101
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O'Connor PB. Considerations for design of a Fourier transform mass spectrometer in the 4.2 K cold bore of a superconducting magnet. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:1160-1167. [PMID: 12112266 DOI: 10.1002/rcm.685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An external source Fourier transform mass spectrometer (FTMS) constructed inside the vertical cold bore of a superconducting magnet will have dramatic advantages in effective magnetic field, noise figures, and base pressure over current commercially available external source FTMS systems. There are substantial, but solvable, difficulties in the design, primarily with regard to control of the helium boiloff rate to an acceptable level, as well as relatively minor design challenges with heat sinks, contraction of metallic ion optic elements in the extreme temperature, and tandem mass spectrometry experiments. However, the ability to construct the FTMS inside the narrow bore tube of existing, commercially available vertical bore NMR magnets will allow access to the upper magnetic field limit currently used by 900 MHz (21 Tesla) - 1 GHz (23.3 Tesla) NMR experiments. The vacuum system, simply by being held inside the cold bore at 4.2 K, will cryopump itself dropping base pressures substantially, and heat sinking the input resistor of the preamplifier to this cryogenically cooled vacuum chamber will allow reduction of the input Johnson noise by a factor of 8.4 with associated 8.4-fold improvement in signal/noise, sensitivity, and dynamic range. The simultaneous improvement of three fundamental limiting factors in the FTMS (field strength, base pressure, and Johnson noise figure) will clearly outweigh the concomitant increased helium boiloff rate particularly if this rate can be dropped to the estimated <5 L/day range. The additional use of modern cryorefrigerators will further reduce helium boiloff to zero except during MS(n) experiments and system cooldown.
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Affiliation(s)
- Peter B O'Connor
- Department of Biochemistry, Mass Spectrometry Resource, Boston University School of Medicine, 715 Albany St., R806, Boston, MA 02118, USA.
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102
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Palmblad M, Buijs J, Håkansson P. Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:1153-1162. [PMID: 11720389 DOI: 10.1016/s1044-0305(01)00301-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
High mass-resolving power has been shown to be useful for studying the conformational dynamics of proteins by hydrogen/deuterium (H/D) exchange. A computer algorithm was developed that automatically identifies peptides and their extent of deuterium incorporation from H/D exchange mass spectra of enzymatic digests or fragment ions produced by collisionally induced dissociation (CID) or electron capture dissociation (ECD). The computer algorithm compares measured and calculated isotopic distributions and uses a fast calculation of isotopic distributions using the fast Fourier transform (FFT). The algorithm facilitates rapid and automated analysis of H/D exchange mass spectra suitable for high-throughput approaches to the study of peptide and protein structures. The algorithm also makes the identification independent on comparisons with undeuterated control samples. The applicability of the algorithm was demonstrated on simulated isotopic distributions as well as on experimental data, such as Fourier transform ion cyclotron resonance (FTICR) mass spectra of myoglobin peptic digests, and CID and ECD spectra of substance P.
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Affiliation(s)
- M Palmblad
- Division of Ion Physics, Angström Laboratory, Uppsala University, Sweden.
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103
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Frankevich V, Zenobi R. Deceleration of high-energy matrix-assisted laser desorption/ionization ions in an open cell for Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2001; 15:2035-2040. [PMID: 11675671 DOI: 10.1002/rcm.474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A new method of ion deceleration in a Fourier transform ion cyclotron resonance (FTICR) open cell is described that improves the performance of FTICR-MS instruments equipped with an internal source for laser desorption/ionization. Ion deceleration occurs in the front trapping cylinder of an open cylindrical cell. Decelerating voltages up to 100 V can be applied for 10-500 micros to the front cylinder during ion introduction. The deceleration field is uniformly distributed along the cylinder length giving a "smooth" deceleration, which means that the deceleration is effective over a large time interval and a large m/z range. This results in improved trapping efficiency of high-energy ions. We demonstrate efficient trapping of high (m/z 66 kDa) mass ions and the possibility to reduce the width of the kinetic energy distribution of MALDI ions with this arrangement.
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Affiliation(s)
- V Frankevich
- Department of Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, CH-8093 Zürich, Switzerland
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104
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Affiliation(s)
- J Godovac-Zimmermann
- Center for Molecular Medicine, Department of Medicine, University College London, 5 University Street, London WC1E 6JJ, United Kingdom.
