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He X, Guo X, Deng F, Zeng P, Wu B, Sun H, Zhao Z, Duan Y. A study of the transient gas flow affected ion transmission in atmospheric pressure interfaces based on large eddy simulation for electrospray ionization mass spectrometry. Talanta 2024; 274:125980. [PMID: 38579418 DOI: 10.1016/j.talanta.2024.125980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024]
Abstract
Modern atmosphere pressure interface (API) enables high-efficiency coupling between mass analyzers in high vacuum and atmosphere ionization sources such as electrospray ionization (ESI) source. The transient gas flow entering API possesses strong compressibility and turbulent characteristics, which exerts a huge impact on ion transmission. However, the instantaneous nature and vortical morphology of the turbulence in API and its affection in ion transmission were hardly covered in the reported research. Here we conduct a transient turbulent flow-affected ion transmission evaluation for two typical APIs, the ion funnel and the S-lens, based on scale-resolving large eddy simulation and electro-hydrodynamical ion tracing simulation. In our simulation, the transient properties of the gas flow in the two APIs are illustrated and analyzed in-depth. After experimentally validated on a homemade ESI-TOF-MS platform, the results suggest that the ion funnel can achieve a higher droplet desolvation rate by introducing a unique droplet recirculation mechanism. Meanwhile, the less-dispersed gas flow in S-lens is beneficial in actuating ions axially. In conclusion, the application of the scale-resolving turbulence model helps us to understand the complicated fluid-ion interaction mechanism in APIs and is promising in the development of mass spectrometry instruments of higher performance.
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Affiliation(s)
- Xingliang He
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China
| | - Xing Guo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China
| | - Fulong Deng
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China
| | - Pengyu Zeng
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China
| | - Bin Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China
| | - Hong'en Sun
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China
| | - Zhongjun Zhao
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China; Aliben Science & Technology, China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, China; Aliben Science & Technology, China.
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2
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Li H, Jing-Hao Q, Ya-Qing L, Shen-Shu C, Xin-Qiong L. Development and characterization of discontinuous atmospheric pressure interface - Dual pressure chamber miniature mass spectrometer. Anal Biochem 2024; 690:115531. [PMID: 38574796 DOI: 10.1016/j.ab.2024.115531] [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: 02/10/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/06/2024]
Abstract
Miniaturized mass spectrometers have become increasingly prevalent for real-time detection and analysis, owing to their compact size and portability. The pursuit of performance enhancement in these instruments is a pivotal objective within the domain of mass spectrometry miniaturization. This study introduces a novel miniature mass spectrometer featuring a discontinuous atmospheric pressure interface and a dual pressure chamber. Compared to conventional single-chamber, discontinuous sampling interface mass spectrometers, the newly developed instrument demonstrates a more than tenfold improvement in detection efficiency. This significant enhancement is achieved without the need for complex control of switch coupling time series, thereby streamlining the circuit design and improving the instrument's fault tolerance. Furthermore, by capitalizing on the benefits of discontinuous sampling, the instrument reduces the operational pressure relative to traditional continuous sampling in differential pressure vacuum chambers. It accommodates larger inlet capillary (0.38 mm) and skimmer (0.5 mm) diameters, leading to a ninefold increase in response strength for risperidone and lowering the detection limit to 0.5 ppb. The instrument's capacity for rapid drug detection, along with enhanced resolution and detection limits, underscores its potential utility. Additionally, it facilitates the use of smaller mechanical pumps, significantly diminishing both the instrument's volume and power consumption. This presents a promising avenue for further miniaturization of mass spectrometers.
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Affiliation(s)
- Hua Li
- School of Life and Environmental Sciences, GuiLin University of Electronic Technology, GuiLin 541004, China.
| | - Qi Jing-Hao
- School of Life and Environmental Sciences, GuiLin University of Electronic Technology, GuiLin 541004, China
| | - Li Ya-Qing
- Guangdong Nantian Institute of Judicial Expertise, Shenzhen 518055, China
| | - Chen Shen-Shu
- Guangdong Nantian Institute of Judicial Expertise, Shenzhen 518055, China
| | - Lu Xin-Qiong
- Shenzhen ZhiQin Instrument Co., LTD, Shenzhen 518055, China.
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3
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Jung JE, Ewing MA, Valentine SJ, Clemmer DE. Structural Insights into Linkage-Specific Ubiquitin Chains Using Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:982-991. [PMID: 38597281 DOI: 10.1021/jasms.4c00019] [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
The structural characterization and differentiation of four types of oligoubiquitin conjugates [linear (Met1)-, Lys11-, Lys48-, Lys63-linked di-, tri-, and tetraubiquitin chains] using ion mobility mass spectrometry are reported. A comparison of collision cross sections for the same linkage of di-, tri-, and tetraubiquitin chains shows differences in conformational elongation for higher charge states due to the interplay of linkage-derived structure and Coulombic repulsion. For di- and triubiquitin chains, this elongation results in a single narrow feature representing an elongated conformation type for multiple higher charge state species. In contrast, higher charge state tetraubiquitin species do not form a single conformer type as readily. A comparison of different linkages in tetraubiquitin chains reveals greater similarity in conformation type at lower charge states; with increasing charge state, the four linkage types diverge in the relative proportions of elongated conformer types with Met1- ≥ Lys11- > Lys63- > Lys48-linkage. These differences in conformational trends could be discussed with respect to biological functions of linkage-specific polyubiquitinated proteins.
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Affiliation(s)
- Ji Eun Jung
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Forensic Chemistry Division, National Forensic Service, Wonju 26460, Korea
| | - Michael A Ewing
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Roche Infomatics, F. Hoffman-La Roche AG, Basel, CH 4070, Switzerland
| | - Stephen J Valentine
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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4
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Salvi M, Uma NN, Dinesan H, Roy A, Kumar SS. A versatile 16-pole ion trap setup for investigating photophysics of biomolecular ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:093203. [PMID: 37721505 DOI: 10.1063/5.0160407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023]
Abstract
A linear 16-pole ion trap-based experimental setup has been designed, implemented, and characterized to investigate the photophysics of biomolecules in the gas phase. Electrospray ionization is employed to generate the ions in the gas phase at atmospheric pressure. The voltage configuration on the ion funnel, the ion optic device in the first vacuum interface, is used to control the energy of the ions. A home-built quadrupole mass-filter is utilized for the mass-selection of the ions of interest. A 16-pole ion trap designed and built in-house is implemented for ion trapping. The instrument's versatility and capability are showcased by demonstrating the fragmentation patterns of protonated and deprotonated tryptophan, as well as describing the photodetachment decay of deprotonated indole.
