1
|
Ross DH, Bredeweg EL, Eder JG, Orton DJ, Burnet MC, Kyle JE, Nakayasu ES, Zheng X. A deep learning-guided automated workflow in LipidOz for detailed characterization of fungal fatty acid unsaturation by ozonolysis. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5078. [PMID: 39132905 DOI: 10.1002/jms.5078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/10/2024] [Accepted: 07/02/2024] [Indexed: 08/13/2024]
Abstract
Understanding fungal lipid biology and metabolism is critical for antifungal target discovery as lipids play central roles in cellular processes. Nuances in lipid structural differences can significantly impact their functions, making it necessary to characterize lipids in detail to understand their roles in these complex systems. In particular, lipid double bond (DB) locations are an important component of lipid structure that can only be determined using a few specialized analytical techniques. Ozone-induced dissociation mass spectrometry (OzID-MS) is one such technique that uses ozone to break lipid DBs, producing pairs of characteristic fragments that allow the determination of DB positions. In this work, we apply OzID-MS and LipidOz software to analyze the complex lipids of Saccharomyces cerevisiae yeast strains transformed with different fatty acid desaturases from Histoplasma capsulatum to determine the specific unsaturated lipids produced. The automated data analysis in LipidOz made the determination of DB positions from this large dataset more practical, but manual verification for all targets was still time-consuming. The DL model reduces manual involvement in data analysis, but since it was trained using mammalian lipid extracts, the prediction accuracy on yeast-derived data was reduced. We addressed both shortcomings by retraining the DL model to act as a pre-filter to prioritize targets for automated analysis, providing confident manually verified results but requiring less computational time and manual effort. Our workflow resulted in the determination of detailed DB positions and enzymatic specificity.
Collapse
Affiliation(s)
- Dylan H Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Erin L Bredeweg
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Josie G Eder
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| |
Collapse
|
2
|
Yang HC, Scruggs SS, Chai M, Mathai G, Taylor JS, Gross ML. Distinguishing Isomeric Cyclobutane Thymidine Dimers by Ion Mobility and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1768-1774. [PMID: 38952267 PMCID: PMC11305913 DOI: 10.1021/jasms.4c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Irradiation of the major conformation of duplex DNA found in cells (B form) produces cyclobutane pyrimidine dimers (CPDs) from adjacent pyrimidines in a head-to-head orientation (syn) with the C5 substituents in a cis stereochemistry. These CPDs have crucial implications in skin cancer. Irradiation of G-quadruplexes and other non-B DNA conformations in vitro produces, however, CPDs between nonadjacent pyrimidines in nearby loops with syn and head-to-tail orientations (anti) with both cis and trans stereochemistry to yield a mixture of six possible isomers of the T=T dimer. This outcome is further complicated by formation of mixtures of nonadjacent CPDs of C=T, T=C, and C=C, and successful analysis depends on development of specific and sensitive methods. Toward meeting this need, we investigated whether ion mobility mass spectrometry (IMMS) and MS/MS can distinguish the cis,syn and trans,anti T=T CPDs. Ion mobility can afford baseline separation and give relative mobilities that are in accord with predicted cross sections. Complementing this ability to distinguish isomers is MS/MS collisional activation where fragmentation also distinguishes the two isomers and confirms conclusions drawn from ion mobility analysis. The observations offer early support that ion mobility and MS/MS can enable the distinction of DNA photoproduct isomers.
Collapse
Affiliation(s)
- Hsin-Chieh Yang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Savannah S. Scruggs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Mengqi Chai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - George Mathai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - John-Stephen Taylor
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| |
Collapse
|
3
|
Blakley B, Zlibut E, Gupta RM, May JC, McLean JA. Direct Enantiomer Differentiation of Drugs and Drug-Like Compounds via Noncovalent Copper-Amino Acid Complexation and Ion Mobility-Mass Spectrometry. Anal Chem 2024; 96:12892-12900. [PMID: 39051631 PMCID: PMC11307251 DOI: 10.1021/acs.analchem.4c02710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
Drug enantiomers can possess vastly different pharmacological properties, yet they are identical in their chemical composition and structural connectivity. Thus, resolving enantiomers poses a great challenge in the field of separation science. Enantiomer separations necessitate interaction of the analyte with a chiral environment─in mass spectrometry-based analysis, a common approach is through a three-point interaction with a chiral selector commonly introduced during sample preparation. In select cases, the structural difference imparted through noncovalent complexation results in enantiomer-specific structural differences, facilitating measurement using a structurally selective analytical technique such as ion mobility-mass spectrometry (IM-MS). In this work, we investigate the direct IM-MS differentiation of chiral drug compounds using mononuclear copper complexes incorporating an amino acid chiral selector. A panel of 20 chiral drugs and drug-like compounds were investigated for separation, and four l-amino acids (l-histidine, l-tryptophan, l-proline, and l-tyrosine) were evaluated as chiral selectors (CS) to provide the chiral environment necessary for differentiation. Enantiomer differentiation was achieved for four chiral molecule pairs (R/S-thalidomide, R/S-baclofen, R/S-metoprolol, and d/l-panthenol) with two-peak resolution (Rp-p) values ranging from 0.7 (>10% valley) to 1.5 (baseline separation). Calibration curves relating IM peak areas to enantiomeric concentrations enabled enantiomeric excess quantitation of racemic thalidomide and metoprolol with residuals of 5.7 and 2.5%, respectively. Theoretical models suggest that CuII and l-histidine complexation around the analyte chiral center is important for gas-phase stereoselectivity. This study demonstrates the potential of combining enantioselective noncovalent copper complexation with structurally selective IM-MS for differentiating chiral drugs and drug-like compounds.
Collapse
Affiliation(s)
- Benjamin
K. Blakley
- Department of Chemistry, Center for
Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt-Ingram
Cancer Center, and Vanderbilt Institute for Integrated Biosystems
Research and Education, Vanderbilt University, Nashville, Tennessee 37235-1822, United
States
| | | | - Rashi M. Gupta
- Department of Chemistry, Center for
Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt-Ingram
Cancer Center, and Vanderbilt Institute for Integrated Biosystems
Research and Education, Vanderbilt University, Nashville, Tennessee 37235-1822, United
States
| | - Jody C. May
- Department of Chemistry, Center for
Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt-Ingram
Cancer Center, and Vanderbilt Institute for Integrated Biosystems
Research and Education, Vanderbilt University, Nashville, Tennessee 37235-1822, United
States
| | - John A. McLean
- Department of Chemistry, Center for
Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt-Ingram
Cancer Center, and Vanderbilt Institute for Integrated Biosystems
Research and Education, Vanderbilt University, Nashville, Tennessee 37235-1822, United
States
| |
Collapse
|
4
|
Xia C, Mernie E, Zaia J, Costello CE, Lin C. Accurate Collisional Cross Section Measurement by Multipass Cyclic Ion Mobility Spectrometry. Anal Chem 2024; 96:11959-11968. [PMID: 38990519 DOI: 10.1021/acs.analchem.4c01758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Ion mobility-mass spectrometry (IM-MS) is a powerful analytical tool for structural characterization. IM measurement provides collision cross section (CCS) values that facilitate analyte identification. While CCS values can be directly calculated from mobility measurements obtained using drift tube ion mobility spectrometry (DT-IMS), this method has limited mobility resolution due to the practical constraints on the length of the ion drift path. Consequently, DT-IMS cannot differentiate analytes with similar mobilities or resolve fine mobility features of individual ions. Cyclic IMS (cIMS) instruments leverage a cyclic path enabled by traveling wave ion mobility (TWIM) technology and offer increased mobility solution to address this challenge. While TWIM devices must first be calibrated to enable CCS measurements, current calibration strategies are primarily tailored for single-pass analyses. This preference is partly attributed to the challenges associated with multipass calibration methods, which require both calibrants and analytes to experience the same number of passes. Achieving this consistency can be complicated due to factors like peak splitting and diffusion, and may not be feasible for online IM-MS analyses. A recent report employed average ion velocities obtained from multiple measurements under different separation pathlengths as a path length-independent metric for CCS calibration. However, the ability to exploit this averaging approach is limited by observed variation in ion drift time/velocity in these measurements. In this study, we introduce a novel calibration strategy designed for multipass cIMS analyses, directly targeting the root cause for the path length- and mobility-dependent variations in ion drift time. With this method, we demonstrate that CCS values derived from multipass measurements closely align with those obtained from single-pass analyses, with an average deviation of 0.1%. We apply this method to characterize four isomeric trisaccharides. Our approach not only results in excellent agreement between our measured cIMSCCS values and the reported DTCCS values, with an average difference of only 0.5%, but also allows us to effectively identify subtle mobility characteristics of each compound and determine their respective CCS values. This level of detail and accuracy was previously unattainable using DT-IMS or single-pass cIMS measurements. We developed an algorithm for reconstructing arrival time distribution in cases where wrap-around has resulted in peak splitting. Collectively, the new calibration strategy and the reconstruction procedure maintain reproducibility and precision in CCS measurements while largely eliminating the need for meticulous selection of separation times. We expect that our method will empower researchers to harness the high mobility resolution offered by multipass cIMS analyses without compromising the accuracy of CCS measurement, making it appropriate for straightforward use across a wide range of applications.
Collapse
Affiliation(s)
- Chaoshuang Xia
- Department of Biochemistry & Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Elias Mernie
- Department of Biochemistry & Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Joseph Zaia
- Department of Biochemistry & Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Catherine E Costello
- Department of Biochemistry & Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Cheng Lin
- Department of Biochemistry & Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| |
Collapse
|
5
|
Haack A, Schaefer C, Zimmermann S. On the Arrival Time Distribution of Reacting Systems in Ion Mobility Spectrometry. Anal Chem 2024; 96. [PMID: 39009503 PMCID: PMC11295131 DOI: 10.1021/acs.analchem.4c02010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/13/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
Ion mobility spectrometry (IMS) is a widely used gas-phase separation technique, particularly when coupled with mass spectrometry (MS). Modern IMS instruments often apply elevated reduced field strengths for improved ion separation and ion focusing. These alter the collision dynamics and further drive ion reaction processes that can change the analyte's structure. As a result, the measured arrival time distribution (ATD) can change with the applied reduced field strengths. In this work, we systematically study how the ion collision dynamics and the ion reaction dynamics, as a function of the reduced field strength, can alter the ATD. To this end, we investigate 2,6-di-tert-butylpyridine, methanol, and ethyl acetate using a home-built drift tube IMS coupled to a home-built MS and extensive first-principles Monte Carlo modeling. We show how elevated reduced field strengths can actually lower resolving power through increased ion diffusion and how the field dependency of the ion mobility can introduce uncertainties to collision cross sections (CCS) calculated from the measured mobilities. On top of the collision dynamics, we show how chemical transformation processes that alter the analyte's CCS, e.g., dynamic clustering or fragmentation, can lead to broadened, shifted, or non-Gaussian ATDs and how sensitive these processes are to the applied field strengths. We highlight how first-principles ion dynamics simulations can help to understand and even harness the mentioned effects.
