1
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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2
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Pizzala NJ, Bhanot JS, Carrick IJ, Dziekonski ET, McLuckey SA. Ion parking in native mass spectrometry. Analyst 2024; 149:2966-2977. [PMID: 38600834 PMCID: PMC11089522 DOI: 10.1039/d4an00242c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
A forced, damped harmonic oscillator model for gas-phase ion parking using single-frequency resonance excitation is described and applied to high-mass ions of relevance to native mass spectrometry. Experimental data are provided to illustrate key findings revealed by the modelling. These include: (i) ion secular frequency spacings between adjacent charge states of a given protein are essentially constant and decrease with the mass of the protein (ii) the mechanism for ion parking of high mass ions is the separation of the ion clouds of the oppositely-charged ions with much less influence from an increase in the relative ion velocity due to resonance excitation, (iii) the size of the parked ion cloud ultimately limits ion parking at high m/z ratio, and (iv) the extent of ion parking of off-target ions is highly sensitive to the bath gas pressure in the ion trap. The model is applied to ions of 17 kDa, 467 kDa, and 2 MDa while experimental data are also provided for ions of horse skeletal muscle myoglobin (≈17 kDa) and β-galactosidase (≈467 kDa). The model predicts and data show that it is possible to effect ion parking on a 17 kDa protein to the 1+ charge state under trapping conditions that are readily accessible with commercially available ion traps. It is also possible to park β-galactosidase efficiently to a roughly equivalent m/z ratio (i.e., the 26+ charge state) under the same trapping conditions. However, as charge states decrease, analyte ion cloud sizes become too large to allow for efficient ion trapping. The model allows for a semi-quantitative prediction of ion trapping performance as a function of ion trapping, resonance excitation, and pressure conditions.
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Affiliation(s)
- Nicolas J Pizzala
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Jay S Bhanot
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Ian J Carrick
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Eric T Dziekonski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
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3
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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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4
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Fabijanczuk KC, Foreman DJ, McLuckey SA. Charge Inversion of Mono- and Dianions to Cations via Triply Charged Metal Complexes: Application to Lipid Mixtures. Anal Chem 2023; 95:16289-16297. [PMID: 37871251 DOI: 10.1021/acs.analchem.3c03345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Electrospray ionization (ESI) of mixtures can give rise to ions with different masses and charges with overlapping mass-to-charge (m/z) ratios. Such a scenario can be particularly problematic for the detection of low-abundance species in the presence of more highly abundant mixture components. For example, negative mode ESI of polar lipid extracts can result in highly abundant singly charged glyerophospholipids (GPLs), such as phosphatidylethanolamines (PE) and phosphatidylglycerols (PG), that can obscure much less abundant cardiolipins (CLs), which are complex phospholipids with masses roughly double those of GPLs that mostly form doubly charged anions. Despite their low relative abundance, CLs are lipidome components that perform vital biological functions. To facilitate the study of CLs in lipid mixtures without resorting to offline or online separations, we have developed a gas-phase approach employing ion/ion reactions to charge invert anionic lipid species using a trivalent metal-complex. Specifically, ytterbium(III) is shown to readily complex with three neutral ligands, N,N,N',N'-tetra-2-ethylhexyl diglycolamide (TEHDGA), to form [Yb(TEHDGA3)]3+ using ESI. Herein, we describe pilot studies to evaluate [Yb(TEHDGA)3]3+ as an ion/ion reagent to allow for chemical separation of doubly and singly charged anions, using lipid mixtures as examples, without neutralizing ions of either charge state.
