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Fu L, Ellin NR, Pizzala NJ, Baez Bolivar EG, McLuckey SA. Digital Ion Trap Isolation and Mass Analysis of Macromolecular Analytes with Multiply Charged Ion Attachment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2237-2247. [PMID: 39158841 DOI: 10.1021/jasms.4c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Multiply charged ions produced by electrospray ionization (ESI) of heterogeneous mixtures of macromolecular analytes under native conditions are typically confined to relatively narrow ranges of mass-to-charge (m/z) ratio, often with extensive overlap. This scenario makes charge and mass assignments extremely challenging, particularly when individual charge states are unresolved. An ion/ion reaction strategy involving multiply charged ion attachment (MIA) to the mixture components in a narrow range of m/z can facilitate charge and mass assignment. In MIA operation, multiply charged reagent ions are attached to the analyte ions of opposite polarity to provide large m/z displacements resulting from both large changes in mass and charge. However, charge reduction of the high m/z ions initially generated under native ESI conditions requires the ability to isolate high m/z ions and to analyze even higher m/z product ions. Digital ion trap (DIT) operation offers means for both high m/z ion isolation and high m/z mass analysis, in addition to providing conditions for the reaction of oppositely charged ions. The feasibility of conducting MIA experiments in a DIT that takes advantage of high m/z ion operation is demonstrated here using a tandem 2D-3D DIT instrument. Proof-of-concept MIA experiments with cations derived from β-galactosidase using the 20- charge state of human serum immunoglobulin G (IgG, ∼149 kDa) as the reagent anion are described. MIA experiments involving mixtures of ions derived from the E. coli. ribosome are also described. For example, three components in a mixture of 70S particles (>2.2 MDa) were resolved and assigned with masses and charges following an MIA experiment involving the 20- charge state of human serum IgG.
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Affiliation(s)
- Liangxuan Fu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicholas R Ellin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicolas J Pizzala
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Erick G Baez Bolivar
- 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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2
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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024; 23:2733-2749. [PMID: 38442041 PMCID: PMC11296938 DOI: 10.1021/acs.jproteome.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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3
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Wang Q, Wang Q, Qi Z, Moeller W, Wysocki VH, Sun L. Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590970. [PMID: 38712154 PMCID: PMC11071496 DOI: 10.1101/2024.04.24.590970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Native proteomics measures endogenous proteoforms and protein complexes under a near physiological condition using native mass spectrometry (nMS) coupled with liquid-phase separations. Native proteomics should provide the most accurate bird's-eye view of proteome dynamics within cells, which is fundamental for understanding almost all biological processes. nMS has been widely employed to characterize well-purified protein complexes. However, there are only very few trials of utilizing nMS to measure proteoforms and protein complexes in a complex sample (i.e., a whole cell lysate). Here, we pioneer the native proteomics measurement of large proteoforms or protein complexes up to 400 kDa from a complex proteome via online coupling of native capillary zone electrophoresis (nCZE) to an ultra-high mass range (UHMR) Orbitrap mass spectrometer. The nCZE-MS technique enabled the measurement of a 115-kDa standard protein complex while consuming only about 0.1 ng of protein material. nCZE-MS analysis of an E . coli cell lysate detected 72 proteoforms or protein complexes in a mass range of 30-400 kDa in a single run while consuming only 50-ng protein material. The mass distribution of detected proteoforms or protein complexes agreed well with that from mass photometry measurement. This work represents a technical breakthrough in native proteomics for measuring complex proteomes.
