1
|
Sarbu M, Seidler DG, Clemmer DE, Zamfir AD. Introducing Ion Mobility Mass Spectrometry in Brain Glycosaminoglycomics: Application to Chondroitin/Dermatan Sulfate Octasaccharide Domains. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2102-2117. [PMID: 39178342 DOI: 10.1021/jasms.4c00159] [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: 08/25/2024]
Abstract
Glycosaminoglycans (GAGs) are sulfated linear O-glycan chains abundantly expressed in the extracellular matrix (ECM). Among GAGs, chondroitin sulfate (CS) and dermatan sulfate (DS) play important roles at the brain level, where the distribution and location of the sulfates within the CS/DS chains are responsible for numerous biological events. The diversity of the neural hybrid CS/DS expressed in the brain and the need to elucidate their structure gave rise to considerable efforts toward the development of analytical methods able to discover novel regularly and irregularly sulfated domains. In this context, we report here the introduction of ion mobility separation (IMS) mass spectrometry (MS) in brain glycosaminoglycomics. Based on IMS MS and tandem MS (MS/MS) by collision-induced dissociation (CID), we have developed a powerful approach for the screening and structural analysis of neural CS/DS and optimized and validated the method for the structural analysis of octasaccharides that were released from brain proteoglycans by β-elimination and pooled after chain depolymerization using chondroitin AC lyase. The IMS MS data revealed the separation of CS/DS octamers into mobility families based on the amount of sulfation. Among the discovered oversulfated domains, of major biological importance is the pentasulfated-[4,5-Δ-GlcAGalNAc(IdoAGalNAc)3], for which the (-) nanoESI IMS CID MS/MS analysis disclosed through the presence of distinct drift times, the incidence of two isomers. Moreover, the generated fragment ions revealed an uncommon trisulfated motif and an uncommon pentasulfated motif. Hence, using IMS MS and CID MS/MS, novel brain-related CS/DS domains of atypical sulfation patterns were discovered and structurally characterized in detail.
Collapse
Affiliation(s)
- Mirela Sarbu
- Department of Condensed Matter, National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara 300224, Romania
| | | | - David E Clemmer
- Department of Chemistry, The College of Arts & Science, Indiana University, Bloomington, Indiana 47405, United States
| | - Alina D Zamfir
- Department of Condensed Matter, National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara 300224, Romania
- Department of Technical and Natural Sciences, "Aurel Vlaicu" University of Arad, Arad 310330, Romania
| |
Collapse
|
2
|
Liu R, Lu G, Hu X, Li J, Zhang Z, Tang K. Capillary zone electrophoresis-tandem mass spectrometry for in-depth proteomics analysis via data-independent acquisition. Anal Bioanal Chem 2024:10.1007/s00216-024-05502-7. [PMID: 39196334 DOI: 10.1007/s00216-024-05502-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024]
Abstract
A capillary zone electrophoresis (CZE) system was coupled to an Orbitrap mass spectrometer operating in a data-independent acquisition (DIA) mode for in-depth proteomics analysis. The performance of this CZE-DIA-MS system was systemically evaluated and optimized under different operating conditions. The performance of the fully optimized CZE-DIA-MS system was subsequently compared to the one by using the same CZE-MS system operating in a data-dependent acquisition (DDA) mode. The experimental results show that the numbers of identified peptides and proteins acquired in the DIA mode are much higher than the ones acquired in the DDA mode, especially with the small sample loading amount. Specifically, the numbers of identified peptides and proteins acquired in the DIA mode are 1.8-fold and 2-fold higher than the ones acquired in the DDA mode by using 12.5 ng Hela digests. The proteins identified in the DIA mode also cover almost all the proteins identified in the DDA mode. In addition, a potential cancer biomarker protein, carbohydrate antigen 125, undetected in the DDA mode, can be easily identified in the DIA mode even with 12.5 ng Hela digests. The performance of the CZE-DIA-MS system for in-depth proteomics analysis with a limited sample amount has been fully demonstrated for the first time through this study.
Collapse
Affiliation(s)
- Rong Liu
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Gang Lu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, PR China
| | - Xiaozhong Hu
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Junhui Li
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Zhenbin Zhang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, PR China
| | - Keqi Tang
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, PR China.
- Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China.