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Affiliation(s)
- Kimberly C Fabijanczuk
- 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
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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5
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Walker JN, Lam R, Brodbelt JS. Enhanced Characterization of Histones Using 193 nm Ultraviolet Photodissociation and Proton Transfer Charge Reduction. Anal Chem 2023; 95:5985-5993. [PMID: 36989418 DOI: 10.1021/acs.analchem.2c05765] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Top-down characterization of histones, proteins that are critical participants in an array of DNA-dependent processes, offers the potential to examine the relationship between histone structure and mechanisms of genetic regulation. Mapping patterns of post-translational modifications (PTMs) of histones requires extensive backbone cleavages to bracket the sites of mass shifts corresponding to specific PTMs. Ultraviolet photodissociation (UVPD) causes substantial fragmentation of proteins, which is well-suited for PTM localization, but the resulting spectra are congested with fragment ions that may have overlapping isotopic distributions that confound deconvolution. Gas-phase proton transfer charge reduction (PTCR) decreases the charge states of highly charged ions, thus alleviating this congestion and facilitating the identification of additional sequence-determining and PTM-localizing fragment ions. By integrating UVPD with PTCR for histone proteoform analyses, sequence coverages up to 91% were achieved for calf thymus histone H4 containing acetylation marks at the N-terminus and Lys12 as well as a dimethylation at Arg3. UVPD-PTCR exhibited large gains in characterization for other histones, such as histone H2A, increasing the sequence coverage from 59 to 77% for monoacetylated H2A.
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Affiliation(s)
- Jada N Walker
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Raymond Lam
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - 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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Lin Y, Agarwal AM, Anderson LC, Marshall AG. Discovery of a biomarker for β-Thalassemia by HPLC-MS and improvement from Proton Transfer Reaction - Parallel Ion Parking. J Mass Spectrom Adv Clin Lab 2023; 28:20-26. [PMID: 36814695 PMCID: PMC9939715 DOI: 10.1016/j.jmsacl.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
β-thalassemia is a quantitative hemoglobin (Hb) disorder resulting in reduced production of Hb A and increased levels of Hb A2. Diagnosis of β-thalassemia can be problematic when combined with other structural Hb variants, so that the separation approaches in routine clinical centers are not sufficiently decisive to obtain accurate results. Here, we separate the intact Hb subunits by high-performance liquid chromatography, followed by top-down tandem mass spectrometry of intact subunits to distinguish Hb variants. Proton transfer reaction-parallel ion parking (PTR-PIP), in which a radical anion removes protons from multiply charged precursor ions and produces charge-reduced ions spanning a limited m/z range, was used to increase the signal-to-noise ratio of the subunits of interest. We demonstrate that the δ/β ratio can act as a biomarker to identify β-thalassemia in normal electrospray ionization MS1 and PTR-PIP MS1. The application of PTR-PIP significantly increases the sensitivity and specificity of the HPLC-MS method to identify δ/β ratio as a thalassemia biomarker.
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Key Words
- ACN, Acetonitrile
- AUC, Areas under the curve
- CID, Collision-induced dissociation
- ESI, Electrospray ionization
- ETD, Electron-transfer dissociation
- FA, Formic acid
- FN, False-negative
- FP, False-positive
- FT-ICR
- FT-ICR, MS Fourier transform ion cyclotron resonance mass spectrometer
- FTMS
- Fourier transform ion cyclotron resonance
- Hb A, Normal adult Hb
- Hb, Hemoglobin
- HbA1d, Hb β with glutathione
- IFCC, International Federation of Clinical Chemistry and Laboratory Medicine
- IQR, Interquartile range
- J, Youden Index
- MCW, Methanol/chloroform/water
- MS, Mass spectrometry
- PTM, Post-translational modification
- PTR-PIP, Proton transfer reaction-parallel ion parking
- ROC, Receiver operating characteristic
- S/N, Signal-to-noise ratios
- Se(c), Sensitivity, the probability of a true positive)
- Sp(c), Specificity, the probability of a true negative)
- TIC, Total ion chromatogram
- TN, True negative
- TP, True positive
- Top-down
- XIC, Extracted ion chromatograms
- m/z, Mass-to-charge ratios
- δ/β ratio
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Affiliation(s)
- Yuan Lin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States
| | - Archana M. Agarwal
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, United States,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, United States
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States,Corresponding authors at: Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States (A.G. Marshall).
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States,Corresponding authors at: Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States (A.G. Marshall).
