1
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Steigerwald S, Sinha A, Fort KL, Zeng WF, Niu L, Wichmann C, Kreutzmann A, Mourad D, Aizikov K, Grinfeld D, Makarov A, Mann M, Meier F. Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis. Mol Cell Proteomics 2024; 23:100713. [PMID: 38184013 PMCID: PMC10851225 DOI: 10.1016/j.mcpro.2024.100713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024] Open
Abstract
Optimizing data-independent acquisition methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here, we describe a real-time full mass range implementation of the phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2 h analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here, the number of identified protein groups and peptides increased by >15% in comparison to enhanced Fourier transformation processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.
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Affiliation(s)
- Sophia Steigerwald
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kyle L Fort
- Thermo Fisher Scientific (GmbH), Bremen, Germany
| | - Wen-Feng Zeng
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lili Niu
- Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christoph Wichmann
- Department Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | | | - Matthias Mann
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Florian Meier
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Functional Proteomics, Jena University Hospital, Jena, Germany.
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2
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James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Expanding Orbitrap Collision Cross-Section Measurements to Native Protein Applications Through Kinetic Energy and Signal Decay Analysis. Anal Chem 2023; 95:7656-7664. [PMID: 37133913 DOI: 10.1021/acs.analchem.3c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The measurement of collision cross sections (CCS, σ) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the modified hard collision model, thus deviating from the prior FT-MS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision induced unfolding and tandem mass spectrometry experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.
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Affiliation(s)
- Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Kyle L Fort
- Thermo Fisher Scientific, Bremen 28199, Germany
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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3
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Phaneuf CG, Aizikov K, Grinfeld D, Kreutzmann A, Mourad D, Lange O, Dai D, Zhang B, Belenky A, Makarov AA, Ivanov AR. Experimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays. Commun Chem 2023; 6:64. [PMID: 37024568 PMCID: PMC10079678 DOI: 10.1038/s42004-023-00861-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Mass spectrometry (MS)-based thermal stability assays have recently emerged as one of the most promising solutions for the identification of protein-ligand interactions. Here, we have investigated eight combinations of several recently introduced MS-based advancements, including the Phase-Constrained Spectral Deconvolution Method, Field Asymmetric Ion Mobility Spectrometry, and the implementation of a carrier sample as improved MS-based acquisition approaches for thermal stability assays (iMAATSA). We used intact Jurkat cells treated with a commercially available MEK inhibitor, followed by heat treatment, to prepare a set of unfractionated isobarically-labeled proof-of-concept samples to compare the performance of eight different iMAATSAs. Finally, the best-performing iMAATSA was compared to a conventional approach and evaluated in a fractionation experiment. Improvements of up to 82% and 86% were demonstrated in protein identifications and high-quality melting curves, respectively, over the conventional approach in the proof-of-concept study, while an approximately 12% improvement in melting curve comparisons was achieved in the fractionation experiment.