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Affiliation(s)
- M Salvi
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
| | - N N Uma
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
| | - Hemanth Dinesan
- CNRS Laboratoire de Physique des Lasers (LPL), Université Sorbonne Paris Nord Villetaneuse, Villetaneuse 93430, France
| | - Abheek Roy
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
| | - S Sunil Kumar
- Department of Physics and the Center for Atomic, Molecular, and Optical Sciences & Technologies (CAMOST), Indian Institute of Science Education and Research Tirupati, AP, Tirupati 517507, India
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5
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Yan Y, Schmitt L, Khramchenkova A, Lengyel J. Ion transmission in an electrospray ionization-mass spectrometry interface using an S-lens. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4955. [PMID: 37401114 DOI: 10.1002/jms.4955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/24/2023] [Accepted: 06/03/2023] [Indexed: 07/05/2023]
Abstract
We present the design and performance of an in-house built electrospray ionization-mass spectrometry (ESI-MS) interface equipped with an S-lens ion guide. The ion source was designed specifically for our ion beam experiments to investigate the chemical reactivity and deposition of the clusters and nanoparticles. It includes standard ESI-MS interface components, such as nanoelectrospray, ion transfer capillary, and the S-lens. A custom design enables systematic optimization of all relevant factors influencing ion formation and transfer through the interface. By varying the ESI voltage and flow rate, we determined the optimal operating conditions for selected silica emitters. A comparison of the pulled silica emitters with different tip inner diameters reveals that the total ion current is highest for the largest tip, whereas a tip with the smallest diameter exhibited the highest transmission efficiency through the ESI-MS interface. Ion transmission through the transfer capillary is strongly limited by its length, but the loss of ions can be reduced by increasing the capillary voltage and temperature. The S-lens was characterized over a wide range of RF frequencies and amplitudes. Maximum ion current was detected at RF amplitudes greater than 50 V peak-to-peak (p/p) and frequencies above 750 kHz, with a stable ion transmission region of about 20%. A factor of 2.6 increase in total ion current is observed for 650 kHz as RF amplitudes reach 400 V p/p. Higher RF amplitudes also focus the ions into a narrow beam, which mitigates their losses when passing through the ion guide.
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Affiliation(s)
- Yihui Yan
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Lucas Schmitt
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Anastasiya Khramchenkova
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Jozef Lengyel
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
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6
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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.
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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.
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7
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Lamont L, Hadavi D, Bowman AP, Flinders B, Cooper‐Shepherd D, Palmer M, Jordens J, Mengerink Y, Honing M, Langridge J, Porta Siegel T, Vreeken RJ, Heeren RMA. High-resolution ion mobility spectrometry-mass spectrometry for isomeric separation of prostanoids after Girard's reagent T derivatization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9439. [PMID: 36415963 PMCID: PMC10078546 DOI: 10.1002/rcm.9439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE Isomeric separation of prostanoids is often a challenge and requires chromatography and time-consuming sample preparation. Multiple prostanoid isomers have distinct in vivo functions crucial for understanding the inflammation process, including prostaglandins E2 (PGE2 ) and D2 (PGD2 ). High-resolution ion mobility spectrometry (IMS) based on linear ion transport in low-to-moderate electric fields and nonlinear ion transport in strong electric fields emerges as a broad approach for rapid separations prior to mass spectrometry. METHODS Derivatization with Girard's reagent T (GT) was used to overcome inefficient ionization of prostanoids in negative ionization mode due to poor deprotonation of the carboxylic acid group. Three high-resolution IMS techniques, namely linear cyclic IMS, linear trapped IMS, and nonlinear high-field asymmetric waveform IMS, were compared for the isomeric separation and endogenous detection of prostanoids present in intestinal tissue. RESULTS Direct infusion of GT-derivatized prostanoids proved to increase the ionization efficiency in positive ionization mode by a factor of >10, which enabled detection of these molecules in endogenous concentration levels. The high-resolution IMS comparison revealed its potential for rapid isomeric analysis of biologically relevant prostanoids. Strengths and weaknesses of both linear and nonlinear IMS are discussed. Endogenous prostanoid detection in intestinal tissue extracts demonstrated the applicability of our approach in biomedical research. CONCLUSIONS The applied derivatization strategy offers high sensitivity and improved stereoisomeric separation for screening of complex biological systems. The high-resolution IMS comparison indicated that the best sensitivity and resolution are achieved by linear and nonlinear IMS, respectively.
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Affiliation(s)
- Lieke Lamont
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Darya Hadavi
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Andrew P. Bowman
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Bryn Flinders
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | | | | | - Jan Jordens
- DSM Materials Science CenterGeleenMDThe Netherlands
| | | | - Maarten Honing
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | | | - Tiffany Porta Siegel
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Rob J. Vreeken
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
- Janssen R&DBeerseBelgium
| | - Ron M. A. Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
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8
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Yang F, Armentrout PB. Periodic trends in the hydration energies and critical sizes of alkaline earth and transition metal dication water complexes. MASS SPECTROMETRY REVIEWS 2023:e21830. [PMID: 36644985 DOI: 10.1002/mas.21830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/19/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
This review encompasses guided ion beam tandem mass spectrometry studies of hydrated metal dication complexes. Metals include the Group 2 alkaline earths (Mg, Ca, Sr, and Ba), late first-row transition metals (Mn, Fe, Co, Ni, Cu, and Zn), along with Cd. In all cases, threshold collision-induced dissociation experiments are used to quantitatively determine the sequential hydration energies for M2+ (H2 O)x complexes ranging in size from one to 11 water molecules. Periodic trends in these bond dissociation energies are examined and discussed. Values are compared to other experimental results when available. In addition to dissociation by simple water ligand loss, complexes at a select size (which differs from metal to metal) are also observed to undergo charge separation to yield a hydrated metal hydroxide cation and a hydrated proton. This leads to the concept of a critical size, xcrit , and the periodic trends in this value are also discussed.
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Affiliation(s)
- Fan Yang
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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9
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Wang CF, Li L. Instrument-type effects on chemical isotope labeling LC-MS metabolome analysis: Quadrupole time-of-flight MS vs. Orbitrap MS. Anal Chim Acta 2022; 1226:340255. [PMID: 36068057 DOI: 10.1016/j.aca.2022.340255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022]
Abstract
Chemical isotope labeling (CIL) LC-MS is a powerful tool for metabolome analysis with markedly improved metabolomic coverage and quantification accuracy over the conventional LC-MS technique. In addition, with differential isotope labeling, each labeled metabolite is detected as a peak pair in the mass spectra, offering the possibility of differentiating true metabolite peaks from the singlet noise or background peaks. In this study, we examined the effects of instrument type on the detectability of true metabolites with a focus on the comparison of quadrupole time-of-flight (QTOF) and Orbitrap mass spectrometers. Using the same ultra-high-performance liquid chromatography setup and optimized running conditions for QTOF and Orbitrap, we compared the total number of peak pairs detected and identified from the two instruments using human urine and serum as the test samples. Many common peak pairs were detected from the two instruments; however, there were a significant number of unique peak pairs detected in each type of instrument. By combining the datasets obtained using QTOF and Orbitrap, the total number of peak pairs detected could be significantly increased. We also examined the effect of mass resolving power on peak pair detection in Orbitrap (60,000 vs. 120,000 resolution). The observed differences in peak pair detectability were much less than those of QTOF vs. Orbitrap. However, the type of peak pairs detected using different resolutions could be somewhat different, offering the possibility of increasing the overall number of peak pairs by combining the two datasets obtained at two different resolutions. The results from this study clearly indicate that instrument type can have a profound effect on metabolite detection in CIL LC-MS. Therefore, comparison of metabolome data generated using different instruments needs to be carefully done. Moreover, future research (e.g., hardware modifications) is warranted to minimize the differences in order to generate more reproducible metabolome data from different types of instruments.
