1
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Capek GO, Howdieshell CJ, Garand E. Square Parametric Excitation: A Digital Resonant Method for the Quadrupole Ion Trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1846-1853. [PMID: 39012076 DOI: 10.1021/jasms.4c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Digital ion trap technology is an alternate method for driving quadrupole ion traps and mass filters using variable frequency, fixed amplitude RF square waves in place of variable amplitude, fixed frequency RF sine waves. This technique offers some advantages such as an increase in the high mass analysis range by varying frequency and lower overall voltage requirements. Here, we present a complex square waveform developed for resonant parametric excitation in a quadrupole linear ion trap. Unlike traditional resonance methods, the driving RF square wave and auxiliary square wave are coupled using the same digital circuitry without the need for transformer coupling. In this work, we use this complex waveform to selectively excite the first order parametric resonances of ion motion. The square parametric excitation method presented here employs a simple and repetitive circuit design consisting of a low-voltage waveform generator followed by a series of high-voltage MOSFET switches. This design allows for resonance methods to be easily implemented in the all-digital quadrupole. The complex square waveform can perform the same useful functions as sine wave auxiliary signals, such as selective mass elimination and mass isolation. We also demonstrate that the mass resolution performance and S/N of our digital mass spectrometer is improved by applying the complex square waveform during ion ejection.
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Affiliation(s)
- Grace O Capek
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Casey J Howdieshell
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
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2
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Dunham SD, Brodbelt JS. Enhancing Top-Down Analysis of Proteins by Combining Ultraviolet Photodissociation (UVPD), Proton-Transfer Charge Reduction (PTCR), and Gas-Phase Fractionation to Alleviate the Impact of Nondissociated Precursor Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:255-265. [PMID: 38150423 DOI: 10.1021/jasms.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Recent advances in top-down mass spectrometry strategies continue to improve the analysis of intact proteins. 193 nm ultraviolet photodissociation (UVPD) is one method well-suited for top-down analysis. UVPD is often performed using relatively low photon flux in order to limit multiple-generation dissociation of fragment ions and maximize sequence coverage. Consequently, a large portion of the precursor ion survives the UVPD process, dominates the spectrum, and may impede identification of fragment ions. Here, we explore the isolation of subpopulations of fragment ions lower and higher than the precursor ion after UVPD as a means to eliminate the impact of the surviving precursor ion on the detection of low abundance fragment ions. This gas-phase fractionation method improved sequence coverage harvested from fragment ions found in the m/z regions lower and higher than the precursor by an average factor of 1.3 and 2.3, respectively. Combining this gas-phase fractionation method with proton transfer charge reduction (PTCR) further increased the sequence coverage obtained from these m/z regions by another factor of 1.3 and 1.4, respectively. Implementing a post-UVPD fractionation + PTCR strategy with six fractionation events resulted in a sequence coverage of 75% for enolase, the highest reported for 193 nm UVPD.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
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3
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Prakash P, Manchanda P, Paouri E, Bisht K, Sharma K, Wijewardhane PR, Randolph CE, Clark MG, Fine J, Thayer EA, Crockett A, Gasmi N, Stanko S, Prayson RA, Zhang C, Davalos D, Chopra G. Amyloid β Induces Lipid Droplet-Mediated Microglial Dysfunction in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.04.543525. [PMID: 37333071 PMCID: PMC10274698 DOI: 10.1101/2023.06.04.543525] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Several microglia-expressed genes have emerged as top risk variants for Alzheimer's disease (AD). Impaired microglial phagocytosis is one of the main proposed outcomes by which these AD-risk genes may contribute to neurodegeneration, but the mechanisms translating genetic association to cellular dysfunction remain unknown. Here we show that microglia form lipid droplets (LDs) upon exposure to amyloid-beta (Aβ), and that their LD load increases with proximity to amyloid plaques in brains from human patients and the AD mouse model 5xFAD. LD formation is dependent upon age and disease progression and is more prominent in the hippocampus in mice and humans. Despite variability in LD load between microglia from male versus female animals and between cells from different brain regions, LD-laden microglia exhibited a deficit in Aβ phagocytosis. Unbiased lipidomic analysis identified a substantial decrease in free fatty acids (FFAs) and a parallel increase in triacylglycerols (TAGs) as the key metabolic transition underlying LD formation. We demonstrate that DGAT2, a key enzyme for the conversion of FFAs to TAGs, promotes microglial LD formation, is increased in microglia from 5xFAD and human AD brains, and that inhibiting DGAT2 improved microglial uptake of Aβ. These findings identify a new lipid-mediated mechanism underlying microglial dysfunction that could become a novel therapeutic target for AD.
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Affiliation(s)
- Priya Prakash
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Palak Manchanda
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Evi Paouri
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Kanchan Bisht
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Kaushik Sharma
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | | | - Matthew G. Clark
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Jonathan Fine
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Alexis Crockett
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Nadia Gasmi
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Sarah Stanko
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Richard A. Prayson
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Chi Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Dimitrios Davalos
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case, Western Reserve University, Cleveland, OH 44106, USA
| | - Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
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4
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Fabijanczuk KC, Hager JW, McLuckey SA. Separation and Simultaneous Trapping of Multiply Charged and Singly Charged Ions for Mass Spectrometry: Application to Lipid Mixtures. Anal Chem 2023; 95:6115-6121. [PMID: 37000630 PMCID: PMC10129443 DOI: 10.1021/acs.analchem.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Conventional electrospray ionization (ESI) of mixtures can give rise to singly and multiply charged analyte species that overlap in mass-to-charge (m/z) ratios, which can complicate the analysis of individual components. The overlap in m/z for ions of different mass and charge is particularly problematic when ions of low relative abundance are of interest. For example, cardiolipins (CLs) are structurally complex phospholipids present in low relative abundance in the lipidome but play crucial roles in mitochondrial metabolism and various regulatory processes. ESI of CLs in negative ion mode shows abundant doubly deprotonated ions and minor singly deprotonated ions. In the ESI of lipid extracts, highly abundant singly charged phospholipids extensively overlap in m/z space with CL dianions of much lesser abundance, thereby complicating the study of the CLs. To address this challenge, we employed a gas-phase approach to separate singly charged ions from a population of ions of mixed charge states while allowing for the storage of one or both of the separated ion populations. Herein, we describe the considerations for applying enhanced singly charged (ESC) and enhanced multiply charged (EMC) scans to perform a gas-phase separation of singly charged lipids from doubly charged lipids in an Escherichia coli extract. This method allows for improved signal-to-noise (S/N) ratio of low abundance ions with minimal overall signal loss, removal of "chemical noise" arising from singly charged ions, and allows for retention of spatially separated ions within a mass spectrometer.
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Affiliation(s)
| | - James W. Hager
- Sciex, 71 Four Valley Road, Concord, ON, L4K 4V8, Canada
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
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5
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Shenault DM, McLuckey SA, Franklin ET. Localization of cyclopropyl groups and alkenes within glycerophospholipids using gas-phase ion/ion chemistry. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4913. [PMID: 36916143 PMCID: PMC10014902 DOI: 10.1002/jms.4913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Shotgun lipid analysis using electrospray ionization tandem mass spectrometry (ESI-MS/MS) is a common approach for the identification and characterization of glycerophohspholipids GPs. ESI-MS/MS, with the aid of collision-induced dissociation (CID), enables the characterization of GP species at the headgroup and fatty acyl sum compositional levels. However, important structural features that are often present, such as carbon-carbon double bond(s) and cyclopropane ring(s), can be difficult to determine. Here, we report the use of gas-phase charge inversion reactions that, in combination with CID, allow for more detailed structural elucidation of GPs. CID of a singly deprotonated GP, [GP - H]- , generates FA anions, [FA - H]- . The fatty acid anions can then react with doubly charged cationic magnesium tris-phenanthroline complex, [Mg(Phen)3 ]2+ , to form charge inverted complex cations of the form [FA - H + MgPhen2 ]+ . CID of the complex generates product ion spectral patterns that allow for the identification of carbon-carbon double bond position(s) as well as the sites of cyclopropyl position(s) in unsaturated lipids. This approach to determining both double bond and cyclopropane positions is demonstrated with GPs for the first time using standards and is applied to lipids extracted from Escherichia coli.