Collapse
Affiliation(s)
- Alexander Haack
- Department of Sensors and
Measurement Technology, Institute of Electrical Engineering and Measurement
Technology, Leibniz University Hannover, 30167 Hannover, Germany
| | - Christoph Schaefer
- Department of Sensors and
Measurement Technology, Institute of Electrical Engineering and Measurement
Technology, Leibniz University Hannover, 30167 Hannover, Germany
| | - Stefan Zimmermann
- Department of Sensors and
Measurement Technology, Institute of Electrical Engineering and Measurement
Technology, Leibniz University Hannover, 30167 Hannover, Germany
| |
Collapse
|
6
|
Höving S, Schomacher J, Schiller A, Franzke J. Setting the Separation Factor α for Ketone Monomers and Dimers by the Use of Different Drift Gases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1622-1628. [PMID: 38866725 DOI: 10.1021/jasms.4c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
This study investigates the influence of different drift gases on ion mobility in ion mobility spectrometry (IMS) using ketones as model substances within a custom-built drift tube spectrometer. Different binary mixtures of nitrogen, helium, and argon were used as drift gases to investigate the influence of mobility on the monomers and dimers of the different ketones. Experimental results reveal shifts in ion drift times and separation factors (α) with varying gas compositions, in accordance with Blanc's Law. Furthermore, the study underscores the device-independent nature of α and the device-dependent resolution, emphasizing the importance of comparative analyses. Employing 2-hexanone and 2-decanone in the same sample but with different drift gases is used to show the impact of different drift gases. By changing the drift gas composition, total alignment of drift times and therefore no possible resolution or baseline resolution could be achieved. Through different experiments and analyses, this research provides insights into the interactions between gas composition and ion mobility, offering implications for diverse analytical applications from environmental monitoring to chemical detection.
Collapse
Affiliation(s)
- Simon Höving
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
| | - Jos Schomacher
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
| | - Arthur Schiller
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
| | - Joachim Franzke
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
| |
Collapse
|
7
|
Baines C, Sargeant J, Fage CD, Pugh H, Alkhalaf LM, Challis GL, Oldham NJ. Native ESI-MS and Collision-Induced Unfolding (CIU) of the Complex between Bacterial Elongation Factor-Tu and the Antibiotic Enacyloxin IIa. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1490-1496. [PMID: 38830009 PMCID: PMC11228974 DOI: 10.1021/jasms.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
Collision-induced unfolding (CIU) of protein ions, monitored by ion mobility-mass spectrometry, can be used to assess the stability of their compact gas-phase fold and hence provide structural information. The bacterial elongation factor EF-Tu, a key protein for mRNA translation in prokaryotes and hence a promising antibiotic target, has been studied by CIU. The major [M + 12H]12+ ion of EF-Tu unfolded in collision with Ar atoms between 40 and 50 V, corresponding to an Elab energy of 480-500 eV. Binding of the cofactor analogue GDPNP and the antibiotic enacyloxin IIa stabilized the compact fold of EF-Tu, although dissociation of the latter from the complex diminished its stabilizing effect at higher collision energies. Molecular dynamics simulations of the [M + 12H]12+ EF-Tu ion showed similar qualitative behavior to the experimental results.
Collapse
Affiliation(s)
- Cameron Baines
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United
Kingdom
| | - Jacob Sargeant
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christopher D. Fage
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hannah Pugh
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Lona M. Alkhalaf
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, United Kingdom
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute,
Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Neil J. Oldham
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United
Kingdom
| |
Collapse
|
8
|
Ross DH, Lee JY, Gao Y, Hollerbach AL, Bilbao A, Shi T, Ibrahim YM, Smith RD, Zheng X. Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-Based High-Resolution Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1539-1549. [PMID: 38864778 DOI: 10.1021/jasms.4c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Ion mobility spectrometry (IMS) is a gas-phase analytical technique that separates ions with different sizes and shapes and is compatible with mass spectrometry (MS) to provide an additional separation dimension. The rapid nature of the IMS separation combined with the high sensitivity of MS-based detection and the ability to derive structural information on analytes in the form of the property collision cross section (CCS) makes IMS particularly well-suited for characterizing complex samples in -omics applications. In such applications, the quality of CCS from IMS measurements is critical to confident annotation of the detected components in the complex -omics samples. However, most IMS instrumentation in mainstream use requires calibration to calculate CCS from measured arrival times, with the most notable exception being drift tube IMS measurements using multifield methods. The strategy for calibrating CCS values, particularly selection of appropriate calibrants, has important implications for CCS accuracy, reproducibility, and transferability between laboratories. The conventional approach to CCS calibration involves explicitly defining calibrants ahead of data acquisition and crucially relies upon availability of reference CCS values. In this work, we present a novel reference-free approach to CCS calibration which leverages trends among putatively identified features and computational CCS prediction to conduct calibrations post-data acquisition and without relying on explicitly defined calibrants. We demonstrated the utility of this reference-free CCS calibration strategy for proteomics application using high-resolution structures for lossless ion manipulations (SLIM)-based IMS-MS. We first validated the accuracy of CCS values using a set of synthetic peptides and then demonstrated using a complex peptide sample from cell lysate.
Collapse
Affiliation(s)
- Dylan H Ross
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jung Yun Lee
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yuqian Gao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Adam L Hollerbach
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aivett Bilbao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tujin Shi
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
9
|
Colley ME, Esselman AB, Scott CF, Spraggins JM. High-Specificity Imaging Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:1-24. [PMID: 38594938 DOI: 10.1146/annurev-anchem-083023-024546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Imaging mass spectrometry (IMS) enables highly multiplexed, untargeted tissue mapping for a broad range of molecular classes, facilitating in situ biological discovery. Yet, challenges persist in molecular specificity, which is the ability to discern one molecule from another, and spatial specificity, which is the ability to link untargeted imaging data to specific tissue features. Instrumental developments have dramatically improved IMS spatial resolution, allowing molecular observations to be more readily associated with distinct tissue features across spatial scales, ranging from larger anatomical regions to single cells. High-performance mass analyzers and systems integrating ion mobility technologies are also becoming more prevalent, further improving molecular coverage and the ability to discern chemical identity. This review provides an overview of recent advancements in high-specificity IMS that are providing critical biological context to untargeted molecular imaging, enabling integrated analyses, and addressing advanced biomedical research applications.
Collapse
Affiliation(s)
- Madeline E Colley
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison B Esselman
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Claire F Scott
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffrey M Spraggins
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- 5Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
10
|
Gass DT, Quintero AV, Hatvany JB, Gallagher ES. Metal adduction in mass spectrometric analyses of carbohydrates and glycoconjugates. MASS SPECTROMETRY REVIEWS 2024; 43:615-659. [PMID: 36005212 DOI: 10.1002/mas.21801] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Glycans, carbohydrates, and glycoconjugates are involved in many crucial biological processes, such as disease development, immune responses, and cell-cell recognition. Glycans and carbohydrates are known for the large number of isomeric features associated with their structures, making analysis challenging compared with other biomolecules. Mass spectrometry has become the primary method of structural characterization for carbohydrates, glycans, and glycoconjugates. Metal adduction is especially important for the mass spectrometric analysis of carbohydrates and glycans. Metal-ion adduction to carbohydrates and glycoconjugates affects ion formation and the three-dimensional, gas-phase structures. Herein, we discuss how metal-ion adduction impacts ionization, ion mobility, ion activation and dissociation, and hydrogen/deuterium exchange for carbohydrates and glycoconjugates. We also compare the use of different metals for these various techniques and highlight the value in using metals as charge carriers for these analyses. Finally, we provide recommendations for selecting a metal for analysis of carbohydrate adducts and describe areas for continued research.
Collapse
Affiliation(s)
- Darren T Gass
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Ana V Quintero
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| |
Collapse
|
11
|
Matney R, Gadkari VV. Recent advances in gas phase unfolding: Instrumentation and applications. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5059. [PMID: 38894609 DOI: 10.1002/jms.5059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Broader adoption of native mass spectrometry (MS) and ion mobility-mass spectrometry (IM-MS) has propelled the development of several techniques which take advantage of the selectivity, sensitivity, and speed of MS to make measurements of complex biological molecules in the gas phase. One such method, collision induced unfolding (CIU), has risen to prominence in recent years, due to its well documented capability to detect shifts in structural stability of biological molecules in response to external stimuli (e.g., mutations, stress, non-covalent interactions, sample conditions etc.). This increase in reported CIU measurements is enabled partly due to advances in IM-MS instrumentation by vendors, and also innovative method development by researchers. This perspective highlights a few of these advances and concludes with a look forward toward the future of the gas phase unfolding field.
Collapse
Affiliation(s)
- Rowan Matney
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Varun V Gadkari
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
12
|
Bouwmeester R, Richardson K, Denny R, Wilson ID, Degroeve S, Martens L, Vissers JPC. Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling. Talanta 2024; 274:125970. [PMID: 38621320 DOI: 10.1016/j.talanta.2024.125970] [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: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
The use of collision cross section (CCS) values derived from ion mobility studies is proving to be an increasingly important tool in the characterization and identification of molecules detected in complex mixtures. Here, a novel machine learning (ML) based method for predicting CCS integrating both molecular modeling (MM) and ML methodologies has been devised and shown to be able to accurately predict CCS values for singly charged small molecular weight molecules from a broad range of chemical classes. The model performed favorably compared to existing models, improving compound identifications for isobaric analytes in terms of ranking and assigning identification probability values to the annotation. Furthermore, charge localization was seen to be correlated with CCS prediction accuracy and with gas-phase proton affinity demonstrating the potential to provide a proxy for prediction error based on chemical structural properties. The presented approach and findings represent a further step towards accurate prediction and application of computationally generated CCS values.