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4
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Panczyk EM, Lin YF, Harvey SR, Snyder DT, Liu FC, Ridgeway ME, Park MA, Bleiholder C, Wysocki VH. Evaluation of a Commercial TIMS-Q-TOF Platform for Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1394-1402. [PMID: 38905538 DOI: 10.1021/jasms.3c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
Mass-spectrometry based assays in structural biology studies measure either intact or digested proteins. Typically, different mass spectrometers are dedicated for such measurements: those optimized for rapid analysis of peptides or those designed for high molecular weight analysis. A commercial trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) platform is widely utilized for proteomics and metabolomics, with ion mobility providing a separation dimension in addition to liquid chromatography. The ability to perform high-quality native mass spectrometry of protein complexes, however, remains largely uninvestigated. Here, we evaluate a commercial TIMS-Q-TOF platform for analyzing noncovalent protein complexes by utilizing the instrument's full range of ion mobility, MS, and MS/MS (both in-source activation and collision cell CID) capabilities. The TIMS analyzer is able to be tuned gently to yield collision cross sections of native-like complexes comparable to those previously reported on various instrument platforms. In-source activation and collision cell CID were robust for both small and large complexes. TIMS-CID was performed on protein complexes streptavidin (53 kDa), avidin (68 kDa), and cholera toxin B (CTB, 58 kDa). Complexes pyruvate kinase (237 kDa) and GroEL (801 kDa) were beyond the trapping capabilities of the commercial TIMS analyzer, but TOF mass spectra could be acquired. The presented results indicate that the commercial TIMS-Q-TOF platform can be used for both omics and native mass spectrometry applications; however, modifications to the commercial RF drivers for both the TIMS analyzer and quadrupole (currently limited to m/z 3000) are necessary to mobility analyze protein complexes greater than about 60 kDa.
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Affiliation(s)
- Erin M Panczyk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Yu-Fu Lin
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dalton T Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Fanny C Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Mark E Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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5
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XUE J, LIU Z, WANG F. [Applications of native mass spectrometry and ultraviolet photodissociation in protein structure and interaction analysis]. Se Pu 2024; 42:681-692. [PMID: 38966976 PMCID: PMC11224945 DOI: 10.3724/sp.j.1123.2024.01021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Indexed: 07/06/2024] Open
Abstract
Dynamic changes in the structures and interactions of proteins are closely correlated with their biological functions. However, the precise detection and analysis of these molecules are challenging. Native mass spectrometry (nMS) introduces proteins or protein complexes into the gas phase by electrospray ionization, and then performs MS analysis under near-physiological conditions that preserve the folded state of proteins and their complexes in solution. nMS can provide information on stoichiometry, assembly, and dissociation constants by directly determining the relative molecular masses of protein complexes through high-resolution MS. It can also integrate various MS dissociation technologies, such as collision-induced dissociation (CID), surface-induced dissociation (SID), and ultraviolet photodissociation (UVPD), to analyze the conformational changes, binding interfaces, and active sites of protein complexes, thereby revealing the relationship between their interactions and biological functions. UVPD, especially 193 nm excimer laser UVPD, is a rapidly evolving MS dissociation method that can directly dissociate the covalent bonds of protein backbones with a single pulse. It can generate different types of fragment ions, while preserving noncovalent interactions such as hydrogen bonds within these ions, thereby enabling the MS analysis of protein structures with single-amino-acid-site resolution. This review outlines the applications and recent progress of nMS and UVPD in protein dynamic structure and interaction analyses. It covers the nMS techniques used to analyze protein-small-molecule ligand interactions, the structures of membrane proteins and their complexes, and protein-protein interactions. The discussion on UVPD includes the analysis of gas-phase protein structures and interactions, as well as alterations in protein dynamic structures, and interactions resulting from mutations and ligand binding. Finally, this review describes the future development prospects for protein analysis by nMS and new-generation advanced extreme UV light sources with higher brightness and shorter pulses.
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6
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Escobar EE, Yang W, Lanzillotti MB, Juetten KJ, Shields S, Siegel D, Zhang YJ, Brodbelt JS. Tracking Inhibition of Human Small C-Terminal Domain Phosphatase 1 Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1330-1341. [PMID: 38662915 PMCID: PMC11384422 DOI: 10.1021/jasms.4c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Working in tandem with kinases via a dynamic interplay of phosphorylation and dephosphorylation of proteins, phosphatases regulate many cellular processes and thus represent compelling therapeutic targets. Here we leverage ultraviolet photodissociation to shed light on the binding characteristics of two covalent phosphatase inhibitors, T65 and rabeprazole, and their respective interactions with the human small C-terminal domain phosphatase 1 (SCP1) and its single-point mutant C181A, in which a nonreactive alanine replaces one key reactive cysteine. Top-down MS/MS analysis is used to localize the binding of T65 and rabeprazole on the two proteins and estimate the relative reactivities of each cysteine residue.