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Affiliation(s)
- De’Shovon M. Shenault
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, United States, 47907-2084
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, United States, 47907-2084
| | - Elissia T. Franklin
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, United States, 47907-2084
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6
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Dunham SD, Wei B, Lantz C, Loo JA, Brodbelt JS. Impact of Internal Fragments on Top-Down Analysis of Intact Proteins by 193 nm UVPD. J Proteome Res 2023; 22:170-181. [PMID: 36503236 DOI: 10.1021/acs.jproteome.2c00583] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
193 nm ultraviolet photodissociation (UVPD) allows high sequence coverage to be obtained for intact proteins using terminal fragments alone. However, internal fragments, those that contain neither N- nor C- terminus, are typically ignored, neglecting their potential to bolster characterization of intact proteins. Here, we explore internal fragments generated by 193 nm UVPD for proteins ranging in size from 17-47 kDa and using the ClipsMS algorithm to facilitate searches for internal fragments. Internal fragments were only retained if identified in multiple replicates in order to reduce spurious assignments and to explore the reproducibility of internal fragments generated by UVPD. Inclusion of internal fragment improved sequence coverage by an average of 18% and 32% for UVPD and HCD, respectively, across all proteins and charge states studied. However, only an average of 18% of UVPD internal fragments were identified in two out of three replicates relative to the average number identified across all replicates for all proteins studied. Conversely, for HCD, an average of 63% of internal fragments were retained across replicates. These trends reflect an increased risk of false-positive identifications and a need for caution when considering internal fragments for UVPD. Additionally, proton-transfer charge reduction (PTCR) reactions were performed following UVPD or HCD to assess the impact on internal fragment identifications, allowing up to 20% more fragment ions to be retained across multiple replicates. At this time, it is difficult to recommend the inclusion of the internal fragment when searching UVPD spectra without further work to develop strategies for reducing the possibilities of false-positive identifications. All mass spectra are available in the public repository jPOST with the accession number JPST001885.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benqian Wei
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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7
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Randolph CE, Beveridge CH, Iyer S, Blanksby SJ, McLuckey SA, Chopra G. Identification of Monomethyl Branched-Chain Lipids by a Combination of Liquid Chromatography Tandem Mass Spectrometry and Charge-Switching Chemistries. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2156-2164. [PMID: 36218280 PMCID: PMC10173259 DOI: 10.1021/jasms.2c00225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
While various mass spectrometric approaches have been applied to lipid analysis, unraveling the extensive structural diversity of lipids remains a significant challenge. Notably, these approaches often fail to differentiate between isomeric lipids─a challenge that is particularly acute for branched-chain fatty acids (FAs) that often share similar (or identical) mass spectra to their straight-chain isomers. Here, we utilize charge-switching strategies that combine ligated magnesium dications with deprotonated fatty acid anions. Subsequent activation of these charge inverted anions yields mass spectra that differentiate anteiso-branched- from straight-chain and iso-branched-chain FA isomers with the predictable fragmentation enabling de novo assignment of anteiso branch points. The application of these charge-inversion chemistries in both gas- and solution-phase modalities is demonstrated to assign the position of anteiso-methyl branch-points in FAs and, with the aid of liquid chromatography, can be extended to de novo assignment of additional branching sites via predictable fragmentation patterns as methyl branching site(s) move closer to the carboxyl carbon. The gas-phase approach is shown to be compatible with top-down structure elucidation of complex lipids such as phosphatidylcholines, while the integration of solution-phase charge-inversion with reversed phase liquid chromatography enables separation and unambiguous identification of FA structures within isomeric mixtures. Taken together, the presented charge-switching MS-based technique, in combination with liquid chromatography, enables the structural identification of branched-chain FA without the requirement of authentic methyl-branched FA reference standards.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Connor H. Beveridge
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Sanjay Iyer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Stephen J. Blanksby
- Central Analytical Research Facility and the School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
- Department of Computer Science (by courtesy), Purdue Institutes of Drug Discovery and Integrative Neuroscience, Purdue Center for Cancer Research, West Lafayette, Indiana, 47907, USA
- Address reprint requests to: Dr. Gaurav Chopra, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 496-6108, Fax: (765) 494-0239,
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8
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Bhanot JS, Fabijanczuk KC, Abdillahi AM, Chao HC, Pizzala NJ, Londry FA, Dziekonski ET, Hager JW, McLuckey SA. Adaptation and Operation of a Quadrupole/Time-of-Flight Tandem Mass Spectrometer for High Mass Ion/Ion Reaction Studies. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2022; 478:116874. [PMID: 37032994 PMCID: PMC10081487 DOI: 10.1016/j.ijms.2022.116874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A commercial quadrupole/time-of-flight tandem mass spectrometer has been modified and evaluated for its performance in conducting ion/ion reaction studies involving high mass (>100 kDa) ions. Modifications include enabling the application of dipolar AC waveforms to opposing rods in three quadrupole arrays in the ion path. This modification allows for resonance excitation of ions to effect ion activation, selective ion isolation, and ion parking. The other set of opposing rods in each array is enabled for the application of dipolar DC voltages for the purpose of broad-band (non-selective) ion heating. The plates between each quadrupole array are enabled for the application of either DC or AC (or both) voltages. The use of AC voltages allows for the simultaneous storage of ions of opposite polarity, thereby enabling mutual storage ion/ion reactions. Ions derived from nano-electrospray ionization of GroEL and β-galactosidase under native conditions were used to evaluate limits of instrument performance, in terms of m/z range, ion isolation, and ion storage. After adjustment of the pulser frequency, ions as high in m/z as 400,000 were detected. Significant losses in efficiency were noted above m/z 250,000 that is likely due to roll-over in the ion detector efficiency and possibly also due to limitations in ion transfer efficiency from the collision quadrupole to the pulser region of the mass analyzer. No measurable decrease in the apparent mass resolving power was noted upon charge state reduction of the model ions. Resonance ejection techniques that employ the dipolar AC capabilities of the quadrupoles allow for ion isolation at m/z values much greater than the RF/DC limitation of Q1 of m/z = 2100. For example, at the highest low-mass cutoff achievable in the collision quadrupole (m/z = 500), it is possible to isolate ions of m/z as high as 62,000. This is limited by the lowest dipolar AC frequency (5 kHz) that can be applied. A simple model is included to provide for an estimate of the ion cloud radius based on ion m/z, ion z, and ion trap operating conditions. The model predicts that singly charged ions of 1 MDa and thermal energy can be contained in the ion trap at the maximum low-mass cutoff, although such an ion would not be detected efficiently. Doubly charged GroEL ions were observed experimentally. Collectively, the performance characteristics at high m/z, the functionality provided by the standard instrument capabilities, the modifications described above, and highly flexible instrument control software provide for a highly versatile platform for the study of high mass ion/ion reactions.
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Affiliation(s)
- Jay S. Bhanot
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
| | | | | | - Hsi-Chun Chao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
| | - Nicolas J. Pizzala
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
| | | | | | | | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
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9
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Fabijanczuk KC, Altalhi WAO, Aldajani AMO, Canty AJ, McLuckey SA, O'Hair RAJ. Ion-pairs as a gateway to transmetalation: aryl transfer from boron to nickel and magnesium. Dalton Trans 2022; 51:5699-5705. [PMID: 35323833 DOI: 10.1039/d2dt00746k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas-phase ion-ion reactions between tris-1,10-phenantholine metal dications, [(phen)3M]2+ (where M = Ni and Mg), and the tetraphenylborate anion yield the ion-pairs {[(phen)3M]2+[BPh4]-}+. The ion-pairs undergo transmetalation upon loss of a phen ligand to give the organometallic complexes [(phen)2M(Ph)]+. DFT calculations, used to determine the energy barriers for the transmetalation reactions and the hydrolysis reactions, are entirely consistent with the experimental results.
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Affiliation(s)
| | - Weam A O Altalhi
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Victoria 3010, Australia. .,Department of Chemistry, Prince Sattam Bin Abdulaziz University, Hotat Bani Tamim, 16511 Saudi Arabia
| | - Asma M O Aldajani
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Victoria 3010, Australia. .,Department of Chemistry, College of Science, University of Bisha, Bisha 61922, P.O. Box 551, Saudi Arabia
| | - Allan J Canty
- School of Physical Sciences - Chemistry, University of Tasmania, Private Bag 75, Hobart, Tasmania 7001, Australia
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Richard A J O'Hair
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Victoria 3010, Australia.
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10
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Dunham SD, Sanders JD, Holden DD, Brodbelt JS. Improving the Center Section Sequence Coverage of Large Proteins Using Stepped-Fragment Ion Protection Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:446-456. [PMID: 35119856 DOI: 10.1021/jasms.1c00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry has gained attention in recent years for its ability to provide high sequence coverage of intact proteins. However, secondary dissociation of fragment ions, in which fragment ions subjected to multiple laser pulses decompose into small products, is a common phenomenon during UVPD that contributes to limited coverage in the midsection of protein sequences. To counter secondary dissociation, a method involving the application of notched waveforms to modulate the trajectories of fragment ions away from the laser beam, termed fragment ion protection (FIP), was previously developed to reduce the probability of secondary dissociation. This, in turn, increased the number of identified large fragment ions. In the present study, FIP was applied to UVPD of large proteins ranging in size from 29 to 55 kDa, enhancing the abundances of large fragment ions. A stepped-FIP strategy was implemented in which UVPD mass spectra were collected using multiple different amplitudes of the FIP waveforms and then the results from the mass spectra were combined. By using stepped-FIP, the number of fragment ions in the midsections of the sequences increased for all proteins. For example, whereas no fragment ions were identified in the middle section of the sequence for glutamate dehydrogenase (55 kDa, 55+ charge state), 10 sequence ions were identified by using UVPD-FIP.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Dustin D Holden
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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11
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Pitts-McCoy AM, Abdillahi AM, Lee KW, McLuckey SA. Multiply Charged Cation Attachment to Facilitate Mass Measurement in Negative-Mode Native Mass Spectrometry. Anal Chem 2022; 94:2220-2226. [PMID: 35029382 PMCID: PMC9670251 DOI: 10.1021/acs.analchem.1c04875] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Native mass spectrometry (MS) is usually conducted in the positive-ion mode; however, in some cases, it is advantageous to use the negative-ion polarity. Challenges associated with native MS using ensemble measurements (i.e., the measurement of many ions at a time as opposed to the measurement of the charge and the mass-to-charge ratio of individual ions) include narrow charge state distributions with the potential for an overlap in neighboring charge states. These issues can either compromise or preclude confident charge state (and hence mass) determination. Charge state determination in challenging instances can be enabled via the attachment of multiply charged ions of opposite polarity. Multiply charged ion attachment facilitates the resolution of charge states and generates mass-to-charge (m/z) information across a broad m/z range. In this work, we demonstrated the attachment of multiply charged cations to anionic complexes generated under native MS conditions. To illustrate the flexibility available in selecting the mass and charge of the reagents, the 15+ and 20+ charge states of horse skeletal muscle apomyoglobin and the 20+ and 30+ charge states of bovine carbonic anhydrase were demonstrated to attach to model complex anions derived from either β-galactosidase or GroEL. The exclusive attachment of reagent ions is observed with no evidence for proton transfer, which is the key for the unambiguous interpretation of the post-ion/ion reaction product ion spectrum. To illustrate the application to mixtures of complex ions, the 10+ charge state of bovine ubiquitin was attached to mixtures of anions generated from the 30S and 50S particles of the Escherichia coli ribosome. Six and five major components were revealed, respectively. In the case of the 50S anion population, it was shown that the attachment of two 30+ cations of carbonic anhydrase revealed the same information as the attachment of six 10+ cations of ubiquitin. In neither case was the intact 50S particle observed. Rather, particles with different combinations of missing components were observed. This work demonstrated the utility of multiply charged cation attachment to facilitate charge state assignments in native MS ensemble measurements of heterogeneous mixtures.