Collapse
Affiliation(s)
- Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | | | | | - Ian D Wilson
- Computational & Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, United Kingdom
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | |
Collapse
|
13
|
He G, He Q, Cheng J, Yu R, Shuai J, Cao Y. ProPept-MT: A Multi-Task Learning Model for Peptide Feature Prediction. Int J Mol Sci 2024; 25:7237. [PMID: 39000344 PMCID: PMC11241495 DOI: 10.3390/ijms25137237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
In the realm of quantitative proteomics, data-independent acquisition (DIA) has emerged as a promising approach, offering enhanced reproducibility and quantitative accuracy compared to traditional data-dependent acquisition (DDA) methods. However, the analysis of DIA data is currently hindered by its reliance on project-specific spectral libraries derived from DDA analyses, which not only limits proteome coverage but also proves to be a time-intensive process. To overcome these challenges, we propose ProPept-MT, a novel deep learning-based multi-task prediction model designed to accurately forecast key features such as retention time (RT), ion intensity, and ion mobility (IM). Leveraging advanced techniques such as multi-head attention and BiLSTM for feature extraction, coupled with Nash-MTL for gradient coordination, ProPept-MT demonstrates superior prediction performance. Integrating ion mobility alongside RT, mass-to-charge ratio (m/z), and ion intensity forms 4D proteomics. Then, we outline a comprehensive workflow tailored for 4D DIA proteomics research, integrating the use of 4D in silico libraries predicted by ProPept-MT. Evaluation on a benchmark dataset showcases ProPept-MT's exceptional predictive capabilities, with impressive results including a 99.9% Pearson correlation coefficient (PCC) for RT prediction, a median dot product (DP) of 96.0% for fragment ion intensity prediction, and a 99.3% PCC for IM prediction on the test set. Notably, ProPept-MT manifests efficacy in predicting both unmodified and phosphorylated peptides, underscoring its potential as a valuable tool for constructing high-quality 4D DIA in silico libraries.
Collapse
Affiliation(s)
- Guoqiang He
- Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Qingzu He
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Jinyan Cheng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Rongwen Yu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Jianwei Shuai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Yi Cao
- Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| |
Collapse
|
14
|
Iwamoto K, Inoue G, Matsubara H. Structural analysis of C 8H 6˙ + fragment ion from quinoline using ion-mobility spectrometry/mass spectrometry. Phys Chem Chem Phys 2024; 26:17205-17212. [PMID: 38855902 DOI: 10.1039/d4cp01676a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
This study investigated the structures of fragment ions derived from the quinoline (C9H7N) radical cation using ion-mobility spectrometry and mass spectrometry. Ion mobility and mass analysis revealed that C8H6˙+ is the primary dissociation product resulting from the loss of HCN during collision-induced dissociation of the quinoline radical cation. The reduced mobility (K0) of the C8H6˙+ fragment product in helium gas was measured over a range of reduced electric fields (E/N = 20.8-27.4 Td) at room temperature. The experimental K0 values indicated that C8H6˙+ is a mixture of phenylacetylene and pentalene radical cations. Furthermore, quantum chemical calculations revealed two potential energy surfaces delineating the loss of HCN from the quinoline radical cation to form phenylacetylene radical cations.
Collapse
Affiliation(s)
- Kenichi Iwamoto
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan.
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan
| | - Genki Inoue
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan.
| | - Hiroshi Matsubara
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan.
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 1-1 Gakuencho Nakaku, Sakai, Osaka 599-8531, Japan
| |
Collapse
|
15
|
Williams-Pavlantos K, Mokarizadeh AH, Curole BJ, Grayson SM, Tsige M, Wesdemiotis C. Elucidation of Dithiol-yne Comb Polymer Architectures by Tandem Mass Spectrometry and Ion Mobility Techniques. Polymers (Basel) 2024; 16:1665. [PMID: 38932016 PMCID: PMC11207239 DOI: 10.3390/polym16121665] [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: 02/07/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Polymers have a wide range of applications depending on their composition, size, and architecture. Varying any of these three characteristics can greatly impact the resulting chemical, physical, and mechanical properties. While many techniques are available to determine polymer composition and size, determining the exact polymer architecture is more challenging. Herein, tandem mass spectrometry (MS/MS) and ion mobility mass spectrometry (IM-MS) methods are utilized to derive crucial architectural information about dithiol-yne comb polymers. Based on their unique fragmentation products and IM drift times, dithiol-yne oligomers with distinct architectures were successfully differentiated and characterized. Additionally, experimental collision cross-sections (Ω) derived via IM-MS were compared to theoretically extracted Ω values from molecular dynamics simulated structures to deduce the architectural motif of these comb oligomers. Overall, this work demonstrates the benefits of combining various mass spectrometry techniques in order to gain a complete understanding of a complex polymer mixture.
Collapse
Affiliation(s)
| | - Abdol Hadi Mokarizadeh
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
| | - Brennan J. Curole
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA;
| | - Scott M. Grayson
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA;
| | - Mesfin Tsige
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
| | - Chrys Wesdemiotis
- Department of Chemistry, University of Akron, Akron, OH 44325, USA;
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
| |
Collapse
|
16
|
Jurček O, Chattopadhyay S, Kalenius E, Linnanto JM, Kiesilä A, Jurček P, Radiměřský P, Marek R. Unsymmetric Chiral Ligands for Large Metallo-Macrocycles: Selectivity of Orientational Self-Sorting. Angew Chem Int Ed Engl 2024:e202409134. [PMID: 38845398 DOI: 10.1002/anie.202409134] [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: 05/14/2024] [Indexed: 08/02/2024]
Abstract
Nature uses various chiral and unsymmetric building blocks to form substantial and complex supramolecular assemblies. In contrast, the majority of organic ligands used in metallosupramolecular chemistry are symmetric and achiral. Here we extend the group of unsymmetric chiral bile acids used as a scaffold for organic bispyridyl ligands by employing chenodeoxycholic acid (CDCA), an epimer of the previously used ursodeoxycholic acid (UDCA). The epimerism, flexibility, and bulkiness of the ligands leads to large structural differences in coordination products upon reaction with Pd(NO3)2. The UDCA-bispyridyl ligand self-assembles quantitatively into a single crown-like Pd3L6 complex, whereas the CDCA ligand provides a mixture of coordination complexes of general formula PdnL2n, i.e., Pd2L4, Pd3L6, Pd4L8, Pd5L10, and even Pd6L12 containing an impressive 120 chiral centers. The coordination products were studied by a combination of analytical methods, with ion-mobility mass spectrometry (IM-MS) providing valuable details on their structure and allowed an effective separation of m/z 1461 to individual signals according to the arrival time distribution, thereby revealing four different ions of [Pd3L6(NO3)3]3+, [Pd4L8(NO3)4]4+, [Pd5L10(NO3)5]5+, and [Pd6L12(NO3)6]6+. The structures of all the complexes were modelled using DFT calculations. Finally, the challenges and conclusions in determining the specific structural identity of these unsymmetric species are discussed.
Collapse
Affiliation(s)
- Ondřej Jurček
- Department of Natural Drugs, Faculty of Pharmacy, Masaryk University, Palackého 1946/1, CZ-61200, Brno, Czechia
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Subhasis Chattopadhyay
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Elina Kalenius
- Department of Chemistry, University of Jyvaskyla P. O. Box 35, FI-40014, Jyväskylä, Finland
| | - Juha M Linnanto
- Institute of Physics, University of Tartu, W. Ostwald Street 1, 50411, Tartu, Estonia
| | - Anniina Kiesilä
- Department of Chemistry, University of Jyvaskyla P. O. Box 35, FI-40014, Jyväskylä, Finland
| | - Pia Jurček
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Petr Radiměřský
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| | - Radek Marek
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czechia
| |
Collapse
|
17
|
Ross DH, Bhotika H, Zheng X, Smith RD, Burnum-Johnson KE, Bilbao A. Computational tools and algorithms for ion mobility spectrometry-mass spectrometry. Proteomics 2024; 24:e2200436. [PMID: 38438732 DOI: 10.1002/pmic.202200436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/06/2024]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.
Collapse
Affiliation(s)
- Dylan H Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Harsh Bhotika
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aivett Bilbao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| |
Collapse
|
18
|
Kumari S, Causon T. CCSfind: A tool for chemically informed LC-IM-MS database building. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5040. [PMID: 38736147 DOI: 10.1002/jms.5040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
In addition to providing critical knowledge of the accurate mass of ions, ion mobility-mass spectrometry (IM-MS) delivers complementary data relating to the conformation and size of ions in the form of an ion mobility spectrum and derived parameters, namely, the ion's mobility (K) and the IM-derived collision cross section (CCS). However, the maximum amount of information obtained in IM-MS measurements is not currently transferred into analytical databases including the full mobility spectra (CCS distributions) as well as capturing of additional ion species (e.g., adducts) into the same compound entry. We introduce CCSfind, a new tool for building comprehensive databases from experimental IM-MS measurements of small molecules. CCSfind allows predicted ion species to be chosen for input chemical formulae, which are then targeted by CCSfind after parsing open source mzML input files to provide a unified set of results within a single data processing step. CCSfind can handle both chromatographically separated isomers and IM separation of isomeric ions (e.g., "protomers" or conformers of the same ion species) with simple user control over the output for new database entries in SQL format. Files of up to 1 GB can be processed in less than 2 min on a desktop computer with 32 GB RAM with computational time scaling linearly with the size of the input mzML file or the number of input molecular formulae. Results are manually reviewed, annotated with experimental settings, before committing the database where the full dataset can be retrieved.