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Affiliation(s)
| | | | | | | | | | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, United States
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7
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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] [Grants] [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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8
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Habeck T, Brown KA, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W, Keener JE, Volny M, Wilson JW, Ying Y, Agar JN, Danis PO, Ge Y, Kelleher NL, Li H, Loo JA, Marty MT, Paša-Tolić L, Sandoval W, Lermyte F. Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nat Methods 2024:10.1038/s41592-024-02279-6. [PMID: 38744918 DOI: 10.1038/s41592-024-02279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.
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Affiliation(s)
- Tanja Habeck
- Technische Universität Darmstadt, Darmstadt, Germany
| | - Kyle A Brown
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, WA, USA
- Zhejiang University, Zhejiang, China
| | | | | | | | | | | | - Jesse W Wilson
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yujia Ying
- Sun Yat-sen University, Guangzhou, China
| | - Jeffrey N Agar
- Northeastern University, Boston, MA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Ying Ge
- University of Wisconsin-Madison, Madison, WI, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Neil L Kelleher
- Northwestern University, Evanston, IL, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Huilin Li
- Sun Yat-sen University, Guangzhou, China
| | - Joseph A Loo
- University of California, Los Angeles, CA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | | | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, WA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
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9
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Jordan JS, Lee KJ, Williams ER. Overcoming aggregation with laser heated nanoelectrospray mass spectrometry: thermal stability and pathways for loss of bicarbonate from carbonic anhydrase II. Analyst 2024; 149:2281-2290. [PMID: 38497240 DOI: 10.1039/d4an00229f] [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: 03/19/2024]
Abstract
Variable temperature electrospray mass spectrometry is useful for multiplexed measurements of the thermal stabilities of biomolecules, but the ionization process can be disrupted by aggregation-prone proteins/complexes that have irreversible unfolding transitions. Resistively heating solutions containing a mixture of bovine carbonic anhydrase II (BCAII), a CO2 fixing enzyme involved in many biochemical pathways, and cytochrome c leads to complete loss of carbonic anhydrase signal and a significant reduction in cytochrome c signal above ∼72 °C due to aggregation. In contrast, when the tips of borosilicate glass nanoelectrospray emitters are heated with a laser, complete thermal denaturation curves for both proteins are obtained in <1 minute. The simultaneous measurements of the melting temperature of BCAII and BCAII bound to bicarbonate reveal that the bicarbonate stabilizes the folded form of this protein by ∼6.4 °C. Moreover, the temperature dependences of different bicarbonate loss pathways are obtained. Although protein analytes are directly heated by the laser for only 140 ms, heat conduction further up the emitter leads to a total analyte heating time of ∼41 s. Pulsed laser heating experiments could reduce this time to ∼0.5 s for protein aggregation that occurs on a faster time scale. Laser heating provides a powerful method for studying the detailed mechanisms of cofactor/ligand loss with increasing temperature and promises a new tool for studying the effect of ligands, drugs, growth conditions, buffer additives, or other treatments on the stabilities of aggregation-prone biomolecules.
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Affiliation(s)
- Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Katherine J Lee
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
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10
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Villacob RA, Feizi N, Beno SC, Solouki T. Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:13-30. [PMID: 38095581 DOI: 10.1021/jasms.3c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.
