1
|
Kostyukevich Y, Osipenko S, Borisova L, Kireev A. In-Electrospray source Hydrogen/Deuterium exchange coupled to multistage fragmentation for the investigation of the protonation and fragmentation pathways of gas phase ions. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5032. [PMID: 38736146 DOI: 10.1002/jms.5032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Identification of molecules in complex natural matrices relies on matching the fragmentation spectra of ions under investigation and the spectra acquired for the corresponding analytical standards. Currently, there are many databases of experimentally measured tandem mass spectrometry spectra (such as NIST, MzCloud, and Metlin), and considerable progress has been made in the development of software for predicting tandem mass spectrometry fragments in silico using combinatorial, machine learning, and quantum chemistry approaches (such as MetFrag, CFM-ID, and QCxMS). However, the electrospray ionization molecules can be ionized at different sites (protonated or deprotonated), and the fragmentation spectra of such ions are different. Here, we are using the combination of the in-ESI source hydrogen/deuterium exchange reaction and MSn fragmentation for the investigation of the fragmentation pathways for different protomers of organic molecules. It is shown that the distribution of the deuterium in the fragment ions reflects the presence of different protomers. For several molecules, the distribution of deuterium was traced up to the MS5 level of fragmentation revealing many unusual and unexpected effects. For example, we investigated the loss of HF from the ciprofloxacin and norfloxacin ions and observed that for ions protonated at -COOH group, the eliminating hydrogen always comes from -NH group. When ions are protonated at another site, the elimination of hydrogen with a probability of 30% occurs from the -NH group, and with a probability of 70%, it originates from other sites on the molecule. Such effects were not described previously. Quantum chemical simulation was used for the verification of the protonated structures and simulation of the corresponding fragmentation spectra.
Collapse
Affiliation(s)
| | - Sergey Osipenko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Albert Kireev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| |
Collapse
|
2
|
Cajka T, Hricko J, Rakusanova S, Brejchova K, Novakova M, Rudl Kulhava L, Hola V, Paucova M, Fiehn O, Kuda O. Hydrophilic Interaction Liquid Chromatography-Hydrogen/Deuterium Exchange-Mass Spectrometry (HILIC-HDX-MS) for Untargeted Metabolomics. Int J Mol Sci 2024; 25:2899. [PMID: 38474147 DOI: 10.3390/ijms25052899] [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: 01/15/2024] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Liquid chromatography with mass spectrometry (LC-MS)-based metabolomics detects thousands of molecular features (retention time-m/z pairs) in biological samples per analysis, yet the metabolite annotation rate remains low, with 90% of signals classified as unknowns. To enhance the metabolite annotation rates, researchers employ tandem mass spectral libraries and challenging in silico fragmentation software. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) may offer an additional layer of structural information in untargeted metabolomics, especially for identifying specific unidentified metabolites that are revealed to be statistically significant. Here, we investigate the potential of hydrophilic interaction liquid chromatography (HILIC)-HDX-MS in untargeted metabolomics. Specifically, we evaluate the effectiveness of two approaches using hypothetical targets: the post-column addition of deuterium oxide (D2O) and the on-column HILIC-HDX-MS method. To illustrate the practical application of HILIC-HDX-MS, we apply this methodology using the in silico fragmentation software MS-FINDER to an unknown compound detected in various biological samples, including plasma, serum, tissues, and feces during HILIC-MS profiling, subsequently identified as N1-acetylspermidine.