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Affiliation(s)
- Anthony M. Pitts-McCoy
- 560 Oval Drive, Department of Chemistry, Purdue University, West
Lafayette, IN, USA 47907-2084
| | - Abdirahman M. Abdillahi
- 560 Oval Drive, Department of Chemistry, Purdue University, West
Lafayette, IN, USA 47907-2084
| | - Kenneth W. Lee
- 560 Oval Drive, Department of Chemistry, Purdue University, West
Lafayette, IN, USA 47907-2084
| | - Scott A. McLuckey
- 560 Oval Drive, Department of Chemistry, Purdue University, West
Lafayette, IN, USA 47907-2084
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12
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Bonney JR, Prentice BM. Perspective on Emerging Mass Spectrometry Technologies for Comprehensive Lipid Structural Elucidation. Anal Chem 2021; 93:6311-6322. [PMID: 33856206 PMCID: PMC8177724 DOI: 10.1021/acs.analchem.1c00061] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Lipids and metabolites are of interest in many clinical and research settings because it is the metabolome that is increasingly recognized as a more dynamic and sensitive molecular measure of phenotype. The enormous diversity of lipid structures and the importance of biological structure-function relationships in a wide variety of applications makes accurate identification a challenging yet crucial area of research in the lipid community. Indeed, subtle differences in the chemical structures of lipids can have important implications in cellular metabolism and many disease pathologies. The speed, sensitivity, and molecular specificity afforded by modern mass spectrometry has led to its widespread adoption in the field of lipidomics on many different instrument platforms and experimental workflows. However, unambiguous and complete structural identification of lipids by mass spectrometry remains challenging. Increasingly sophisticated tandem mass spectrometry (MS/MS) approaches are now being developed and seamlessly integrated into lipidomics workflows to meet this challenge. These approaches generally either (i) alter the type of ion that is interrogated or (ii) alter the dissociation method in order to improve the structural information obtained from the MS/MS experiment. In this Perspective, we highlight recent advances in both ion type alteration and ion dissociation methods for lipid identification by mass spectrometry. This discussion is aimed to engage investigators involved in fundamental ion chemistry and technology developments as well as practitioners of lipidomics and its many applications. The rapid rate of technology development in recent years has accelerated and strengthened the ties between these two research communities. We identify the common characteristics and practical figures of merit of these emerging approaches and discuss ways these may catalyze future directions of lipid structural elucidation research.
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Affiliation(s)
- Julia R Bonney
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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13
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Randolph CE, Shenault DM, Blanksby SJ, McLuckey SA. Localization of Carbon-Carbon Double Bond and Cyclopropane Sites in Cardiolipins via Gas-Phase Charge Inversion Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:455-464. [PMID: 33370110 PMCID: PMC8557092 DOI: 10.1021/jasms.0c00348] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cardiolipins (CLs) are comprised of two phosphatic acid moieties bound to a central glycerol backbone and are substituted with four acyl chains. Consequently, a vast number of distinct CL structures are possible in different biological contexts, representing a significant analytical challenge. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) has become a widely used approach for the detection, characterization, and quantitation of complex lipids, including CLs. Central to this approach is fragmentation of the [CLs - H]- or [CL - 2H]2- anions by collision-induced dissociation (CID). Product ions in the resulting tandem mass spectra confirm the CL subclass assignment and reveal the numbers of carbons and degrees of unsaturation in each of the acyl chains. Conventional CID, however, affords limited structural elucidation of the fatty acyl chains, failing to discriminate isomers arising from different site(s) of unsaturation or cyclopropanation and potentially obscuring their metabolic origins. Here, we report the application of charge inversion ion/ion chemistry in the gas phase to enhance the structural elucidation of CLs. Briefly, CID of [CL - H]2- anions generated via negative ion ESI allowed for the assignment of individual fatty acyl substituents and phosphatidic acid moieties. Next, gas-phase derivatization of the resulting CL product ions, including fatty acyl carboxylate anions, was effected with gas-phase ion/ion charge inversion reactions with tris-phenanthroline magnesium reagent dications. Subsequent isolation and activation of the charge-inverted fatty acyl complex cations permitted the localization of both carbon-carbon double bond and cyclopropane motifs within each of the four acyl chains of CLs. This approach was applied to the de novo elucidation of unknown CLs in a biological extract revealing distinct isomeric populations and regiochemical relationships between double bonds and carbocyles.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | | | - Stephen J. Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
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14
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Abdillahi AM, Lee KW, McLuckey SA. Mass Analysis of Macro-molecular Analytes via Multiply-Charged Ion Attachment. Anal Chem 2020; 92:16301-16306. [PMID: 33275425 DOI: 10.1021/acs.analchem.0c04335] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A novel gas-phase charge and mass manipulation approach is demonstrated to facilitate the mass measurement of high mass complexes within the context of native mass spectrometry. Electrospray ionization applied to solutions generated under native or near-native conditions has been demonstrated to be capable of preserving biologically relevant complexes into the gas phase as multiply charged ions suitable for mass spectrometric analysis. However, charge state distributions tend to be narrow and extensive salt adduction, heterogeneity, and so on tend to lead to significantly broadened peaks. These issues can compromise mass measurement of high mass bio-complexes, particularly when charge states are not clearly resolved. In this work, we show that the attachment of high mass ions of known mass and charge to populations of ions of interest can lead to well-separated signals that can yield confident charge state and mass assignments from otherwise poorly resolved signals.
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Affiliation(s)
- Abdirahman M Abdillahi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Kenneth W Lee
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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15
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Randolph CE, Blanksby SJ, McLuckey SA. Enhancing detection and characterization of lipids using charge manipulation in electrospray ionization-tandem mass spectrometry. Chem Phys Lipids 2020; 232:104970. [PMID: 32890498 PMCID: PMC7606777 DOI: 10.1016/j.chemphyslip.2020.104970] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022]
Abstract
Heightened awareness regarding the implication of disturbances in lipid metabolism with respect to prevalent human-related pathologies demands analytical techniques that provide unambiguous structural characterization and accurate quantitation of lipids in complex biological samples. The diversity in molecular structures of lipids along with their wide range of concentrations in biological matrices present formidable analytical challenges. Modern mass spectrometry (MS) offers an unprecedented level of analytical power in lipid analysis, as many advancements in the field of lipidomics have been facilitated through novel applications of and developments in electrospray ionization tandem mass spectrometry (ESI-MS/MS). ESI allows for the formation of intact lipid ions with little to no fragmentation and has become widely used in contemporary lipidomics experiments due to its sensitivity, reproducibility, and compatibility with condensed-phase modes of separation, such as liquid chromatography (LC). Owing to variations in lipid functional groups, ESI enables partial chemical separation of the lipidome, yet the preferred ion-type is not always formed, impacting lipid detection, characterization, and quantitation. Moreover, conventional ESI-MS/MS approaches often fail to expose diverse subtle structural features like the sites of unsaturation in fatty acyl constituents or acyl chain regiochemistry along the glycerol backbone, representing a significant challenge for ESI-MS/MS. To overcome these shortcomings, various charge manipulation strategies, including charge-switching, have been developed to transform ion-type and charge state, with aims of increasing sensitivity and selectivity of ESI-MS/MS approaches. Importantly, charge manipulation approaches afford enhanced ionization efficiency, improved mixture analysis performance, and access to informative fragmentation channels. Herein, we present a critical review of the current suite of solution-based and gas-phase strategies for the manipulation of lipid ion charge and type relevant to ESI-MS/MS.
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Affiliation(s)
- Caitlin E Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Stephen J Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
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16
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Randolph CE, Fabijanczuk KC, Blanksby SJ, McLuckey SA. Proton Transfer Reactions for the Gas-Phase Separation, Concentration, and Identification of Cardiolipins. Anal Chem 2020; 92:10847-10855. [PMID: 32639138 PMCID: PMC7490759 DOI: 10.1021/acs.analchem.0c02545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cardiolipin (CL) analysis demands high specificity, due to the extensive diversity of CL structures, and high sensitivity, due to their low relative abundance within the lipidome. While electrospray ionization mass spectrometry (ESI-MS) is the most widely used technology in lipidomics, the potential for multiple charging presents unique challenges for CL identification and quantification. Depending on the conditions, ESI-MS of lipid extracts in negative ion mode can give rise to cardiolipins ionized as both singly and doubly deprotonated anions. This signal degeneracy diminishes the signal-to-noise ratio, while in addition (for direct infusion), the dianion population falls within a m/z range already heavily congested with monoanions from more abundant glycerophospholipid subclasses. Herein, we describe a direct infusion strategy for CL profiling from total lipid extracts utilizing gas-phase proton-transfer ion/ion reactions. In this approach, lipid extracts are ionized by negative ion ESI generating both singly deprotonated phospholipids and doubly deprotonated CL anions. Charge reduction of the negative ion population by ion/ion reactions leads to an enhancement in singly deprotonated [CL - H]- species via proton transfer to the corresponding [CL - 2H]2-̅ dianions. To concentrate the [CL - H]- anion signal, multiple iterations of ion accumulation and proton-transfer ion/ion reaction can be performed prior to subsequent interrogation. Mass selection and collisional activation of the enriched population of [CL - H]- anions facilitates the assignment of individual fatty acyl substituents and phosphatidic acid moieties. Demonstrated advantages of this new approach derive from the improved performance in complex mixture analysis affording detailed characterization of low abundant CLs directly from a total biological extract.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | | | - Stephen J. Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
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17
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Randolph CE, Marshall DL, Blanksby SJ, McLuckey SA. Charge-switch derivatization of fatty acid esters of hydroxy fatty acids via gas-phase ion/ion reactions. Anal Chim Acta 2020; 1129:31-39. [PMID: 32891388 DOI: 10.1016/j.aca.2020.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 01/30/2023]
Abstract
Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are a recently discovered class of endogenous bioactive lipids with anti-diabetic and anti-inflammatory effects. Identification of FAHFAs is challenging due to both the relatively low abundance of these metabolites in most biological samples and the significant structural diversity arising from the co-occurrence of numerous regioisomers. Ultimately, development of sensitive analytical techniques that enable rapid and unambiguous identification of FAHFAs is integral to understanding their diverse physiological functions in health and disease. While a battery of mass spectrometry (MS) based methods for complex lipid analysis has been developed, FAHFA identification presents specific challenges to conventional approaches. Notably, while the MS2 product ion spectra of [FAHFA - H]¯ anions afford the assignment of fatty acid (FA) and hydroxy fatty acid (HFA) constituents, FAHFA regioisomers are usually indistinguishable by this approach. Here, we report the development of a novel MS-based technique employing charge inversion ion/ion reactions with tris-phenanthroline magnesium complex dications, Mg(Phen)32+, to selectively and efficiently derivatize [FAHFA - H]¯ anions in the gas phase, yielding fixed-charge cations. Subsequent activation of [FAHFA - H + MgPhen2]+ cations yield product ions that facilitate the assignment of FA and HFA constituents, pinpoints unsaturation sites within the FA moiety, and elucidates ester linkage regiochemistry. Collectively, the presented approach represents a rapid, entirely gas-phase method for near-complete FAHFA structural elucidation and confident isomer discrimination without the requirement for authentic FAHFA standards.