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Affiliation(s)
- Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Neda Feizi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sarah C Beno
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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11
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Lermyte F, Habeck T, Brown K, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W, Keener J, Volny M, Wilson J, Ying Y, Agar J, Danis P, Ge Y, Kelleher N, Li H, Loo J, Marty M, Pasa-Tolic L, Sandoval W. Top-down mass spectrometry of native proteoforms and their complexes: A community study. RESEARCH SQUARE 2023:rs.3.rs-3228472. [PMID: 37674709 PMCID: PMC10479449 DOI: 10.21203/rs.3.rs-3228472/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
The combination of native electrospray ionisation with top-down fragmentation in mass spectrometry allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and co-factors. While this approach is powerful, both native mass spectrometry and top-down mass spectrometry are not yet well standardised, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics (CTDP) initiated a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. The outcomes are summarised in this report to provide robust benchmarks and a valuable entry point for the scientific community.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jeffrey Agar
- Department of Chemistry and Chemical Biology, Northeastern University
| | | | - Ying Ge
- University of Wisconsin-Madison
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12
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Ventouri IK, Veelders S, Passamonti M, Endres P, Roemling R, Schoenmakers PJ, Somsen GW, Haselberg R, Gargano AFG. Micro-flow size-exclusion chromatography for enhanced native mass spectrometry of proteins and protein complexes. Anal Chim Acta 2023; 1266:341324. [PMID: 37244657 DOI: 10.1016/j.aca.2023.341324] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 05/29/2023]
Abstract
Size-exclusion chromatography (SEC) employing aqueous mobile phases with volatile salts at neutral pH combined with native mass spectrometry (nMS) is a valuable tool to characterize proteins and protein aggregates in their native state. However, the liquid-phase conditions (high salt concentrations) frequently used in SEC-nMS hinder the analysis of labile protein complexes in the gas phase, necessitating higher desolvation-gas flow and source temperature, leading to protein fragmentation/dissociation. To overcome this issue, we investigated narrow SEC columns (1.0 mm internal diameter, I.D.) operated at 15-μL/min flow rates and their coupling to nMS for the characterization of proteins, protein complexes and higher-order structures (HOS). The reduced flow rate resulted in a significant increase in the protein-ionization efficiency, facilitating the detection of low-abundant impurities and HOS up to 230 kDa (i.e., the upper limit of the Orbitrap-MS instrument used). More-efficient solvent evaporation and lower desolvation energies allowed for softer ionization conditions (e.g., lower gas temperatures), ensuring little or no structural alterations of proteins and their HOS during transfer into the gas phase. Furthermore, ionization suppression by eluent salts was decreased, permitting the use of volatile-salt concentrations up to 400 mM. Band broadening and loss of resolution resulting from the introduction of injection volumes exceeding 3% of the column volume could be circumvented by incorporating an online trap-column containing a mixed-bed ion-exchange (IEX) material. The online IEX-based solid-phase extraction (SPE) or "trap-and-elute" set-up provided on-column focusing (sample preconcentration). This allowed the injection of large sample volumes on the 1-mm I.D. SEC column without compromising the separation. The enhanced sensitivity attained by the micro-flow SEC-MS, along with the on-column focusing achieved by the IEX precolumn, provided picogram detection limits for proteins.
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Affiliation(s)
- Iro K Ventouri
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands.
| | - Sharene Veelders
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands
| | - Marta Passamonti
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands
| | - Patrick Endres
- Tosoh Bioscience GmbH, Im Leuschnerpark 4, 64347, Griesheim, Germany
| | - Regina Roemling
- Tosoh Bioscience GmbH, Im Leuschnerpark 4, 64347, Griesheim, Germany
| | - Peter J Schoenmakers
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands
| | - Govert W Somsen
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Division of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV Amsterdam, the Netherlands
| | - Rob Haselberg
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Division of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV Amsterdam, the Netherlands
| | - Andrea F G Gargano
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands.
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13
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McGee JP, Senko MW, Jooß K, Des Soye BJ, Compton PD, Kelleher NL, Kafader JO. Automated Control of Injection Times for Unattended Acquisition of Multiplexed Individual Ion Mass Spectra. Anal Chem 2022; 94:16543-16548. [PMID: 36416365 PMCID: PMC9969899 DOI: 10.1021/acs.analchem.2c03495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Charge detection mass spectrometry (CDMS) provides mass domain spectra of large and highly heterogeneous analytes. Over the past few years, we have multiplexed CDMS on Orbitrap instruments, an approach termed Individual Ion Mass Spectrometry (I2MS). Until now, I2MS required manual adjustment of injection times to collect spectra in the individual ion regime. To increase sample adaptability, enable online separations, and reduce the barrier for entry, we report an automated method for adjusting ion injection times in I2MS for image current detectors like the Orbitrap. Automatic Ion Control (AIC) utilizes the density of signals in the m/z domain to adjust an ensemble of ions down to the individual ion regime in real-time. The AIC technique was applied to both denatured and native proteins yielding high quality data without human intervention directly in the mass domain.