Collapse
Affiliation(s)
- Tomas Cajka
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Jiri Hricko
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Stanislava Rakusanova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Kristyna Brejchova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Novakova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Lucie Rudl Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Veronika Hola
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Paucova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Ondrej Kuda
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| |
Collapse
|
3
|
Xue L, Liu K, Yan C, Dun J, Xu Y, Wu L, Yang H, Liu H, Xie L, Wang G, Liang Y. Schisandra lignans ameliorate nonalcoholic steatohepatitis by regulating aberrant metabolism of phosphatidylethanolamines. Acta Pharm Sin B 2023; 13:3545-3560. [PMID: 37655337 PMCID: PMC10465965 DOI: 10.1016/j.apsb.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/16/2023] [Accepted: 04/19/2023] [Indexed: 09/02/2023] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is a spectrum of chronic liver disease characterized by hepatic lipid metabolism disorder. Recent reports emphasized the contribution of triglyceride and diglyceride accumulation to NASH, while the other lipids associated with the NASH pathogenesis remained unexplored. The specific purpose of our study was to explore a novel pathogenesis and treatment strategy of NASH via profiling the metabolic characteristics of lipids. Herein, multi-omics techniques based on LC-Q-TOF/MS, LC-MS/MS and MS imaging were developed and used to screen the action targets related to NASH progress and treatment. A methionine and choline deficient (MCD) diet-induced mouse model of NASH was then constructed, and Schisandra lignans extract (SLE) was applied to alleviate hepatic damage by regulating the lipid metabolism-related enzymes CES2A and CYP4A14. Hepatic lipidomics indicated that MCD-diet led to aberrant accumulation of phosphatidylethanolamines (PEs), and SLE could significantly reduce the accumulation of intrahepatic PEs. Notably, exogenous PE (18:0/18:1) was proved to significantly aggravate the mitochondrial damage and hepatocyte apoptosis. Supplementing PE (18:0/18:1) also deteriorated the NASH progress by up regulating intrahepatic proinflammatory and fibrotic factors, while PE synthase inhibitor exerted a prominent hepatoprotective role. The current work provides new insights into the relationship between PE metabolism and the pathogenesis of NASH.
Collapse
Affiliation(s)
- Lijuan Xue
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Keanqi Liu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Caixia Yan
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, Department of Clinical Pharmacy, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Junling Dun
- Analytical Applications Center, Shimadzu (China) Co., Ltd., Shanghai 200233, China
| | - Yexin Xu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Linlin Wu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Huizhu Yang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Huafang Liu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lin Xie
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Guangji Wang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Liang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
4
|
Kostyukevich Y, Stekolshikova E, Levashova A, Kovalenko A, Vishnevskaya A, Bashilov A, Kireev A, Tupertsev B, Rumiantseva L, Khaitovich P, Osipenko S, Nikolaev E. Untargeted Lipidomics after D 2O Administration Reveals the Turnover Rate of Individual Lipids in Various Organs of Living Organisms. Int J Mol Sci 2023; 24:11725. [PMID: 37511483 PMCID: PMC10380497 DOI: 10.3390/ijms241411725] [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: 06/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The administration of low doses of D2O to living organisms was used for decades for the investigation of metabolic pathways and for the measurement of the turnover rate for specific compounds. Usually, the investigation of the deuterium uptake in lipids is performed by measuring the deuteration level of the palmitic acid residue using GC-MS instruments, and to our knowledge, the application of the modern untargeted LC-MS/MS lipidomics approaches was only reported a few times. Here, we investigated the deuterium uptake for >500 lipids for 13 organs and body liquids of mice (brain, lung, heart, liver, kidney, spleen, plasma, urine, etc.) after 4 days of 100% D2O administration. The maximum deuteration level was observed in the liver, plasma, and lung, while in the brain and heart, the deuteration level was lower. Using MS/MS, we demonstrated the incorporation of deuterium in palmitic and stearic fragments in lipids (PC, PE, TAG, PG, etc.) but not in the corresponding free forms. Our results were analyzed based on the metabolic pathways of lipids.
