó Grabarics
- Department of Biology
- Chemistry and Pharmacy
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
| | - Maike Lettow
- Department of Biology
- Chemistry and Pharmacy
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
| | - Ansgar T. Kirk
- Institute of Electrical Engineering and Measurement Technology
- Department of Sensors and Measurement Technology
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society
- Department of Molecular Physics
- 14195 Berlin
- Germany
| | - Tim J. Causon
- Department of Chemistry
- Institute of Analytical Chemistry
- University of Natural Resources and Life Sciences
- Vienna
- 1190 Vienna
| | - Kevin Pagel
- Department of Biology
- Chemistry and Pharmacy
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
| |
Collapse
|
43
|
Chen X, Zhou Z, Zhu ZJ. The Use of LipidIMMS Analyzer for Lipid Identification in Ion Mobility-Mass Spectrometry-Based Untargeted Lipidomics. Methods Mol Biol 2020; 2084:269-282. [PMID: 31729667 DOI: 10.1007/978-1-0716-0030-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Untargeted lipidomics aims to comprehensively measure and characterize all lipid species in biological systems. Ion mobility-mass spectrometry (IM-MS) has showed a great potential for untargeted lipidomic analysis. Coupling with liquid chromatography and data-independent tandem MS techniques, acquired IM-MS data set contains four-dimensional information for lipid identification, including m/z of MS1 ion, retention time (RT), collision cross section (CCS), and MS/MS spectra. In this protocol, we introduced a data processing workflow using an integrative web server, namely, LipidIMMS Analyzer, to support accurate lipid identification. The protocol demonstrated the integration of all four dimensional information to achieve unambiguous identifications of lipids in complex biological samples.
Collapse
Affiliation(s)
- Xi Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
44
|
Hernández-Mesa M, Ropartz D, García-Campaña AM, Rogniaux H, Dervilly-Pinel G, Le Bizec B. Ion Mobility Spectrometry in Food Analysis: Principles, Current Applications and Future Trends. Molecules 2019; 24:E2706. [PMID: 31349571 PMCID: PMC6696101 DOI: 10.3390/molecules24152706] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
In the last decade, ion mobility spectrometry (IMS) has reemerged as an analytical separation technique, especially due to the commercialization of ion mobility mass spectrometers. Its applicability has been extended beyond classical applications such as the determination of chemical warfare agents and nowadays it is widely used for the characterization of biomolecules (e.g., proteins, glycans, lipids, etc.) and, more recently, of small molecules (e.g., metabolites, xenobiotics, etc.). Following this trend, the interest in this technique is growing among researchers from different fields including food science. Several advantages are attributed to IMS when integrated in traditional liquid chromatography (LC) and gas chromatography (GC) mass spectrometry (MS) workflows: (1) it improves method selectivity by providing an additional separation dimension that allows the separation of isobaric and isomeric compounds; (2) it increases method sensitivity by isolating the compounds of interest from background noise; (3) and it provides complementary information to mass spectra and retention time, the so-called collision cross section (CCS), so compounds can be identified with more confidence, either in targeted or non-targeted approaches. In this context, the number of applications focused on food analysis has increased exponentially in the last few years. This review provides an overview of the current status of IMS technology and its applicability in different areas of food analysis (i.e., food composition, process control, authentication, adulteration and safety).
Collapse
Affiliation(s)
- Maykel Hernández-Mesa
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071 Granada, Spain.
- INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes, France.
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRA UMR 1329, Route de Gachet-CS 50707, F-44307 Nantes CEDEX 3, France.
| | - David Ropartz
- INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes, France
| | - Ana M García-Campaña
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071 Granada, Spain
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes, France
| | - Gaud Dervilly-Pinel
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRA UMR 1329, Route de Gachet-CS 50707, F-44307 Nantes CEDEX 3, France
| | - Bruno Le Bizec
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRA UMR 1329, Route de Gachet-CS 50707, F-44307 Nantes CEDEX 3, France
| |
Collapse
|
45
|
Angel TE, Naylor BC, Price JC, Evans C, Szapacs M. Improved Sensitivity for Protein Turnover Quantification by Monitoring Immonium Ion Isotopologue Abundance. Anal Chem 2019; 91:9732-9740. [PMID: 31259532 DOI: 10.1021/acs.analchem.9b01329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an analytical strategy allowing for the direct quantification of stable isotope label incorporation in newly synthesized proteins following administration of the stable isotope tracer deuterium oxide. We present a demonstration of coupling high-resolution mass spectrometry, metabolic stable isotope labeling, and MS/MS-based isotopologue quantification for the measurement of protein turnover. Stable isotope labeling with deuterium oxide, followed by immonium ion isotopologue quantification, is a more sensitive strategy for determining protein fractional synthesis rates compared to peptide centric mass isotopomer distribution analysis approaches when labeling time and/or stable isotope tracer exposure is limited and, as such, offers a great advantage for human studies.
Collapse
Affiliation(s)
- Thomas E Angel
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - John C Price
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Christopher Evans
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Matthew Szapacs
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| |
Collapse
|
46
|
Tu J, Zhou Z, Li T, Zhu ZJ. The emerging role of ion mobility-mass spectrometry in lipidomics to facilitate lipid separation and identification. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
47
|
Piendl SK, Raddatz CR, Hartner NT, Thoben C, Warias R, Zimmermann S, Belder D. 2D in Seconds: Coupling of Chip-HPLC with Ion Mobility Spectrometry. Anal Chem 2019; 91:7613-7620. [DOI: 10.1021/acs.analchem.9b00302] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian K. Piendl
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Christian-Robert Raddatz
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstrasse 9A, 30167 Hannover, Germany
| | - Nora T. Hartner
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Christian Thoben
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstrasse 9A, 30167 Hannover, Germany
| | - Rico Warias
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Stefan Zimmermann
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstrasse 9A, 30167 Hannover, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| |
Collapse
|
48
|
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.
Collapse
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
| | | |
Collapse
|
49
|
Kirk AT, Bohnhorst A, Raddatz CR, Allers M, Zimmermann S. Ultra-high-resolution ion mobility spectrometry-current instrumentation, limitations, and future developments. Anal Bioanal Chem 2019; 411:6229-6246. [PMID: 30957205 DOI: 10.1007/s00216-019-01807-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 12/29/2022]
Abstract
With recent advances in ionization sources and instrumentation, ion mobility spectrometers (IMS) have transformed from a detector for chemical warfare agents and explosives to a widely used tool in analytical and bioanalytical applications. This increasing measurement task complexity requires higher and higher analytical performance and especially ultra-high resolution. In this review, we will discuss the currently used ion mobility spectrometers able to reach such ultra-high resolution, defined here as a resolving power greater than 200. These instruments are drift tube IMS, traveling wave IMS, trapped IMS, and field asymmetric or differential IMS. The basic operating principles and the resulting effects of experimental parameters on resolving power are explained and compared between the different instruments. This allows understanding the current limitations of resolving power and how ion mobility spectrometers may progress in the future. Graphical abstract.
Collapse
Affiliation(s)
- Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany.
| | - Alexander Bohnhorst
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Christian-Robert Raddatz
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Maria Allers
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| |
Collapse
|
50
|
Fingerprinting of traditionally produced red wines using liquid chromatography combined with drift tube ion mobility-mass spectrometry. Anal Chim Acta 2019; 1052:179-189. [DOI: 10.1016/j.aca.2018.11.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/23/2018] [Accepted: 11/20/2018] [Indexed: 12/11/2022]
|