Collapse
Affiliation(s)
- Sangeeta Kumari
- Core Facility Bioinformatics, BOKU University, Vienna, Austria
| | - Tim Causon
- Department of Chemistry, Institute of Analytical Chemistry, BOKU University, Vienna, Austria
| |
Collapse
|
19
|
Girgis M, Petruncio G, Russo P, Peyton S, Paige M, Campos D, Sanda M. Analysis of N- and O-linked site-specific glycosylation by ion mobility mass spectrometry: State of the art and future directions. Proteomics 2024; 24:e2300281. [PMID: 38171879 DOI: 10.1002/pmic.202300281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
Glycosylation, the major post-translational modification of proteins, significantly increases the diversity of proteoforms. Glycans are involved in a variety of pivotal structural and functional roles of proteins, and changes in glycosylation are profoundly connected to the progression of numerous diseases. Mass spectrometry (MS) has emerged as the gold standard for glycan and glycopeptide analysis because of its high sensitivity and the wealth of fragmentation information that can be obtained. Various separation techniques have been employed to resolve glycan and glycopeptide isomers at the front end of the MS. However, differentiating structures of isobaric and isomeric glycopeptides constitutes a challenge in MS-based characterization. Many reports described the use of various ion mobility-mass spectrometry (IM-MS) techniques for glycomic analyses. Nevertheless, very few studies have focused on N- and O-linked site-specific glycopeptidomic analysis. Unlike glycomics, glycoproteomics presents a multitude of inherent challenges in microheterogeneity, which are further exacerbated by the lack of dedicated bioinformatics tools. In this review, we cover recent advances made towards the growing field of site-specific glycosylation analysis using IM-MS with a specific emphasis on the MS techniques and capabilities in resolving isomeric peptidoglycan structures. Furthermore, we discuss commonly used software that supports IM-MS data analysis of glycopeptides.
Collapse
Affiliation(s)
- Michael Girgis
- Department of Bioengineering, College of Engineering & Computing, George Mason University, Fairfax, Virginia, USA
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
| | - Gregory Petruncio
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
- Department of Chemistry & Biochemistry, College of Science, George Mason University, Fairfax, Virginia, USA
| | - Paul Russo
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Steven Peyton
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
| | - Mikell Paige
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
- Department of Chemistry & Biochemistry, College of Science, George Mason University, Fairfax, Virginia, USA
| | - Diana Campos
- Max-Planck-Institut fuer Herz- und Lungenforschung, Bad Nauheim, Germany
| | - Miloslav Sanda
- Max-Planck-Institut fuer Herz- und Lungenforschung, Bad Nauheim, Germany
| |
Collapse
|
20
|
Geue N. Modern Electrospray Ionization Mass Spectrometry Techniques for the Characterization of Supramolecules and Coordination Compounds. Anal Chem 2024; 96:7332-7341. [PMID: 38686955 PMCID: PMC11099892 DOI: 10.1021/acs.analchem.4c01028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Mass spectrometry is routinely used for myriad applications in clinical, industrial, and research laboratories worldwide. Developments in the areas of ionization sources, high-resolution mass analyzers, tandem mass spectrometry, and ion mobility have significantly extended the repertoire of mass spectrometrists; however, for coordination compounds and supramolecules, mass spectrometry remains underexplored and arguably underappreciated. Here, the reader is guided through different tools of modern electrospray ionization mass spectrometry that are suitable for larger inorganic complexes. All steps, from sample preparation and technical details to data analysis and interpretation are discussed. The main target audience of this tutorial is synthetic chemists as well as technicians/mass spectrometrists with little experience in characterizing labile inorganic compounds.
Collapse
Affiliation(s)
- Niklas Geue
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, Department
of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
21
|
Hildebrand F, Koellensperger G, Causon T. MobiLipid: A Tool for Enhancing CCS Quality Control of Ion Mobility-Mass Spectrometry Lipidomics by Internal Standardization. Anal Chem 2024; 96:7380-7385. [PMID: 38693701 PMCID: PMC11099887 DOI: 10.1021/acs.analchem.4c01253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Ion mobility-mass spectrometry (IM-MS) offers benefits for lipidomics by obtaining IM-derived collision cross sections (CCS), a conditional property of an ion that can enhance lipid identification. While drift tube (DT) IM-MS retains a direct link to the primary experimental method to derive CCS values, other IM technologies rely solely on external CCS calibration, posing challenges due to dissimilar chemical properties between lipids and calibrants. To address this, we introduce MobiLipid, a novel tool facilitating the CCS quality control of IM-MS lipidomics workflows by internal standardization. MobiLipid utilizes a newly established DTCCSN2 library for uniformly (U)13C-labeled lipids, derived from a U13C-labeled yeast extract, containing 377 DTCCSN2 values. This automated open-source R Markdown tool enables internal monitoring and straightforward compensation for CCSN2 biases. It supports lipid class- and adduct-specific CCS corrections, requiring only three U13C-labeled lipids per lipid class-adduct combination across 10 lipid classes without requiring additional external measurements. The applicability of MobiLipid is demonstrated for trapped IM (TIM)-MS measurements of an unlabeled yeast extract spiked with U13C-labeled lipids. Monitoring the CCSN2 biases of TIMCCSN2 values compared to DTCCSN2 library entries utilizing MobiLipid resulted in mean absolute biases of 0.78% and 0.33% in positive and negative ionization mode, respectively. By applying the CCS correction integrated into the tool for the exemplary data set, the mean absolute CCSN2 biases of 10 lipid classes could be reduced to approximately 0%.
Collapse
Affiliation(s)
- Felina Hildebrand
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- Vienna
Metabolomics Center (VIME), University of
Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Tim Causon
- BOKU
University, Department of Chemistry, Institute
of Analytical Chemistry, Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|
22
|
Habeck T, Brown KA, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W, Keener JE, Volny M, Wilson JW, Ying Y, Agar JN, Danis PO, Ge Y, Kelleher NL, Li H, Loo JA, Marty MT, Paša-Tolić L, Sandoval W, Lermyte F. Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nat Methods 2024:10.1038/s41592-024-02279-6. [PMID: 38744918 DOI: 10.1038/s41592-024-02279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.
Collapse
Affiliation(s)
- Tanja Habeck
- Technische Universität Darmstadt, Darmstadt, Germany
| | - Kyle A Brown
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, WA, USA
- Zhejiang University, Zhejiang, China
| | | | | | | | | | | | - Jesse W Wilson
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yujia Ying
- Sun Yat-sen University, Guangzhou, China
| | - Jeffrey N Agar
- Northeastern University, Boston, MA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Ying Ge
- University of Wisconsin-Madison, Madison, WI, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Neil L Kelleher
- Northwestern University, Evanston, IL, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Huilin Li
- Sun Yat-sen University, Guangzhou, China
| | - Joseph A Loo
- University of California, Los Angeles, CA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | | | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, WA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | | | | |
Collapse
|
23
|
York EM, Miller A, Stopka SA, Martínez-François JR, Hossain MA, Baquer G, Regan MS, Agar NYR, Yellen G. The dentate gyrus differentially metabolizes glucose and alternative fuels during rest and stimulation. J Neurochem 2024; 168:533-554. [PMID: 37929637 PMCID: PMC11070451 DOI: 10.1111/jnc.16004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/16/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023]
Abstract
The metabolic demands of neuronal activity are both temporally and spatially dynamic, and neurons are particularly sensitive to disruptions in fuel and oxygen supply. Glucose is considered an obligate fuel for supporting brain metabolism. Although alternative fuels are often available, the extent of their contribution to central carbon metabolism remains debated. Differential fuel metabolism likely depends on cell type, location, and activity state, complicating its study. While biosensors provide excellent spatial and temporal information, they are limited to observations of only a few metabolites. On the other hand, mass spectrometry is rich in chemical information, but traditionally relies on cell culture or homogenized tissue samples. Here, we use mass spectrometry imaging (MALDI-MSI) to focus on the fuel metabolism of the dentate granule cell (DGC) layer in murine hippocampal slices. Using stable isotopes, we explore labeling dynamics at baseline, as well as in response to brief stimulation or fuel competition. We find that at rest, glucose is the predominant fuel metabolized through glycolysis, with little to no measurable contribution from glycerol or fructose. However, lactate/pyruvate, β-hydroxybutyrate (βHB), octanoate, and glutamine can contribute to TCA metabolism to varying degrees. In response to brief depolarization with 50 mM KCl, glucose metabolism was preferentially increased relative to the metabolism of alternative fuels. With an increased supply of alternative fuels, both lactate/pyruvate and βHB can outcompete glucose for TCA cycle entry. While lactate/pyruvate modestly reduced glucose contribution to glycolysis, βHB caused little change in glycolysis. This approach achieves broad metabolite coverage from a spatially defined region of physiological tissue, in which metabolic states are rapidly preserved following experimental manipulation. Using this powerful methodology, we investigated metabolism within the dentate gyrus not only at rest, but also in response to the energetic demand of activation, and in states of fuel competition.
Collapse
Affiliation(s)
- Elisa M. York
- Department of Neurobiology, Harvard Medical School,
Boston, MA 02115 USA
| | - Anne Miller
- Department of Neurobiology, Harvard Medical School,
Boston, MA 02115 USA
| | - Sylwia A. Stopka
- Surgical Molecular Imaging Laboratory, Department of
Neurosurgery, Brigham and Women's Hospital; Department of Radiology, Brigham
and Women's Hospital; Department of Cancer Biology, Dana-Farber Cancer
Institute; Harvard Medical School, Boston, MA, 02115 USA
| | | | - Md Amin Hossain
- Surgical Molecular Imaging Laboratory, Department of
Neurosurgery, Brigham and Women's Hospital; Department of Radiology, Brigham
and Women's Hospital; Department of Cancer Biology, Dana-Farber Cancer
Institute; Harvard Medical School, Boston, MA, 02115 USA
| | - Gerard Baquer
- Surgical Molecular Imaging Laboratory, Department of
Neurosurgery, Brigham and Women's Hospital; Department of Radiology, Brigham
and Women's Hospital; Department of Cancer Biology, Dana-Farber Cancer
Institute; Harvard Medical School, Boston, MA, 02115 USA
| | - Michael S. Regan
- Surgical Molecular Imaging Laboratory, Department of
Neurosurgery, Brigham and Women's Hospital; Department of Radiology, Brigham
and Women's Hospital; Department of Cancer Biology, Dana-Farber Cancer
Institute; Harvard Medical School, Boston, MA, 02115 USA
| | - Nathalie Y. R. Agar
- Surgical Molecular Imaging Laboratory, Department of
Neurosurgery, Brigham and Women's Hospital; Department of Radiology, Brigham
and Women's Hospital; Department of Cancer Biology, Dana-Farber Cancer
Institute; Harvard Medical School, Boston, MA, 02115 USA
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School,
Boston, MA 02115 USA
| |
Collapse
|
24
|
Zimnicka MM. Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:526-559. [PMID: 37260128 DOI: 10.1002/mas.21851] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.