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Affiliation(s)
- John P McGee
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California95134, United States
| | - Kevin Jooß
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Benjamin J Des Soye
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Philip D Compton
- Integrated Protein Technologies, Inc., Evanston, Illinois60201, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
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14
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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15
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Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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16
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Abstract
Recent advancements place a comprehensive catalog of protein structure, oligomeric state, sequence, and modification status tentatively within reach, thus providing an unprecedented roadmap to therapies for many human diseases. To achieve this goal, revolutionary technologies capable of bridging key gaps in our ability to simultaneously measure protein composition and structure must be developed. Much of the current progress in this area has been catalyzed by mass spectrometry (MS) tools, which have become an indispensable resource for interrogating the structural proteome. For example, methods associated with native proteomics seek to comprehensively capture and quantify the endogenous assembly states for all proteins within an organism. Such technologies have often been partnered with ion mobility (IM) separation, from which collision cross section (CCS) information can be rapidly extracted to provide protein size information. IM technologies are also being developed that utilize CCS values to enhance the confidence of protein identification workflows derived from liquid chromatography-IM-MS analyses of enzymatically produced peptide mixtures. Such parallel advancements in technology beg the question: can CCS values prove similarly useful for the identification of intact proteins and their complexes in native proteomics? In this perspective, I examine current evidence and technology trends to explore the promise and limitations of such CCS information for the comprehensive analysis of multiprotein complexes from cellular mixtures.
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Affiliation(s)
- Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Lebede M, Di Marco F, Esser-Skala W, Hennig R, Wohlschlager T, Huber CG. Exploring the Chemical Space of Protein Glycosylation in Noncovalent Protein Complexes: An Expedition along Different Structural Levels of Human Chorionic Gonadotropin by Employing Mass Spectrometry. Anal Chem 2021; 93:10424-10434. [PMID: 34288669 PMCID: PMC8340079 DOI: 10.1021/acs.analchem.1c02199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Modern analytical
approaches employing high-resolution mass spectrometry
(MS) facilitate the generation of a vast amount of structural data
of highly complex glycoproteins. Nevertheless, systematic interpretation
of this data at different structural levels remains an analytical
challenge. The glycoprotein utilized as a model system in this study,
human chorionic gonadotropin (hCG), exists as a heterodimer composed
of two heavily glycosylated subunits. In order to unravel the multitude
of glycoforms of recombinant hCG (drug product Ovitrelle), we combine
established techniques, such as released glycan and glycopeptide analysis,
with novel approaches employing high-performance liquid chromatography-mass
spectrometry (HPLC-MS) to characterize protein subunits and native
MS to analyze the noncovalent hCG complex. Starting from the deconvoluted
mass spectrum of dimeric hCG comprising about 50 signals, it was possible
to explore the chemical space of hCG glycoforms and elucidate the
complexity that hides behind just 50 signals. Systematic, stepwise
integration of data obtained at the levels of released glycans, glycopeptides,
and subunits using a computational annotation tool allowed us to reveal
1031 underlying glycoforms. Additionally, critical quality attributes
such as sialylation and core fucosylation were compared for two batches
of Ovitrelle to assess the potential product variability.
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Affiliation(s)
- Maximilian Lebede
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Fiammetta Di Marco
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Wolfgang Esser-Skala
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Department of Biosciences, Computational Systems Biology Group, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - René Hennig
- glyXera GmbH, Brenneckestraße 20 - ZENIT, 39120 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Therese Wohlschlager
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
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18
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Schachner LF, Tran DP, Lee A, McGee JP, Jooss K, Durbin K, Seckler HDS, Adams L, Cline E, Melani R, Ives AN, Des Soye B, Kelleher NL, Patrie SM. Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 465:116591. [PMID: 34539228 PMCID: PMC8445521 DOI: 10.1016/j.ijms.2021.116591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The combined use of electrospray ionization run in so-called "native mode" with top-down mass spectrometry (nTDMS) is enhancing both structural biology and discovery proteomics by providing three levels of information in a single experiment: the intact mass of a protein or complex, the masses of its subunits and non-covalent cofactors, and fragment ion masses from direct dissociation of subunits that capture the primary sequence and combinations of diverse post-translational modifications (PTMs). While intact mass data are readily deconvoluted using well-known software options, the analysis of fragmentation data that result from a tandem MS experiment - essential for proteoform characterization - is not yet standardized. In this tutorial, we offer a decision-tree for the analysis of nTDMS experiments on protein complexes and diverse bioassemblies. We include an overview of strategies to navigate this type of analysis, provide example data sets, and highlight software for the hypothesis-driven interrogation of fragment ions for localization of PTMs, metals, and cofactors on native proteoforms. Throughout we have emphasized the key features (deconvolution, search mode, validation, other) that the reader can consider when deciding upon their specific experimental and data processing design using both open-access and commercial software.