Collapse
Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Elena Stekolshikova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anna Levashova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Scientific Center of Biomedical Technologies of the Federal Medical and Biological Agency, Krasnogorsky District, Village Light Mountains, Bld. 1, 143442 Moscow, Russia
| | - Anna Kovalenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anna Vishnevskaya
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anton Bashilov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Albert Kireev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Boris Tupertsev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Lidiia Rumiantseva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Sergey Osipenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| |
Collapse
|
5
|
Wei Y, Sun Y, Jia S, Yan P, Xiong C, Qi M, Wang C, Du Z, Jiang H. Identification of endogenous carbonyl steroids in human serum by chemical derivatization, hydrogen/deuterium exchange mass spectrometry and the quantitative structure-retention relationship. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1226:123776. [PMID: 37311272 DOI: 10.1016/j.jchromb.2023.123776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/09/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023]
Abstract
Steroids are tetracyclic aliphatic compounds, and most of them contain carbonyl groups. The disordered homeostasis of steroids is closely related to the occurrence and progression of various diseases. Due to high structural similarity, low concentrations in vivo, poor ionization efficiency, and interference from endogenous substances, it is very challenging to comprehensively and unambiguously identify endogenous steroids in biological matrix. Herein, an integrated strategy was developed for the characterization of endogenous steroids in serum based on chemical derivatization, ultra-performance liquid chromatography quadrupole Exactive mass spectrometry (UPLC-Q-Exactive-MS/MS), hydrogen/deuterium (H/D) exchange, and a quantitative structure-retention relationship (QSRR) model. To enhance the mass spectrometry (MS) response of carbonyl steroids, the ketonic carbonyl group was derivatized by Girard T (GT). Firstly, the fragmentation rules of derivatized carbonyl steroid standards by GT were summarized. Then, carbonyl steroids in serum were derivatized by GT and identified based on the fragmentation rules or by comparing retention time and MS/MS spectra with those of standards. H/D exchange MS was utilized to distinguish derivatized steroid isomers for the first time. Finally, a QSRR model was constructed to predict the retention time of the unknown steroid derivatives. With this strategy, 93 carbonyl steroids were identified from human serum, and 30 of them were determined to be dicarbonyl steroids by the charge number of characteristic ions and the number of exchangeable hrdrogen or comparing with standards. The QSRR model built by the machine learning algorithms has an excellent regression correlation, thus the accurate structures of 14 carbonyl steroids were determined, among which three steroids were reported for the first time in human serum. This study provides a new analytical method for the comprehensive and reliable identification of carbonyl steroids in biological matrix.
Collapse
Affiliation(s)
- Yinyu Wei
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yi Sun
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuailong Jia
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Pan Yan
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410028, China
| | - Chaomei Xiong
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Meiling Qi
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chenxi Wang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhifeng Du
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Hongliang Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
| |
Collapse
|
6
|
Williamson DL, Trimble TK, Nagy G. Hydrogen-Deuterium-Exchange-Based Mass Distribution Shifts in High-Resolution Cyclic Ion Mobility Separations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37098274 DOI: 10.1021/jasms.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The mass distribution of ions influences separations in ion mobility spectrometry-mass spectrometry (IMS-MS). Herein, we introduce a method to induce mass distribution shifts for various analytes using hydrogen-deuterium exchange (HDX) immediately prior to ionization using a dual syringe approach. By replacing labile hydrogens on analytes with deuteriums, we were able to differentiate isomers using separations of isotopologues. For each analyte studied, every possible level of deuteration (from undeuterated to fully deuterated) was generated and then separated using cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS). The information gained from such separations (relative arrival times; tRel. values) was found to be orthogonal to conventional IMS-MS separations. Additionally, the observed shifts were linearly additive with increasing deuteration, suggesting that this methodology could be extended to analytes with a larger number of labile hydrogens. For one isomer pair, as few as two deuteriums were able to produce a large enough mass distribution shift to differentiate isomers. In another experiment, we found that the mass distribution shift was large enough to overcome the reduced mass contribution, resulting in a "flipped" arrival time where the heavier deuterated isotopologue arrived before the lighter one. In this work, we present a proof-of-concept demonstration that mass-distribution-based shifts, tRel. values, could potentially act as an added dimension to characterize molecules in IMS-MS. We anticipate, along with future work in this area, that mass-distribution-based shifts could enable the identification of unknown molecules through a database-driven approach in an analogous fashion to collision cross section (CCS) measurements.