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Affiliation(s)
- Caitlin E Randolph
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - David L Marshall
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Stephen J Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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18
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Randolph CE, Shenault DM, Blanksby SJ, McLuckey SA. Structural Elucidation of Ether Glycerophospholipids Using Gas-Phase Ion/Ion Charge Inversion Chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1093-1103. [PMID: 32251588 PMCID: PMC7328668 DOI: 10.1021/jasms.0c00025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ether lipids represent a unique subclass of glycerophospholipid (GPL) that possesses a 1-O-alkyl (i.e., plasmanyl subclass) or a 1-O-alk-1'-enyl (i.e., plasmenyl subclass) group linked at the sn-1 position of the glycerol backbone. As changes in ether GPL composition and abundance are associated with numerous human pathologies, analytical strategies capable of providing high-level structural detail are desirable. While mass spectrometry (MS) has emerged as a prominent tool for lipid structural elucidation in biological extracts, distinctions between the various isomeric forms of ether-linked GPLs have remained a significant challenge for tandem MS, principally due to similarities in the conventional tandem mass spectra obtained from the two ether-linked subclasses. To distinguish plasmanyl and plasmenyl GPLs, a multistage (i.e., MSn where n = 3 or 4) mass spectrometric approach reliant on low-energy collision-induced dissociation (CID) is required. While this method facilitates assignment of the sn-1 bond type (i.e., 1-O-alkyl versus 1-O-alk-1'-enyl), a composite distribution of isomers is left unresolved, as carbon-carbon double-bond (C=C) positions cannot be localized in the sn-2 fatty acyl substituent. In this study, we combine a systematic MSn approach with two unique gas-phase charge inversion ion/ion chemistries to elucidate ether GPL structures with high-level detail. Ultimately, we assign both the sn-1 bond type and sites of unsaturation in the sn-2 fatty acyl substituent using an entirely gas-phase MS-based workflow. Application of this workflow to human blood plasma extract permitted isomeric resolution and in-depth structural identification of major and, in some cases, minor isomeric contributors to ether GPLs that have been previously unresolved when examined via conventional methods.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | | | - Stephen J. Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
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19
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Randolph CE, Blanksby SJ, McLuckey SA. Toward Complete Structure Elucidation of Glycerophospholipids in the Gas Phase through Charge Inversion Ion/Ion Chemistry. Anal Chem 2020; 92:1219-1227. [PMID: 31763816 PMCID: PMC6949391 DOI: 10.1021/acs.analchem.9b04376] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Shotgun lipidomics has recently gained popularity for lipid analysis. Conventionally, shotgun analysis of glycerophospholipids via direct electrospray ionization tandem mass spectrometry (ESI-MS/MS) provides glycerophospholipid (GPL) class (i.e., headgroup composition) and fatty acyl composition. Reliant on low-energy collision-induced dissociation (CID), traditional ESI-MS/MS fails to define fatty acyl regiochemistry along the glycerol backbone or carbon-carbon double bond position(s) in unsaturated fatty acyl substituents. Therefore, isomeric GPLs are often unresolved, representing a significant challenge for shotgun-MS approaches. We developed a top-down shotgun-MS method utilizing gas-phase ion/ion charge inversion chemistry that provides near-complete GPL structural identification. First, in negative ion mode, CID of mass-selected GPL anions generates fatty acyl carboxylate anions via fragmentation of ester bonds linking the fatty acyl substituents at the sn-1 and sn-2 positions of the glycerol backbone. Product anions, including fatty acyl carboxylate ions, were then derivatized in the mass spectrometer via an ion/ion charge inversion reaction with tris-phenanthroline magnesium dications. Subsequent CID of charge-inverted fatty acyl complex cations yielded isomer-specific product ion spectra that permit (i) unambiguous assignment of carbon-carbon double bond position(s) and (ii) relative quantitation of isomeric fatty acyl substituents. The outlined strategy was applied to the analysis of targeted GPLs extracted from human plasma, including several proposed plasma biomarkers. A single experiment thus facilitates assignment of the GPL headgroup, fatty acyl composition, carbon-carbon double bond position(s) in unsaturated fatty acyl chains, and, in some cases, fatty acyl sn-position and relative abundances for isomeric fatty acyl substituents. Ultimately, this MSn platform paired with ion/ion chemistry permitted identification of major, and some minor, isomeric contributors that are unresolved using conventional ESI-MS/MS.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Stephen J. Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
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20
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Foreman DJ, Lawler JT, Niedrauer ML, Hostetler MA, McLuckey SA. Gold(I) Cationization Promotes Ring Opening in Lysine-Containing Cyclic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1914-1922. [PMID: 31250319 PMCID: PMC6812625 DOI: 10.1007/s13361-019-02247-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
A strategy to sequence lysine-containing cyclic peptides by MSn is presented. Doubly protonated cyclic peptides ions are transformed into gold (I) cationized peptide ions via cation switching ion/ion reaction. Gold(I) cationization facilitates the oxidation of neutral lysine residues in the gas phase, weakening the adjacent amide bond. Upon activation, facile cleavage N-terminal to the oxidized lysine residue provides a site-specific ring opening pathway that converts cyclic peptides into acyclic analogs. The ensuing ion contains a cyclic imine as the new N-terminus and an oxazolone, or structural equivalent, as the new C-terminus. Product ions are formed from subsequent fragmentation events of the linearized peptide ion. Such an approach simplifies MS/MS data interpretation as a series of fragment ions with common N- and C-termini are generated. Results are presented for two cyclic peptides, sunflower trypsin inhibitor and the model cyclic peptide, β-Loop. The power of this strategy lies in the ability to generate the oxidized peptide, which is easily identified via the loss of HAuNH3 from [M + Au]+. While some competitive processes are observed, the site of ring opening can be pinpointed to the lysine residue upon MS4 enabling the unambiguous sequencing of cyclic peptides.
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Affiliation(s)
- David J Foreman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - John T Lawler
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Mary L Niedrauer
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Matthew A Hostetler
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA.
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21
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Randolph CE, Foreman DJ, Blanksby SJ, McLuckey SA. Generating Fatty Acid Profiles in the Gas Phase: Fatty Acid Identification and Relative Quantitation Using Ion/Ion Charge Inversion Chemistry. Anal Chem 2019; 91:9032-9040. [PMID: 31199126 PMCID: PMC6882335 DOI: 10.1021/acs.analchem.9b01333] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Representing the most fundamental lipid class, fatty acids (FA) play vital biological roles serving as energy sources, cellular signaling molecules, and key architectural components of complex lipids. Direct infusion electrospray ionization spectrometry, also known as shotgun lipidomics, has emerged as a rapid and powerful toolbox for lipid analysis. While shotgun lipidomics can be a sensitive approach to FA detection, the diverse molecular structure of FA presents challenges for unambiguous identification and the relative quantification of isomeric contributors. In particular, pinpointing double bond position(s) in unsaturated FA and determining the relative contribution of double bond isomers has limited the application of the shotgun approach. Recently, we reported the use of gas-phase ion/ion reactions to facilitate the identification of FA. Briefly, singly deprotonated FA anions undergo charge inversion when reacted in the gas phase with tris-phenanthroline magnesium dications by forming [FA - H + MgPhen]+ complex ions. These charge-inverted FA complex cations fragment upon ion-trap collision-induced dissociation (CID) to generate product ion spectra unique to individual FA isomers. Herein, we report the development of a mass spectral library comprised of [FA - H + MgPhen]+ product ion spectra. The developed FA library permits confident FA identification, including polyunsaturated FA isomers. Furthermore, we demonstrate the ability to determine relative contributions of isomeric FA using multiple linear regression analysis paired with gas-phase ion/ion reactions. We successfully applied the presented method to generate a FA profile for bovine liver phospholipidome based entirely on gas-phase chemistries.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - David J. Foreman
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Stephen J. Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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22
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Ye S, Li M, Jiang Y, Gong X, Xiong X, Liu D, Zhao B, Fang X. Ion manipulation and enrichment mass spectrometer for cleavage of disulfide bond via ion/ion reaction. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:311-315. [PMID: 30672057 DOI: 10.1002/jms.4333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/27/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
A novel mass spectrometer with the capability of ion manipulation and enrichment was developed to perform gas-phase ion/ion reactions followed by product ions accumulation. The development of this apparatus opens opportunities for more complex sequences of ion manipulations, thus offers the potential on extensive application involving ion/ion reaction. Here, cleavage of disulfide bond in peptide was demonstrated based upon this ion manipulation and enrichment mass spectrometer. Two typical peptides including S-glutathionylated ARACAKA with an intermolecular disulfide bond, and oxytocin with an intramolecular disulfide bond were chosen as typical samples to demonstrate the ability of the apparatus. After ion/ion reaction between selected peptide cations and periodate ions (IO4 - ), two kinds of product ions (eg, [M + O + H]+ and [M + H + Na + IO4 ]+ ) were enriched with a number of accumulation events. Afterwards, the enriched ions were subjected to activation, and the disulfide bond cleavage was clearly observed from the tandem mass spectra. These results illustrate the potential of this apparatus for ion manipulation performing ion/ion reaction, and low abundance product ion enrichment.