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Affiliation(s)
- Chu-Fan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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10
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Covey T. Where have all the ions gone, long time passing? Tandem quadrupole mass spectrometers with atmospheric pressure ionization sensitivity gains since the mid-1970s. A perspective. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022:e9354. [PMID: 35830299 DOI: 10.1002/rcm.9354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/09/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
The gains in sensitivity since 1975 for quadrupole mass spectrometers equipped with atmospheric pressure ionization (API), and in particular triple quadrupole mass spectrometers (QqQs) since 1981, have been driven by the needs of the environmental, biomedical, agricultural, and other scientific research, industrial, regulatory, legal, and sporting communities to continually achieve lower limits of quantitation and identification. QqQs have realized a one-million-fold improvement in sensitivity attempting to address these needs over the past two score years. It is the purpose of this article to describe how that came about, not through an exhaustive review of the literature, but rather by describing what general approaches were used across the industry to improve sensitivity and provide some examples to illustrate its evolution. The majority of the gains came from the ion source and its interface to the vacuum system. "Sampling efficiency" is a measurement of the losses in this area so will be a focus of this review. The discovery of the phenomenon of collisional focusing was key to improving sampling efficiency because it enabled designs that increased the ion-containing gas loads from the ion source, using staged differential pumping backed by increasingly larger pumps, and prevented the scattering losses of ions in the resulting gas expansion inside vacuum. Likewise, systems with smaller pumps and lower ion-containing gas loads could be designed with size and cost reduction in mind while maintaining reasonable sampling efficiencies. As a consequence, advancements in the designs of both larger and smaller turbomolecular vacuum pumps were accelerated by pump manufacturers to accommodate the explosive growth in the use of API-QqQ and API-ion trap mass spectrometers that occurred in the 1990s and continued into the new millennium. Sampling efficiency was further improved by increasing the ion yield from electrospray by increasing the rate of droplet desolvation. An estimate of the practical limit to further sensitivity improvements beyond what has been achieved to date is provided to shed light on what to expect in the future. Lastly, the implications and unforeseen consequences of the sensitivity gains are considered with a particular focus on how they have enabled a dramatic increase in daily sample throughput on triple quadrupole and other types of mass spectrometers.
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11
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Walz A, Stoiber K, Huettig A, Schlichting H, Barth JV. Navigate Flying Molecular Elephants Safely to the Ground: Mass-Selective Soft Landing up to the Mega-Dalton Range by Electrospray Controlled Ion-Beam Deposition. Anal Chem 2022; 94:7767-7778. [PMID: 35609119 PMCID: PMC9178560 DOI: 10.1021/acs.analchem.1c04495] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The prototype of a highly versatile and efficient preparative mass spectrometry system used for the deposition of molecules in ultrahigh vacuum (UHV) is presented, along with encouraging performance data obtained using four model species that are thermolabile or not sublimable. The test panel comprises two small organic compounds, a small and very large protein, and a large DNA species covering a 4-log mass range up to 1.7 MDa as part of a broad spectrum of analyte species evaluated to date. Three designs of innovative ion guides, a novel digital mass-selective quadrupole (dQMF), and a standard electrospray ionization (ESI) source are combined to an integrated device, abbreviated electrospray controlled ion-beam deposition (ES-CIBD). Full control is achieved by (i) the square-wave-driven radiofrequency (RF) ion guides with steadily tunable frequencies, including a dQMF allowing for investigation, purification, and deposition of a virtually unlimited m/z range, (ii) the adjustable landing energy of ions down to ∼2 eV/z enabling integrity-preserving soft landing, (iii) the deposition in UHV with high ion beam intensity (up to 3 nA) limiting contaminations and deposition time, and (iv) direct coverage control via the deposited charge. The maximum resolution of R = 650 and overall efficiency up to Ttotal = 4.4% calculated from the solution to UHV deposition are advantageous, whereby the latter can be further enhanced by optimizing ionization performance. In the setup presented, a scanning tunneling microscope (STM) is attached for in situ UHV investigations of deposited species, demonstrating a selective, structure-preserving process and atomically clean layers.
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Affiliation(s)
- Andreas Walz
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Karolina Stoiber
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Annette Huettig
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Hartmut Schlichting
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Johannes V Barth
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
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12
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Su P, Chen X, Smith AJ, Espenship MF, Samayoa Oviedo HY, Wilson SM, Gholipour-Ranjbar H, Larriba-Andaluz C, Laskin J. Multiplexing of Electrospray Ionization Sources Using Orthogonal Injection into an Electrodynamic Ion Funnel. Anal Chem 2021; 93:11576-11584. [PMID: 34378383 DOI: 10.1021/acs.analchem.1c02092] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this contribution, we report an efficient approach to multiplex electrospray ionization (ESI) sources for applications in analytical and preparative mass spectrometry. This is achieved using up to four orthogonal injection inlets implemented on the opposite sides of an electrodynamic ion funnel interface. We demonstrate that both the total ion current transmitted through the mass spectrometer and the signal-to-noise ratio increase by 3.8-fold using four inlets compared to one inlet. The performance of the new multiplexing approach was examined using different classes of analytes covering a broad range of mass and ionic charge. A deposition rate of >10 μg of mass-selected ions per day may be achieved by using the multiplexed sources coupled to preparative mass spectrometry. The almost proportional increase in the ion current with the number of ESI inlets observed experimentally is confirmed using gas flow and ion trajectory simulations. The simulations demonstrate a pronounced effect of gas dynamics on the ion trajectories in the ion funnel, indicating that the efficiency of multiplexing strongly depends on gas velocity field. The study presented herein opens up exciting opportunities for the development of bright ion sources, which will advance both analytical and preparative mass spectrometry applications.
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Affiliation(s)
- Pei Su
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Xi Chen
- Department of Mechanical and Energy Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Andrew J Smith
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Michael F Espenship
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hugo Y Samayoa Oviedo
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Solita M Wilson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Habib Gholipour-Ranjbar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Carlos Larriba-Andaluz
- Department of Mechanical and Energy Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Julia Laskin
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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13
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Javaheri H, Schneider BB. Ion Guide for Improved Atmosphere to Mass Spectrometer Vacuum Ion Transfer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1945-1951. [PMID: 33400869 DOI: 10.1021/jasms.0c00394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Various approaches for transmitting ions from atmosphere to the deep vacuum required for mass analysis have been developed with the goal to increase the ion to gas ratio while maintaining high ion transmission efficiency. Since the vast majority of ion losses occurs in the atmospheric pressure ion source, an effective way to improve sampling of those ions is to increase the atmosphere to vacuum aperture diameter. However, as the aperture diameter is increased, the resulting intense free jet gas expansion and subsequent gas beam can scatter ions in the first vacuum region. The interface described here provides an optimized flow field to the second vacuum stage, with a unique geometry to counter the ion losses from scattering collisions with the gas. Two additional differentially pumped quadrupole ion guides are used to further improve the ion to gas ratio, resulting in an ion transfer efficiency improvement of 5-6× over a two-stage differentially pumped interface with quadrupole ion guides. The interface also demonstrates efficient declustering and fragmentation capabilities beneficial for reducing background chemical noise.
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Affiliation(s)
- Hassan Javaheri
- SCIEX, 71 Four Valley Drive, Concord, Ontario, Canada L4K 4V8
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14
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Demireva M, Armentrout PB. Relative Energetics of the Gas Phase Protomers of p-Aminobenzoic Acid and the Effect of Protonation Site on Fragmentation. J Phys Chem A 2021; 125:2849-2865. [DOI: 10.1021/acs.jpca.0c11540] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maria Demireva
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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15
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Zhou S, Tang K, Wu H, Xie Z, Wu Y, Yu J. Performance optimization of an ion funnel driven by novel radiofrequency waveforms. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8924. [PMID: 32779286 DOI: 10.1002/rcm.8924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE In mass spectrometry, ion transmission is usually achieved by driving an ion funnel with a reversed sine wave radiofrequency. However, the mass range of this conventional ion funnel is limited. In order to overcome this limitation, and to improve the transmission efficiency of the ion funnel, we explore the use of different radiofrequency waveforms for different m/z ranges. METHODS Right triangle, sawtooth, and variable phase sine (VPS) waves are used in different m/z ranges to improve ion transmission efficiency. We use SIMION-based numerics to simulate their potential field distributions and ion flight trajectories. We compare transmission and focusing performances with those of a conventional ion funnel. RESULTS Ions with high m/z values require a larger potential gradient to limit their flight trajectory. Right triangle waves can quickly adjust electrode potential through a step change. The equipotential line distribution of VPS waves is wider than that of a sine wave which improves focusing performance. At the same time, the local ion trap effect at the outlet of the ion funnel is improved because of the "snake potential". The maximum effective potential of the sawtooth wave is smaller than that of the sine wave, which is suitable for low m/z ion transmission. CONCLUSIONS Sawtooth and VPS waves may improve the transmission performance of the ion funnel in the low m/z regime whereas right triangle waves may improve the transmission performance in the high m/z regime.