Collapse
Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Tyson K Trimble
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| |
Collapse
|
7
|
Raznikov V, Raznikova M, Sulimenkov I, Zelenov V. Separation of mass spectra of hydrogen-deuterium exchanged ions obtained by electrospray of solutions of biopolymers with unknown primary structure. Anal Bioanal Chem 2023; 415:2193-2207. [PMID: 36943444 DOI: 10.1007/s00216-023-04625-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 03/23/2023]
Abstract
The work is dedicated to further development of our described method for analyzing mass spectra of biomolecules acquired as a result of hydrogen-deuterium exchange reactions (HDXs). The modified method consists of separating HDX distributions via their approximations by a minimum number of components corresponding to independent H/D substitutions and independent charge carrier retentions in different spatial isoforms or conformations of biomolecules with unknown primary structures. In this case, neither the natural isotopic distribution nor the exact number of active sites involved in HDXs and H+ or D+ attachments can be determined in advance. Original H/D electrospray mass spectra of an apamin solution were taken from our previous work. In that work, taking into account the natural isotopic distribution of apamin molecules, three main conformations of apamin ions were found as a result of separating the H/D mass spectra of the apamin solution for the gas flow with the addition of about 10% ND3 molecules. Using the proposed modified method that does not require knowledge of the primary structure of the biomolecules gave similar results with slight deviations of calculated HDX distributions of the apamin ions from those obtained earlier. The maximum difference between mean values of the calculated HDX distributions for ions of the same charge in both cases does not exceed a few percent. In addition, HDX mass spectra of the apamin complex with an adduct of unknown structure were processed. Such analysis gave also three main fractions of ions with relatively large contributions when ND3 was injected into a radio-frequency quadrupole. In the absence of ND3 flow, the results of calculations for apamin and its complex were close to each other too. The formation of the apamin complex most probably in solution was confirmed by performed calculations.
Collapse
Affiliation(s)
- Valery Raznikov
- Chernogolovka Branch of the N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia.
| | - Marina Raznikova
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia.
| | - Ilia Sulimenkov
- Chernogolovka Branch of the N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia
| | - Vladislav Zelenov
- Chernogolovka Branch of the N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia
| |
Collapse
|
8
|
Bookmeyer C, Röhling U, Dreisewerd K, Soltwisch J. Single‐Photon‐Induced Post‐Ionization to Boost Ion Yields in MALDI Mass Spectrometry Imaging**. Angew Chem Int Ed Engl 2022; 61:e202202165. [PMID: 35727295 PMCID: PMC9546322 DOI: 10.1002/anie.202202165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Indexed: 12/15/2022]
Abstract
Matrix‐assisted laser desorption/ionization mass spectrometry imaging (MALDI‐MSI) is a rapidly growing method in the life sciences. However, for many analyte classes, its sensitivity is limited due to poor ionization efficiencies. To mitigate this problem, we here introduce a novel post‐ionization scheme based on single‐photon induced chemical ionization using pulsed RF‐Kr lamps. The fine‐vacuum conditions of a dual ion‐funnel ion source effectively thermalize the evolving MALDI plume and enable ample gas‐phase reactions. Injected chemical dopants crucially support fragment‐less ionization to [M+H]+/[M−H]− species. Based on this interplay, numerous glycerophospho‐, sphingo‐, and further lipids, registered from mammalian tissue sections, were boosted by up to three orders of magnitude, similar to results obtained with laser‐based post‐ionization (MALDI‐2). Experiments with deuterated matrix and dopant, however, indicated complex chemical ionization pathways different from MALDI‐2.
Collapse
Affiliation(s)
- Christoph Bookmeyer
- Institute of Hygiene University of Münster Robert-Koch-Str. 41 48149 Münster Germany
- Metabolomics Interdisciplinary Laboratory University of Tarragona Avinguda Països Catalans 26 43007 Tarragona (Spain)
| | - Ulrich Röhling
- Institute of Medical Physics and Biophysics University of Münster Robert-Koch-Str. 31 48149 Münster Germany
| | - Klaus Dreisewerd
- Institute of Hygiene University of Münster Robert-Koch-Str. 41 48149 Münster Germany
| | - Jens Soltwisch
- Institute of Hygiene University of Münster Robert-Koch-Str. 41 48149 Münster Germany
| |
Collapse
|
9
|
Rensner JJ, Lee YJ. Efficient Hydrogen-Deuterium Exchange in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging for Confident Metabolite Identification. Anal Chem 2022; 94:11129-11133. [PMID: 35917496 DOI: 10.1021/acs.analchem.2c00978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Highly efficient hydrogen-deuterium exchange (HDX) is developed for mass spectrometry imaging (MSI) with low-vacuum matrix-assisted laser desorption/ionization (MALDI). A HDX efficiency of 73-85% is achieved by introducing D2O vapor into a heated MALDI source in combination with a deuterium-labeled matrix, which allows correct determination of the number of possible H/D exchanges for up to 17 labile hydrogens. This provides valuable orthogonal information to supplement m/z, allowing for increased confidence in metabolite identification while retaining the spatial information MSI supplies. When combined with high-throughput METASPACE annotation, this approach can systematically improve untargeted metabolite annotations in MALDI-MS imaging. The developed method was applied to MALDI-MS imaging of the top surface, bottom surface, and middle section of Lemna minor fronds. Out of a total of 56 on-sample annotations made with the BraChem database using a 10% false discovery rate, 31 of these annotations (55%) matched our HDX data, providing additional confidence. For the remaining 45%, our data allowed us to narrow down structural possibilities and eliminate incorrect structures, greatly increasing confidence in metabolite identification.