Collapse
Affiliation(s)
- Magdalena M Zimnicka
- Mass Spectrometry Group, Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
25
|
Gozzo TA, Bush MF. Effects of charge on protein ion structure: Lessons from cation-to-anion, proton-transfer reactions. MASS SPECTROMETRY REVIEWS 2024; 43:500-525. [PMID: 37129026 DOI: 10.1002/mas.21847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Collision cross-section values, which can be determined using ion mobility experiments, are sensitive to the structures of protein ions and useful for applications to structural biology and biophysics. Protein ions with different charge states can exhibit very different collision cross-section values, but a comprehensive understanding of this relationship remains elusive. Here, we review cation-to-anion, proton-transfer reactions (CAPTR), a method for generating a series of charge-reduced protein cations by reacting quadrupole-selected cations with even-electron monoanions. The resulting CAPTR products are analyzed using a combination of ion mobility, mass spectrometry, and collisional activation. We compare CAPTR to other charge-manipulation strategies and review the results of various CAPTR-based experiments, exploring their contribution to a deeper understanding of the relationship between protein ion structure and charge state.
Collapse
Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| |
Collapse
|
26
|
Kurilung A, Limjiasahapong S, Kaewnarin K, Wisanpitayakorn P, Jariyasopit N, Wanichthanarak K, Sartyoungkul S, Wong SCC, Sathirapongsasuti N, Kitiyakara C, Sirivatanauksorn Y, Khoomrung S. Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples. J Pharm Anal 2024; 14:100921. [PMID: 38799238 PMCID: PMC11127212 DOI: 10.1016/j.jpha.2023.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/17/2023] [Accepted: 12/13/2023] [Indexed: 05/29/2024] Open
Abstract
The collision cross-sections (CCS) measurement using ion mobility spectrometry (IMS) in combination with mass spectrometry (MS) offers a great opportunity to increase confidence in metabolite identification. However, owing to the lack of sensitivity and resolution, IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites (VLMs ≤ 250 Da). Here, we describe an analytical method using ultrahigh-performance liquid chromatography (UPLC) coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine samples. The experimental CCS values, along with mass spectral properties, were reported for the 174 metabolites. The experimental data included the mass-to-charge ratio (m/z), retention time (RT), tandem MS (MS/MS) spectra, and CCS values. Among the studied metabolites, 263 traveling wave ion mobility spectrometry (TWIMS)-derived CCS values (TWCCSN2) were reported for the first time, and more than 70% of these were CCS values of VLMs. The TWCCSN2 values were highly repeatable, with inter-day variations of <1% relative standard deviation (RSD). The developed method revealed excellent TWCCSN2 accuracy with a CCS difference (ΔCCS) within ±2% of the reported drift tube IMS (DTIMS) and TWIMS CCS values. The complexity of the urine matrix did not affect the precision of the method, as evidenced by ΔCCS within ±1.92%. According to the Metabolomics Standards Initiative, 55 urinary metabolites were identified with a confidence level of 1. Among these 55 metabolites, 53 (96%) were VLMs. The larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values, which clearly increased metabolite identification confidence.
Collapse
Affiliation(s)
- Alongkorn Kurilung
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Suphitcha Limjiasahapong
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Khwanta Kaewnarin
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- SingHealth Duke-NUS Institute of Biodiversity Medicine, National Cancer Centre Singapore, 168583, Singapore
| | - Pattipong Wisanpitayakorn
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Narumol Jariyasopit
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Kwanjeera Wanichthanarak
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sitanan Sartyoungkul
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | | | - Nuankanya Sathirapongsasuti
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, 10540, Thailand
| | - Chagriya Kitiyakara
- Department of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sakda Khoomrung
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| |
Collapse
|
27
|
Brodmerkel MN, Thiede L, De Santis E, Uetrecht C, Caleman C, Marklund EG. Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles. Phys Chem Chem Phys 2024; 26:13094-13105. [PMID: 38628116 DOI: 10.1039/d3cp06344e] [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: 05/02/2024]
Abstract
Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the gas-phase unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation, together with CIU experiments. The dimers have highly similar structures, but their CIU reveals different stability that can be explained by the different dynamics that arises in response to the activation seen in the simulations, including a part of the sequence with previously observed strain-specific dynamics in solution. Our findings show how similar protein variants can be examined using mass spectrometric techniques in conjunction with atomistic molecular dynamics simulations to reveal differences in stability as well as differences in how and where unfolding takes place upon activation.
Collapse
Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
| | - Lars Thiede
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
| |
Collapse
|
28
|
Ito R, Ohshimo K, Misaizu F. Intra-host π-π interactions in crown ether complexes revealed by cryogenic ion mobility-mass spectrometry. Phys Chem Chem Phys 2024; 26:12537-12544. [PMID: 38619106 DOI: 10.1039/d4cp00835a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Cryogenic ion mobility-mass spectrometry was performed to investigate the relative abundance of conformers of dinaphtho-24-crown-8 (DN24C8) complexes with alkali metal cations M+ (M = Li, Na, K, Rb, and Cs). The "closed" conformers of M+(DN24C8) with short distances between two naphthalene rings in the crown ethers were predominantly observed for all complexes at 86 K. The two noncovalent interactions, host-guest and intra-host interactions, were analyzed separately by density functional theory calculations to reveal the origin of the stability of the closed conformers. As a result, it was revealed that the intra-host π-π interactions have a more critical role in determining the stability of the conformers than the host-guest interactions. The closed conformers of M+(DN24C8) also have wider regions of the π-π interactions than those of the M+(dibenzo-24-crown-8) complexes.
Collapse
Affiliation(s)
- Ryosuke Ito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| |
Collapse
|
29
|
Critch-Doran O, Jenkins K, Hashemihedeshi M, Mommers AA, Green MK, Dorman FL, Jobst KJ. Toward Part-per-Million Precision in the Determination of an Ion's Collision Cross Section Using Multipass Cyclic Ion Mobility. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:775-783. [PMID: 38498916 DOI: 10.1021/jasms.4c00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
In cyclic ion mobility (cIMS), ions are permitted to travel multiple passes around the drift cell, increasing the distance traveled and the relative separation between ions. This study tests the hypothesis that multiple passes around the cell can also result in improved precision when measuring an ion's mobility and the collision cross section (TWCCS) derived therefrom. Experiments were performed with a diverse set of compounds, including 16 polycyclic aromatic hydrocarbons using gas chromatographic atmospheric pressure chemical ionization and a set of drug molecules by direct infusion electrospray ionization. The average periodic drift time, viz., the average time required for the ion to travel around the cIMS cell once, shifts dramatically, approaching part-per-million (ppm) precision as the number of passes increases to ∼100. Extrapolation of the precision of the CCS values with respect to the number of passes led to the prediction that the precision will reach 1000 ppm after 50 passes, 100 ppm after 100 passes, and <10 ppm after 150 passes. Experiments wherein the number of passes exceeded 100 produced TWCCS values having within-run precisions ranging between 15 and 117 ppm. The improved precision with an increasing number of passes may be a consequence of mitigating space-charge effects by allowing the ions to occupy a larger region of the cIMS cell. A method is proposed to enable practical measurements of TWCCS with ppm precision and is demonstrated to characterize an unknown drug mixture.
Collapse
Affiliation(s)
- Olivia Critch-Doran
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
| | - Kevin Jenkins
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
| | - Mahin Hashemihedeshi
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
| | - Alexander A Mommers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - M Kirk Green
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Frank L Dorman
- Department of Chemistry, Dartmouth College, Hannover, New Hampshire 03755, United States
- Waters Corporation, 34 Maple St., Milford, Massachusetts 01757, United States
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
| |
Collapse
|
30
|
Geue N, Winpenny REP, Barran PE. Ion Mobility Mass Spectrometry for Large Synthetic Molecules: Expanding the Analytical Toolbox. J Am Chem Soc 2024; 146:8800-8819. [PMID: 38498971 PMCID: PMC10996010 DOI: 10.1021/jacs.4c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024]
Abstract
Understanding the composition, structure and stability of larger synthetic molecules is crucial for their design, yet currently the analytical tools commonly used do not always provide this information. In this perspective, we show how ion mobility mass spectrometry (IM-MS), in combination with tandem mass spectrometry, complementary techniques and computational methods, can be used to structurally characterize synthetic molecules, make and predict new complexes, monitor disassembly processes and determine stability. Using IM-MS, we present an experimental and computational framework for the analysis and design of complex molecular architectures such as (metallo)supramolecular cages, nanoclusters, interlocked molecules, rotaxanes, dendrimers, polymers and host-guest complexes.
Collapse
Affiliation(s)
- Niklas Geue
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Richard E. P. Winpenny
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| |
Collapse
|
31
|
George AC, Schmitz I, Colsch B, Afonso C, Fenaille F, Loutelier-Bourhis C. Impact of Source Conditions on Collision Cross Section Determination by Trapped Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:696-704. [PMID: 38430122 DOI: 10.1021/jasms.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Collision cross section (CCS) values determined in ion mobility-mass spectrometry (IM-MS) are increasingly employed as additional descriptors in metabolomics studies. CCS values must therefore be reproducible and the causes of deviations must be carefully known and controlled. Here, we analyzed lipid standards by trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) to evaluate the effects of solvent and flow rate in flow injection analysis (FIA), as well as electrospray source parameters including nebulizer gas pressure, drying gas flow rate, and temperature, on the ion mobility and CCS values. The stability of ion mobility experiments was studied over 10 h, which established the need for a delay-time of 20 min to stabilize source parameters (mostly pressure and temperature). Modifications of electrospray source parameters induced shifts of ion mobility peaks and even the occurrence of an additional peak in the ion mobility spectra. This behavior could be essentially explained by ion-solvent cluster formation. Changes in source parameters were also found to impact CCS value measurements, resulting in deviations up to 0.8%. However, internal calibration with the Tune Mix calibrant reduced the CCS deviations to 0.1%. Thus, optimization of source parameters is essential to achieve a good desolvation of lipid ions and avoid misinterpretation of peaks in ion mobility spectra due to solvent effects. This work highlights the importance of internal calibration to ensure interoperable CCS values, usable in metabolomics annotation.