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Affiliation(s)
- Sijian Ye
- Department of Chemistry & Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, PR China
- College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Ming Li
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - You Jiang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - Xiaoyun Gong
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - Xingchuang Xiong
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
| | - Dajun Liu
- Department of Chemistry & Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, PR China
| | - Bo Zhao
- Department of Chemistry & Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, PR China
| | - Xiang Fang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, PR China
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23
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Pitts-McCoy AM, Harrilal CP, McLuckey SA. Gas-Phase Ion/Ion Chemistry as a Probe for the Presence of Carboxylate Groups in Polypeptide Cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:329-338. [PMID: 30341581 PMCID: PMC6347497 DOI: 10.1007/s13361-018-2079-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/04/2018] [Indexed: 05/31/2023]
Abstract
The reactivity of 1-hydroxybenzoyl triazole (HOBt) esters with the carboxylate functionality present in peptides is demonstrated in the gas phase with a doubly deprotonated dianion. The reaction forms an anhydride linkage at the carboxylate site. Upon ion trap collisional-induced dissociation (CID) of the modified peptide, the resulting spectrum shows a nominal loss of the mass of the reagent and a water molecule. Analogous phenomenology was also noted for model peptide cations that likely contain zwitterionic/salt-bridged motifs in reactions with a negatively charged HOBt ester. Control experiments indicate that a carboxylate group is the likely reactive site, rather than other possible nucleophilic sites present in the peptide. These observations suggest that HOBt ester chemistry may be used as a chemical probe for the presence and location of carboxylate groups in net positively charged polypeptide ions. As an illustration, deprotonated sulfobenzoyl HOBt was reacted with the [M+7H]7+ ion of ubiquitin. The ion was shown to react with the reagent and CID of the covalent reaction product yielded an abundant [M+6H-H2O]6+ ion. Comparison of the CID product ion spectrum of this ion with that of the water loss product generated from CID of the unmodified [M+6H]6+ ion revealed the glutamic acid at residue 64 as a reactive site, suggesting that it is present in the deprotonated form. Graphical Abstract ᅟ.
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Affiliation(s)
- Anthony M Pitts-McCoy
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Christopher P Harrilal
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA.
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24
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Foreman DJ, Dziekonski ET, McLuckey SA. Maximizing Selective Cleavages at Aspartic Acid and Proline Residues for the Identification of Intact Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:34-44. [PMID: 29713964 PMCID: PMC6207472 DOI: 10.1007/s13361-018-1965-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 05/03/2023]
Abstract
A new approach for the identification of intact proteins has been developed that relies on the generation of relatively few abundant products from specific cleavage sites. This strategy is intended to complement standard approaches that seek to generate many fragments relatively non-selectively. Specifically, this strategy seeks to maximize selective cleavage at aspartic acid and proline residues via collisional activation of precursor ions formed via electrospray ionization (ESI) under denaturing conditions. A statistical analysis of the SWISS-PROT database was used to predict the number of arginine residues for a given intact protein mass and predict a m/z range where the protein carries a similar charge to the number of arginine residues thereby enhancing cleavage at aspartic acid residues by limiting proton mobility. Cleavage at aspartic acid residues is predicted to be most favorable in the m/z range of 1500-2500, a range higher than that normally generated by ESI at low pH. Gas-phase proton transfer ion/ion reactions are therefore used for precursor ion concentration from relatively high charge states followed by ion isolation and subsequent generation of precursor ions within the optimal m/z range via a second proton transfer reaction step. It is shown that the majority of product ion abundance is concentrated into cleavages C-terminal to aspartic acid residues and N-terminal to proline residues for ions generated by this process. Implementation of a scoring system that weights both ion fragment type and ion fragment area demonstrated identification of standard proteins, ranging in mass from 8.5 to 29.0 kDa. Graphical Abstract ᅟ.
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Affiliation(s)
- David J Foreman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | | | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA.
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25
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Wang N, Pilo AL, Zhao F, Bu J, McLuckey SA. Gas-phase rearrangement reaction of Schiff-base-modified peptide ions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:2166-2173. [PMID: 30280440 PMCID: PMC6657513 DOI: 10.1002/rcm.8298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/18/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Schiff base modification of peptides has been shown to facilitate their primary structural characterization via tandem mass spectrometry. However, we have discovered a novel rearrangement reaction via ion trap collisional activation involving the imine of the Schiff base and one of several functional groups, particularly the side chains of the basic residues lysine, arginine, and histidine, in the peptide. METHODS Gas-phase ion/ion reactions involving an aldehyde-containing reagent were used to generate Schiff-base-modified model peptides in a hybrid triple quadrupole/linear ion trap tandem mass spectrometer. Subsequent ion trap collisional activation was used to study the rearrangement reaction. RESULTS Schiff-base-modified peptide ions were found to undergo a rearrangement reaction that was observed to be either a major or minor contributor to the product ion spectrum, depending upon a variety of factors that include, for example, ion polarity, identity of the nucleophile in the peptide (e.g., side chains of lysine, histidine, and arginine), and the position of the nucleophile relative to the imine. CONCLUSIONS Relatively low-energy rearrangement reactions can occur in Schiff-base-modified peptide ions that involve the imine of the Schiff base and a nucleophile present in the polypeptide. While this rearrangement process does not appear to compromise the structural information that can be generated via collisional activation of Schiff-base-modified peptide ions, it can siphon away signal from the structurally diagnostic processes in some instances.
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Affiliation(s)
| | | | | | | | - Scott A. McLuckey
- Address reprint requested to: Dr. S. A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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26
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Randolph CE, Foreman DJ, Betancourt SK, Blanksby SJ, McLuckey SA. Gas-Phase Ion/Ion Reactions Involving Tris-Phenanthroline Alkaline Earth Metal Complexes as Charge Inversion Reagents for the Identification of Fatty Acids. Anal Chem 2018; 90:12861-12869. [PMID: 30260210 PMCID: PMC6688842 DOI: 10.1021/acs.analchem.8b03441] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fatty acids (FA) play vital biological roles as energy sources, signaling molecules and key building blocks of complex lipids in cell membranes. Modifications to FA structure and composition are associated with the onset and progression of a number of chronic diseases. Consequently, the sensitive detection and unambiguous structure elucidation of FA is integral to the advancement of biomedical sciences. Recent advances in FA analysis have taken advantage of wet chemical derivatization to enhance detection and drive unique fragmentation in tandem mass spectrometry protocols. Here, we significantly further this approach through demonstrating gas-phase charge inversion of singly deprotonated FA ions, [M - H]-, using doubly charged tris-phenanthroline alkaline earth metal complexes, [Cat(Phen)3]2+ (Cat = Mg2+, Ca2+, Sr2+, or Ba2+). Metal cationized FA, [M - H + Cat]+ are obtained after the gas-phase ion/ion reaction. Low-energy collision-induced dissociation (CID) of the [M - H + Cat]+ cations facilitates double bond localization for a variety of monounsaturated and polyunsaturated FAs. Ultimately, detailed characterization presented unambiguous distinction among FA double bond positional isomers, such as n-3 and n-6 isomers. The method was successfully used to identify the FA profile of corn oil, including double bond localization for unsaturated FAs present.
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Affiliation(s)
- Caitlin E. Randolph
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - David J. Foreman
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Stella K. Betancourt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Stephen J. Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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27
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Foreman DJ, Betancourt SK, Pilo AL, McLuckey SA. Novel Peptide Ion Chemistry Associated with Gold (I) Cationization: Preferential Cleavage at Lysine Residues. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:114-122. [PMID: 29881326 PMCID: PMC5985815 DOI: 10.1016/j.ijms.2017.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Novel peptide ion chemistry associated with gold (I) cationization is described. Cation switching ion/ion reactions, involving gold dichloride reagent anion, [AuCl2]-, are used to replace protons with a gold (I) cation on a polypeptide. Collision induced dissociation of aurated, lysine-containing peptides results in the elimination of gold hydride and ammonia, generating a [M - H - NH3]+ oxidized species. The oxidized product is likely a cyclic iminium ion. This fragmentation pathway is specific to lysine side-chains as polypeptides containing arginine or histidine in the absence of lysine were not observed to form the oxidized product. While oxidation can occur on N-terminal, internal, and C-terminal lysine residues, it is observed to a lesser extent at lysines found at internal and C-terminal positions. However, isolation and subsequent activation of the [M - H - NH3]+ species derived from the internal or C-terminal positions results in preferential cleavage N-terminal to the oxidized lysine residue. This chemistry has been demonstrated using a variety of model peptides and has also been applied to the analysis of melittin.
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Affiliation(s)
| | | | | | - Scott A. McLuckey
- Address reprint requests to: Dr. Scott A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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28
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Munshi M, Craig SM, Berden G, Martens J, DeBlase AF, Foreman DJ, McLuckey SA, Oomens J, Johnson MA. Preparation of Labile Ni +(cyclam) Cations in the Gas Phase Using Electron-Transfer Reduction through Ion-Ion Recombination in an Ion Trap and Structural Characterization with Vibrational Spectroscopy. J Phys Chem Lett 2017; 8:5047-5052. [PMID: 28961009 PMCID: PMC5677246 DOI: 10.1021/acs.jpclett.7b02223] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/29/2017] [Indexed: 05/31/2023]
Abstract
Gas-phase ion chemistry methods that capture and characterize the degree of activation of small molecules in the active sites of homogeneous catalysts form a powerful new tool to unravel how ligand environments affect reactivity. A key roadblock in this development, however, is the ability to generate the fragile metal oxidation states that are essential for catalytic activity. Here we demonstrate the preparation of the key Ni(I) center in the widely used cyclam scaffold using ion-ion recombination as a gas-phase alternative to electrochemical reduction. The singly charged Ni+(cyclam) coordination complex is generated by electron transfer from fluoranthene and azobenzene anions to doubly charged Ni2+(cyclam), using the electron-transfer dissociation protocol in a commercial quadrupole ion trap instrument and in a custom-built octopole RF ion trap. The successful preparation of the Ni+(cyclam) cation is verified through analysis of its vibrational spectrum obtained using the infrared free electron laser FELIX.