Collapse
Affiliation(s)
- Josiah J Rensner
- Department of Chemistry, Iowa State University, Ames Iowa 50011, United States
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames Iowa 50011, United States
| |
Collapse
|
10
|
Bookmeyer C, Röhling U, Dreisewerd K, Soltwisch J. Single‐Photon‐Induced Post‐Ionization to Boost Ion Yields in MALDI Mass Spectrometry Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christoph Bookmeyer
- University of Münster: Westfälische Wilhelms-Universität Münster Institute of Hygiene Robert-Koch.Str. 41 48149 Münster GERMANY
| | - Ulrich Röhling
- University of Münster: Westfälische Wilhelms-Universität Münster Institute of Medical Physics and Biophysics GERMANY
| | - Klaus Dreisewerd
- University of Münster: Westfälische Wilhelms-Universität Münster Institute of Hygiene GERMANY
| | - Jens Soltwisch
- Westfalische Wilhelms-Universität Munster Institute of Hygiene Robert-Koch-Str. 41 48149 Munster GERMANY
| |
Collapse
|
11
|
Analysis of 16O/ 18O and H/D Exchange Reactions between Carbohydrates and Heavy Water Using High-Resolution Mass Spectrometry. Int J Mol Sci 2022; 23:ijms23073585. [PMID: 35408942 PMCID: PMC8998639 DOI: 10.3390/ijms23073585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/16/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023] Open
Abstract
Mono- and polysaccharides are an essential part of every biological system. Identifying underivatized carbohydrates using mass spectrometry is still a challenge because carbohydrates have a low capacity for ionization. Normally, the intensities of protonated carbohydrates are relatively low, and in order to increase the corresponding peak height, researchers add Na+, K+, or NH4+to the solution. However, the fragmentation spectra of the corresponding ions are very poor. Based on this, reliably identifying carbohydrates in complex natural and biological objects can benefit frommeasuring additional molecular descriptors, especially those directly connected to the molecular structure. Previously, we reported that the application of the isotope exchange approach (H/D and 16O/18O) to high-resolution mass spectrometry can increase the reliability of identifying drug-like compounds. Carbohydrates possess many -OH and -COOH groups, making it reasonable to expect that the isotope exchange approach would have considerable potential for detecting carbohydrates. Here, we used a collection of standard carbohydrates to investigate the isotope exchange reaction (H/D and 16O/18O) in carbohydrates and estimate its analytical applications.
Collapse
|
12
|
Kostyukevich Y, Sosnin S, Osipenko S, Kovaleva O, Rumiantseva L, Kireev A, Zherebker A, Fedorov M, Nikolaev EN. PyFragMS-A Web Tool for the Investigation of the Collision-Induced Fragmentation Pathways. ACS OMEGA 2022; 7:9710-9719. [PMID: 35350354 PMCID: PMC8945079 DOI: 10.1021/acsomega.1c07272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 05/13/2023]
Abstract
Dissociation induced by the accumulation of internal energy via collisions of ions with neutral molecules is one of the most important fragmentation techniques in mass spectrometry (MS), and the identification of small singly charged molecules is based mainly on the consideration of the fragmentation spectrum. Many research studies have been dedicated to the creation of databases of experimentally measured tandem mass spectrometry (MS/MS) spectra (such as MzCloud, Metlin, etc.) and developing software for predicting MS/MS fragments in silico from the molecular structure (such as MetFrag, CFM-ID, CSI:FingerID, etc.). However, the fragmentation mechanisms and pathways are still not fully understood. One of the limiting obstacles is that protomers (positive ions protonated at different sites) produce different fragmentation spectra, and these spectra overlap in the case of the presence of different protomers. Here, we are proposing to use a combination of two powerful approaches: computing fragmentation trees that carry information of all consecutive fragmentations and consideration of the MS/MS data of isotopically labeled compounds. We have created PyFragMS-a web tool consisting of a database of annotated MS/MS spectra of isotopically labeled molecules (after H/D and/or 16O/18O exchange) and a collection of instruments for computing fragmentation trees for an arbitrary molecule. Using PyFragMS, we investigated how the site of protonation influences the fragmentation pathway for small molecules. Also, PyFragMS offers capabilities for performing database search when MS/MS data of the isotopically labeled compounds are taken into account.