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| |
Collapse
|
3
|
Li J, Liu R, Hu Z, Fu S, Yu J, Tang K. Racetrack FAIMS for High-Resolution and High-Sensitivity Characterization of Peptide Conformers. Anal Chem 2024. [PMID: 39153009 DOI: 10.1021/acs.analchem.4c02750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Abstract
A racetrack field asymmetric waveform ion mobility spectrometry (r-FAIMS) device, which consists of both cylindrical FAIMS (c-FAIMS) and planar FAIMS (p-FAIMS) sections with a 1 mm gap width, was developed and applied for high-resolution and high-sensitivity exploration of conformational diversity for peptides. The optimal operating conditions of r-FAIMS were systemically studied, and the performance of the fully optimized r-FAIMS was compared to a previously developed p-FAIMS in detail by using pure nitrogen as the FAIMS carrier gas. Relying on the ion focusing effect in the c-FAIMS section, the intensity of the FAIMS spectrum for doubly charged bradykinin ions acquired by using r-FAIMS is ∼8.5-fold higher than that acquired by using p-FAIMS under the same resolving power/resolution condition, implying about an order of magnitude better sensitivity of r-FAIMS. In addition, the peak separation resolution of r-FAIMS was ∼1.70-fold higher than p-FAIMS under a similar sensitivity condition for doubly charged bradykinin ions. Due to a reduced gap width of the newly designed r-FAIMS (1 mm) as compared to the previously developed p-FAIMS (1.88 mm), r-FAIMS can operate at a much higher separation field with a similar FAIMS dispersion voltage (DV) to gain significantly higher resolving power. For triply charged syntide 2 ions, the resolving power of r-FAIMS can easily exceed 120 at -3.5 kV DV by using pure nitrogen as the FAIMS carrier gas as compared to 44.2 resolving power obtained by using p-FAIMS at -4.0 kV DV. All of the experimental results have confirmed that r-FAIMS can perform structural characterization of biomolecules with both high resolution and high sensitivity.
Collapse
Affiliation(s)
- Junhui Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, P. R. China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| | - Rong Liu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, P. R. China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| | - Zhonghan Hu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, P. R. China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| | - Shoushuai Fu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, P. R. China
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Jiancheng Yu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, P. R. China
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, P. R. China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P. R. China
| |
Collapse
|
4
|
Hu X, Zhou J, Li J, Gao W, Zhou J, Yu J, Tang K. An improved algorithm for resolving overlapping peaks in ion mobility spectrometry and its application to the separation of glycan isomers. Analyst 2023; 148:5514-5524. [PMID: 37791632 DOI: 10.1039/d3an01042b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Despite the popularity of ion mobility spectrometry (IMS) for glycan analysis, its limited structural resolution hinders the effective separation of many glycan isomers. This leads to the overlap of IMS peaks, consequently impacting the accurate identification of glycan compositions. To this end, an improved algorithm, namely second-order differentiation combined with a simulated annealing particle swarm optimization algorithm based on sine adaptive weights (DWSA-PSO), was proposed for the separation of overlapping IMS peaks formed by glycan isomers. DWSA-PSO first performed second-order differentiation to automatically determine the number of components in overlapping peaks and exclude impossible single-peak combinations. It then introduced sinusoidal adaptive weights and a simulated annealing mechanism to improve the algorithm's search capability and global optimization performance, thereby enabling accurate and efficient separation of individual peaks. To evaluate the performance of DWSA-PSO and its application to the separation of glycan isomers, multiple sets of overlapping peaks with different degrees of overlap were simulated, and various types of multi-component overlapping peaks were formed using six disaccharide and four trisaccharide isomers. The experimental results consistently demonstrated that the DWSA-PSO algorithm outperformed both the improved particle swarm optimization (IPSO) algorithm and the dynamic inertia weight particle swarm optimization (DIWPSO) algorithm in terms of separation accuracy, running time, and fitness values. In addition, the DWSA-PSO algorithm was successfully applied to the separation of glycan isomers in malt milk beverage. All these results reveal the capability of the DWSA-PSO algorithm to facilitate the accurate identification of glycan isomers.
Collapse
Affiliation(s)
- Xiangyang Hu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, P. R. China.
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, P. R. China.
| | - Junfei Zhou
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, P. R. China.