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105
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Stoeber L, Sustic A, Simonsick WJ, Vogl O. FUNCTIONAL POLYMERS 64. POTASSIUM IONIZATION OF DESORBED SPECIES (K+IDS) OF 2(2-HYDROXYPHENYL)2H-BENZOTRIAZOLES. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2000. [DOI: 10.1081/ma-100101154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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106
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Belkić D, Dando PA, Main J, Taylor HS. Three novel high-resolution nonlinear methods for fast signal processing. J Chem Phys 2000. [DOI: 10.1063/1.1310612] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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107
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Rodgers RP, Blumer EN, Hendrickson CL, Marshall AG. Stable isotope incorporation triples the upper mass limit for determination of elemental composition by accurate mass measurement. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:835-840. [PMID: 11014445 DOI: 10.1016/s1044-0305(00)00158-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
By comparing electrospray ionization Fourier-transform ion cyclotron resonance (FT-ICR) mass spectra and collision-induced dissociation (CID) FT-ICR mass spectra of a phospholipid (851 Da) extracted from natural abundance and 99% 13C bacterial growth media, we are able to reduce its number of possible elemental compositions (based on +/-10 ppm externally calibrated mass accuracy and biologically relevant compositional constraints) from 394 to 1. The basic idea is simply that the mass of a molecule containing N carbon atoms increases by N Da when 12C is replaced by 13C. Once the number of carbons is known, the number of possible combinations of other atoms in the molecule is greatly reduced. We demonstrate the method for a stored-waveform inverse Fourier transform-isolated phospholipid from an extract of membrane lipids from Rhodococcus rhodochrous hydrocarbon-degrading bacteria grown on either natural abundance or 99% 13C-enriched mixtures of n-hexadecane and n-octadecane. We project that this method raises the upper mass limit for unique determination of elemental composition from accurate mass measurement by a factor of at least 3, thereby extending "chemical formula" determination to identification and sequencing of larger synthetic and bio-polymers: phospholipids, oligopeptides of more than three to four amino acids, DNA or RNA of more than two nucleotides, oligosaccharides of more than three sugars, etc. The method can also be extended to determination of the number of other atoms for which heavy isotopes are available (e.g., 15N, 34S, 18O, etc.).
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Affiliation(s)
- R P Rodgers
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Florida State University, Tallahassee 32310, USA
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108
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Horn DM, Zubarev RA, McLafferty FW. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc Natl Acad Sci U S A 2000; 97:10313-7. [PMID: 10984529 PMCID: PMC27020 DOI: 10.1073/pnas.97.19.10313] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2000] [Indexed: 11/18/2022] Open
Abstract
A de novo sequencing program for proteins is described that uses tandem MS data from electron capture dissociation and collisionally activated dissociation of electrosprayed protein ions. Computer automation is used to convert the fragment ion mass values derived from these spectra into the most probable protein sequence, without distinguishing Leu/Ile. Minimum human input is necessary for the data reduction and interpretation. No extra chemistry is necessary to distinguish N- and C-terminal fragments in the mass spectra, as this is determined from the electron capture dissociation data. With parts-per-million mass accuracy (now available by using higher field Fourier transform MS instruments), the complete sequences of ubiquitin (8.6 kDa) and melittin (2.8 kDa) were predicted correctly by the program. The data available also provided 91% of the cytochrome c (12.4 kDa) sequence (essentially complete except for the tandem MS-resistant region K(13)-V(20) that contains the cyclic heme). Uncorrected mass values from a 6-T instrument still gave 86% of the sequence for ubiquitin, except for distinguishing Gln/Lys. Extensive sequencing of larger proteins should be possible by applying the algorithm to pieces of approximately 10-kDa size, such as products of limited proteolysis.
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Affiliation(s)
- D M Horn
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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109
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Fourier transform ion cyclotron resonance mass spectrometry as a high throughput affinity screen to identify RNA binding ligands. Trends Analyt Chem 2000. [DOI: 10.1016/s0165-9936(00)00029-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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110
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Horn DM, Zubarev RA, McLafferty FW. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:320-332. [PMID: 10757168 DOI: 10.1016/s1044-0305(99)00157-9] [Citation(s) in RCA: 364] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Here a fully automated computer algorithm is applied to complex mass spectra of peptides and proteins. This method uses a subtractive peak finding routine to locate possible isotopic clusters in the spectrum, subjecting these to a combination of the previous Fourier transform/Patterson method for primary charge determination and the method for least-squares fitting to a theoretically derived isotopic abundance distribution for m/z determination of the most abundant isotopic peak, and the statistical reliability of this determination. If a predicted protein sequence is available, each such m/z value is checked for assignment as a sequence fragment. A new signal-to-noise calculation procedure has been devised for accurate determination of baseline and noise width for spectra with high peak density. In 2 h, the program identified 824 isotopic clusters representing 581 mass values in the spectrum of a GluC digest of a 191 kDa protein; this is >50% more than the number of mass values found by the extremely tedious operator-applied methodology used previously. The program should be generally applicable to classes of large molecules, including DNA and polymers. Thorough high resolution analysis of spectra by Horn (THRASH) is proposed as the program's verb.