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7
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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: 4] [Impact Index Per Article: 4.0] [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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8
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Papanastasiou D, Kounadis D, Lekkas A, Orfanopoulos I, Mpozatzidis A, Smyrnakis A, Panagiotopoulos E, Kosmopoulou M, Reinhardt-Szyba M, Fort K, Makarov A, Zubarev RA. The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1990-2007. [PMID: 36113052 PMCID: PMC9850925 DOI: 10.1021/jasms.2c00214] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.
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Affiliation(s)
- Dimitris Papanastasiou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Diamantis Kounadis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Alexandros Lekkas
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Ioannis Orfanopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Andreas Mpozatzidis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Athanasios Smyrnakis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Elias Panagiotopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Mariangela Kosmopoulou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | | | - Kyle Fort
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Alexander Makarov
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Roman A. Zubarev
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
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9
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Brodbelt JS. Deciphering combinatorial post-translational modifications by top-down mass spectrometry. Curr Opin Chem Biol 2022; 70:102180. [PMID: 35779351 PMCID: PMC9489649 DOI: 10.1016/j.cbpa.2022.102180] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications (PTMs) create vast structural and functional diversity of proteins, ultimately modulating protein function and degradation, influencing cellular signaling, and regulating transcription. The combinatorial patterns of PTMs increase the heterogeneity of proteins and further mediates their interactions. Advances in mass spectrometry-based proteomics have resulted in identification of thousands of proteins and allowed characterization of numerous types and sites of PTMs. Examination of intact proteins, termed the top-down approach, offers the potential to map protein sequences and localize multiple PTMs on each protein, providing the most comprehensive cataloging of proteoforms. This review describes some of the dividends of using mass spectrometry to analyze intact proteins and showcases innovative strategies that have enhanced the promise of top-down proteomics for exploring the impact of combinatorial PTMs in unsurpassed detail.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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10
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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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11
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Fornelli L, Toby TK. Characterization of large intact protein ions by mass spectrometry: What directions should we follow? BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140758. [PMID: 35077914 DOI: 10.1016/j.bbapap.2022.140758] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Theoretically, the gas-phase interrogation of whole proteoforms via mass spectrometry, known as top-down proteomics, bypasses the protein inference problem that afflicts peptide-centric proteomic approaches. Despite this obvious advantage, the application of top-down proteomics remains rare, mainly due to limited throughput and difficulty of analyzing proteins >30 kDa. Here we will discuss some of the problems encountered during the characterization of large proteoforms, and guided by a combination of theoretical background and experimental evidence we will describe some innovative data acquisition strategies and novel mass spectrometry technologies that can at least partially overcome such limitations.
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Affiliation(s)
- Luca Fornelli
- University of Oklahoma, Department of Biology, 730 Van Vleet oval, Norman, OK 73109, United States of America; University of Oklahoma, Department Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73109, United States of America.
| | - Timothy K Toby
- DiscernDx, 2478 Embarcadero Way, Palo Alto, CA 94303, United States of America
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12
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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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13
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Bailey AO, Huguet R, Mullen C, Syka JEP, Russell WK. Ion-Ion Charge Reduction Addresses Multiple Challenges Common to Denaturing Intact Mass Analysis. Anal Chem 2022; 94:3930-3938. [PMID: 35189062 DOI: 10.1021/acs.analchem.1c04973] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Complete LC-MS-based protein primary sequence characterization requires measurement of intact protein profiles under denaturing and/or reducing conditions. To address issues of protein overcharging of unstructured proteins under acidic, denaturing conditions and sample heterogeneity (macro- and micro-scales) which often confound denaturing intact mass analysis of a wide variety of protein samples, we propose the use of broadband isolation of entire charge state distributions of intact proteins followed by ion-ion proton transfer charge reduction, which we have termed "full scan PTCR" (fsPTCR). Using rapid denaturing size exclusion chromatography coupled to fsPTCR-Orbitrap MS and time-resolved deconvolution data analysis, we demonstrate a strategy for method optimization, leading to significant analytical advantages over conventional MS1. Denaturing analysis of the flexible bacterial translation initiation factor 2 (91 kDa) using fsPTCR reduced overcharging and showed an 11-fold gain in S/N compared to conventional MS1. Analysis by fsPTCR-MS of the microheterogeneous glycoprotein fetuin revealed twice as many proteoforms as MS1 (112 vs 56). In a macroheterogeneous mixture of proteins ranging from 14 to 148 kDa, fsPTCR provided more than 10-fold increased sensitivity and quantitative accuracy for diluted bovine serum albumin (66 kDa). Finally, our analysis shows that collisional gas pressure is a key parameter which can be utilized during fsPTCR to retain or remove larger proteins from acquired spectra.