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Affiliation(s)
- Shao Zhou
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, China
| | - Keqi Tang
- Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China
| | - Huanming Wu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, China
| | - Zhijun Xie
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, China
| | - Yong Wu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, China
| | - Jiancheng Yu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, China
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16
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Berdnikov AS, Verenchikov AN, Gall NR, Kuzmin AG, Masyukevich SV, Lapushkin MN, Titov YA. Radio-Frequency Ion Guides with Periodical Electrodes and Pulse Voltages. JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1134/s1061934820140063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Eldrid C, Thalassinos K. Developments in tandem ion mobility mass spectrometry. Biochem Soc Trans 2020; 48:2457-2466. [PMID: 33336686 PMCID: PMC7752082 DOI: 10.1042/bst20190788] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 01/09/2023]
Abstract
Ion Mobility (IM) coupled to mass spectrometry (MS) is a useful tool for separating species of interest out of small quantities of heterogenous mixtures via a combination of m/z and molecular shape. While tandem MS instruments are common, instruments which employ tandem IM are less so with the first commercial IM-MS instrument capable of multiple IM selection rounds being released in 2019. Here we explore the history of tandem IM instruments, recent developments, the applications to biological systems and expected future directions.
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Affiliation(s)
- Charles Eldrid
- Institute of Structural and Molecular Biology, UCL, Gower St, London WC1E 6BT, U.K
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, UCL, Gower St, London WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Birkbeck University, Malet Place, London WC1E 7HX, U.K
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18
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Ahmed E, Xiao D, Kabir KMM, Fletcher J, Donald WA. Ambient Pressure Ion Funnel: Concepts, Simulations, and Analytical Performance. Anal Chem 2020; 92:15811-15817. [DOI: 10.1021/acs.analchem.0c02938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ezaz Ahmed
- School of Chemistry, University of New South Wales, Sydney, NSW 2052 Australia
| | - Dan Xiao
- School of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, NSW 2052 Australia
| | - K. M. Mohibul Kabir
- School of Chemistry, University of New South Wales, Sydney, NSW 2052 Australia
| | - John Fletcher
- School of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, NSW 2052 Australia
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, NSW 2052 Australia
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19
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Raab SA, El-Baba TJ, Woodall DW, Liu W, Liu Y, Baird Z, Hales DA, Laganowsky A, Russell DH, Clemmer DE. Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements. J Am Chem Soc 2020; 142:17372-17383. [PMID: 32866376 DOI: 10.1021/jacs.0c05365] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chymotrypsin inhibitor 2 (CI-2) is a classic model for two-state cooperative protein folding and is one of the most extensively studied systems. Alan Fersht, a pioneer in the field of structural biology, has studied the wild-type (wt) and over 100 mutant forms of CI-2 with traditional analytical and biochemical techniques. Here, we examine wt CI-2 and three mutant forms (A16G, K11A, L32A) to demonstrate the utility of variable-temperature (vT) electrospray ionization (ESI) paired with ion mobility spectrometry (IMS) and mass spectrometry (MS) to map the free energy folding landscape. As the solution temperature is increased, the abundance of each of the six ESI charge states for wt CI-2 and each mutant is found to vary independently. These results require that at least six unique types of CI-2 solution conformers are present. Ion mobility analysis reveals that within each charge state there are additional conformers having distinct solution temperature profiles. A model of the data at ∼30 different temperatures for all four systems suggests the presence of 41 unique CI-2 solution conformations. A thermodynamic analysis of this system yields values of ΔCp as well as ΔG, ΔH, and ΔS for each state at every temperature studied. Detailed energy landscapes derived from these data provide a rare glimpse into Anfinsen's thermodynamic hypothesis and the process of thermal denaturation, normally thought of as a cooperative two-state transition involving the native state and unstructured denatured species. Specifically, as the temperature is varied, the entropies and enthalpies of different conformers undergo dramatic changes in magnitude and relative order to maintain the delicate balance associated with equilibrium.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Wen Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zane Baird
- Baxter Healthcare Corporation, 927 South Curry Pike, Bloomington, Indiana 47403, United States
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, Arkansas 72032, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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20
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Schlottmann F, Allers M, Kirk AT, Bohnhorst A, Zimmermann S. A Simple Printed Circuit Board-Based Ion Funnel for Focusing Low m/z Ratio Ions with High Kinetic Energies at Elevated Pressure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1813-1823. [PMID: 31140080 DOI: 10.1007/s13361-019-02241-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Ion funnels are one of the key components for transferring ions from higher pressure into the vacuum. Typically, ion funnels are constructed of several different plate ring electrodes with a decreasing inner diameter where radio frequency (RF) voltages and electric DC fields are applied to the electrodes to focus and transport ion clouds. In this work, we developed and investigated a simple and low-cost ion funnel design that is based on standard printed circuit boards (PCB) with integrated planar electrodes including the signal distribution network. This ion funnel is capable of withstanding high electric fields with superimposed RF voltages due to its buried capacitors. To evaluate the ion focusing efficiency of the ion funnel, we simulated the movement of ions inside this funnel and experimentally evaluated the ion transfer. Our simulations show that a rectangular ion funnel like the PCB ion funnel has similar performance compared with conventional stacked ring funnels. Due to the hundredfold lower parasitic capacitance between the planar electrodes compared with conventional ion funnels, high RF voltage amplitudes up to 195 V and reduced electric DC field strengths up to 100 Td can be reached at a frequency of about 5 MHz. Thus, the funnel is appropriate to focus light ions at elevated pressures up to 20 mbar. Graphical Abstract .
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Affiliation(s)
- Florian Schlottmann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstr. 9A, Hannover, 30167, Germany.
| | - Maria Allers
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstr. 9A, Hannover, 30167, Germany
| | - Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstr. 9A, Hannover, 30167, Germany
| | - Alexander Bohnhorst
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstr. 9A, Hannover, 30167, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz University Hannover, Appelstr. 9A, Hannover, 30167, Germany
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21
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Rahrt R, Auth T, Demireva M, Armentrout PB, Koszinowski K. Benzhydrylpyridinium Ions: A New Class of Thermometer Ions for the Characterization of Electrospray-Ionization Mass Spectrometers. Anal Chem 2019; 91:11703-11711. [DOI: 10.1021/acs.analchem.9b02257] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Rene Rahrt
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Thomas Auth
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Maria Demireva
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112, United States
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112, United States
| | - Konrad Koszinowski
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
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22
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Giles K, Ujma J, Wildgoose J, Pringle S, Richardson K, Langridge D, Green M. A Cyclic Ion Mobility-Mass Spectrometry System. Anal Chem 2019; 91:8564-8573. [PMID: 31141659 DOI: 10.1021/acs.analchem.9b01838] [Citation(s) in RCA: 265] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Improvements in the performance and availability of commercial instrumentation have made ion mobility-mass spectrometry (IM-MS) an increasingly popular approach for the structural analysis of ionic species as well as for separation of complex mixtures. Here, a new research instrument is presented which enables complex experiments, extending the current scope of IM technology. The instrument is based on a Waters SYNAPT G2-S i IM-MS platform, with the IM separation region modified to accept a cyclic ion mobility (cIM) device. The cIM region consists of a 98 cm path length, closed-loop traveling wave (TW)-enabled IM separator positioned orthogonally to the main ion optical axis. A key part of this geometry and its flexibility is the interface between the ion optical axis and the cIM, where a planar array of electrodes provides control over the TW direction and subsequent ion motion. On either side of the array, there are ion guides used for injection, ejection, storage, and activation of ions. In addition to single and multipass separations around the cIM, providing selectable mobility resolution, the instrument design and control software enable a range of "multifunction" experiments such as mobility selection, activation, storage, IMS n, and importantly custom combinations of these functions. Here, the design and performance of the cIM-MS instrument is highlighted, with a mobility resolving power of approximately 750 demonstrated for 100 passes around the cIM device using a reverse sequence peptide pair. The multifunction capabilities are demonstrated through analysis of three isomeric pentasaccharide species and the small protein ubiquitin.