Collapse
|
13
|
Osipenko S, Nikolaev E, Kostyukevich Y. Amine additives for improved in-ESI H/D exchange. Analyst 2022; 147:3180-3185. [DOI: 10.1039/d2an00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In-ESI H/D exchange is a convenient technique for analyzing small-molecular complex mixtures.
Collapse
Affiliation(s)
- Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Yury Kostyukevich
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| |
Collapse
|
14
|
Zhvansky ES, Ivanov DG, Sorokin AA, Bugrova AE, Nikolaev EN, Popov IA. Interactive Estimation of Heterogeneity from Mass Spectrometry Imaging. Anal Chem 2021; 93:3706-3709. [PMID: 33591173 DOI: 10.1021/acs.analchem.1c00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we demonstrate a new approach for interactively assessing hyperspectral data spatial structures for heterogeneity using mass spectrometry imaging. This approach is based on the visualization of the cosine distance as the similarity levels between mass spectra of a chosen region and the rest of the image (sample). The applicability of the method is demonstrated on a set of mass spectrometry images of frontal mouse brain slices. Selection of the reference pixel of the mass spectrometric image and a further view of the corresponding cosine distance map helps to prepare supporting vectors for further analysis, select features, and carry out biological interpretation of different tissues in the mass spectrometry context with or without histological annotation. Visual inspection of the similarity maps reveals the spatial distribution of features in tissue samples, which can serve as the molecular histological annotation of a slide.
Collapse
Affiliation(s)
- Evgeny S Zhvansky
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Daniil G Ivanov
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia.,Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Kosygina st. 4, 119334 Moscow, Russia
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia.,Institute of Cell Biophysics RAS, Institutskaya st., 3, 142290 Pushchino, Russia.,Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Anna E Bugrova
- Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Kosygina st. 4, 119334 Moscow, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Novaya Street, 100, 143025 Skolkovo, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia
| |
Collapse
|
15
|
Sarycheva A, Grigoryev A, Sidorchuk D, Vladimirov G, Khaitovich P, Efimova O, Gavrilenko O, Stekolshchikova E, Nikolaev EN, Kostyukevich Y. Structure-Preserving and Perceptually Consistent Approach for Visualization of Mass Spectrometry Imaging Datasets. Anal Chem 2021; 93:1677-1685. [PMID: 33373190 DOI: 10.1021/acs.analchem.0c04256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry imaging (MSI) has become an important tool for 2D profiling of biological tissues, allowing for the visualization of individual compound distributions in the sample. Based on this information, it is possible to investigate the molecular organization within any particular tissue and detect abnormal regions (such as tumor regions) and many other biologically relevant phenomena. However, the large number of compounds present in the spectra hinders the productive analysis of large MSI datasets when utilizing standard tools. The heterogeneity of samples makes exploratory visualization (a presentation of the general idea of the molecular and structural organization of the inspected tissues) challenging. Here, we explore the application of various dimensionality reduction techniques that have been used extensively in the visualization of hyperspectral images and the MSI data specifically, such as principal component analysis, independent component analysis, non-negative matrix factorization, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection. Further, we propose a new approach based on a combination of structure preserving visualization with nonlinear manifold embedding of normalized spectral data. This way, we aim to preserve as much spatially overlapping signals as possible while augmenting them with information on compositional (spectral) variation. The proposed approach can be used for exploratory visualization of MSI datasets without prior deep chemical or histological knowledge of the sample. Thus, different datasets can be visually compared employing the proposed method. The proposed approach allowed for the clear visualization of the molecular layer, granular layer, and white matter in chimpanzee and macaque cerebellum slices.