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Affiliation(s)
- Aaron O Bailey
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - William K Russell
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
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14
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Duselis EM, Panepinto MC, Syka JEP, Mullen C, D'Ippolito RA, English AM, Ugrin SA, Shabanowitz J, Hunt DF. Improved Sequence Analysis of Intact Proteins by Parallel Ion Parking during Electron Transfer Dissociation. Anal Chem 2021; 93:15728-15735. [PMID: 34788003 DOI: 10.1021/acs.analchem.1c03652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transfer dissociation (ETD) is an analytically useful tool for primary structure interrogation of intact proteins, but its utility is limited by higher-order reactions with the products. To inhibit these higher-order reactions, first-generation fragment ions are kinetically excited by applying an experimentally tailored parallel ion parking waveform during ETD (ETD-PIP). In combination with subsequent ion/ion proton transfer reactions, precursor-to-product conversion was maximized as evidenced by the consumption of more than 90% of the 21 kDa Protein G precursor to form ETD product ions. The employment of ETD-PIP increased sequence coverage to 90% from 80% with standard ETD. Additionally, the inhibition of sequential electron transfers was reflected in the high number of complementary ion pairs from ETD-PIP (90%) compared to standard ETD (39%).
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Affiliation(s)
- Elizabeth M Duselis
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Maria C Panepinto
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - John E P Syka
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Robert A D'Ippolito
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - A Michelle English
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Scott A Ugrin
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Pathology, University of Virginia, Charlottesville, Virginia 22903, United States
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15
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Panepinto MC, Duselis EM, Shabanowitz J, Hunt DF. Nitrogen-Containing Aromatic Radical Anions Perform Multiple Proton and Electron Transfers Near-Simultaneously with Multiply Protonated Cations. Anal Chem 2021; 93:14365-14368. [PMID: 34670079 DOI: 10.1021/acs.analchem.1c03801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas phase ion/ion reactions between singly charged radical reagent anions and multiply charged cation precursors primarily result in either proton or electron transfer. These ion/ion reactions have been extensively studied for bioanalysis, and many reagent anions have been tested and reported. Here, nitrogen-containing aromatic radical anions were tested for the ability to conduct proton or electron transfer by their reaction with the ubiquitin [M + 13H]+13 precursor. The singly charged anion of 2,2'-biquinoline was found to undergo charge inversion to singly protonated cations via near-simultaneous proton and electron transfers while reactants were bound in a single ion/ion reaction complex. Although the focus of this paper was 2,2'-biquinoline, all three nitrogen-containing aromatic compounds tested produced similar results.