Collapse
Affiliation(s)
- Anaïs C George
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Isabelle Schmitz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - Benoit Colsch
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, F-91191 Gif sur Yvette, France
| | - Carlos Afonso
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| | - François Fenaille
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, F-91191 Gif sur Yvette, France
| | - Corinne Loutelier-Bourhis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France
| |
Collapse
|
32
|
Wang N, Dixit SM, Lee T, DeFiglia SA, Ruotolo BT, Håkansson K. Salt-Bridged Peptide Anion Gaseous Structures Enable Efficient Negative Ion Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:784-792. [PMID: 38489759 DOI: 10.1021/jasms.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
We previously discovered that electron attachment to gaseous peptide anions can occur within a relatively narrow electron energy range. The resulting charge-increased radical ions undergo dissociation analogous to conventional cation electron capture/transfer dissociation (ECD/ETD), thus enabling a novel tandem mass spectrometry (MS/MS) technique that we termed negative ion electron capture dissociation (niECD). We proposed that gaseous zwitterionic structures are required for niECD with electron capture either occurring at or being directed by a positively charged site. Here, we further evaluate this zwitterion mechanism by performing niECD of peptides derivatized to alter their ability to form zwitterionic gaseous structures. Introduction of a fixed positive charge tag, a highly basic guanidino group, or a highly acidic sulfonate group to promote zwitterionic structures in singly charged anions, rescued the niECD ability of a peptide refractory to niECD in its unmodified form. We also performed a systematic study of five sets of synthetic peptides with decreasing zwitterion propensity and found that niECD efficiency decreased accordingly, further supporting the zwitterion mechanism. However, traveling-wave ion mobility-mass spectrometry experiments, performed to gain further insight into the gas-phase structures of peptides showing high niECD efficiency, exhibited an inverse correlation between the orientationally averaged collision cross sections and niECD efficiency. These results indicate that compact salt-bridged structures are also a requirement for effective niECD.
Collapse
Affiliation(s)
- Ning Wang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Teresa Lee
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
33
|
Bechtella L, Chunsheng J, Fentker K, Ertürk GR, Safferthal M, Polewski Ł, Götze M, Graeber SY, Vos GM, Struwe WB, Mall MA, Mertins P, Karlsson NG, Pagel K. Ion mobility-tandem mass spectrometry of mucin-type O-glycans. Nat Commun 2024; 15:2611. [PMID: 38521783 PMCID: PMC10960840 DOI: 10.1038/s41467-024-46825-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
The dense O-glycosylation of mucins plays an important role in the defensive properties of the mucus hydrogel. Aberrant glycosylation is often correlated with inflammation and pathology such as COPD, cancer, and Crohn's disease. The inherent complexity of glycans and the diversity in the O-core structure constitute fundamental challenges for the analysis of mucin-type O-glycans. Due to coexistence of multiple isomers, multidimensional workflows such as LC-MS are required. To separate the highly polar carbohydrates, porous graphitized carbon is often used as a stationary phase. However, LC-MS workflows are time-consuming and lack reproducibility. Here we present a rapid alternative for separating and identifying O-glycans released from mucins based on trapped ion mobility mass spectrometry. Compared to established LC-MS, the acquisition time is reduced from an hour to two minutes. To test the validity, the developed workflow was applied to sputum samples from cystic fibrosis patients to map O-glycosylation features associated with disease.
Collapse
Affiliation(s)
- Leïla Bechtella
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Jin Chunsheng
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Fentker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Güney R Ertürk
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
| | - Marc Safferthal
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Łukasz Polewski
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Michael Götze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gaël M Vos
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Weston B Struwe
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany.
| |
Collapse
|
34
|
Thoben C, Stadtler JJ, Simon PR, Raddatz CR, Sehlmeyer M, Zimmermann S. Coated Blade Spray Ion Mobility Spectrometry. Anal Chem 2024; 96:3593-3599. [PMID: 38347729 PMCID: PMC10902811 DOI: 10.1021/acs.analchem.3c05586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/28/2024]
Abstract
Coated blade spray (CBS) is a microextraction technology with blades that serve as both the extraction device and the electrospray ionization (ESI) emitter. CBS is designed for easy and rapid extraction of analytes in complex matrices as well as ESI directly from the blade. The technology selectively enriches the components of interest on a coated metal blade. The coating consists of a selective polymer. So far, CBS has only been coupled with mass spectrometry but never with ion mobility spectrometry (IMS), where ions are separated and detected based on their ion mobility in a drift gas under the influence of an electric field, while instrumentation is compact and easy to operate so that the advantages of CBS can be particularly well exploited. Therefore, this work focuses on coupling CBS with our previously described ESI-IMS. The ion mobility spectrometer has a drift length of only 75 mm and provides a high resolving power of RP = 100. In this work, preliminary measurements of CBS-IMS are presented. In particular, the detection of benzodiazepines and ketamine in drinks and the pesticide isoproturon in water samples is shown to demonstrate the feasibility of CBS-IMS.
Collapse
Affiliation(s)
- Christian Thoben
- Institute of Electrical Engineering
and Measurement Technology, Department of Sensors and Measurement
Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Jannie J. Stadtler
- Institute of Electrical Engineering
and Measurement Technology, Department of Sensors and Measurement
Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Paul R. Simon
- Institute of Electrical Engineering
and Measurement Technology, Department of Sensors and Measurement
Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, 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
| | - Merle Sehlmeyer
- Institute of Electrical Engineering
and Measurement Technology, Department of Sensors and Measurement
Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering
and Measurement Technology, Department of Sensors and Measurement
Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| |
Collapse
|
35
|
Chung NA, May JC, Robinson RAS, McLean JA. Solvent Composition Can Have a Measurable Influence on the Ion Mobility-Derived Collision Cross Section of Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:234-243. [PMID: 38082535 DOI: 10.1021/jasms.3c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Ion mobility (IM) is an important analytical technique for increasing identification coverage of metabolites in untargeted studies, especially when integrated into traditional liquid chromatography-mass spectrometry workflows. While there has been extensive work surrounding best practices to obtain and standardize collision cross section (CCS) measurements necessary for comparing across different IM techniques and laboratories, there has been little investigation into experimental factors beyond the mobility separation region that could potentially influence CCS measurements. The first-principles derived CCS of 15 chemical standards were evaluated across 27 aqueous:organic solvent compositions using a high-precision drift tube instrument. A small but measurable dependency of the CCS on the solvent composition was observed, with the larger analytes from this study (m/z > 400) exhibiting a characteristic increase in CCS at the intermediate (40-60%) solvent compositions. Parallels to the behavior of solvent viscosity and protonation site tautomers (protomers) were noted, although the origin of these solvent-dependent CCS trends is as yet unclear. Taken together, these findings document a solvent dependency on CCS, which, while minor (<0.5%), identifies an important need for reporting the solvent system when utilizing CCS in comparative ion mobility studies.
Collapse
Affiliation(s)
- Nadjali A Chung
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jody C May
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A McLean
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
36
|
Li Y, Bai J, Tseng K, Zhang X, Zhang L, Zhang J, Sun W, Guo Y. Intramolecular Ring-Chain Equilibrium Elimination Strategy for Pinpointing C═C Positional and Geometric Isomers of N-Alkylpyridinium Unsaturated Fatty Acid Derivatives via Ion Mobility-Mass Spectrometry. Anal Chem 2024; 96:1977-1984. [PMID: 38258619 DOI: 10.1021/acs.analchem.3c04320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Free unsaturated fatty acids (UFA) are key intermediates of lipid metabolism and participate in many metabolic pathways with specific biological functions. Although various fragmentation-based methods for pinpointing C═C locations in UFA were developed, the current mass spectrometry methods are difficult to simultaneously differentiate geometric isomers and positional isomers in trace samples due to low ionization efficiency, low conversion, and low resolution. Herein, an intramolecular ring-chain equilibrium elimination strategy via 4-plex stable isotope labeling dual derivatization-assisted ion mobility-mass spectrometry was developed, thereby one-pot specifically labeling C═C and carboxyl groups among the trace and unstable UFA with high sensitivity, high efficiency, and good substrate generality. It achieved fast separation of both C═C positional and geometric isomers with high resolution, which benefited from eliminating the intramolecular ring-chain equilibrium by suppressing the formation of salt bridges between free carboxyl groups and pyridine cations. 4-plex stable isotope labeling reagents showed similar reactivity, enabling high-throughput quantitative analysis of omics. This method was successfully applied for accurate and rapid identification of the UFA composition in olive oil extract. These results suggest that the developed method provides new insight for rapid characterization of UFA C═C positional and geometric isomers in complex samples to explore disease biomarkers and food quality control indicators.
Collapse
Affiliation(s)
- Yuling Li
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Shimadzu Research Laboratory (Shanghai) Co. Ltd., Shanghai 201206, China
| | - Jiahui Bai
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kuofeng Tseng
- Shimadzu Research Laboratory (Shanghai) Co. Ltd., Shanghai 201206, China
| | - Xiaoqiang Zhang
- Shimadzu Research Laboratory (Shanghai) Co. Ltd., Shanghai 201206, China
| | - Li Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjian Sun
- Shimadzu Research Laboratory (Shanghai) Co. Ltd., Shanghai 201206, China
| | - Yinlong Guo
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
37
|
Briš A, Baltussen MG, Tripodi GL, Huck WTS, Franceschi P, Roithová J. Direct Analysis of Complex Reaction Mixtures: Formose Reaction. Angew Chem Int Ed Engl 2024; 63:e202316621. [PMID: 38100204 DOI: 10.1002/anie.202316621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Indexed: 12/31/2023]
Abstract
Complex reaction mixtures, like those postulated on early Earth, present an analytical challenge because of the number of components, their similarity, and vastly different concentrations. Interpreting the reaction networks is typically based on simplified or partial data, limiting our insight. We present a new approach based on online monitoring of reaction mixtures formed by the formose reaction by ion-mobility-separation mass-spectrometry. Monitoring the reaction mixtures led to large data sets that we analyzed by non-negative matrix factorization, thereby identifying ion-signal groups capturing the time evolution of the network. The groups comprised ≈300 major ion signals corresponding to sugar-calcium complexes formed during the formose reaction. Multivariate analysis of the kinetic profiles of these complexes provided an overview of the interconnected kinetic processes in the solution, highlighting different pathways for sugar growth and the effects of different initiators on the initial kinetics. Reconstructing the network's topology further, we revealed so far unnoticed fast retro-aldol reaction of ketoses, which significantly affects the initial reaction dynamics. We also detected the onset of sugar-backbone branching for C6 sugars and cyclization reactions starting for C5 sugars. This top-down analytical approach opens a new way to analyze complex dynamic mixtures online with unprecedented coverage and time resolution.
