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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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Yan J, Zhou M, Gilbert JD, Wolff JJ, Somogyi Á, Pedder RE, Quintyn RS, Morrison LJ, Easterling ML, Paša-Tolić L, Wysocki VH. Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Anal Chem 2016; 89:895-901. [DOI: 10.1021/acs.analchem.6b03986] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jing Yan
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joshua D. Gilbert
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Árpád Somogyi
- OSU
Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Royston S. Quintyn
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lindsay J. Morrison
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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Snyder DT, Fedick PW, Cooks RG. Multigenerational Collision-Induced Dissociation for Characterization of Organic Compounds. Anal Chem 2016; 88:9572-9581. [PMID: 27622856 DOI: 10.1021/acs.analchem.6b02209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Dalton T. Snyder
- Department
of Chemistry and
Center for Analytical Instrumentation Development, Purdue University, West Lafayette, Indiana 47907, United States
| | - Patrick W. Fedick
- Department
of Chemistry and
Center for Analytical Instrumentation Development, Purdue University, West Lafayette, Indiana 47907, United States
| | - R. Graham Cooks
- Department
of Chemistry and
Center for Analytical Instrumentation Development, Purdue University, West Lafayette, Indiana 47907, United States
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Ma X, Lai LB, Lai SM, Tanimoto A, Foster MP, Wysocki VH, Gopalan V. Uncovering the Stoichiometry of Pyrococcus furiosusRNase P, a Multi-Subunit Catalytic Ribonucleoprotein Complex, by Surface-Induced Dissociation and Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ma X, Lai LB, Lai SM, Tanimoto A, Foster MP, Wysocki VH, Gopalan V. Uncovering the stoichiometry of Pyrococcus furiosus RNase P, a multi-subunit catalytic ribonucleoprotein complex, by surface-induced dissociation and ion mobility mass spectrometry. Angew Chem Int Ed Engl 2014; 53:11483-7. [PMID: 25195671 DOI: 10.1002/anie.201405362] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/16/2014] [Indexed: 01/02/2023]
Abstract
We demonstrate that surface-induced dissociation (SID) coupled with ion mobility mass spectrometry (IM-MS) is a powerful tool for determining the stoichiometry of a multi-subunit ribonucleoprotein (RNP) complex assembled in a solution containing Mg(2+). We investigated Pyrococcus furiosus (Pfu) RNase P, an archaeal RNP that catalyzes tRNA 5' maturation. Previous step-wise, Mg(2+)-dependent reconstitutions of Pfu RNase P with its catalytic RNA subunit and two interacting protein cofactor pairs (RPP21⋅RPP29 and POP5⋅RPP30) revealed functional RNP intermediates en route to the RNase P enzyme, but provided no information on subunit stoichiometry. Our native MS studies with the proteins showed RPP21⋅RPP29 and (POP5⋅RPP30)2 complexes, but indicated a 1:1 composition for all subunits when either one or both protein complexes bind the cognate RNA. These results highlight the utility of SID and IM-MS in resolving conformational heterogeneity and yielding insights on RNP assembly.
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Affiliation(s)
- Xin Ma
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210 (USA)
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Ma X, Zhou M, Wysocki VH. Surface induced dissociation yields quaternary substructure of refractory noncovalent phosphorylase B and glutamate dehydrogenase complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:368-379. [PMID: 24452296 DOI: 10.1007/s13361-013-0790-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/11/2013] [Accepted: 11/19/2013] [Indexed: 06/03/2023]
Abstract
Ion mobility (IM) and tandem mass spectrometry (MS/MS) coupled with native MS are useful for studying noncovalent protein complexes. Collision induced dissociation (CID) is the most common MS/MS dissociation method. However, some protein complexes, including glycogen phosphorylase B kinase (PHB) and L-glutamate dehydrogenase (GDH) examined in this study, are resistant to dissociation by CID at the maximum collision energy available in the instrument. Surface induced dissociation (SID) was applied to dissociate the two refractory protein complexes. Different charge state precursor ions of the two complexes were examined by CID and SID. The PHB dimer was successfully dissociated to monomers and the GDH hexamer formed trimeric subcomplexes that are informative of its quaternary structure. The unfolding of the precursor and the percentages of the distinct products suggest that the dissociation pathways vary for different charge states. The precursors at lower charge states (+21 for PHB dimer and +27 for GDH hexamer) produce a higher percentage of folded fragments and dissociate more symmetrically than the precusors at higher charge states (+29 for PHB dimer and +39 for GDH hexamer). The precursors at lower charge state may be more native-like than the higher charge state because a higher percentage of folded fragments and a lower percentage of highly charged unfolded fragments are detected. The combination of SID and charge reduction is shown to be a powerful tool for quaternary structure analysis of refractory noncovalent protein complexes, as illustrated by the data for PHB dimer and GDH hexamer.