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Affiliation(s)
- Maria C Panepinto
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Elizabeth M Duselis
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Pathology, University of Virginia, Charlottesville, Virginia 22903, United States
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16
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Kline JT, Mullen C, Durbin KR, Oates RN, Huguet R, Syka JEP, Fornelli L. Sequential Ion-Ion Reactions for Enhanced Gas-Phase Sequencing of Large Intact Proteins in a Tribrid Orbitrap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2334-2345. [PMID: 33900069 DOI: 10.1021/jasms.1c00062] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Obtaining extensive sequencing of an intact protein is essential in order to simultaneously determine both the nature and exact localization of chemical and genetic modifications which distinguish different proteoforms arising from the same gene. To effectively achieve such characterization, it is necessary to take advantage of the analytical potential offered by the top-down mass spectrometry approach to protein sequence analysis. However, as a protein increases in size, its gas-phase dissociation produces overlapping, low signal-to-noise fragments. The application of advanced ion dissociation techniques such as electron transfer dissociation (ETD) and ultraviolet photodissociation (UVPD) can improve the sequencing results compared to slow-heating techniques such as collisional dissociation; nonetheless, even ETD- and UVPD-based approaches have thus far fallen short in their capacity to reliably enable extensive sequencing of proteoforms ≥30 kDa. To overcome this issue, we have applied proton transfer charge reduction (PTCR) to limit signal overlap in tandem mass spectra (MS2) produced by ETD (alone or with supplemental ion activation, EThcD). Compared to conventional MS2 experiments, following ETD/EThcD MS2 with PTCR MS3 prior to m/z analysis of deprotonated product ions in the Orbitrap mass analyzer proved beneficial for the identification of additional large protein fragments (≥10 kDa), thus improving the overall sequencing and in particular the coverage of the central portion of all four analyzed proteins spanning from 29 to 56 kDa. Specifically, PTCR-based data acquisition led to 39% sequence coverage for the 56 kDa glutamate dehydrogenase, which was further increased to 44% by combining fragments obtained via HCD followed by PTCR MS3.
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Affiliation(s)
- Jake T Kline
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | | | - Ryan N Oates
- Department of Chemistry and Biochemistry, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
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17
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Weisbrod CR, Anderson LC, Hendrickson CL, Schaffer LV, Shortreed MR, Smith LM, Shabanowitz J, Hunt DF. Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal Chem 2021; 93:9119-9128. [PMID: 34165955 DOI: 10.1021/acs.analchem.1c00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer reactions (PTRs) have emerged as a powerful tool for the study of intact proteins. When coupled with m/z-selective kinetic excitation, such as parallel ion parking (PIP), one can exert exquisite control over rates of reaction with a high degree of specificity. This allows one to "concentrate", in the gas phase, nearly all the signals from an intact protein charge state envelope into a single charge state, improving the signal-to-noise ratio (S/N) by 10× or more. While this approach has been previously reported, here we show that implementing these technologies on a 21 T FT-ICR MS provides a tremendous advantage for intact protein analysis. Advanced strategies for performing PTR with PIP were developed to complement this unique instrument, including subjecting all analyte ions entering the mass spectrometer to PTR and PIP. This experiment, which we call "PTR-MS1-PIP", generates a pseudo-MS1 spectrum derived from ions that are exposed to the PTR reagent and PIP waveforms but have not undergone any prior true mass filtering or ion isolation. The result is an extremely rapid and significant improvement in the spectral S/N of intact proteins. This permits the observation of many more proteoforms and reduces ion injection periods for subsequent tandem mass spectrometry characterization. Additionally, the product ion parking waveform has been optimized to enhance the PTR rate without compromise to the parking efficiency. We demonstrate that this process, called "rapid park", can improve reaction rates by 5-10× and explore critical factors discovered to influence this process. Finally, we demonstrate how coupling PTR-MS1 and rapid park provides a 10-fold reduction in ion injection time, improving the rate of tandem MS sequencing.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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18
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Yu D, Wang Z, Cupp-Sutton KA, Guo Y, Kou Q, Smith K, Liu X, Wu S. Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1336-1344. [PMID: 33725447 PMCID: PMC8323476 DOI: 10.1021/jasms.0c00464] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Labeling approaches using isobaric chemical tags (e.g., isobaric tagging for relative and absolute quantification, iTRAQ and tandem mass tag, TMT) have been widely applied for the quantification of peptides and proteins in bottom-up MS. However, until recently, successful applications of these approaches to top-down proteomics have been limited because proteins tend to precipitate and "crash" out of solution during TMT labeling of complex samples making the quantification of such samples difficult. In this study, we report a top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples. To reduce the sample complexity and remove large proteins from complex samples, we developed a filter-SEC technique that combines a molecular weight cutoff filtration step with high-performance size exclusion chromatography (SEC) separation. No protein precipitation was observed in filtered samples under the intact protein-level TMT labeling conditions. The proposed top-down TMT MS platform enables high-throughput analysis of intact proteoforms, allowing for the identification and quantification of hundreds of intact proteoforms from Escherichia coli cell lysates. To our knowledge, this represents the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.