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Affiliation(s)
- Musleh
U. Munshi
- Radboud
University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld
7c, 6525ED Nijmegen, The Netherlands
| | - Stephanie M. Craig
- Sterling
Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
| | - Giel Berden
- Radboud
University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld
7c, 6525ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud
University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld
7c, 6525ED Nijmegen, The Netherlands
| | - Andrew F. DeBlase
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Spectral
Energies,
LLC, Beavercreek, Ohio 45430, United States
| | - David J. Foreman
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Scott A. McLuckey
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jos Oomens
- Radboud
University, Institute for Molecules and
Materials, FELIX Laboratory, Toernooiveld
7c, 6525ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, 1098XH Amsterdam, Science Park 908, The Netherlands
| | - Mark A. Johnson
- Sterling
Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, United States
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29
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Peng Z, Bu J, McLuckey SA. The Generation of Dehydroalanine Residues in Protonated Polypeptides: Ion/Ion Reactions for Introducing Selective Cleavages. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1765-1774. [PMID: 28497355 PMCID: PMC5681889 DOI: 10.1007/s13361-017-1672-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/02/2017] [Accepted: 03/19/2017] [Indexed: 06/07/2023]
Abstract
We examine a gas-phase approach for converting a subset of amino acid residues in polypeptide cations to dehydroalanine (Dha). Subsequent activation of the modified polypeptide ions gives rise to specific cleavage N-terminal to the Dha residue. This process allows for the incorporation of selective cleavages in the structural characterization of polypeptide ions. An ion/ion reaction within the mass spectrometer between a multiply protonated polypeptide and the sulfate radical anion introduces a radical site into the multiply protonated polypeptide reactant. Subsequent collisional activation of the polypeptide radical cation gives rise to radical side chain loss from one of several particular amino acid side chains (e.g., leucine, asparagine, lysine, glutamine, and glutamic acid) to yield a Dha residue. The Dha residues facilitate preferential backbone cleavages to produce signature c- and z-ions, demonstrated with cations derived from melittin, mechano growth factor (MGF), and ubiquitin. The efficiencies for radical side chain loss and for subsequent generation of specific c- and z-ions have been examined as functions of precursor ion charge state and activation conditions using cations of ubiquitin as a model for a small protein. It is noted that these efficiencies are not strongly dependent on ion trap collisional activation conditions but are sensitive to precursor ion charge state. Moderate to low charge states show the greatest overall yields for the specific Dha cleavages, whereas small molecule losses (e.g., water/ammonia) dominate at the lowest charge states and proton catalyzed amide bond cleavages that give rise to b- and y-ions tend to dominate at high charge states. Graphical Abstract ᅟ.
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Affiliation(s)
- Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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30
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Patil AA, Chou SW, Chang PY, Lee CW, Cheng CY, Chu ML, Peng WP. High Mass Ion Detection with Charge Detector Coupled to Rectilinear Ion Trap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1066-1078. [PMID: 27966174 DOI: 10.1007/s13361-016-1548-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Conventional linear ion trap mass analyzers (LIT-MS) provide high ion capacity and show their MS n ability; however, the detection of high mass ions is still challenging because LIT-MS with secondary electron detectors (SED) cannot detect high mass ions. To detect high mass ions, we coupled a charge detector (CD) to a rectilinear ion trap mass spectrometer (RIT-MS). Immunoglobulin G ions (m/z ~150,000) are measured successfully with controlled ion kinetic energy. In addition, when mass-to-charge (m/z) ratios of singly charged ions exceed 10 kTh, the detection efficiency of CD is found to be greater than that of SED. The CD can be coupled to LIT-MS to extend the detection mass range and provide the potential to perform MS n of high mass ions inside the ion trap. Graphical Abstract ᅟ.
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Affiliation(s)
- Avinash A Patil
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Szu-Wei Chou
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
- AcroMass technologies Inc., Hukou, Hsinchu, Taiwan, 30352, Republic of China
| | - Pei-Yu Chang
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Chen-Wei Lee
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Chun-Yen Cheng
- AcroMass technologies Inc., Hukou, Hsinchu, Taiwan, 30352, Republic of China
| | - Ming-Lee Chu
- Institute of Physics, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China.
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31
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Pilo AL, Zhao F, McLuckey SA. Gas-Phase Oxidation via Ion/Ion Reactions: Pathways and Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:991-1004. [PMID: 28050870 PMCID: PMC5438755 DOI: 10.1007/s13361-016-1554-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/31/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
Here, we provide an overview of pathways available upon the gas-phase oxidation of peptides and DNA via ion/ion reactions and explore potential applications of these chemistries. The oxidation of thioethers (i.e., methionine residues and S-alkyl cysteine residues), disulfide bonds, S-nitrosylated cysteine residues, and DNA to the [M+H+O]+ derivative via ion/ion reactions with periodate and peroxymono-sulfate anions is demonstrated. The oxidation of neutral basic sites to various oxidized structures, including the [M+H+O]+, [M-H]+, and [M-H-NH3]+ species, via ion/ion reactions is illustrated and the oxidation characteristics of two different oxidizing reagents, periodate and persulfate anions, are compared. Lastly, the highly efficient generation of molecular radical cations via ion/ion reactions with sulfate radical anion is summarized. Activation of the newly generated molecular radical peptide cations results in losses of various neutral side chains, several of which generate dehydroalanine residues that can be used to localize the amino acid from which the dehydroalanine was generated. The chemistries presented herein result in a diverse range of structures that can be used for a variety of applications, including the identification and localization of S-alkyl cysteine residues, the oxidative cleavage of disulfide bonds, and the generation of molecular radical cations from even-electron doubly protonated peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Feifei Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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32
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Pilo AL, Bu J, McLuckey SA. Gas-Phase Oxidation of Neutral Basic Residues in Polypeptide Cations by Periodate. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1979-1988. [PMID: 27644939 PMCID: PMC5088057 DOI: 10.1007/s13361-016-1491-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The gas-phase oxidation of doubly protonated peptides containing neutral basic residues to various products, including [M + H + O]+, [M - H]+, and [M - H - NH3]+, is demonstrated here via ion/ion reactions with periodate. It was previously demonstrated that periodate anions are capable of oxidizing disulfide bonds and methionine, tryptophan, and S-alkyl cysteine residues. However, in the absence of these easily oxidized sites, we show here that systems containing neutral basic residues can undergo oxidation. Furthermore, we show that these neutral basic residues primarily undergo different types of oxidation (e.g., hydrogen abstraction) reactions than those observed previously (i.e., oxygen transfer to yield the [M + H + O]+ species) upon gas-phase ion/ion reactions with periodate anions. This chemistry is illustrated with a variety of systems, including a series of model peptides, a cell-penetrating peptide containing a large number of unprotonated basic sites, and ubiquitin, a roughly 8.6 kDa protein. Graphical Abstract ᅟ.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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33
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Pilo AL, Peng Z, McLuckey SA. The dehydroalanine effect in the fragmentation of ions derived from polypeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:857-866. [PMID: 27484024 PMCID: PMC5068825 DOI: 10.1002/jms.3831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 05/11/2023]
Abstract
The fragmentation of peptides and proteins upon collision-induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non-proteinogenic amino acid with an unsaturated side-chain, undergo enhanced cleavage of the N-Cα bond of the dehydroalanine residue to generate c- and z-ions. Because these fragment ion types are not commonly observed upon activation of positively charged even-electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S-alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas-phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S-alkyl cysteine residues and conversion of multiply-protonated peptides to radical cations. In the latter case, loss of radical side-chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue-specific backbone cleavage of polypeptide ions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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34
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Pilo AL, McLuckey SA. Selective Gas-Phase Ion/Ion Reactions: Enabling Disulfide Mapping via Oxidation and Cleavage of Disulfide Bonds in Intermolecularly-Linked Polypeptide Ions. Anal Chem 2016; 88:8972-9. [PMID: 27531151 DOI: 10.1021/acs.analchem.6b01043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The selective gas-phase oxidation of disulfide bonds to their thiosulfinate form using ion/ion reactions and subsequent cleavage is demonstrated here. Oxidizing reagent anions are observed to attach to all polypeptides, regardless of amino acid composition. Direct proton transfer yielding a charge-reduced peptide is also frequently observed. Activation of the ion/ion complex between an oxidizing reagent anion and a disulfide-containing peptide cation results in oxygen transfer from the reagent anion to the peptide cation to form the [M+H+O](+) species. This thiosulfinate derivative can undergo one of several rearrangements that result in cleavage of the disulfide bond. Species containing an intermolecular disulfide bond undergo separation of the two chains upon activation. Further activation can be used to generate more sequence information from each chain. These oxidation ion/ion reactions have been used to illustrate the identification of S-glutathionylated and S-cysteinylated peptides, in which low molecular weight thiols are attached to cysteine residues in peptides via disulfide bonds. The oxidation chemistry effectively labels peptide ions with readily oxidized groups, such as disulfide bonds. This enables a screening approach for the identification of disulfide-linked peptides in a disulfide mapping application involving enzymatic digestion. The mixtures of ions generated by tryptic and peptic digestions of lysozyme and insulin, respectively, without prior separation or isolation were subjected both to oxidation and proton transfer ion/ion chemistry to illustrate the identification of peptides in the mixtures with readily oxidized groups.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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35
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Pilo AL, Zhao F, McLuckey SA. Selective Gas-Phase Oxidation and Localization of Alkylated Cysteine Residues in Polypeptide Ions via Ion/Ion Chemistry. J Proteome Res 2016; 15:3139-46. [PMID: 27476698 DOI: 10.1021/acs.jproteome.6b00266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The thiol group in cysteine residues is susceptible to several post-translational modifications (PTMs), including prenylation, nitrosylation, palmitoylation, and the formation of disulfide bonds. Additionally, cysteine residues involved in disulfide bonds are commonly reduced and alkylated prior to mass spectrometric analysis. Several of these cysteine modifications, specifically S-alkyl modifications, are susceptible to gas-phase oxidation via selective ion/ion reactions with periodate anions. Multiply protonated peptides containing modified cysteine residues undergo complex formation upon ion/ion reaction with periodate anions. Activation of the ion/ion complexes results in oxygen transfer from the reagent to the modified sulfur residue to create a sulfoxide functionality. Further activation of the sulfoxide derivative yields abundant losses of the modification with the oxidized sulfur as a sulfenic acid (namely, XSOH) to generate a dehydroalanine residue. This loss immediately indicates the presence of an S-alkyl cysteine residue, and the mass of the loss can be used to easily deduce the type of modification. An additional step of activation can be used to localize the modification to a specific residue within the peptide. Selective cleavage to create c- and z-ions N-terminal to the dehydroalanine residue is often noted. As these types of ions are not typically observed upon collision-induced dissociation (CID), they can be used to immediately indicate where in the peptide the PTM was originally located.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Feifei Zhao
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
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36
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Bu J, Fisher CM, Gilbert JD, Prentice BM, McLuckey SA. Selective Covalent Chemistry via Gas-Phase Ion/ion Reactions: An Exploration of the Energy Surfaces Associated with N-Hydroxysuccinimide Ester Reagents and Primary Amines and Guanidine Groups. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1089-1098. [PMID: 27020926 DOI: 10.1007/s13361-016-1359-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 01/28/2016] [Accepted: 01/30/2016] [Indexed: 06/05/2023]
Abstract
Selective covalent bond forming reactions (referred to as covalent reactions) can occur in gas-phase ion/ion reactions and take place via the formation of a long-lived chemical complex. The gas-phase ion/ion reactivity between sulfo-N-hydroxysuccinimide (sulfo-NHS) ester reagent anions and peptide cations containing a primary amine or guanidine group has been examined via DFT calculations and complex dissociation rate measurements. The results reveal insights regarding the roles of the barriers of competing processes within the complex. When the covalent reaction is exothermic, two prototypical cases, determined by the nature of the energy surface, are apparent. The product partitioning between covalent reaction and simple proton transfer upon dissociation of the long-lived complex is sensitive to activation conditions when the transition state barrier for covalent reaction is relatively high (case 1) but is insensitive to activation conditions when the transition state barrier is relatively low (case 2). Covalent reaction efficiencies are very high in case 2 scenarios, such as when the reactive site is a guanidine and the anion attachment site is a guanidinium ion. Covalent reaction efficiencies are variable, and generally low, in case 1 scenarios, such as when an amine is the reactive site and an ammonium ion is the site of anion attachment. A relatively long slow-heating step prior to the complex dissociation step, however, can dramatically increase covalent reaction yield in case 1 scenarios. Graphical Abstract ᅟ.