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Affiliation(s)
- Xin Ma
- Department of Chemistry and Biochemistry, The Ohio State University, 876 Biological Sciences Building, 484 W 12th Ave, Columbus, OH, 43210, USA
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Yoon SH, Gamage CM, Gillig KJ, Wysocki VH. Kinetics of surface-induced dissociation of N(CH3)4(+) and N(CD3)4(+) using silicon nanoparticle assisted laser desorption/ionization and laser desorption/ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:957-964. [PMID: 19321360 DOI: 10.1016/j.jasms.2009.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 03/01/2009] [Accepted: 03/02/2009] [Indexed: 05/27/2023]
Abstract
The implementation of surface-induced dissociation (SID) to study the fast dissociation kinetics (sub-microsecond dissociation) of peptides in a MALDI TOF instrument has been reported previously. Silicon nanoparticle assisted laser desorption/ionization (SPALDI) now allows the study of small molecule dissociation kinetics for ions formed with low initial source internal energy and without MALDI matrix interference. The dissociation kinetics of N(CH(3))(4)(+) and N(CD(3))(4)(+) were chosen for investigation because the dissociation mechanisms of N(CH(3))(4)(+) have been studied extensively, providing well-characterized systems to investigate by collision with a surface. With changes in laboratory collision energy, changes in fragmentation timescale and dominant fragment ions were observed, verifying that these ions dissociate via unimolecular decay. At lower collision energies, methyl radical (CH(3)) loss with a sub-microsecond dissociation rate is dominant, but consecutive H loss after CH(3) loss becomes dominant at higher collision energies. These observations are consistent with the known dissociation pathways. The dissociation rate of CH(3) loss from N(CH(3))(4)(+) formed by SPALDI and dissociated by an SID lab collision energy of 15 eV corresponds to log k = 8.1, a value achieved by laser desorption ionization (LDI) and SID at 5 eV. The results obtained with SPALDI SID and LDI SID confirm that (1) the dissociation follows unimolecular decay as predicted by RRKM calculations; (2) the SPALDI process deposits less initial energy than LDI, which has advantages for kinetics studies; and (3) fluorinated self-assembled monolayers convert about 18% of laboratory collision energy into internal energy. SID TOF experiments combined with SPALDI and peak shape analysis enable the measurement of dissociation rates for fast dissociation of small molecules.
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Affiliation(s)
- Sung Hwan Yoon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
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Wysocki VH, Joyce KE, Jones CM, Beardsley RL. Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:190-208. [PMID: 18191578 PMCID: PMC2709493 DOI: 10.1016/j.jasms.2007.11.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 10/23/2007] [Accepted: 11/03/2007] [Indexed: 05/12/2023]
Abstract
This article provides a perspective on collisions of ions with surfaces, including surface-induced dissociation (SID) and reactive ion scattering spectrometry (RISS). The content is organized into sections on surface-induced dissociation of small ions, surface characterization of organic thin films by collision of well-characterized ions into surfaces, the use of SID to probe peptide fragmentation, and the dissociation of large non-covalent complexes by SID. Examples are given from the literature with a focus on experiments from the authors' laboratory. The article is not a comprehensive review but is designed to provide the reader with an overview of the types of results possible by collisions of ions into surfaces.
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Affiliation(s)
- Vicki H Wysocki
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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Dodds ED, German JB, Lebrilla CB. Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation. Anal Chem 2007; 79:9547-56. [PMID: 18001128 DOI: 10.1021/ac701763t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a central tool for proteomic analysis, yet the singly protonated tryptic peptide ions produced by MALDI are significantly more difficult to dissociate for tandem mass spectrometry (MS/MS) than the corresponding multiply protonated ions. In order to overcome this limitation, current proteomic approaches using MALDI-MS/MS involve high-energy collision-induced dissociation (CID). Unfortunately, the use of high-energy CID complicates product ion spectra with a significant proportion of irrelevant fragments while also reducing mass accuracy and mass resolution. In order to address the lack of a high-resolution, high mass accuracy MALDI-MS/MS platform for proteomics, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and a recently developed MS/MS technique termed CIRCA (for combination of infrared and collisional activation) have been applied to proteomic analysis. Here, CIRCA is shown to be suitable for dissociating singly protonated tryptic peptides, providing greater sequence coverage than either CID or infrared multiphoton dissociation (IRMPD) alone. Furthermore, the CIRCA fragmentation spectra are of sufficient quality to allow protein identification based on the MS/MS spectra alone or in concert with the peptide mass fingerprint (PMF). This is accomplished without compromising mass accuracy or mass resolution. As a result, CIRCA serves to enable MALDI-FTICR-MS/MS for high-performance proteomics experiments.