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Affiliation(s)
- Kevin Giles
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jakub Ujma
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jason Wildgoose
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Steven Pringle
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Keith Richardson
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - David Langridge
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Martin Green
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
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23
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Eldrid C, Ujma J, Kalfas S, Tomczyk N, Giles K, Morris M, Thalassinos K. Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device. Anal Chem 2019; 91:7554-7561. [PMID: 31117399 PMCID: PMC7006968 DOI: 10.1021/acs.analchem.8b05641] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Ion
mobility mass spectrometry (IM-MS) allows separation of native
protein ions into “conformational families”. Increasing
the IM resolving power should allow finer structural information to
be obtained and can be achieved by increasing the length of the IM
separator. This, however, increases the time that protein ions spend
in the gas phase and previous experiments have shown that the initial
conformations of small proteins can be lost within tens of milliseconds.
Here, we report on investigations of protein ion stability using a
multipass traveling wave (TW) cyclic IM (cIM) device. Using this device,
minimal structural changes were observed for Cytochrome C after hundreds
of milliseconds, while no changes were observed for a larger multimeric
complex (Concanavalin A). The geometry of the instrument (Q-cIM-ToF)
also enables complex tandem IM experiments to be performed, which
were used to obtain more detailed collision-induced unfolding pathways
for Cytochrome C. The instrument geometry provides unique capabilities
with the potential to expand the field of protein analysis via IM-MS.
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Affiliation(s)
- Charles Eldrid
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Jakub Ujma
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Symeon Kalfas
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Nick Tomczyk
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Kevin Giles
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Mike Morris
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College , University of London , London , WC1E 7HX , United Kingdom
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24
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Zhai Y, Xu Q, Tang Y, Liu S, Li D, Xu W. Boosting the Sensitivity and Selectivity of a Miniature Mass Spectrometer Using a Hybrid Ion Funnel. Anal Chem 2019; 91:7911-7919. [DOI: 10.1021/acs.analchem.9b01770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yanbing Zhai
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Qian Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yang Tang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Siyu Liu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Dayu Li
- School of Computer Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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25
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Humphrey SJ, Karayel O, James DE, Mann M. High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform. Nat Protoc 2019; 13:1897-1916. [PMID: 30190555 DOI: 10.1038/s41596-018-0014-9] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mass spectrometry has transformed the field of cell signaling by enabling global studies of dynamic protein phosphorylation ('phosphoproteomics'). Recent developments are enabling increasingly sophisticated phosphoproteomics studies, but practical challenges remain. The EasyPhos workflow addresses these and is sufficiently streamlined to enable the analysis of hundreds of phosphoproteomes at a depth of >10,000 quantified phosphorylation sites. Here we present a detailed and updated workflow that further ensures high performance in sample-limited conditions while also reducing sample preparation time. By eliminating protein precipitation steps and performing the entire protocol, including digestion, in a single 96-well plate, we now greatly minimize opportunities for sample loss and variability. This results in very high reproducibility and a small sample size requirement (≤200 μg of protein starting material). After cell culture or tissue collection, the protocol takes 1 d, whereas mass spectrometry measurements require ~1 h per sample. Applied to glioblastoma cells acutely treated with epidermal growth factor (EGF), EasyPhos quantified 20,132 distinct phosphopeptides from 200 μg of protein in less than 1 d of measurement time, revealing thousands of EGF-regulated phosphorylation events.
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Affiliation(s)
- Sean J Humphrey
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia. .,The Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.
| | - Ozge Karayel
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David E James
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,The Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Martinsried, Germany. .,NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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26
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Singh JT. A new concept for searching for time-reversal symmetry violation using Pa-229 ions trapped in optical crystals. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s10751-019-1573-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Couvillion SP, Zhu Y, Nagy G, Adkins JN, Ansong C, Renslow RS, Piehowski PD, Ibrahim YM, Kelly RT, Metz TO. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst 2019; 144:794-807. [PMID: 30507980 PMCID: PMC6349538 DOI: 10.1039/c8an01574k] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass-spectrometry based omics technologies - namely proteomics, metabolomics and lipidomics - have enabled the molecular level systems biology investigation of organisms in unprecedented detail. There has been increasing interest for gaining a thorough, functional understanding of the biological consequences associated with cellular heterogeneity in a wide variety of research areas such as developmental biology, precision medicine, cancer research and microbiome science. Recent advances in mass spectrometry (MS) instrumentation and sample handling strategies are quickly making comprehensive omics analyses of single cells feasible, but key breakthroughs are still required to push through remaining bottlenecks. In this review, we discuss the challenges faced by single cell MS-based omics analyses and highlight recent technological advances that collectively can contribute to comprehensive and high throughput omics analyses in single cells. We provide a vision of the potential of integrating pioneering technologies such as Structures for Lossless Ion Manipulations (SLIM) for improved sensitivity and resolution, novel peptide identification tactics and standards free metabolomics approaches for future applications in single cell analysis.
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Affiliation(s)
- Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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28
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Research Progress and Application of Ion Funnel Technique. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(18)61133-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Li X, Zhang Y, Ge S, Qian J, Miao W. Portable linear ion trap mass spectrometer with compact multistage vacuum system and continuous atmospheric pressure interface. Analyst 2019; 144:5127-5135. [PMID: 31338496 DOI: 10.1039/c9an01047e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A portable linear ion trap mass spectrometer featuring a compact three-stage vacuum system, a continuous atmospheric pressure interface (CAPI), and a miniature ion funnel was developed and characterized. The dimensions and weight of the instrument were 38 × 26 × 23 cm3 and ∼20 kg, respectively. The combination of a three-stage vacuum system and CAPI reduced the pressure smoothly from atmospheric to ∼5 × 10-4 Torr, ensuring that the miniature ion funnel, quadrupole ion guide, and linear ion trap operated in a suitable and stable vacuum environment. The analytical performance of the instrument was evaluated with a nano-electron spray ionization source and a reserpine sample solution. A satisfactory mass resolution up to 4060 (m/Δm, FWHM) was achieved at m/z 609 when the mass scan rate was 495 Da s-1. Unit mass resolution was achieved at a mass scan rate of 6000 Da s-1. In addition, a limit of detection of 5 ng mL-1 was achieved and tandem mass spectrometry (MS3) was successfully performed with the instrument. Furthermore, the measurements showed high repeatability and stability (RSD < 6%). This portable mass spectrometer shows great potential for practical applications in on-site analyses, such as those required for food safety, drug analysis, environmental protection, forensic investigations, and homeland security.
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Affiliation(s)
- Xiaoxu Li
- School of Mechanical and Electrical Engineering, Soochow University, Suzhou, 215021, China.