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, P. R. China.
| | - Junhui Li
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, P. R. China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, P.R. China
| | - Wenqing Gao
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, P. R. China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, P.R. China
| | - Jun Zhou
- Zhejiang Ningbo Ecological and Environmental Monitoring Center, Ningbo, P.R. China.
| | - Jiancheng Yu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, P. R. China.
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, P. R. China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, P.R. China
| | - Keqi Tang
- Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, P. R. China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, P.R. China
| |
Collapse
|
5
|
Long CC, Antevska A, Mast DH, Okyem S, Sweedler JV, Do TD. Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1898-1907. [PMID: 37102735 PMCID: PMC10524105 DOI: 10.1021/jasms.3c00092] [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: 06/19/2023]
Abstract
Posttranslational modifications (PTMs) play vital roles in cellular homeostasis and are implicated in various pathological conditions. This work uses two ion mobility spectrometry-mass spectrometry (IMS-MS) modalities, drift-tube IMS (DT-IMS) and trapped IMS (TIMS), to characterize three important nonenzymatic PTMs that induce no mass loss: l/d isomerization, aspartate/isoaspartate isomerization, and cis/trans proline isomerization. These PTMs are assessed in a single peptide system, the recently discovered pleurin peptides, Plrn2, from Aplysia californica. We determine that the DT-IMS-MS/MS can capture and locate asparagine deamidation into aspartate and its subsequent isomerization to isoaspartate, a key biomarker for age-related diseases. Additionally, nonenzymatic peptide cleavage via in-source fragmentation is evaluated for differences in the intensities and patterns of fragment peaks between these PTMs. Peptide fragments resulting from in-source fragmentation, preceded by peptide denaturation by liquid chromatography (LC) mobile phase, exhibited cis/trans proline isomerization. Finally, the effects of differing the fragmentation voltage at the source and solution-based denaturation conditions on in-source fragmentation profiles are evaluated, confirming that LC denaturation and in-source fragmentation profoundly impact N-terminal peptide bond cleavages of Plrn2 and the structures of their fragment ions. With that, LC-IMS-MS/MS coupled with in-source fragmentation could be a robust method to identify three important posttranslational modifications: l/d isomerization, Asn-deamidation leading to Asp/IsoAsp isomerization, and cis/trans proline isomerization.
Collapse
Affiliation(s)
- Connor C. Long
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - David H. Mast
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Samuel Okyem
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Thanh D. Do
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
6
|
Li J, Liu R, Gao W, Yu J, Tang K. Ion storage biases in the ion funnel trap of a Hybrid ion mobility spectrometer/time of flight mass spectrometer. Talanta 2023; 260:124621. [PMID: 37149942 DOI: 10.1016/j.talanta.2023.124621] [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: 02/25/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
A detailed experimental characterization on the ion storage biases in an ion funnel trap, related to ion structure, charge state and RF voltage applied to the ion funnel trap, is reported by using both cytochrome C and ubiquitin samples. It was first observed experimentally that an unavoidable ion overflow would occur when the incoming ions exceeded the capacity of ion funnel trap. The conformers with extended structures would lose preferentially in the ion overflow process. Accordingly, a significant structural bias in the ion mobility spectrometry/time of flight mass spectrometry (IMS-TOF MS) spectrum was created, as the peak intensities for conformers with compact structures and extended structures would continuously increase and decrease, respectively, when the ion overflow time of the ion funnel trap was increased. Furthermore, the experimental results also showed that the effect of this ion structural bias was more significant when the RF voltage applied to the ion funnel trap was increased. In addition, an ion charge state bias in the ion funnel trap was also observed. The effect of the ion structural bias depends significantly on the specific charge state of the ions. For a given analyte, its lower charge state ions show a greater sensitivity to the ion structural bias than the higher charge state ones under the same ion funnel trap operating conditions. Therefore, it is extremely important to set a reasonable operation condition for the ion funnel trap to avoid ion storage biases in IMS-TOF MS.