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Affiliation(s)
- D M Horn
- Department of Chemistry, Cornell University, Ithaca, New York 14853-1301, USA
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111
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He F, Hendrickson CL, Marshall AG. Unequivocal determination of metal atom oxidation state in naked heme proteins: Fe(III)myoglobin, Fe(III)cytochrome c, Fe(III)cytochrome b5, and Fe(III)cytochrome b5 L47R. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:120-126. [PMID: 10689664 DOI: 10.1016/s1044-0305(99)00132-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Unambiguous determination of metal atom oxidation state in an intact metalloprotein is achieved by matching experimental (electrospray ionization 9.4 tesla Fourier transform ion cyclotron resonance) and theoretical isotopic abundance mass distributions for one or more holoprotein charge states. The ion atom oxidation state is determined unequivocally as Fe(III) for each of four gas-phase unhydrated heme proteins electrosprayed from H2O: myoglobin, cytochrome c, cytochrome b5, and cytochrome b5 L47R (i.e., the solution-phase oxidation state is conserved following electrospray to produce gas-phase ions). However, the same Fe(III) oxidation state in all four heme proteins is observed after prior reduction by sodium dithionite to produce Fe(II) heme proteins in solution: thus proving that oxygen was present during the electrospray process. Those results bear directly on the issue of similarity (or lack thereof) of solution-phase and gas-phase protein conformations. Finally, infrared multiphoton irradiation of the gas-phase Fe(III)holoproteins releases Fe(III)heme from each of the noncovalently bound Fe(III)heme proteins (myoglobin, cytochrome b5 and cytochrome b5 L47R), but yields Fe(II)heme from the covalently bound heme in cytochrome c.
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Affiliation(s)
- F He
- Center for Interdisciplinary Magnetic Resonance, Florida State University, Tallahassee 32306, USA
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112
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Speir JP, Perkins G, Berg C, Pullen F. Fast, generic gradient high performance liquid chromatography coupled to fourier transform ion cyclotron resonance mass spectrometry for the accurate mass analysis of mixtures. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2000; 14:1937-1942. [PMID: 11013423 DOI: 10.1002/1097-0231(20001030)14:20<1937::aid-rcm115>3.0.co;2-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Fast gradient high performance liquid chromatography (HPLC) has been combined with a commercially available Fourier transform ion cyclotron resonance (FTICR) mass spectrometer for the routine and high performance analysis of mixtures. With this combination we were able to separate and detect, under high mass accuracy conditions, a six-component drug mixture in less than 5 minutes. The fast gradients described are now possible due to the development of mechanically robust, ultra pure silica packing materials, which allow relatively high flow rates (ca. 1 mL/min for a 2 mm diameter column). For the six compounds present in the model mixture, relative mass errors of less than 1 ppm were obtained (based on an external calibration) providing sufficient mass accuracy to make unequivocal assignments of empirical formulae. Preliminary results of fast gradient HPLC/FTICR-MS/MS are also shown for the same six-component mixture. Copyright 2000 John Wiley & Sons, Ltd.
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Affiliation(s)
- JP Speir
- Bruker Daltonics, Inc., Manning Park, Billerica, MA 01821, USA
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113
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Hendrickson CL, Emmett MR. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Annu Rev Phys Chem 1999; 50:517-36. [PMID: 10575730 DOI: 10.1146/annurev.physchem.50.1.517] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The basic principles and recent advances in electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry are reviewed. A brief history of electrospray ionization is provided, along with a complete technical description of the technique, electrospray ionization variations, and advantages. Next, the fundamental principles of Fourier transform ion cyclotron resonance mass spectrometry are covered, including ion cyclotron motion, ion cyclotron resonance excitation, and image current detection. Instrumentation and methods used to couple these techniques are then described. Topics include ion source configuration, ion transport through a strong magnetic field gradient, and ion trapping methods. The article concludes with selected applications that highlight the strengths of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.
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Affiliation(s)
- C L Hendrickson
- Center for Interdisciplinary Magnetic Resonance, Florida State University, Tallahassee 32310, USA.
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114
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Abstract
Mass spectrometry is capable of examining very large, dynamic proteins and this ability, coupled with its relatively high throughput and low sample requirements, is reflected by its increasing importance for the characterisation of protein structure. Recent developments in mass spectrometry, in particular the refinement of the electrospray process and its coupling with time-of-flight mass analysis, mean that it is poised to contribute not only as a complementary tool but also with a defined role in many areas of chemical biology.
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Affiliation(s)
- A M Last
- Oxford Centre for Molecular Sciences, South Parks Road, Oxford, OX1 3QT, UK
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