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Affiliation(s)
- Clifford G Phaneuf
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | | | | | | | - Daniel Dai
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | - Bailin Zhang
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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4
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Cai R, Huang W, Meder M, Bourgain F, Aizikov K, Riva M, Bianchi F, Ehn M. Improving the Sensitivity of Fourier Transform Mass Spectrometer (Orbitrap) for Online Measurements of Atmospheric Vapors. Anal Chem 2022; 94:15746-15753. [DOI: 10.1021/acs.analchem.2c03403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Runlong Cai
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Wei Huang
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Melissa Meder
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Frederic Bourgain
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON, Villeurbanne 69626, France
| | | | - Matthieu Riva
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, IRCELYON, Villeurbanne 69626, France
| | - Federico Bianchi
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Mikael Ehn
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
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5
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James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Advancing Orbitrap Measurements of Collision Cross Sections to Multiple Species for Broad Applications. Anal Chem 2022; 94:15613-15620. [DOI: 10.1021/acs.analchem.2c02146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Virginia K. James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D. Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | | | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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6
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Hilkert A, Böhlke JK, Mroczkowski SJ, Fort KL, Aizikov K, Wang XT, Kopf SH, Neubauer C. Exploring the Potential of Electrospray-Orbitrap for Stable Isotope Analysis Using Nitrate as a Model. Anal Chem 2021; 93:9139-9148. [PMID: 34165950 DOI: 10.1021/acs.analchem.1c00944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Widely used isotope ratio mass spectrometers have limited capabilities to measure metabolites, drugs, or small polyatomic ions without the loss of structural isotopic information. A new approach has recently been introduced that uses electrospray ionization Orbitrap to measure multidimensional isotope signatures of intact polar compounds. Using nitrate as a model compound, this study aims to establish performance metrics for comparisons with conventional IRMS at the natural abundance level. We present a framework on how to convert isotopolog intensities to δ values that are commonly used in the isotope geochemistry community. The quantification of seven nitrate isotopologs provides multiple pathways for obtaining the primary N and O δ values including non-mass-dependent O isotope variations, as well as opportunities to explore nonrandom isotopic distributions (i.e., clumping effects) within molecular nitrate. Using automation and the adaptation of measurement principles that are specific to isotope ratio analysis, nitrate δ15NAIR, δ18OVSMOW, and δ17OVSMOW were measured with a long-term precision of 0.4‰ or better for isotopic reference materials and purified nitrate from environmental samples. In addition, we demonstrate promising results for unpurified environmental samples in liquid form. With these new developments, this study connects the two largely disparate mass spectrometry fields of bioanalytical MS and isotope ratio MS, thus providing a route to measure new isotopic signatures in diverse organic and inorganic solutes.
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Affiliation(s)
- Andreas Hilkert
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - John K Böhlke
- U.S. Geological Survey, Reston, Virginia 20192, United States
| | | | - Kyle L Fort
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Konstantin Aizikov
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Xingchen T Wang
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Sebastian H Kopf
- Department of Geological Sciences, University of Colorado, Boulder, Colorado 80309, United States.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado 80303, United States
| | - Cajetan Neubauer
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado 80303, United States
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7
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Kelstrup CD, Aizikov K, Batth TS, Kreutzman A, Grinfeld D, Lange O, Mourad D, Makarov AA, Olsen JV. Limits for Resolving Isobaric Tandem Mass Tag Reporter Ions Using Phase-Constrained Spectrum Deconvolution. J Proteome Res 2018; 17:4008-4016. [PMID: 30220210 DOI: 10.1021/acs.jproteome.8b00381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A popular method for peptide quantification relies on isobaric labeling such as tandem mass tags (TMT), which enables multiplexed proteome analyses. Quantification is achieved by reporter ions generated by fragmentation in a tandem mass spectrometer. However, with higher degrees of multiplexing, the smaller mass differences between the reporter ions increase the mass resolving power requirements. This contrasts with faster peptide sequencing capabilities enabled by lowered mass resolution on Orbitrap instruments. It is therefore important to determine the mass resolution limits for highly multiplexed quantification when maximizing proteome depth. Here, we defined the lower boundaries for resolving TMT reporter ions with 0.0063 Da mass differences using an ultra-high-field Orbitrap mass spectrometer. We found the optimal method depends on the relative ratio between closely spaced reporter ions and that 64 ms transient acquisition time provided sufficient resolving power for separating TMT reporter ions with absolute ratio changes up to 16-fold. Furthermore, a 32 ms transient processed with phase-constrained spectrum deconvolution provides >50% more identifications with >99% quantified but with a slight loss in quantification precision and accuracy. These findings should guide decisions on what Orbitrap resolution settings to use in future proteomics experiments, relying on isobaric TMT reporter ion quantification.