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Abstract
INTRODUCTION Nanoproteomics, which is defined as quantitative proteome profiling of small populations of cells (<5000 cells), can reveal critical information related to rare cell populations, hard-to-obtain clinical specimens, and the cellular heterogeneity of pathological tissues. Areas covered: We present a brief review of the recent technological advances in nanoproteomics. These advances include new technologies or approaches covering major areas of proteomics workflow ranging from sample isolation, sample processing, high-resolution separations, to MS instrumentation. Expert commentary: We comment on the current state of nanoproteomics and discuss perspectives on both future technological directions and potential enabling applications.
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Affiliation(s)
- Ying Zhu
- a Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland , WA , USA
| | - Paul D Piehowski
- b Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Ryan T Kelly
- a Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- b Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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31
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ZHU H, ZHAO GS, XU L, PENG Z, FENG B, DONG JG, CHENG P, ZHOU Z. Development of a SIMION-Simulated Ion Funnel Tube for Proton Transfer Reaction Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61101-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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de Ruette N, Wolf M, Giacomozzi L, Alexander JD, Gatchell M, Stockett MH, Haag N, Zettergren H, Schmidt HT, Cederquist H. DESIREE electrospray ion source test bench and setup for collision induced dissociation experiments. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:075102. [PMID: 30068131 DOI: 10.1063/1.5030528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this paper, we give a detailed description of an electrospray ion source test bench and a single-pass setup for ion fragmentation studies at the Double ElectroStatic Ion Ring ExpEriment infrastructure at Stockholm University. This arrangement allows for collision-induced dissociation experiments at the center-of-mass energies between 10 eV and 1 keV. Charged fragments are analyzed with respect to their kinetic energies (masses) by means of an electrostatic energy analyzer with a wide angular acceptance and adjustable energy resolution.
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Affiliation(s)
- N de Ruette
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - M Wolf
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - L Giacomozzi
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - J D Alexander
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - M Gatchell
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - M H Stockett
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - N Haag
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - H Zettergren
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - H T Schmidt
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - H Cederquist
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
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33
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Prentice BM, Ryan DJ, Van de Plas R, Caprioli RM, Spraggins JM. Enhanced Ion Transmission Efficiency up to m/ z 24 000 for MALDI Protein Imaging Mass Spectrometry. Anal Chem 2018; 90:5090-5099. [PMID: 29444410 PMCID: PMC6905630 DOI: 10.1021/acs.analchem.7b05105] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The molecular identification of species of interest is an important part of an imaging mass spectrometry (IMS) experiment. The high resolution accurate mass capabilities of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) have recently been shown to facilitate the identification of proteins in matrix-assisted laser desorption/ionization (MALDI) IMS. However, these experiments are typically limited to proteins giving rise to ions of relatively low m/ z due to difficulties transmitting and measuring large molecular weight ions of low charge states. Herein we have modified the source gas manifold of a commercial MALDI FT-ICR MS to regulate the gas flow and pressure to maximize the transmission of large m/ z protein ions through the ion funnel region of the instrument. By minimizing the contribution of off-axis gas disruption to ion focusing and maximizing the effective potential wall confining the ions through pressure optimization, the signal-to-noise ratios (S/N) of most protein species were improved by roughly 1 order of magnitude compared to normal source conditions. These modifications enabled the detection of protein standards up to m/ z 24 000 and the detection of proteins from tissue up to m/ z 22 000 with good S/N, roughly doubling the mass range for which high quality protein ion images from rat brain and kidney tissue could be produced. Due to the long time-domain transients (>4 s) required to isotopically resolve high m/ z proteins, we have used these data as part of an FT-ICR IMS-microscopy data-driven image fusion workflow to produce estimated protein images with both high mass and high spatial resolutions.
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Affiliation(s)
- Boone M. Prentice
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Daniel J. Ryan
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, Delft 2628 CD, The Netherlands
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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34
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Coates RA, Armentrout PB. Binding energies of hydrated cobalt(ii) by collision-induced dissociation and theoretical studies: evidence for a new critical size. Phys Chem Chem Phys 2018; 20:802-818. [PMID: 29210383 DOI: 10.1039/c7cp05828d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The experimental sequential bond energies for loss of water from Co2+(H2O)x complexes, x = 5-11, are determined by threshold collision-induced dissociation (TCID) using a guided ion beam tandem mass spectrometer with a thermal electrospray ionization source. Kinetic energy dependent TCID cross sections are analyzed to yield 0 K thresholds for sequential loss of neutral water molecules. The thresholds are converted from 0 to 298 K values to give hydration enthalpies and free energies. Theoretical geometry optimizations and single point energy calculations at several levels of theory are performed for the reactant and product ion complexes. Theoretical bond energies for ground structures are used for direct comparison with experimental values to obtain structural information on these complexes. In addition, the dissociative charge separation process, Co2+(H2O)x → CoOH+(H2O)m + H+(H2O)x-m-1, is observed at x = 4, 6, and 7 in competition with primary water loss products. Energies for the charge separation rate-limiting transition states are calculated and compared to experimental threshold measurements. Results suggest that the critical size for which charge separation is energetically favored over water loss is xcrit = 6, in contrast to lower values in previous literature reports.
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Affiliation(s)
- Rebecca A Coates
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, UT 84112, USA.
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35
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Rezaee M, McNary CP, Armentrout PB. Threshold collision-induced dissociation and theoretical study of protonated azobenzene. J Chem Phys 2017; 147:164308. [DOI: 10.1063/1.5000683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Mohammadreza Rezaee
- Department of Physics, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Christopher P. McNary
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm. 2020, Salt Lake City, Utah 84112, USA
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm. 2020, Salt Lake City, Utah 84112, USA
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36
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McNary CP, Armentrout PB. Non-adiabatic behavior in the homolytic and heterolytic bond dissociation of protonated hydrazine: A guided ion beam and theoretical investigation. J Chem Phys 2017; 147:124306. [DOI: 10.1063/1.4997415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Christopher P. McNary
- Department of Chemistry, University of Utah, 315 S. 1400 E,
Room 2020, Salt Lake City, Utah 84112, USA
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E,
Room 2020, Salt Lake City, Utah 84112, USA
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37
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Carpenter JE, McNary CP, Furin A, Sweeney AF, Armentrout PB. How Hot are Your Ions Really? A Threshold Collision-Induced Dissociation Study of Substituted Benzylpyridinium "Thermometer" Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1876-1888. [PMID: 28500582 DOI: 10.1007/s13361-017-1693-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/17/2017] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
The first absolute experimental bond dissociation energies (BDEs) for the main heterolytic bond cleavages of four benzylpyridinium "thermometer" ions are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. In this experiment, substituted benzylpyridinium ions are introduced into the apparatus using an electrospray ionization source, thermalized, and collided with Xe at varied kinetic energies to determine absolute cross-sections for these reactions. Various effects are accounted for, including kinetic shifts, multiple collisions, and internal and kinetic energy distributions. These experimentally measured 0 K BDEs are compared with computationally predicted values at the B3LYP-GD3BJ, M06-GD3, and MP2(full) levels of theory with a 6-311+G(2d,2p) basis set using vibrational frequencies and geometries determined at the B3LYP/6-311+G(d,p) level. Additional dissociation pathways are observed for nitrobenzylpyridinium experimentally and investigated using these same levels of theory. Experimental BDEs are also compared against values in the literature at the AM1, HF, B3LYP, B3P86, and CCSD(T) levels of theory. Of the calculated values obtained in this work, the MP2(full) level of theory with counterpoise corrections best reproduces the experimental results, as do the similar literature CCSD(T) values. Lastly, the survival yield method is used to determine the characteristic temperature (Tchar) of the electrospray source prior to the thermalization region and to confirm efficient thermalization. Graphical Abstract ᅟ.