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Affiliation(s)
- Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Christine M Fisher
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Joshua D Gilbert
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Boone M Prentice
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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Peng Z, McLuckey SA. C-terminal peptide extension via gas-phase ion/ion reactions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 391:17-23. [PMID: 26640400 PMCID: PMC4666559 DOI: 10.1016/j.ijms.2015.07.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The formation of peptide bonds is of great importance from both a biological standpoint and in routine organic synthesis. Recent work from our group demonstrated the synthesis of peptides in the gas-phase via ion/ion reactions with sulfo-NHS reagents, which resulted in conjugation of individual amino acids or small peptides to the N-terminus of an existing 'anchor' peptide. Here, we demonstrate a complementary approach resulting in the C-terminal extension of peptides. Individual amino acids or short peptides can be prepared as reagents by incorporating gas phase-labile protecting groups to the reactive C-terminus and then converting the N-terminal amino groups to the active ketenimine reagent. Gas-phase ion/ion reactions between the anionic reagents and doubly protonated "anchor" peptide cations results in extension of the "anchor" peptide with new amide bond formation at the C-terminus. We have demonstrated that ion/ion reactions can be used as a fast, controlled, and efficient means for C-terminal peptide extension in the gas phase.
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Affiliation(s)
- Zhou Peng
- Department of Chemistry Purdue University West Lafayette, Indiana, USA 47907-2084
| | - Scott A McLuckey
- Department of Chemistry Purdue University West Lafayette, Indiana, USA 47907-2084
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38
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Peng Z, Pilo AL, Luongo CA, McLuckey SA. Gas-Phase Amidation of Carboxylic Acids with Woodward's Reagent K Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1686-94. [PMID: 26122523 PMCID: PMC4567925 DOI: 10.1007/s13361-015-1209-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 05/13/2023]
Abstract
Gas-phase amidation of carboxylic acids in multiply-charged peptides is demonstrated via ion/ion reactions with Woodward's reagent K (wrk) in both positive and negative mode. Woodward's reagent K, N-ethyl-3-phenylisoxazolium-3'-sulfonate, is a commonly used reagent that activates carboxylates to form amide bonds with amines in solution. Here, we demonstrate that the analogous gas-phase chemistry occurs upon reaction of the wrk ions and doubly protonated (or doubly deprotonated) peptide ions containing the carboxylic acid functionality. The reaction involves the formation of the enol ester intermediate in the electrostatic complex. Upon collisional activation, the ethyl amine on the reagent is transferred to the activated carbonyl carbon on the peptide, resulting in the formation of an ethyl amide (addition of 27 Da to the peptide) with loss of a neutral ketene derivative. Further collision-induced dissociation (CID) of the products and comparison with solution-phase amidation product confirms the structure of the ethyl amide.
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Affiliation(s)
- Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Carl A Luongo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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39
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Pilo AL, Bu J, McLuckey SA. Transformation of [M + 2H](2+) Peptide Cations to [M - H](+), [M + H + O](+), and M(+•) Cations via Ion/Ion Reactions: Reagent Anions Derived from Persulfate. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1103-14. [PMID: 25944366 PMCID: PMC4475491 DOI: 10.1007/s13361-015-1125-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 05/25/2023]
Abstract
The gas-phase oxidation of doubly protonated peptides is demonstrated here using ion/ion reactions with a suite of reagents derived from persulfate. Intact persulfate anion (HS2O8(-)), peroxymonosulfate anion (HSO5(-)), and sulfate radical anion (SO4(-•)) are all either observed directly upon negative nanoelectrospray ionization (nESI) or easily obtained via beam-type collisional activation of persulfate into the mass spectrometer. Ion/ion reactions between each of these reagents and doubly protonated peptides result in the formation of a long-lived complex. Collisional activation of the complex containing a peroxymonosulfate anion results in oxygen transfer from the reagent to the peptide to generate the [M + H + O](+) species. Activation of the complex containing intact persulfate anion either results in oxygen transfer to generate the [M + H + O](+) species or abstraction of two hydrogen atoms and a proton to generate the [M - H](+) species. Activation of the complex containing sulfate radical anion results in abstraction of one hydrogen atom and a proton to form the peptide radical cation, [M](+•). This suite of reagents allows for the facile transformation of the multiply protonated peptides obtained via nESI into a variety of oxidized species capable of providing complementary information about the sequence and structure of the peptide.
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Affiliation(s)
- Alice L. Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084
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Gilbert JD, Prentice BM, McLuckey SA. Ion/ion reactions with "onium" reagents: an approach for the gas-phase transfer of organic cations to multiply-charged anions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:818-25. [PMID: 25652935 PMCID: PMC4654941 DOI: 10.1007/s13361-015-1077-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/27/2014] [Accepted: 01/08/2015] [Indexed: 05/13/2023]
Abstract
The use of ion/ion reactions to effect gas-phase alkylation is demonstrated. Commonly used fixed-charge "onium" cations are well-suited for ion/ion reactions with multiply deprotonated analytes because of their tendency to form long-lived electrostatic complexes. Activation of these complexes results in an SN2 reaction that yields an alkylated anion with the loss of a neutral remnant of the reagent. This alkylation process forms the basis of a general method for alkylation of deprotonated analytes generated via electrospray, and is demonstrated on a variety of anionic sites. SN2 reactions of this nature are demonstrated empirically and characterized using density functional theory (DFT). This method for modification in the gas phase is extended to the transfer of larger and more complex R groups that can be used in later gas-phase synthesis steps. For example, N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide (CMC) is used to transfer a carbodiimide functionality to a peptide anion containing a carboxylic acid. Subsequent activation yields a selective reaction between the transferred carbodiimide group and a carboxylic acid, suggesting the carbodiimide functionality is retained through the transfer process. Many different R groups are transferable using this method, allowing for new possibilities for charge manipulation and derivatization in the gas phase.
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Affiliation(s)
- Joshua D Gilbert
- Department of Chemistry, Purdue University, West Lafayette, IN, 4907-2084, USA
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41
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Luongo CA, Bu J, Burke NL, Gilbert JD, Prentice BM, Cummings S, Reed CA, McLuckey SA. Selective removal of alkali metal cations from multiply-charged ions via gas-phase ion/ion reactions using weakly coordinating anions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:404-414. [PMID: 25560986 DOI: 10.1007/s13361-014-1052-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/14/2014] [Accepted: 11/15/2014] [Indexed: 06/04/2023]
Abstract
Selective removal of alkali metal cations from mixed cation multiply-charged peptide ions is demonstrated here using gas-phase ion/ion reactions with a series of weakly coordinating anions (WCAs), including hexafluorophosphate (PF6 (-)), tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (BARF), tetrakis(pentafluorophenyl)borate (TPPB), and carborane (CHB11Cl11 (-)). In all cases, a long-lived complex is generated by dication/anion condensation followed by ion activation to compare proton transfer with alkali ion transfer from the peptide to the anion. The carborane anion was the only anion studied to undergo dissociation exclusively through loss of the metallated anion, regardless of the studied metal adduct. All other anions studied yield varying abundances of protonated and metallated peptide depending on the peptide sequence and the metal identity. Density functional theory calculations suggest that for the WCAs studied, metal ion transfer is most strongly favored thermodynamically, which is consistent with the experimental results. The carborane anion is demonstrated to be a robust reagent for the selective removal of alkali metal cations from peptide cations with mixtures of excess protons and metal cations.
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Affiliation(s)
- Carl A Luongo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
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Gilbert JD, Fisher CM, Bu J, Prentice BM, Redwine JG, McLuckey SA. Strategies for generating peptide radical cations via ion/ion reactions. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:418-26. [PMID: 25800024 PMCID: PMC4372815 DOI: 10.1002/jms.3548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 11/14/2014] [Accepted: 11/16/2014] [Indexed: 05/25/2023]
Abstract
Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process.
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Affiliation(s)
| | | | | | | | | | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey 560 Oval Drive Department of Chemistry Purdue University West Lafayette, IN 47907-2084, USA Phone: (765) 494-5270 Fax: (765) 494-0239
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43
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Peng Z, McGee WM, Bu J, Barefoot NZ, McLuckey SA. Gas phase reactivity of carboxylates with N-hydroxysuccinimide esters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:174-80. [PMID: 25338221 PMCID: PMC4654944 DOI: 10.1007/s13361-014-1002-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/06/2014] [Accepted: 09/08/2014] [Indexed: 05/13/2023]
Abstract
N-hydroxysuccinimide (NHS) esters have been used for gas-phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ε-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O(18) were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas phase, where they are shown to be reactive, and the solution phase, where they are not regarded as reactive with NHS esters.