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Affiliation(s)
- Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Qiang Kou
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Xiaowen Liu
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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19
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Srzentić K, Fornelli L, Tsybin YO, Loo JA, Seckler H, Agar JN, Anderson LC, Bai DL, Beck A, Brodbelt JS, van der Burgt YEM, Chamot-Rooke J, Chatterjee S, Chen Y, Clarke DJ, Danis PO, Diedrich JK, D'Ippolito RA, Dupré M, Gasilova N, Ge Y, Goo YA, Goodlett DR, Greer S, Haselmann KF, He L, Hendrickson CL, Hinkle JD, Holt MV, Hughes S, Hunt DF, Kelleher NL, Kozhinov AN, Lin Z, Malosse C, Marshall AG, Menin L, Millikin RJ, Nagornov KO, Nicolardi S, Paša-Tolić L, Pengelley S, Quebbemann NR, Resemann A, Sandoval W, Sarin R, Schmitt ND, Shabanowitz J, Shaw JB, Shortreed MR, Smith LM, Sobott F, Suckau D, Toby T, Weisbrod CR, Wildburger NC, Yates JR, Yoon SH, Young NL, Zhou M. Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1783-1802. [PMID: 32812765 PMCID: PMC7539639 DOI: 10.1021/jasms.0c00036] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product's primary structure accurately and reproducibly. The major objective of the present study is to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up (BU) approaches with regard to confirming protein integrity, sequencing variable domains, avoiding artifacts, and revealing modifications and their locations. We also aim to gather information on the common TD/MD MS methods and practices in the field. A panel of three mAbs was selected and centrally provided to 20 laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). Various MS instrument platforms and ion dissociation techniques were employed. The present study confirms that TD/MD MS tools are available in laboratories worldwide and provide complementary information to the BU approach that can be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. A primary limitation revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS.
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Affiliation(s)
- Kristina Srzentić
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Luca Fornelli
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Joseph A Loo
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Henrique Seckler
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Jeffrey N Agar
- Northeastern University, Boston, Massachusetts 02115, United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Dina L Bai
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Alain Beck
- Centre d'immunologie Pierre Fabre, 74160 Saint-Julien-en-Genevois, France
| | | | | | | | | | - Yunqiu Chen
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | - David J Clarke
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, Massachusetts 02142, United States
| | - Jolene K Diedrich
- The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ying Ge
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Young Ah Goo
- University of Maryland, Baltimore, Maryland 21201, United States
| | - David R Goodlett
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Sylvester Greer
- University of Texas at Austin, Austin, Texas 78712-1224, United States
| | | | - Lidong He
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | | | - Joshua D Hinkle
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Matthew V Holt
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Sam Hughes
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Donald F Hunt
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Neil L Kelleher
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Anton N Kozhinov
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Ziqing Lin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Alan G Marshall
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Florida State University, Tallahassee, Florida 32310-4005, United States
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Robert J Millikin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Simone Nicolardi
- Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Neil R Quebbemann
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | | | - Wendy Sandoval
- Genentech, Inc., South San Francisco, California 94080-4990, United States
| | - Richa Sarin
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | | | | | - Jared B Shaw
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Lloyd M Smith
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Frank Sobott
- University of Antwerp, 2000 Antwerp, Belgium
- University of Leeds, LS2 9JT Leeds, United Kingdom
| | | | - Timothy Toby
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Norelle C Wildburger
- Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - John R Yates
- The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sung Hwan Yoon
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicolas L Young
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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20
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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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21