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Affiliation(s)
- John E Carpenter
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, UT, 84112, USA
| | - Christopher P McNary
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, UT, 84112, USA
| | - April Furin
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, UT, 84112, USA
| | - Andrew F Sweeney
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, UT, 84112, USA
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, UT, 84112, USA.
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38
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Dilger JM, Glover MS, Clemmer DE. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1293-1303. [PMID: 28357817 DOI: 10.1007/s13361-016-1592-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/17/2016] [Accepted: 12/18/2016] [Indexed: 05/18/2023]
Abstract
Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases. Graphical Abstract ᅟ.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
- Spectrum Warfare Systems Department, Naval Surface Warfare Center, Crane Division, Crane, IN, 47522, USA.
| | - Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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39
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Coates RA, Armentrout PB. Thermochemical Investigations of Hydrated Nickel Dication Complexes by Threshold Collision-Induced Dissociation and Theory. J Phys Chem A 2017; 121:3629-3646. [DOI: 10.1021/acs.jpca.7b00635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rebecca A. Coates
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake
City, Utah 84112, United States
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake
City, Utah 84112, United States
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40
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Hoffman NM, Opačić B, Reilly PTA. Note: An inexpensive square waveform ion funnel driver. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:016104. [PMID: 28147692 DOI: 10.1063/1.4974345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
An inexpensive frequency variable square waveform generator (WFG) was developed to use with existing sinusoidal waveform driven ion funnels. The developed WFG was constructed using readily available low voltage DC power supplies and discrete components placed in printed circuit boards. As applied to ion funnels, this WFG represents considerable cost savings over commercially available products without sacrificing performance. Operation of the constructed pulse generator has been demonstrated for a 1 nF ion funnel at an operating frequency of 1 MHz while switching 48 Vp-p.
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Affiliation(s)
- Nathan M Hoffman
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, USA
| | - Bojana Opačić
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, USA
| | - Peter T A Reilly
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, USA
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41
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Electrospray Ionization. Mass Spectrom (Tokyo) 2017. [DOI: 10.1007/978-3-319-54398-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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42
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McNary CP, Armentrout PB. Threshold Collision-Induced Dissociation of Proton-Bound Hydrazine and Dimethylhydrazine Clusters. J Phys Chem A 2016; 120:9690-9701. [PMID: 27973810 DOI: 10.1021/acs.jpca.6b09318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Threshold collision-induced dissociation (TCID) using a guided ion beam tandem mass spectrometer is performed on (N2H4)nH+ where n = 2-4 and on the proton-bound unsymmetrical 1,1-dimethylhydrazine (UDMH) dimer complex. The primary dissociation pathway for all reactants consists of loss of a single hydrazine (or UDMH) molecule followed by the sequential loss of additional hydrazine molecules at higher collision energies for n = 3 and 4. The data were analyzed using a statistical model after accounting for internal and kinetic energy distributions, multiple collisions, and kinetic shifts to obtain 0 K bond dissociation energies (BDEs). These are also converted to values at room temperature by using a rigid rotor/harmonic oscillator approximation and theoretical molecular constants. Experimental BDEs are compared to theoretical BDEs determined at the B3LYP, M06, mPW1PW91, PBE0, MP2(full), and CCSD(T) levels of theory with and without empirical dispersion with a 6-311+G(2d,2p) basis set. The structures of all clusters are explored and exhibit extensive hydrogen bonding.
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Affiliation(s)
- Christopher P McNary
- Department of Chemistry, University of Utah , 315 S. 1400 E. Room 2020, Salt Lake City, Utah 84112, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah , 315 S. 1400 E. Room 2020, Salt Lake City, Utah 84112, United States
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43
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McNary CP, Armentrout PB. Threshold collision-induced dissociation of protonated hydrazine and dimethylhydrazine clustered with water. J Chem Phys 2016; 145:214311. [PMID: 28799395 DOI: 10.1063/1.4971238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Threshold collision-induced dissociation using a guided ion beam tandem mass spectrometer is performed on (N2H4)H+(H2O)n, where n = 1 and 2, and on the protonated unsymmetrical 1,1-dimethylhydrazine one-water complex. The primary dissociation pathway for all clusters is a loss of a single water molecule, which for n = 2 is followed by the sequential loss of an additional water molecule at higher collision energies. The data are analyzed using a statistical model after accounting for internal and kinetic energy distributions, multiple collisions, and kinetic shifts to obtain 0 K bond dissociation energies (BDEs). These are also converted using a rigid rotor/harmonic oscillator approximation to yield thermodynamic values at room temperature. Experimental BDEs compare favorably to theoretical BDEs determined at the B3LYP, M06, mPW1PW91, PBE0, MP2(full), and CCSD(T) levels of theory with a 6-311+G(2d,2p) basis set both with and without empirical dispersion. These calculations also allow visualization of the structures of these complexes, which are simple hydrogen-bonded donor-acceptors.
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Affiliation(s)
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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44
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Wu RR, Chen Y, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2'-deoxyguanosine and guanosine. Phys Chem Chem Phys 2016; 18:2968-80. [PMID: 26740232 DOI: 10.1039/c5cp05738h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental and theoretical investigations suggest that hydrolysis of N-glycosidic bonds generally involves a concerted SN2 or a stepwise SN1 mechanism. While theoretical investigations have provided estimates for the intrinsic activation energies associated with N-glycosidic bond cleavage reactions, experimental measurements to validate the theoretical studies remain elusive. Here we report experimental investigations for N-glycosidic bond cleavage of the protonated guanine nucleosides, [dGuo+H](+) and [Guo+H](+), using threshold collision-induced dissociation (TCID) techniques. Two major dissociation pathways involving N-glycosidic bond cleavage, resulting in production of protonated guanine or the elimination of neutral guanine are observed in competition for both [dGuo+H](+) and [Guo+H](+). The detailed mechanistic pathways for the N-glycosidic bond cleavage reactions observed are mapped via electronic structure calculations. Excellent agreement between the measured and B3LYP calculated activation energies and reaction enthalpies for N-glycosidic bond cleavage of [dGuo+H](+) and [Guo+H](+) in the gas phase is found indicating that these dissociation pathways involve stepwise E1 mechanisms in analogy to the SN1 mechanisms that occur in the condensed phase. In contrast, MP2 is found to significantly overestimate the activation energies and slightly overestimate the reaction enthalpies. The 2'-hydroxyl substituent is found to stabilize the N-glycosidic bond such that [Guo+H](+) requires ∼25 kJ mol(-1) more than [dGuo+H](+) to activate the glycosidic bond.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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45
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Ujma J, Giles K, Morris M, Barran PE. New High Resolution Ion Mobility Mass Spectrometer Capable of Measurements of Collision Cross Sections from 150 to 520 K. Anal Chem 2016; 88:9469-9478. [DOI: 10.1021/acs.analchem.6b01812] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jakub Ujma
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
for Biotechnology, University of Manchester, Manchester M1 7DN, U.K
| | | | | | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
for Biotechnology, University of Manchester, Manchester M1 7DN, U.K
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46
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Wu RR, Rodgers MT. Tautomerization lowers the activation barriers for N-glycosidic bond cleavage of protonated uridine and 2'-deoxyuridine. Phys Chem Chem Phys 2016; 18:24451-9. [PMID: 27536972 DOI: 10.1039/c6cp03620a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The gas-phase conformations of protonated uridine, [Urd+H](+), and its 2'-deoxy form, protonated 2'-deoxyuridine, [dUrd+H](+), have been examined in detail previously by infrared multiple photon dissociation action spectroscopy techniques. Both 2,4-dihydroxy tautomers and O4 protonated conformers of [Urd+H](+) and [dUrd+H](+) were found to coexist in the experiments with the 2,4-dihydroxy tautomers dominating the population. In the present study, the kinetic energy dependence of the collision-induced dissociation behavior of [Urd+H](+) and [dUrd+H](+) are examined using a guided ion beam tandem mass spectrometer to probe the mechanisms and energetics for activated dissociation of these protonated nucleosides. The primary dissociation pathways observed involve N-glycosidic bond cleavage leading to competitive elimination of protonated or neutral uracil. The potential energy surfaces (PESs) for these N-glycosidic bond cleavage pathways are mapped out via electronic structure calculations for the mixture of 2,4-dihydroxy tautomers and O4 protonated conformers of [Urd+H](+) and [dUrd+H](+) populated in the experiments. The calculated activation energies (AEs) and heats of reaction (ΔHrxns) for N-glycosidic bond cleavage at both the B3LYP and MP2(full) levels of theory are compared to the measured values. The agreement between experiment and theory indicates that B3LYP provides better estimates of the energetics of the species along the PESs for N-glycosidic bond cleavage than MP2, and that the 2,4-dihydroxy tautomers, which are stabilized by strong hydrogen-bonding interactions, predominantly influence the observed threshold dissociation behavior of [Urd+H](+) and [dUrd+H](+).