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Affiliation(s)
- Eric D Dodds
- Department of Chemistry, School of Medicine, University of California Davis, One Shields Avenue, Davis, California 95616, USA
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11
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Shukla AK. Bimodal energy distributions in the scattering of Ar+ ions from modified surfaces at hyperthermal energies. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.10.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Liu X, Valentine SJ, Plasencia MD, Trimpin S, Naylor S, Clemmer DE. Mapping the human plasma proteome by SCX-LC-IMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1249-64. [PMID: 17553692 PMCID: PMC2195767 DOI: 10.1016/j.jasms.2007.04.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 04/07/2007] [Accepted: 04/07/2007] [Indexed: 05/10/2023]
Abstract
The advent of on-line multidimensional liquid chromatography-mass spectrometry has significantly impacted proteomic analyses of complex biological fluids such as plasma. However, there is general agreement that additional advances to enhance the peak capacity of such platforms are required to enhance the accuracy and coverage of proteome maps of such fluids. Here, we describe the combination of strong-cation-exchange and reversed-phase liquid chromatographies with ion mobility and mass spectrometry as a means of characterizing the complex mixture of proteins associated with the human plasma proteome. The increase in separation capacity associated with inclusion of the ion mobility separation leads to generation of one of the most extensive proteome maps to date. The map is generated by analyzing plasma samples of five healthy humans; we report a preliminary identification of 9087 proteins from 37,842 unique peptide assignments. An analysis of expected false-positive rates leads to a high-confidence identification of 2928 proteins. The results are catalogued in a fashion that includes positions and intensities of assigned features observed in the datasets as well as pertinent identification information such as protein accession number, mass, and homology score/confidence indicators. Comparisons of the assigned features reported here with other datasets shows substantial agreement with respect to the first several hundred entries; there is far less agreement associated with detection of lower abundance components.
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Affiliation(s)
- Xiaoyun Liu
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | | | - Sarah Trimpin
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Stephen Naylor
- Predictive Physiology & Medicine Inc., Bloomington, IN 47404
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:266-277. [PMID: 17262881 DOI: 10.1002/jms.1071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Williams DK, Hawkridge AM, Muddiman DC. Sub parts-per-million mass measurement accuracy of intact proteins and product ions achieved using a dual electrospray ionization quadrupole fourier transform ion cyclotron resonance mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1-7. [PMID: 16979902 DOI: 10.1016/j.jasms.2006.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/15/2006] [Accepted: 08/15/2006] [Indexed: 05/11/2023]
Abstract
High mass measurement accuracy (MMA) is demonstrated for intact proteins and subsequent collision-induced dissociation product ions using internal calibration. Internal calibration was accomplished using a dual electrospray ionization source coupled with a hybrid quadrupole Fourier transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer. Initially, analyte ions generated via the first electrospray (ESI) emitter are isolated and dissociated in the external quadrupole. This event is followed by a simultaneous switch to the calibrant ion ESI emitter and a disablement of the isolation and activation of the external quadrupole such that a broad m/z range of calibrant ions are accumulated before injecting the analyte/calibrant ion mixture into the ICR cell. Two different internal calibrant solutions were utilized in these studies to evaluate this approach for the top-down characterization of melittin and ubiquitin. While external calibration of protein fragments resulted in absolute MMA greater than 16 ppm, internal standardization significantly improved upon the MMA of both the intact proteins and their products ions which ranged from -2.0 ppm to 1.1 ppm, with an average of -0.9 ppm. This method requires limited modification to ESI-FT-ICR mass spectrometers and is applicable for both positive and negative ionization modes.
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Affiliation(s)
- D Keith Williams
- W M Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University Raleigh, North Carolina 27695, USA
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