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Affiliation(s)
- Christian D Kelstrup
- The Novo Nordisk Foundation Center for Protein Research , University of Copenhagen , 2200 Copenhagen , Denmark
| | | | - Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research , University of Copenhagen , 2200 Copenhagen , Denmark
| | | | | | - Oliver Lange
- Thermo Fisher Scientific , 28199 Bremen , Germany
| | | | | | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research , University of Copenhagen , 2200 Copenhagen , Denmark
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8
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Srzentić K, Nagornov KO, Fornelli L, Lobas AA, Ayoub D, Kozhinov AN, Gasilova N, Menin L, Beck A, Gorshkov MV, Aizikov K, Tsybin YO. Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody. Anal Chem 2018; 90:12527-12535. [DOI: 10.1021/acs.analchem.8b02398] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Luca Fornelli
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Anna A. Lobas
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Daniel Ayoub
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alain Beck
- Centre d’Immunologie Pierre Fabre, 74160 St. Julien-en-Genevois, France
| | - Mikhail V. Gorshkov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology State University, 141707 Dolgoprudny, Moscow Region, Russia
| | | | - Yury O. Tsybin
- Spectroswiss, EPFL Innovation Park, 1015 Lausanne, Switzerland
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9
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Sanders JD, Grinfeld D, Aizikov K, Makarov A, Holden DD, Brodbelt JS. Determination of Collision Cross-Sections of Protein Ions in an Orbitrap Mass Analyzer. Anal Chem 2018; 90:5896-5902. [DOI: 10.1021/acs.analchem.8b00724] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- James D. Sanders
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | | | | | | | - Dustin D. Holden
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
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10
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Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner PA, Makarov A, Beck A, Tsybin YO. Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer. J Proteomics 2017; 159:67-76. [PMID: 28242452 DOI: 10.1016/j.jprot.2017.02.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/22/2017] [Accepted: 02/13/2017] [Indexed: 12/27/2022]
Abstract
The increasing importance of immunoglobulins G (IgGs) as biotherapeutics calls for improved structural characterization methods designed for these large (~150kDa) macromolecules. Analysis workflows have to be rapid, robust, and require minimal sample preparation. In a previous work we showed the potential of Orbitrap Fourier transform mass spectrometry (FTMS) combined with electron transfer dissociation (ETD) for the top-down investigation of an intact IgG1, resulting in ~30% sequence coverage. Here, we describe a top-down analysis of two IgGs1 (adalimumab and trastuzumab) and one IgG2 (panitumumab) performed with ETD on a mass spectrometer equipped with a high-field Orbitrap mass analyzer. For the IgGs1, sequence coverage comparable to the previous results was achieved in a two-fold reduced number of summed transients, which corresponds, taken together with the significantly increased spectra acquisition rate, to ~six-fold improvement in analysis time. Furthermore, we studied the influence of ion-ion interaction times on ETD product ions for IgGs1, and the differences in fragmentation behavior between IgGs1 and IgG2, which present structural differences. Overall, these results reinforce the hypothesis that gas phase dissociation using both energy threshold-based and radical-driven ion activations is directed to specific regions of the polypeptide chains mostly by the location of disulfide bonds. SIGNIFICANCE OF THE STUDY Compared with our previous report, the results presented herein demonstrate the power of technological advances of the next generation Orbitrap™ platform, including the use of a high-field compact (i.e., D20) Orbitrap mass analyzer, and a dedicated manipulation strategy for large protein ions (via their trapping in the HCD collision cell along with reduction of the pressure in the cell). Notably, these important developments became recently commercially available in the top-end Orbitrap platforms under the name of "Protein Mode". Furthermore, we continued exploring the advantages offered by the summation (averaging) of transients (time-domain data) for improving the signal-to-noise ratio of top-down mass spectra. Finally, for the first time we report the application of the hybrid ion activation technique that combines electron transfer dissociation and higher energy collisional dissociation, known as EThcD, on intact monoclonal antibodies. Under these specific instrumental parameters, EThcD produces a partially complementary fragmentation pattern compared to ETD, increasing the overall sequence coverage especially at the protein termini.
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Affiliation(s)
- Luca Fornelli
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Ayoub
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 46202 Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Eugen Damoc
- Thermo Fisher Scientific GmbH, 28199 Bremen, Germany
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California in San Diego, 92093 San Diego, CA, USA
| | | | - Alain Beck
- Centre d'Immunologie Pierre Fabre, 74160 St Julien-en-Genevois, France
| | - Yury O Tsybin
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Spectroswiss Sàrl, EPFL Innovation Park, 1015 Lausanne, Switzerland.