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Lodge JM, Schauer KL, Brademan DR, Riley NM, Shishkova E, Westphall MS, Coon JJ. Top-Down Characterization of an Intact Monoclonal Antibody Using Activated Ion Electron Transfer Dissociation. Anal Chem 2020; 92:10246-10251. [PMID: 32608969 DOI: 10.1021/acs.analchem.0c00705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Monoclonal antibodies (mAbs) are important therapeutic glycoproteins, but their large size and structural complexity make them difficult to rapidly characterize. Top-down mass spectrometry (MS) has the potential to overcome challenges of other common approaches by minimizing sample preparation and preserving endogenous modifications. However, comprehensive mAb characterization requires generation of many, well-resolved fragments and remains challenging. While ETD retains modifications and cleaves disulfide bonds-making it attractive for mAb characterization-it can be less effective for precursors having high m/z values. Activated ion electron transfer dissociation (AI-ETD) uses concurrent infrared photoactivation to promote product ion generation and has proven effective in increasing sequence coverage of intact proteins. Here, we present the first application of AI-ETD to mAb sequencing. For the standard NIST mAb, we observe a high degree of complementarity between fragments generated using standard ETD with a short reaction time and AI-ETD with a long reaction time. Most importantly, AI-ETD reveals disulfide-bound regions that have been intractable, thus far, for sequencing with top-down MS. We conclude AI-ETD has the potential to rapidly and comprehensively analyze intact mAbs.
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22
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Chao HC, Shih M, McLuckey SA. Generation of Multiply Charged Protein Anions from Multiply Charged Protein Cations via Gas-Phase Ion/Ion Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1509-1517. [PMID: 32421340 PMCID: PMC7332380 DOI: 10.1021/jasms.0c00062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report a novel charge inversion ion/ion reaction that converts multiply charged protein cations to multiply charged protein anions via a single ion/ion collision using highly charged anions derived from nanoelectrospray ionization (nESI) of hyaluronic acids (HAs). This type of charge inversion reaction is demonstrated with cations derived from cytochrome c, apo-myoglobin, and carbonic anhydrase (CA) cations. For example, the reaction has been demonstrated to convert the [CA+22H]22+ carbonic anhydrase cation to a distribution of anions as high in absolute charge as [CA-19H]19-. Ion/ion reactions involving multiply charged ions of opposite polarity have previously been observed to result predominantly in the attachment of the reactant ions. All mechanisms for ion/ion charge inversion involving low energy ions proceed via the formation of a long-lived complex. Factors that underlie the charge inversion of protein cations to high anionic charge states in reaction with HA anions are hypothesized to include: (i) the relatively high charge densities of the HA anions that facilitate the extraction of multiple protons from the protein leading to multiply charged protein anions, (ii) the relatively high sum of absolute charges of the reactants that leads to high initial energies in the ion/ion complex, and (iii) the relatively high charge of the ion/ion complex following the multiple proton transfers that tends to destabilize the complex.
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Affiliation(s)
| | | | - Scott A. McLuckey
- Address correspondence 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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23
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Zhou M, Uwugiaren N, Williams SM, Moore RJ, Zhao R, Goodlett D, Dapic I, Paša-Tolić L, Zhu Y. Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform. Anal Chem 2020; 92:7087-7095. [PMID: 32374172 DOI: 10.1021/acs.analchem.0c00467] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. However, one significant technical gap of top-down proteomics is the inability to analyze a low amount of biological samples, which limits its access to isolated rare cells, fine needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (nanodroplet processing in one pot for trace samples), into a top-down proteomic workflow. A unique combination of a nonionic detergent dodecyl-β-d-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing nonspecific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ∼170 to ∼620 proteoforms from ∼70 to ∼770 HeLa cells containing ∼10 to ∼115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical research, particularly where clinical specimens are not available in amounts amenable to standard workflows.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland.,Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Lee KW, Eakins GS, Carlsen MS, McLuckey SA. Ion trap operational modes for ion/ion reactions yielding high mass-to-charge product ions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 451:116313. [PMID: 32351313 PMCID: PMC7189770 DOI: 10.1016/j.ijms.2020.116313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
To better probe large biomolecular complexes, developments in mass spectrometry (MS) have focused on improving technologies used to generate, transmit, and measure high m/z ions. The additional tandem-MS (MSn) capabilities of ion trap mass spectrometers (ITMS) facilitate experiments that facilitate probing complex biomolecular ions. In particular, charge reduction using gas-phase ion/ion reactions increase separation of charge states generated via electrospray ionization (ESI), which increases confidence in charge state assignments and therefore masses determined from the observed charge states. Current ITMS technologies struggle to generate and measure low charge states of large (>50 kDa) proteins and complexes because of power limitations associated with conventional high-frequency sine wave operation. Other approaches, including frequency scanning techniques and use of digital waveforms, reduce or eliminate some of these limitations. The work presented here studies five different operational modes for a quadrupole ion trap (QIT) mass spectrometer used to generate and measure low charge states of bovine serum albumin (BSA), pyruvate kinase (PK), and GroEL. While digital operation of a QIT presents limitations during the ion/ion reaction period of the experiment, it generally provided the best spectra in terms of resolution and signal at m/z > 50,000.