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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47
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Wu RR, Rodgers MT. O2 Protonation Controls Threshold Behavior for N-Glycosidic Bond Cleavage of Protonated Cytosine Nucleosides. J Phys Chem B 2016; 120:4803-11. [PMID: 27159774 DOI: 10.1021/acs.jpcb.6b04388] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
IRMPD action spectroscopy studies of protonated 2'-deoxycytidine and cytidine, [dCyd+H](+) and [Cyd+H](+), have established that both N3 and O2 protonated conformers coexist in the gas phase. Threshold collision-induced dissociation (CID) of [dCyd+H](+) and [Cyd+H](+) is investigated here using guided ion beam tandem mass spectrometry techniques to elucidate the mechanisms and energetics for N-glycosidic bond cleavage. N-Glycosidic bond cleavage is observed as the major dissociation pathways resulting in competitive elimination of either protonated or neutral cytosine for both protonated cytosine nucleosides. Electronic structure calculations are performed to map the potential energy surfaces (PESs) for both N-glycosidic bond cleavage pathways observed. The molecular parameters derived from theoretical calculations are employed for thermochemical analysis of the energy-dependent CID data to determine the minimum energies required to cleave the N-glycosidic bond along each pathway. B3LYP and MP2(full) computed activation energies for N-glycosidic bond cleavage associated with elimination of protonated and neutral cytosine, respectively, are compared to measured values to evaluate the efficacy of these theoretical methods in describing the dissociation mechanisms and PESs for N-glycosidic bond cleavage. The 2'-hydroxyl of [Cyd+H](+) is found to enhance the stability of the N-glycosidic bond vs that of [dCyd+H](+). O2 protonation is found to control the threshold energies for N-glycosidic bond cleavage as loss of neutral cytosine from the O2 protonated conformers is found to require ∼25 kJ/mol less energy than the N3 protonated analogues, and the activation energies and reaction enthalpies computed using B3LYP exhibit excellent agreement with the measured thresholds for the O2 protonated conformers.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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48
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Xu H, Zhang X, Wang Y, Ling X, Tian D. Design and performance evaluation of a novel ion funnel driven by a phase-modulated rectangular wave. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1079-1086. [PMID: 27003045 DOI: 10.1002/rcm.7517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE The ion funnel has proven to be an important ion transport device. It is used in mass spectrometry as a replacement for the ion transmission limited skimmer. However, conventional out-of-phase radiofrequency (RF) supply approaches inevitably produce potential barriers, decreasing transmission efficiency. A novel RF supply method is proposed that produces better transmission performance. METHODS We designed an ion funnel driven by a phase-modulated rectangular wave (PMRW). The potential field distributions of the PMRW ion funnel and a conventional ion funnel were computer simulated to evaluate their focusing properties. A series of simulations were produced using the SIMION ion-optics simulation program to compare the transmission efficiency of the two types of funnel. Preliminary experimental results were obtained using an electrospray ionization mass spectrometry platform with polypropylene glycol, propylamine and butylamine samples. RESULTS The electrical potential distribution of a PMRW ion funnel has a bowl shape at the cross section of the electrodes, rather than in the field-free region; this benefits focusing performance. A comparison of ion trajectories and flight time data produced by the SIMION simulations showed that the potential barrier did not exist in the PMRW mode. The experimental results showed that the PMRW method increased the signal intensity by 150-200% for propylamine and butylamine and 50% for polypropylene glycol. CONCLUSIONS A novel PMRW ion funnel has been designed and developed. The simulation and experimental results indicate that the PMRW ion funnel has better transmission efficiency than the conventional ion funnel, particularly for low mass-to-charge ratio ions.
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Affiliation(s)
- Hualei Xu
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, 130012, China
| | - Xiaohua Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yuzhuo Wang
- National Institute of Metrology, Beijing, 100013, China
| | - Xing Ling
- Beijing Perkinje General Instrument Co., Ltd, Beijing, 100085, China
| | - Di Tian
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, 130012, China
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49
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Gaye MM, Nagy G, Clemmer DE, Pohl NLB. Multidimensional Analysis of 16 Glucose Isomers by Ion Mobility Spectrometry. Anal Chem 2016; 88:2335-44. [PMID: 26799269 DOI: 10.1021/acs.analchem.5b04280] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diastereomeric adducts comprising an enantiomerically pure monosaccharide analyte, a peptide, and/or an amino acid and a divalent metal ion (for 16 different monosaccharide isomers) are generated by electrospray ionization and analyzed by combined ion mobility spectrometry-mass spectrometry (IMS-MS) techniques. Mobility distributions of [l-Ser + M + H](+) (where l-Ser is l-serine and M is a given monosaccharide), [l-Phe-Gly + M + H](+) (where l-Phe-Gly is l-phenylalanine-glycine), and [Mn(II) + (l-Phe-Gly - H) + M](+) complex ions are used to determine collision cross sections (ccs in Å(2)), and groups of cross sections for different clusters are proposed as means of identifying the sugar isomers. Within one type of complex, variations in ccs do not always allow delineation between the 16 glucose isomers, but interestingly, when ccs of three different ions are combined as a spatial vector, enantiomers are partially resolved. As a result of this analysis, l-glucose, d-glucose, l-allose, d-allose, d-gulose, d-galactose, and l-mannose are delineated, and for all eight enantiomeric pairs, d and l entities display different coordinates. In addition, different combinations of amino acids, peptide, and metal ions are surveyed, and the potential for yielding unique coordinates for the generated diastereomeric complexes is assessed.
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Affiliation(s)
- M M Gaye
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - G Nagy
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - D E Clemmer
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - N L B Pohl
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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50
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Wu RR, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability. Phys Chem Chem Phys 2016; 18:16021-32. [DOI: 10.1039/c6cp01445c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
N3 protonation induces base rotation and stabilizes the syn orientation of the adenine nucleobase of [dAdo+H]+ and [Ado+H]+via formation of a strong intramolecular N3H+⋯O5′ hydrogen-bonding interaction, which in turn influences the mechanisms and energetics for N-glycosidic bond cleavage.
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Affiliation(s)
- R. R. Wu
- Department of Chemistry
- Wayne State University
- Detroit
- USA
| | - M. T. Rodgers
- Department of Chemistry
- Wayne State University
- Detroit
- USA
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