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Affiliation(s)
- Luis F. Schachner
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Denise P. Tran
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Alexander Lee
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - John P. McGee
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Kevin Jooss
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Kenneth Durbin
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Henrique Dos Santos Seckler
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Lauren Adams
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Erika Cline
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Rafael Melani
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Ashley N. Ives
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Benjamin Des Soye
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Neil L. Kelleher
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Steven M. Patrie
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
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19
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Jooß K, McGee JP, Melani RD, Kelleher NL. Standard procedures for native CZE-MS of proteins and protein complexes up to 800 kDa. Electrophoresis 2021; 42:1050-1059. [PMID: 33502026 PMCID: PMC8122066 DOI: 10.1002/elps.202000317] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
Native mass spectrometry (nMS) is a rapidly growing method for the characterization of large proteins and protein complexes, preserving "native" non-covalent inter- and intramolecular interactions. Direct infusion of purified analytes into a mass spectrometer represents the standard approach for conducting nMS experiments. Alternatively, CZE can be performed under native conditions, providing high separation performance while consuming trace amounts of sample material. Here, we provide standard operating procedures for acquiring high-quality data using CZE in native mode coupled online to various Orbitrap mass spectrometers via a commercial sheathless interface, covering a wide range of analytes from 30-800 kDa. Using a standard protein mix, the influence of various CZE method parameters were evaluated, such as BGE/conductive liquid composition and separation voltage. Additionally, a universal approach for the optimization of fragmentation settings in the context of protein subunit and metalloenzyme characterization is discussed in detail for model analytes. A short section is dedicated to troubleshooting of the nCZE-MS setup. This study is aimed to help normalize nCZE-MS practices to enhance the CE community and provide a resource for the production of reproducible and high-quality data.
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Affiliation(s)
- Kevin Jooß
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - John P McGee
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Rafael D Melani
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
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20
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Jooß K, Schachner LF, Watson R, Gillespie ZB, Howard SA, Cheek MA, Meiners MJ, Sobh A, Licht JD, Keogh MC, Kelleher NL. Separation and Characterization of Endogenous Nucleosomes by Native Capillary Zone Electrophoresis-Top-Down Mass Spectrometry. Anal Chem 2021; 93:5151-5160. [PMID: 33749242 PMCID: PMC8040852 DOI: 10.1021/acs.analchem.0c04975] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report a novel platform [native capillary zone electrophoresis-top-down mass spectrometry (nCZE-TDMS)] for the separation and characterization of whole nucleosomes, their histone subunits, and post-translational modifications (PTMs). As the repeating unit of chromatin, mononucleosomes (Nucs) are an ∼200 kDa complex of DNA and histone proteins involved in the regulation of key cellular processes central to human health and disease. Unraveling the covalent modification landscape of histones and their defined stoichiometries within Nucs helps to explain epigenetic regulatory mechanisms. In nCZE-TDMS, online Nuc separation is followed by a three-tier tandem MS approach that measures the intact mass of Nucs, ejects and detects the constituent histones, and fragments to sequence the histone. The new platform was optimized with synthetic Nucs to significantly reduce both sample requirements and cost compared to direct infusion. Limits of detection were in the low-attomole range, with linearity of over ∼3 orders of magnitude. The nCZE-TDMS platform was applied to endogenous Nucs from two cell lines distinguished by overexpression or knockout of histone methyltransferase NSD2/MMSET, where analysis of constituent histones revealed changes in histone abundances over the course of the CZE separation. We are confident the nCZE-TDMS platform will help advance nucleosome-level research in the fields of chromatin and epigenetics.