Collapse
Affiliation(s)
- Anastasia Sarycheva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Anton Grigoryev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russian Federation
| | - Dmitry Sidorchuk
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russian Federation
| | - Gleb Vladimirov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Olga Efimova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Olga Gavrilenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Elena Stekolshchikova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| |
Collapse
|
16
|
Linke V, Overmyer KA, Miller IJ, Brademan DR, Hutchins PD, Trujillo EA, Reddy TR, Russell JD, Cushing EM, Schueler KL, Stapleton DS, Rabaglia ME, Keller MP, Gatti DM, Keele GR, Pham D, Broman KW, Churchill GA, Attie AD, Coon JJ. A large-scale genome-lipid association map guides lipid identification. Nat Metab 2020; 2:1149-1162. [PMID: 32958938 PMCID: PMC7572687 DOI: 10.1038/s42255-020-00278-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/11/2020] [Indexed: 12/13/2022]
Abstract
Despite the crucial roles of lipids in metabolism, we are still at the early stages of comprehensively annotating lipid species and their genetic basis. Mass spectrometry-based discovery lipidomics offers the potential to globally survey lipids and their relative abundances in various biological samples. To discover the genetics of lipid features obtained through high-resolution liquid chromatography-tandem mass spectrometry, we analysed liver and plasma from 384 diversity outbred mice, and quantified 3,283 molecular features. These features were mapped to 5,622 lipid quantitative trait loci and compiled into a public web resource termed LipidGenie. The data are cross-referenced to the human genome and offer a bridge between genetic associations in humans and mice. Harnessing this resource, we used genome-lipid association data as an additional aid to identify a number of lipids, for example gangliosides through their association with B4galnt1, and found evidence for a group of sex-specific phosphatidylcholines through their shared locus. Finally, LipidGenie's ability to query either mass or gene-centric terms suggests acyl-chain-specific functions for proteins of the ABHD family.
Collapse
Affiliation(s)
- Vanessa Linke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ian J Miller
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Dain R Brademan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Edna A Trujillo
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Thiru R Reddy
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Emily M Cushing
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary E Rabaglia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Duy Pham
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
17
|
Kostyukevich Y, Zherebker A, Orlov A, Kovaleva O, Burykina T, Isotov B, Nikolaev EN. Hydrogen/Deuterium and 16O/ 18O-Exchange Mass Spectrometry Boosting the Reliability of Compound Identification. Anal Chem 2020; 92:6877-6885. [PMID: 32167749 DOI: 10.1021/acs.analchem.9b05379] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Accurate and reliable identification of chemical compounds is the ultimate goal of mass spectrometry analyses. Currently, identification of compounds is usually based on the measurement of the accurate mass and fragmentation spectrum, chromatographic elution time, and collisional cross section. Unfortunately, despite the growth of databases of experimentally measured MS/MS spectra (such as MzCloud and Metlin) and developing software for predicting MS/MS fragments in silico from SMILES patterns (such as MetFrag, CFM-ID, and Ms-Finder), the problem of identification is still unsolved. The major issue is that the elution time and fragmentation spectra depend considerably on the equipment used and are not the same for different LC-MS systems. It means that any additional descriptors depending only on the structure of the chemical compound will be of big help for LC-MS/MS-based omics. Our approach is based on the characterization of compounds by the number of labile hydrogen and oxygen atoms in the molecule, which can be measured using hydrogen/deuterium and 16O/18O-exchange approaches. The number of labile atoms (those from -OH, -NH, ═O, and -COOH groups) can be predicted from SMILES patterns and serves as an additional structural descriptor when performing a database search. In addition, distribution of isotope labels among MS/MS fragments can be roughly predicted by software such as MetFrag or CFM-ID. Here, we present an approach utilizing the selection of structural candidates from a database on the basis of the number of functional groups and analysis of isotope labels distribution among fragments. It was found that our approach allows reduction of the search space by a factor of 10 and considerably increases the reliability of the compound identification.
Collapse
Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Alexey Orlov
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Oxana Kovaleva
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Tatyana Burykina
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 8-2 Trubetskaya St., Moscow 119048, Russian Federation
| | - Boris Isotov
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 8-2 Trubetskaya St., Moscow 119048, Russian Federation
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| |
Collapse
|