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11
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Grinfeld D, Aizikov K, Kreutzmann A, Damoc E, Makarov A. Phase-Constrained Spectrum Deconvolution for Fourier Transform Mass Spectrometry. Anal Chem 2016; 89:1202-1211. [DOI: 10.1021/acs.analchem.6b03636] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dmitry Grinfeld
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Konstantin Aizikov
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Arne Kreutzmann
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Eugen Damoc
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
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12
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Fornelli L, Ayoub D, Aizikov K, Beck A, Tsybin YO. Middle-Down Analysis of Monoclonal Antibodies with Electron Transfer Dissociation Orbitrap Fourier Transform Mass Spectrometry. Anal Chem 2014; 86:3005-12. [DOI: 10.1021/ac4036857] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Luca Fornelli
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Ayoub
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Alain Beck
- Centre d’Immunologie Pierre Fabre, 74160 St. Julien-en-Genevois, France
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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13
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Fornelli L, Damoc E, Thomas PM, Kelleher NL, Aizikov K, Denisov E, Makarov A, Tsybin YO. Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS. Mol Cell Proteomics 2012; 11:1758-67. [PMID: 22964222 DOI: 10.1074/mcp.m112.019620] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The primary structural information of proteins employed as biotherapeutics is essential if one wishes to understand their structure-function relationship, as well as in the rational design of new therapeutics and for quality control. Given both the large size (around 150 kDa) and the structural complexity of intact immunoglobulin G (IgG), which includes a variable number of disulfide bridges, its extensive fragmentation and subsequent sequence determination by means of tandem mass spectrometry (MS) are challenging. Here, we applied electron transfer dissociation (ETD), implemented on a hybrid Orbitrap Fourier transform mass spectrometer (FTMS), to analyze a commercial recombinant IgG in a liquid chromatography (LC)-tandem mass spectrometry (MS/MS) top-down experiment. The lack of sensitivity typically observed during the top-down MS of large proteins was addressed by averaging time-domain transients recorded in different LC-MS/MS experiments before performing Fourier transform signal processing. The results demonstrate that an improved signal-to-noise ratio, along with the higher resolution and mass accuracy provided by Orbitrap FTMS (relative to previous applications of top-down ETD-based proteomics on IgG), is essential for comprehensive analysis. Specifically, ETD on Orbitrap FTMS produced about 33% sequence coverage of an intact IgG, signifying an almost 2-fold increase in IgG sequence coverage relative to prior ETD-based analysis of intact monoclonal antibodies of a similar subclass. These results suggest the potential application of the developed methodology to other classes of large proteins and biomolecules.
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Affiliation(s)
- Luca Fornelli
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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14
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Aizikov K, Smith DF, Chargin DA, Ivanov S, Lin TY, Heeren RMA, O'Connor PB. Vacuum compatible sample positioning device for matrix assisted laser desorption∕ionization Fourier transform ion cyclotron resonance mass spectrometry imaging. Rev Sci Instrum 2011; 82:054102. [PMID: 21639522 PMCID: PMC3117896 DOI: 10.1063/1.3594099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 05/03/2011] [Indexed: 05/19/2023]
Abstract
The high mass accuracy and resolving power of Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR MS) make them ideal mass detectors for mass spectrometry imaging (MSI), promising to provide unmatched molecular resolution capabilities. The intrinsic low tolerance of FT-ICR MS to RF interference, however, along with typically vertical positioning of the sample, and MSI acquisition speed requirements present numerous engineering challenges in creating robotics capable of achieving the spatial resolution to match. This work discusses a two-dimensional positioning stage designed to address these issues. The stage is capable of operating in ∼1 × 10(-8) mbar vacuum. The range of motion is set to 100 mm × 100 mm to accommodate large samples, while the positioning accuracy is demonstrated to be less than 0.4 micron in both directions under vertical load over the entire range. This device was integrated into three different matrix assisted laser desorption∕ionization (MALDI) FT-ICR instruments and showed no detectable RF noise. The "oversampling" MALDI-MSI experiments, under which the sample is completely ablated at each position, followed by the target movement of the distance smaller than the laser beam, conducted on the custom-built 7T FT-ICR MS demonstrate the stability and positional accuracy of the stage robotics which delivers high spatial resolution mass spectral images at a fraction of the laser spot diameter.