Collapse
Affiliation(s)
- Anamarija Briš
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
- Laboratory for physical-organic chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Mathieu G Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Guilherme L Tripodi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Pietro Franceschi
- Research and innovation Centre, Fondazione E. Mach, Via Edmund Mach, 1, 38098, San Michele All'adige TN, Italy
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| |
Collapse
|
38
|
Chatterjee P, Dutta SS, Agarwal M, Dey S, Chakraborty T. UV-A-Induced Photoisomerization and Photodimerization of Curcumin: An Ion Mobility Mass Spectrometry Study. J Phys Chem A 2024; 128:548-562. [PMID: 38206070 DOI: 10.1021/acs.jpca.3c05933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Curcumin, the bioactive compound present in spice plant turmeric, has been shown to exhibit selective phototoxic activities toward mammalian cancer cells, and it is being used extensively as a photosensitizer (PS) in photodynamic therapies (PDT). However, so far, the fate of curcumin toward photochemical transformations is not well understood. Here we report our findings of a number of novel photochemical reaction channels of curcumin in water-methanol mixture, like photoisomerization, photodimerization, and photooxidation (H2-loss). The reaction was performed by irradiating the curcumin solution with ultraviolet (UV) light of wavelength 350 nm, which is abundant in the earth's troposphere. Product identification and structure elucidation are done by employing an integrated method of drift tube ion mobility mass spectrometry (DTIMS) in combination with high-performance liquid chromatography (HPLC) and collision-induced dissociation (CID) of the mass-selected molecular ions. Two photoisomers of curcumin produced as a result of trans-cis configurational changes about C═C double bonds in the excited state have been identified, and it has been shown that they could serve as the precursors for formation of isomeric dimers via [2 + 2] cycloaddition and H2-loss products. Comparisons of the experimentally measured collision cross-section (CCS) values of the reactant and product ions obtained by the DTIMS method with those predicted by the electronic structure theory are found to be very effective for the discrimination of the produced photoisomers. The observed photochemical reaction channels are potentially significant toward uses of curcumin as a photosensitizer in photodynamic therapy.
Collapse
Affiliation(s)
- Piyali Chatterjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhra Sankar Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Megha Agarwal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Supriyo Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| |
Collapse
|
39
|
Agostini M, Traldi P, Hamdan M. Mass Spectrometry Investigation of Some ATP-Binding Cassette (ABC) Proteins. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:200. [PMID: 38399488 PMCID: PMC10890348 DOI: 10.3390/medicina60020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
Drug resistance remains one of the main causes of poor outcome in cancer therapy. It is also becoming evident that drug resistance to both chemotherapy and to antibiotics is driven by more than one mechanism. So far, there are at least eight recognized mechanisms behind such resistance. In this review, we choose to discuss one of these mechanisms, which is known to be partially driven by a class of transmembrane proteins known as ATP-binding cassette (ABC) transporters. In normal tissues, ABC transporters protect the cells from the toxic effects of xenobiotics, whereas in tumor cells, they reduce the intracellular concentrations of anticancer drugs, which ultimately leads to the emergence of multidrug resistance (MDR). A deeper understanding of the structures and the biology of these proteins is central to current efforts to circumvent resistance to both chemotherapy, targeted therapy, and antibiotics. Understanding the biology and the function of these proteins requires detailed structural and conformational information for this class of membrane proteins. For many years, such structural information has been mainly provided by X-ray crystallography and cryo-electron microscopy. More recently, mass spectrometry-based methods assumed an important role in the area of structural and conformational characterization of this class of proteins. The contribution of this technique to structural biology has been enhanced by its combination with liquid chromatography and ion mobility, as well as more refined labelling protocols and the use of more efficient fragmentation methods, which allow the detection and localization of labile post-translational modifications. In this review, we discuss the contribution of mass spectrometry to efforts to characterize some members of the ATP-binding cassette (ABC) proteins and why such a contribution is relevant to efforts to clarify the link between the overexpression of these proteins and the most widespread mechanism of chemoresistance.
Collapse
Affiliation(s)
| | - Pietro Traldi
- Corso Stati Uniti 4, Istituto di Ricerca Pediatrica Città della Speranza, 35100 Padova, Italy; (M.A.)
| | | |
Collapse
|
40
|
Villacob RA, Feizi N, Beno SC, Solouki T. Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:13-30. [PMID: 38095581 DOI: 10.1021/jasms.3c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.
Collapse
Affiliation(s)
- Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Neda Feizi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sarah C Beno
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| |
Collapse
|
41
|
Ibáñez-Ibáñez L, Mollar-Cuni A, Apaloo-Messan E, Sharma AK, Mata JA, Maseras F, Vicent C. Ion mobility mass spectrometry uncovers regioselectivity in the carboxylate-assisted C-H activation of palladium N-heterocyclic carbene complexes. Dalton Trans 2024; 53:656-665. [PMID: 38073605 DOI: 10.1039/d3dt02793g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Carboxylate-assisted Pd-catalyzed C-H bond activation constitutes a mild and versatile synthetic tool to efficiently and selectively cleave inert C-H bonds. Herein, we demonstrate a simple method to experimentally evaluate both reactivity and selectivity in such systems using mass spectrometry (MS) methods. The N-heterocyclic carbene (NHC) cations [(NHC)PdX]+, bearing as X- ligand bases commonly used to promote the C-H activation (carboxylates and bicarbonate), are generated in the gas-phase by ESI-MS. Their C-H bond activation at the N-bound groups of the NHC is then studied using Collision Induced Dissociation (CID) experiments. Ion Mobility Spectrometry (IM)-MS is exploited to identify a number of regioisomers associated with the distinctive site selective C-H activations. It is demonstrated that such C-H activation concomitant with acetic acid release occurs from a mixture of activated [(NHC-H)Pd(CH3CO2H)]+ and non-activated [(NHC)Pd(CH3CO2)]+ complexes. The identity of the X-type ligands (X = Cl-, carboxylates and bicarbonate) has a significant impact on the regioisomer branching ratio upon CID conditions. IM-MS in conjunction with a DFT mechanistic study is presented for the acetate-assisted C-H activation of the [(NHC)Pd(CH3CO2)]+ cation featuring butyl and aryl as N-donor groups.
Collapse
Affiliation(s)
- Laura Ibáñez-Ibáñez
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Andres Mollar-Cuni
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Edmond Apaloo-Messan
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Akhilesh K Sharma
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Jose A Mata
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Cristian Vicent
- Serveis Centrals d'Instrumentació Científica (SCIC). Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| |
Collapse
|
42
|
Zercher BP, Feng Y, Bush MF. Towards IM n with Electrostatic Drift Fields: Resetting the Potential of Trapped Ions Between Dimensions of Ion Mobility. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117163. [PMID: 37928050 PMCID: PMC10621600 DOI: 10.1016/j.ijms.2023.117163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Increasing the dimensionality of ion mobility (IM) presents an enticing opportunity to increase the information content and selectivity of many analyses. However, for implementations of IM that use constant electrostatic gradients to separate ions in a buffer gas, technical challenges have limited the adoption of the technique and number of dimensions within individual experiments. Here, we introduce a strategy to "reset" the potentials of ions between IM dimensions. To achieve this, mobility-selected ions are trapped between dimensions of IM, using a combination of RF and electrostatic fields, while the subsequent dimension of IM is devoid of any drift field. By applying an incremental voltage ramp, the potential of the trapping region is elevated, simultaneously establishing the drift field in the subsequent dimension of IM. The trapped ions are then released and separated. We measured similar arrival-time distributions of protein ions using this strategy and a method without potential resetting, suggesting that potential resetting can be performed without additional losses or activation of ions. The findings of those experiments were corroborated by ion trajectory simulations, which exhibited a very small changes in ion position and no significant changes in effective temperatures during potential resetting. Finally, we demonstrate that IM information can be preserved during potential resetting by selecting subpopulations of 9+ cytochrome c ions, resetting their potential, subjecting them to a second-dimension IM separation, and observing the retention of conformers within each subpopulation. We anticipate that this strategy will be useful for advancing flexible, multidimensional experiments on electrostatic IM instruments.
Collapse
Affiliation(s)
- Benjamin P. Zercher
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| |
Collapse
|
43
|
Vickers S, Irving J, Lomas DA, Thalassinos K. Native and Ion Mobility Mass Spectrometry Characterization of Alpha 1 Antitrypsin Variants and Oligomers. Methods Mol Biol 2024; 2750:41-55. [PMID: 38108966 DOI: 10.1007/978-1-0716-3605-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In this chapter, we describe a method for analyzing both recombinant and plasma-derived alpha 1 antitrypsin and its oligomers by means of native ion mobility mass spectrometry. Our experimental workflow can be applied to other variants of alpha 1 antitrypsin and its oligomers as well as being used to probe their interactions with small molecules in the gas phase.
Collapse
Affiliation(s)
- Sarah Vickers
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - James Irving
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- UCL Respiratory, University College London, London, UK
| | - David A Lomas
- UCL Respiratory, University College London, London, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.
| |
Collapse
|
44
|
Bell DJ, Zhang T, Geue N, Rogers CJ, Barran PE, Bowen AM, Natrajan LS, Riddell IA. Hexanuclear Ln 6 L 6 Complex Formation by Using an Unsymmetric Ligand. Chemistry 2023; 29:e202302497. [PMID: 37733973 PMCID: PMC10946940 DOI: 10.1002/chem.202302497] [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: 08/01/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 09/23/2023]
Abstract
Multinuclear, self-assembled lanthanide complexes present clear opportunities as sensors and imaging agents. Despite the widely acknowledged potential of this class of supramolecule, synthetic and characterization challenges continue to limit systematic studies into their self-assembly restricting the number and variety of lanthanide architectures reported relative to their transition metal counterparts. Here we present the first study evaluating the effect of ligand backbone symmetry on multinuclear lanthanide complex self-assembly. Replacement of a symmetric ethylene linker with an unsymmetric amide at the center of a homoditopic ligand governs formation of an unusual Ln6 L6 complex with coordinatively unsaturated metal centers. The choice of triflate as a counterion, and the effect of ionic radii are shown to be critical for formation of the Ln6 L6 complex. The atypical Ln6 L6 architecture is characterized using a combination of mass spectrometry, luminescence, DOSY NMR and EPR spectroscopy measurements. Luminescence experiments support clear differences between comparable Eu6 L6 and Eu2 L3 complexes, with relatively short luminescent lifetimes and low quantum yields observed for the Eu6 L6 structure indicative of non-radiative decay processes. Synthesis of the Gd6 L6 analogue allows three distinct Gd⋯Gd distance measurements to be extracted using homo-RIDME EPR experiments.