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Affiliation(s)
| | | | | | - Scott A. McLuckey
- Corresponding author. 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA, (S.A. McLuckey)
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25
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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26
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Foreman DJ, McLuckey SA. Recent Developments in Gas-Phase Ion/Ion Reactions for Analytical Mass Spectrometry. Anal Chem 2020; 92:252-266. [PMID: 31693342 PMCID: PMC6949396 DOI: 10.1021/acs.analchem.9b05014] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- David J Foreman
- 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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27
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Sanders JD, Mullen C, Watts E, Holden DD, Syka JEP, Schwartz JC, Brodbelt JS. Enhanced Sequence Coverage of Large Proteins by Combining Ultraviolet Photodissociation with Proton Transfer Reactions. Anal Chem 2019; 92:1041-1049. [DOI: 10.1021/acs.analchem.9b04026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dustin D. Holden
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - John E. P. Syka
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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28
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Huguet R, Mullen C, Srzentić K, Greer JB, Fellers RT, Zabrouskov V, Syka JEP, Kelleher NL, Fornelli L. Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms. Anal Chem 2019; 91:15732-15739. [PMID: 31714757 DOI: 10.1021/acs.analchem.9b03925] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the recent technological advances in Fourier transform mass spectrometry (FTMS) instrumentation, top-down proteomics (TDP) is currently mostly applied to the characterization of proteoforms <30 kDa due to the poor performance of high-resolution FTMS for the analysis of larger proteoforms and the high complexity of intact proteomes in the 30-60 kDa mass range. Here, we propose a novel data acquisition method based on ion-ion proton transfer, herein termed proton transfer charge reduction (PTCR), to investigate large proteoforms of Pseudomonas aeruginosa in a high-throughput fashion. We designed a targeted data acquisition strategy, named tPTCR, which applies two consecutive gas phase fractionation steps for obtaining intact precursor masses: first, a narrow (1.5 m/z-wide) quadrupole filter m/z transmission window is used to select a subset of charge states from all ionized proteoform cations; second, this aliquot of protein cations is subjected to PTCR in order to reduce their average charge state: upon m/z analysis in an Orbitrap, proteoform mass spectra with minimal m/z peak overlap and easy-to-interpret charge state distributions are obtained, simplifying the proteoform mass calculation. Subsequently, the same quadrupole-selected narrow m/z region of analytes is subjected to collisional dissociation to obtain proteoform sequence information, which used in combination with intact mass information leads to proteoform identification through an off-line database search. The newly proposed method was benchmarked against the previously developed "medium/high" data-dependent acquisition strategy and doubled the number of UniProt entries and proteoforms >30 kDa identified on the liquid chromatography time scale.
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Affiliation(s)
- Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Kristina Srzentić
- Thermo Fisher Scientific , 790 Memorial Drive, Suite 2D , Cambridge , Massachusetts 02139 , United States
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - John E P Syka
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Luca Fornelli
- Department of Biology , University of Oklahoma , 730 Van Vleet Oval , Norman , Oklahoma 73071 , United States
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