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Affiliation(s)
- Konstantin Aizikov
- Cardiovascular Proteomics Center, Boston University School of Medicine, 670 Albany Street, Room 504 Boston, Massachusetts 02118, USA
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Smith DF, Aizikov K, Duursma MC, Giskes F, Spaanderman DJ, McDonnell LA, O’Connor PB, Heeren RMA. An external matrix-assisted laser desorption ionization source for flexible FT-ICR Mass spectrometry imaging with internal calibration on adjacent samples. J Am Soc Mass Spectrom 2011; 22:130-7. [PMID: 21472551 PMCID: PMC3042104 DOI: 10.1007/s13361-010-0003-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 09/02/2010] [Accepted: 10/08/2010] [Indexed: 05/03/2023]
Abstract
We describe the construction and application of a new MALDI source for FT-ICR mass spectrometry imaging. The source includes a translational X-Y positioning stage with a 10×10 cm range of motion for analysis of large sample areas, a quadrupole for mass selection, and an external octopole ion trap with electrodes for the application of an axial potential gradient for controlled ion ejection. An off-line LC MALDI MS/MS run demonstrates the utility of the new source for data- and position-dependent experiments. A FT-ICR MS imaging experiment of a coronal rat brain section yields ∼200 unique peaks from m/z 400-1100 with corresponding mass-selected images. Mass spectra from every pixel are internally calibrated with respect to polymer calibrants collected from an adjacent slide.
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Affiliation(s)
- Donald F. Smith
- FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Konstantin Aizikov
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, MA USA
| | - Marc C. Duursma
- FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Frans Giskes
- FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Dirk-Jan Spaanderman
- FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Liam A. McDonnell
- FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
- Present Address: Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, MA USA
- Present Address: Department of Chemistry, University of Warwick, Coventry, UK
| | - Ron M. A. Heeren
- FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
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Aizikov K, Mathur R, O'Connor PB. The spontaneous loss of coherence catastrophe in Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 2009; 20:247-56. [PMID: 19013078 PMCID: PMC2872030 DOI: 10.1016/j.jasms.2008.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 09/29/2008] [Accepted: 09/29/2008] [Indexed: 05/16/2023]
Abstract
The spontaneous loss of coherence catastrophe (SLCC) is a frequently observed, yet poorly studied, space-charge related effect in Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS). This manuscript presents an application of the filter diagonalization method (FDM) in the analysis of this phenomenon. The temporal frequency behavior reproduced by frequency shift analysis using the FDM shows the complex nature of the SLCC, which can be explained by a combination of factors occurring concurrently, governed by electrostatics and ion packet trajectories inside the ICR cell.
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Affiliation(s)
- Konstantin Aizikov
- Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, Massachusetts, USA
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Aizikov K, O'Connor PB. Use of the filter diagonalization method in the study of space charge related frequency modulation in fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 2006; 17:836-843. [PMID: 16603376 DOI: 10.1016/j.jasms.2006.02.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 02/17/2006] [Accepted: 02/25/2006] [Indexed: 05/08/2023]
Abstract
The filter diagonalization method (FDM) is a recently developed computational technique capable of extracting resonance frequencies and amplitudes from very short transient signals. Although it requires stable resonance frequencies and is slower than the fast Fourier transform (FFT), FDM has a resolution and accuracy that is unmatched by the FFT or any other comparable techniques. This unique feature of FDM makes it an ideal tool for tracing space charge induced frequency modulations in Fourier transform ion cyclotron resonance (FT-ICR) cells, which are shown to reach +/-400 ppm even for such simple spectra as Substance P.
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Affiliation(s)
- Konstantin Aizikov
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 02118, Boston, MA, USA
- the Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA
- the Bioinformatics Program, Boston University, Boston, MA
| | - Peter B O'Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 02118, Boston, MA, USA.
- the Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA.
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