Collapse
Affiliation(s)
- Daniel J. Bell
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Tongtong Zhang
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- Michael Barber Centre for Collaborative Mass SpectrometryDepartment of ChemistryThe University of Manchester131 Princess StreetManchesterM17DNUK
| | - Niklas Geue
- Michael Barber Centre for Collaborative Mass SpectrometryDepartment of ChemistryThe University of Manchester131 Princess StreetManchesterM17DNUK
| | - Ciarán J. Rogers
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- National Research Facility for Electron Paramagnetic ResonancePhoton Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass SpectrometryDepartment of ChemistryThe University of Manchester131 Princess StreetManchesterM17DNUK
| | - Alice M. Bowen
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- National Research Facility for Electron Paramagnetic ResonancePhoton Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Louise S. Natrajan
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Imogen A. Riddell
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| |
Collapse
|
45
|
Duez Q, Marek L, Váňa J, Hanusek J, Roithová J. Autocatalysis in Eschenmoser Coupling Reactions. Chemistry 2023:e202303619. [PMID: 38088237 DOI: 10.1002/chem.202303619] [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: 11/01/2023] [Indexed: 12/22/2023]
Abstract
The Eschenmoser coupling reaction (ECR) of thioamides with electrophiles is believed to proceed via thiirane intermediates. However, little is known about converting the intermediates into ECR products. Previous mechanistic studies involved external thiophiles to remove the sulfur atom from the intermediates. In this work, an ECR proceeding without any thiophilic agent or base is studied by electrospray ionization-mass spectrometry. ESI-MS enables the detection of the so-far elusive polysulfide species Sn , with n ranging from 2 to 16 sulfur atoms, proposed to be the key species leading to product formation. Integrating observations from ion mobility spectrometry, ion spectroscopy, and reaction monitoring via flow chemistry coupled with mass spectrometry provides a comprehensive understanding of the reaction mechanism and uncovers the autocatalytic nature of the ECR reaction.
Collapse
Affiliation(s)
- Quentin Duez
- Institute for Molecules and Materials, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lukáš Marek
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ532 10, Pardubice, The Czech Republic
| | - Jiří Váňa
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ532 10, Pardubice, The Czech Republic
| | - Jiří Hanusek
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ532 10, Pardubice, The Czech Republic
| | - Jana Roithová
- Institute for Molecules and Materials, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| |
Collapse
|
46
|
Will A, Oliinyk D, Bleiholder C, Meier F. Peptide collision cross sections of 22 post-translational modifications. Anal Bioanal Chem 2023; 415:6633-6645. [PMID: 37758903 PMCID: PMC10598134 DOI: 10.1007/s00216-023-04957-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.
Collapse
Affiliation(s)
- Andreas Will
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Denys Oliinyk
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32304, USA
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
| |
Collapse
|
47
|
Schramm HM, Tamadate T, Hogan CJ, Clowers BH. Evaluation of Hydrogen-Deuterium Exchange during Transient Vapor Binding of MeOD with Model Peptide Systems Angiotensin II and Bradykinin. J Phys Chem A 2023; 127:8849-8861. [PMID: 37827113 DOI: 10.1021/acs.jpca.3c04608] [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: 10/14/2023]
Abstract
The advancement of hybrid mass spectrometric tools as an indirect probe of molecular structure and dynamics relies heavily upon a clear understanding between gas-phase ion reactivity and ion structural characteristics. This work provides new insights into gas-phase ion-neutral reactions of the model peptides (i.e., angiotensin II and bradykinin) on a per-residue basis by integrating hydrogen/deuterium exchange, ion mobility, tandem mass spectrometry, selective vapor binding, and molecular dynamics simulations. By comparing fragmentation patterns with simulated probabilities of vapor uptake, a clear link between gas-phase hydrogen/deuterium exchange and the probabilities of localized vapor association is established. The observed molecular dynamics trends related to the sites and duration of vapor binding track closely with experimental observation. Additionally, the influence of additional charges and structural characteristics on exchange kinetics and ion-neutral cluster formation is examined. These data provide a foundation for the analysis of solvation dynamics of larger, native-like conformations of proteins in the gas phase.
Collapse
Affiliation(s)
- Haley M Schramm
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Tomoya Tamadate
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
| |
Collapse
|
48
|
Riboni N, Bianchi F, Mattarozzi M, Caldara M, Gullì M, Graziano S, Maestri E, Marmiroli N, Careri M. Ultra-high Performance Liquid Chromatography-Ion Mobility-High-Resolution Mass Spectrometry to Evaluate the Metabolomic Response of Durum Wheat to Sustainable Treatments. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15407-15416. [PMID: 37796632 PMCID: PMC10591464 DOI: 10.1021/acs.jafc.3c04532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
Sustainable agriculture aims at achieving a healthy food production while reducing the use of fertilizers and greenhouse gas emissions using biostimulants and soil amendments. Untargeted metabolomics by ultra-high performance liquid chromatography-ion mobility-high-resolution mass spectrometry, operating in a high-definition MSE mode, was applied to investigate the metabolome of durum wheat in response to sustainable treatments, i.e., the addition of biochar, commercial plant growth promoting microbes, and their combination. Partial least squares-discriminant analysis provided a good discrimination among treatments with sensitivity, specificity, and a non-error rate close to 1. A total of 88 and 45 discriminant compounds having biological, nutritional, and technological implications were tentatively identified in samples grown in 2020 and 2021. The addition of biochar-biostimulants produced the highest up-regulation of lipids and flavonoids, with the glycolipid desaturation being the most impacted pathway, whereas carbohydrates were mostly down-regulated. The findings achieved suggest the safe use of the combined biochar-biostimulant treatment for sustainable wheat cultivation.
Collapse
Affiliation(s)
- Nicolò Riboni
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
| | - Federica Bianchi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Center
for Energy and Environment (CIDEA), Centro Santa Elisabetta, University of Parma, Parco Area delle Scienze 95, 43124 Parma, Italy
| | - Monica Mattarozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Marina Caldara
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
| | - Mariolina Gullì
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Sara Graziano
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Elena Maestri
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Centro
Santa Elisabetta, National Interuniversity
Center for Environmental Sciences (CINSA), Parco Area delle Scienze 95, 43124 Parma, Italy
| | - Maria Careri
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| |
Collapse
|
49
|
Miller A, York EM, Stopka SA, Martínez-François JR, Hossain MA, Baquer G, Regan MS, Agar NYR, Yellen G. Spatially resolved metabolomics and isotope tracing reveal dynamic metabolic responses of dentate granule neurons with acute stimulation. Nat Metab 2023; 5:1820-1835. [PMID: 37798473 PMCID: PMC10626993 DOI: 10.1038/s42255-023-00890-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 08/09/2023] [Indexed: 10/07/2023]
Abstract
Neuronal activity creates an intense energy demand that must be met by rapid metabolic responses. To investigate metabolic adaptations in the neuron-enriched dentate granule cell (DGC) layer within its native tissue environment, we employed murine acute hippocampal brain slices, coupled with fast metabolite preservation and followed by mass spectrometry (MS) imaging, to generate spatially resolved metabolomics and isotope-tracing data. Here we show that membrane depolarization induces broad metabolic changes, including increased glycolytic activity in DGCs. Increased glucose metabolism in response to stimulation is accompanied by mobilization of endogenous inosine into pentose phosphates via the action of purine nucleotide phosphorylase (PNP). The PNP reaction is an integral part of the neuronal response to stimulation, because inhibition of PNP leaves DGCs energetically impaired during recovery from strong activation. Performing MS imaging on brain slices bridges the gap between live-cell physiology and the deep chemical analysis enabled by MS.
Collapse
Affiliation(s)
- Anne Miller
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Elisa M York
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Md Amin Hossain
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gerard Baquer
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
50
|
Edwards AN, Blue AJ, Conforti JM, Cordes MS, Trakselis MA, Gallagher ES. Gas-phase stability and thermodynamics of ligand-bound, binary complexes of chloramphenicol acetyltransferase reveal negative cooperativity. Anal Bioanal Chem 2023; 415:6201-6212. [PMID: 37542535 DOI: 10.1007/s00216-023-04891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
The biological role of the bacterial chloramphenicol (Chl)-resistance enzyme, chloramphenicol acetyltransferase (CAT), has seen renewed interest due to the resurgent use of Chl against multi-drug-resistant microbes. This looming threat calls for more rationally designed antibiotic derivatives that have improved antimicrobial properties and reduced toxicity in humans. Herein, we utilize native ion mobility spectrometry-mass spectrometry (IMS-MS) to investigate the gas-phase structure and thermodynamic stability of the type I variant of CAT from Escherichia coli (EcCATI) and several EcCATI:ligand-bound complexes. EcCATI readily binds multiple Chl without incurring significant changes to its gas-phase structure or stability. A non-hydrolyzable acetyl-CoA derivative (S-ethyl-CoA, S-Et-CoA) was used to kinetically trap EcCATI and Chl in a ternary, ligand-bound state (EcCATI:S-Et-CoA:Chl). Using collision-induced unfolding (CIU)-IMS-MS, we find that Chl dissociates from EcCATI:S-Et-CoA:Chl complexes at low collision energies, while S-Et-CoA remains bound to EcCATI even as protein unfolding occurs. Gas-phase binding constants further suggest that EcCATI binds S-Et-CoA more tightly than Chl. Both ligands exhibit negative cooperativity of subsequent ligand binding in their respective binary complexes. While we observe no significant change in structure or stability to EcCATI when bound to either or both ligands, we have elucidated novel gas-phase unfolding and dissociation behavior and provided a foundation for further characterization of alternative substrates and/or inhibitors of EcCATI.
Collapse
Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Anthony J Blue
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Jessica M Conforti
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
| |
Collapse
|