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Affiliation(s)
- Zhou Peng
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana USA 47907-2084
| | - William M. McGee
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana USA 47907-2084
| | - Jiexun Bu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana USA 47907-2084
| | - Nathan Z. Barefoot
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana USA 47907-2084
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana USA 47907-2084
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44
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Pilo AL, McLuckey SA. Oxidation of methionine residues in polypeptide ions via gas-phase ion/ion chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1049-57. [PMID: 24671696 PMCID: PMC4020970 DOI: 10.1007/s13361-014-0861-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 05/13/2023]
Abstract
The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying degrees to all polypeptide ions irrespective of amino acid composition. Direct proton transfer yielding a charge-reduced peptide ion is also observed. In the case of methionine and, to a much lesser degree, tryptophan-containing peptide ions, collisional activation of the complex ion generated by periodate attachment yields an oxidized peptide product (i.e., [M + H + O](+)), in addition to periodic acid detachment. Detachment of periodic acid takes place exclusively for peptides that do not contain either a methionine or tryptophan side chain. In the case of methionine-containing peptides, the [M + H + O](+) product is observed at a much greater abundance than the proton transfer product (viz., [M + H](+)). Collisional activation of oxidized Met-containing peptides yields a signature loss of 64 Da from the precursor and/or product ions. This unique loss corresponds to the ejection of methanesulfenic acid from the oxidized methionine side chain and is commonly used in solution-phase proteomics studies to determine the presence of oxidized methionine residues. The present work shows that periodate anions can be used to 'label' methionine residues in polypeptides in the gas phase. The selectivity of the periodate anion for the methionine side chain suggests several applications including identification and location of methionine residues in sequencing applications.
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Affiliation(s)
| | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey 560 Oval Drive Department of Chemistry Purdue University West Lafayette, IN 47907-2084, USA Phone: (765) 494-5270 Fax: (765) 494-0239
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45
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Efficient and directed peptide bond formation in the gas phase via ion/ion reactions. Proc Natl Acad Sci U S A 2014; 111:1288-92. [PMID: 24474750 DOI: 10.1073/pnas.1317914111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amide linkages are among the most important chemical bonds in living systems, constituting the connections between amino acids in peptides and proteins. We demonstrate the controlled formation of amide bonds between amino acids or peptides in the gas phase using ion/ion reactions in a mass spectrometer. Individual amino acids or peptides can be prepared as reagents by (i) incorporating gas phase-labile protecting groups to silence otherwise reactive functional groups, such as the N terminus; (ii) converting the carboxyl groups to the active ester of N-hydroxysuccinimide; and (iii) incorporating a charge site. Protonation renders basic sites (nucleophiles) unreactive toward the N-hydroxysuccinimide ester reagents, resulting in sites with the greatest gas phase basicities being, in large part, unreactive. The N-terminal amines of most naturally occurring amino acids have lower gas phase basicities than the side chains of the basic amino acids (i.e., those of histidine, lysine, or arginine). Therefore, reagents may be directed to the N terminus of an existing "anchor" peptide to form an amide bond by protonating the anchor peptide's basic residues, while leaving the N-terminal amine unprotonated and therefore reactive. Reaction efficiencies of greater than 30% have been observed. We propose this method as a step toward the controlled synthesis of peptides in the gas phase.
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46
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McGee WM, McLuckey SA. Gas Phase Dissociation Behavior of Acyl-Arginine Peptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 354-356:181-187. [PMID: 24465154 PMCID: PMC3899352 DOI: 10.1016/j.ijms.2013.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The gas phase dissociation behavior of peptides containing acyl-arginine residues is investigated. These acylations are generated via a combination of ion/ion reactions between arginine-containing peptides and N-hydroxysuccinimide (NHS) esters and subsequent tandem mass spectrometry (MS/MS). Three main dissociation pathways of acylated arginine, labeled Paths 1-3, have been identified and are dependent on the acyl groups. Path 1 involves the acyl-arginine undergoing deguanidination, resulting in the loss of the acyl group and dissociation of the guanidine to generate an ornithine residue. This pathway generates selective cleavage sites based on the recently discussed "ornithine effect". Path 2 involves the coordinated losses of H2O and NH3 from the acyl-arginine side chain while maintaining the acylation. We propose that Path 2 is initiated via cyclization of the δ-nitrogen of arginine and the C-terminal carbonyl carbon, resulting in rapid rearrangement from the acyl-arginine side chain and the neutral losses. Path 3 occurs when the acyl group contains α-hydrogens and is observed as a rearrangement to regenerate unmodified arginine while the acylation is lost as a ketene.
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Affiliation(s)
| | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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47
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Prentice BM, McGee WM, Stutzman JR, McLuckey SA. Strategies for the Gas Phase Modification of Cationized Arginine via Ion/ion Reactions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 354-355:10.1016/j.ijms.2013.05.026. [PMID: 24273437 PMCID: PMC3835304 DOI: 10.1016/j.ijms.2013.05.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The gas phase acetylation of cationized arginine residues is demonstrated here using ion/ion reactions with sulfosuccinimidyl acetate (sulfo-NHS acetate) anions. Previous reports have demonstrated the gas phase modification of uncharged primary amine (the N-terminus and ε-amino side chain of lysine) and uncharged guanidine (the arginine side chain) functionalities via sulfo-NHS ester chemistry. Herein, charge-saturated arginine-containing peptides that contain sodium ions as the charge carriers, such as [ac-ARAAARA+2Na]2+, are shown to exhibit strong reactivity towards sulfo-NHS acetate whereas the protonated peptide analogues exhibit no such reactivity. This difference in reactivity is attributed to the lower sodium ion (as compared to proton) affinity of the arginine, which results in increased nucleophilicity of the cationized arginine guanidinium functionality. This increased nucleophilicity improves the arginine residue's reactivity towards sulfo-NHS esters and enhances the gas phase covalent modification pathway. No such dramatic increase in reactivity towards sulfo-NHS acetate has been observed upon sodium cationization of lysine amino acid residues, indicating that this behavior appears to be unique to arginine. The sodium cationization process is demonstrated in the condensed phase by simply spiking sodium chloride into the peptide sample solution and in the gas phase by a peptide-sodium cation exchange process with a sulfo-NHS acetate sodium-bound dimer cluster reagent. This methodology demonstrates several ways by which arginine can be covalently modified in the gas phase even when it is charged. Collisional activation of an acetylated arginine product can result in deguanidination of the residue, generating an ornithine. This gas phase ornithination exhibits similar site-specific fragmentation behavior to that observed with peptides ornithinated in solution and may represent a useful approach for inducing selective peptide cleavages.
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Affiliation(s)
| | | | | | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey 560 Oval Drive Department of Chemistry Purdue University West Lafayette, IN 47907-2084, USA Phone: (765) 494-5270 Fax: (765) 494-0239
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48
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Mentinova M, Crizer DM, Baba T, McGee WM, Glish GL, McLuckey SA. Cation recombination energy/coulomb repulsion effects in ETD/ECD as revealed by variation of charge per residue at fixed total charge. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1676-89. [PMID: 23568028 PMCID: PMC3795911 DOI: 10.1007/s13361-013-0606-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 02/28/2013] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation (ECD) and electron transfer dissociation (ETD) experiments in electrodynamic ion traps operated in the presence of a bath gas in the 1-10 mTorr range have been conducted on a common set of doubly protonated model peptides of the form X(AG)nX (X = lysine, arginine, or histidine, n = 1, 2, or 4). The partitioning of reaction products was measured using thermal electrons, anions of azobenzene, and anions of 1,3-dinitrobenzene as reagents. Variation of n alters the charge per residue of the peptide cation, which affects recombination energy. The ECD experiments showed that H-atom loss is greatest for the n = 1 peptides and decreases as n increases. Proton transfer in ETD, on the other hand, is expected to increase as charge per residue decreases (i.e., as n increases). These opposing tendencies were apparent in the data for the K(AG)nK peptides. H-atom loss appeared to be more prevalent in ECD than in ETD and is rationalized on the basis of either internal energy differences, differences in angular momentum transfer associated with the electron capture versus electron transfer processes, or a combination of the two. The histidine peptides showed the greatest extent of charge reduction without dissociation, the arginine peptides showed the greatest extent of side-chain cleavages, and the lysine peptides generally showed the greatest extent of partitioning into the c/z•-product ion channels. The fragmentation patterns for the complementary c- and z•-ions for ETD and ECD were found to be remarkably similar, particularly for the peptides with X = lysine.
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Affiliation(s)
- Marija Mentinova
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | - David M. Crizer
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Takashi Baba
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - William M. McGee
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | - Gary L. Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
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49
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Frese CK, Nolting D, Altelaar AFM, Griep-Raming J, Mohammed S, Heck AJR. Characterization of electron transfer dissociation in the Orbitrap Velos HCD cell. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1663-1670. [PMID: 23605687 DOI: 10.1007/s13361-013-0618-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
Electron transfer dissociation (ETD) is commonly employed in ion traps utilizing rf fields that facilitate efficient electron transfer reactions. Here, we explore performing ETD in the HCD collision cell on an Orbitrap Velos instrument by applying a static DC gradient axially to the rods. This gradient enables simultaneous three dimensional, charge sign independent, trapping of cations and anions, initiating electron transfer reactions in the center of the HCD cell where oppositely charged ions clouds overlap. Here, we evaluate this mode of operation for a number of tryptic peptide populations and the top-down sequence analysis of ubiquitin. Our preliminary data show that performing ETD in the HCD cell provides similar fragmentation as ion trap-ETD but requires further optimization to match performance of ion trap-ETD.
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Affiliation(s)
- Christian K Frese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
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50
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Prentice BM, Stutzman JR, McLuckey SA. Reagent cluster anions for multiple gas-phase covalent modifications of peptide and protein cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1045-52. [PMID: 23702708 PMCID: PMC3715118 DOI: 10.1007/s13361-013-0637-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 03/29/2013] [Accepted: 04/02/2013] [Indexed: 05/13/2023]
Abstract
Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the 'cost' of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K10 + 3H](3+) and the reagent cluster [5R(5Na) - Na](-)). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.
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Affiliation(s)
| | | | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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