Collapse
Affiliation(s)
- Junhui Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, PR China
| | - Rong Liu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Wenqing Gao
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Jiancheng Yu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, PR China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, 315211, PR China; Zhenhai Institute of Mass Spectrometry, Ningbo, 315211, PR China; School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| |
Collapse
|
7
|
Ji X, Liu R, Hao J, Wang C, Li J, Gao W, Yu J, Tang K. Two-step particle swarm optimization algorithm for effective deconvolution and resolution enhancement of various overlapping peaks. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9429. [PMID: 36346291 DOI: 10.1002/rcm.9429] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/30/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
RATIONALE The existing particle swarm optimization (PSO) algorithms are only effective in deconvoluting the overlapping peaks in ion mobility spectra with fewer than four component peaks, which limits the applicability of these algorithms. METHODS A high-performance two-step particle swarm optimization (TSPSO) algorithm was developed. Compared to the existing PSO algorithms, TSPSO can narrow the search ranges of all coefficients for the overlapping peaks through Gaussian model calculation, and thus can deconvolute various overlapping peaks with high accuracy, even for 30-component overlapping peaks. In addition, the TSPSO could be further applied to enhance the resolution of the spectra by narrowing the peak widths after the peak deconvolution. RESULTS Simulated overlapping peaks were first used to evaluate the performance of TSPSO as compared to the dynamic inertia weight particle swarm optimization (DIWPSO) algorithm. The results showed that the profiles of the peaks deconvoluted by using TSPSO were more consistent with the original ones. The fitness values and the standard deviations of the fitness values from TSPSO were also at least an order of magnitude less than those from DIWPSO. By applying TSPSO, the overlapping peaks from both mass spectrometry (MS) and field asymmetric waveform ion mobility spectrometry (FAIMS) spectra can also be well deconvoluted. In addition, the resolutions of the MS and FAIMS spectra can be effectively enhanced after peak deconvolution. The enhanced spectra matched excellently with the experimental ones acquired at high-resolution modes. CONCLUSIONS The experiment results convincingly demonstrate that the TSPSO algorithm is capable of both deconvoluting complex overlapping peaks and enhancing the spectrum resolution with high accuracy.
Collapse
Affiliation(s)
- Xiaoli Ji
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Rong Liu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Jie Hao
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, China
| | - Chenlu Wang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Junhui Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, China
| | - Wenqing Gao
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Jiancheng Yu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| |
Collapse
|
8
|
Fu D, Habtegabir SG, Wang H, Feng S, Han Y. Understanding of protomers/deprotomers by combining mass spectrometry and computation. Anal Bioanal Chem 2023:10.1007/s00216-023-04574-1. [PMID: 36737499 DOI: 10.1007/s00216-023-04574-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.
Collapse
Affiliation(s)
- Dali Fu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Sara Girmay Habtegabir
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Haodong Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Shijie Feng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China.
| |
Collapse
|
9
|
Xu X, Han L, Zheng Z, Zhao R, Li L, Shao X, Li G. Composite Multidimensional Ion Mobility-Mass Spectrometry for Improved Differentiation of Stereochemical Modifications. Anal Chem 2023; 95:2221-2228. [PMID: 36635260 DOI: 10.1021/acs.analchem.2c03522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Stereochemical modifications (SCMs), mostly present in the form of d-amino acid substitution, have been increasingly identified from a wide range of neuropeptides and disease-associated biomarker proteins. Traditional mass spectrometry-based SCM identification has been effectively enhanced with technological and strategic advancements in ion mobility spectrometry. With the additional separation provided by ion mobility, SCM-induced structural changes can be probed both in theory and in practice, although the structural resolution for low-abundance SCMs still requires further improvement to enable accurate quantification or unambiguous identification of stereoisomers. Herein, we present a multi-component-enabled multidimensional ion mobility-mass spectrometry (3M-IM-MS) analytical workflow, based upon the metal-enhanced chiral amplification strategy we proposed previously (Nat. Commun., 2019, 5038). Notably, the 3M-IM-MS strategy comprises and features the powerful mathematical tools of continuous wavelet transform and Gaussian fitting-enabled peak splitting. Consequently, the resolving capability of ion mobility spectrometry for SCM analysis has been significantly enhanced, providing mobility profiles with baseline separation and more than fivefold improvement in resolving power and overall resolution. This study represents an alternative toward ultrahigh-resolution structural interrogation of mixtures with very small differences, featuring an important and long-lasting topic in chemical measurement.
Collapse
Affiliation(s)
- Xia Xu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Li Han
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Rui Zhao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Gongyu Li
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| |
Collapse
|
10
|
High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|