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Affiliation(s)
- Kevin Jooß
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Luis F Schachner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Rachel Watson
- EpiCypher Incorporated, Durham, North Carolina 27709, United States
| | | | - Sarah A Howard
- EpiCypher Incorporated, Durham, North Carolina 27709, United States
| | - Marcus A Cheek
- EpiCypher Incorporated, Durham, North Carolina 27709, United States
| | | | - Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida 32610, United States
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida 32610, United States
| | | | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
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21
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Abdillahi AM, Lee KW, McLuckey SA. Mass Analysis of Macro-molecular Analytes via Multiply-Charged Ion Attachment. Anal Chem 2020; 92:16301-16306. [PMID: 33275425 DOI: 10.1021/acs.analchem.0c04335] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A novel gas-phase charge and mass manipulation approach is demonstrated to facilitate the mass measurement of high mass complexes within the context of native mass spectrometry. Electrospray ionization applied to solutions generated under native or near-native conditions has been demonstrated to be capable of preserving biologically relevant complexes into the gas phase as multiply charged ions suitable for mass spectrometric analysis. However, charge state distributions tend to be narrow and extensive salt adduction, heterogeneity, and so on tend to lead to significantly broadened peaks. These issues can compromise mass measurement of high mass bio-complexes, particularly when charge states are not clearly resolved. In this work, we show that the attachment of high mass ions of known mass and charge to populations of ions of interest can lead to well-separated signals that can yield confident charge state and mass assignments from otherwise poorly resolved signals.
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Affiliation(s)
- Abdirahman M Abdillahi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Kenneth W Lee
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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22
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Mallis CS, Zheng X, Qiu X, McCabe JW, Shirzadeh M, Lyu J, Laganowsky A, Russell DH. Development of Native MS Capabilities on an Extended Mass Range Q-TOF MS. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 458:116451. [PMID: 33162786 PMCID: PMC7641504 DOI: 10.1016/j.ijms.2020.116451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Native mass spectrometry (nMS) is increasingly used for studies of large biomolecules (>100 kDa), especially proteins and protein complexes. The growth in this area can be attributed to advances in native electrospray ionization as well as instrumentation that is capable of accessing high mass-to-charge (m/z) regimes without significant losses in sensitivity and resolution. Here, we describe modifications to the ESI source of an Agilent 6545XT Q-TOF MS that is tailored for analysis of large biomolecules. The modified ESI source was evaluated using both soluble and membrane protein complexes ranging from ~127 to ~232 kDa and the ~801 kDa protein chaperone GroEL. The increased mass resolution of the instrument affords the ability to resolve small molecule adducts and analyze collision-induced dissociation products of the native complexes.
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Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Xi Qiu
- Agilent Technologies, Inc., Wilmington, DE 19808
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Correspondence to David H. Russell;
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23
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Huang RYC, Wang F, Wheeler M, Wang Y, Langish R, Chau B, Dong J, Morishige W, Bezman N, Strop P, Rajpal A, Gudmundsson O, Chen G. Integrated Approach for Characterizing Bispecific Antibody/Antigens Complexes and Mapping Binding Epitopes with SEC/MALS, Native Mass Spectrometry, and Protein Footprinting. Anal Chem 2020; 92:10709-10716. [PMID: 32639723 DOI: 10.1021/acs.analchem.0c01876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bispecific antibodies (BsAbs), with a unique mechanism of recognizing two different epitopes or antigens, have shown potential in various therapeutic areas. Molecular characterization of BsAbs' epitopes not only allows for detailed understanding of their mechanism of actions but also guides the design and selection of drug candidate molecules. In this study, we illustrate the practical utility of an integrated approach, including size exclusion chromatography with multiangle light scattering and native mass spectrometry (MS) for the biophysical characterization of complex formation of a BsAb with two target antigens, cluster of differentiation 3 (CD3) and B-cell maturation antigen (BCMA). MS-based protein footprinting strategies, including hydrogen/deuterium exchange MS, fast photochemical oxidation of proteins, and carboxyl group footprinting with glycine ethyl ester, were further applied to determine BsAb's binding epitopes. This combination approach provides molecular details on the binding mechanisms of BsAb to the two distinct antigens with rapid output and high resolution.
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Affiliation(s)
- Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Feng Wang
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Matthew Wheeler
- Discovery Biology, Research and Early Development, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Yun Wang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Robert Langish
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bryant Chau
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Jia Dong
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Winse Morishige
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Natalie Bezman
- Discovery Biology, Research and Early Development, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Pavel Strop
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Arvind Rajpal
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Olafur Gudmundsson
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
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24
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Allison TM, Barran P, Cianférani S, Degiacomi MT, Gabelica V, Grandori R, Marklund EG, Menneteau T, Migas LG, Politis A, Sharon M, Sobott F, Thalassinos K, Benesch JLP. Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology. Anal Chem 2020; 92:10872-10880. [DOI: 10.1021/acs.analchem.9b05791] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Timothy M. Allison
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Matteo T. Degiacomi
- Department of Physics, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | - Erik G. Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Thomas Menneteau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College of London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Konstantinos Thalassinos
- Department of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
| | - Justin L. P. Benesch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
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25
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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26
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Kafader JO, Durbin KR, Melani RD, Des Soye BJ, Schachner LF, Senko MW, Compton PD, Kelleher NL. Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry. J Proteome Res 2020; 19:1346-1350. [PMID: 32032494 PMCID: PMC7060802 DOI: 10.1021/acs.jproteome.9b00797] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Charge detection mass spectrometry (CDMS) is mainly utilized to determine the mass of intact molecules. Previous applications of CDMS have determined the mass-to-charge ratio and the charge of large polymers, DNA molecules, and native protein complexes, from which corresponding mass values could be assigned. Recent advances have demonstrated that CDMS using an Orbitrap mass analyzer yields the reliable assignment of integer charge states that enables individual ion mass spectrometry (I2MS) and spectral output directly into the mass domain. Here I2MS analysis was extended to isotopically resolved fragment ions from intact proteoforms for the first time. With a radically different bias for ion readout, I2MS identified low-abundance fragment ions containing many hundreds of residues that were undetectable by standard Orbitrap measurements, leading to a doubling in the sequence coverage of triosephosphate isomerase. Thus MS/MS with the detection of individual ions (MS/I2MS) provides a far greater ability to detect high mass fragment ions and exhibits strong complementarity to traditional spectral readout in this, its first application to top-down mass spectrometry.
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Affiliation(s)
- Jared O. Kafader
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Kenneth R. Durbin
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Benjamin J. Des Soye
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Luis F. Schachner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Michael W. Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Philip D. Compton
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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27
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McGee JP, Melani RD, Goodwin M, McAlister G, Huguet R, Senko MW, Compton PD, Kelleher NL. Voltage Rollercoaster Filtering of Low-Mass Contaminants During Native Protein Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:763-767. [PMID: 32126774 PMCID: PMC7274025 DOI: 10.1021/jasms.9b00037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Intact protein mass spectrometry (MS) via electrospray-based methods is often degraded by low-mass contaminants, which can suppress the spectral quality of the analyte of interest via space-charge effects. Consequently, selective removal of contaminants by their mobilities would benefit native MS if achieved without additional hardware and before the mass analyzer regions used for selection, analyte readout, or tandem MS. Here, we use the high-pressure multipole within the source of an Orbitrap Tribrid as the foundation for a coarse ion filter. Using this method, we show complete filtration of 2 mM polyethylene glycol (PEG-1000) during native MS of SILu mAb antibody present at a 200× lower concentration. We also show the generality of the process by rescuing 10 μM tetrameric pyruvate kinase from 2 mM PEG-1000, asserting this voltage rollercoaster filtering (VRF) method for use in native MS as an efficient alternative to conventional purification methods.
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Affiliation(s)
- John P McGee
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Michael Goodwin
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Graeme McAlister
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Philip D Compton
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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28
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Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes. Nat Methods 2020; 17:391-394. [PMID: 32123391 PMCID: PMC7131870 DOI: 10.1038/s41592-020-0764-5] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/25/2019] [Accepted: 01/24/2020] [Indexed: 12/26/2022]
Abstract
A new Orbitrap-based ion analysis procedure is shown to be possible by determining the direct charge for numerous individual protein ions to generate true mass spectra. The deployment of an Orbitrap system for charge detection enables the characterization of highly complicated mixtures of proteoforms and their complexes in both denatured and native modes of operation, revealing information not obtainable by traditional measurement of an ensemble of ions.
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29
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Williams JP, Morrison LJ, Brown JM, Beckman JS, Voinov VG, Lermyte F. Top-Down Characterization of Denatured Proteins and Native Protein Complexes Using Electron Capture Dissociation Implemented within a Modified Ion Mobility-Mass Spectrometer. Anal Chem 2020; 92:3674-3681. [PMID: 31999103 DOI: 10.1021/acs.analchem.9b04763] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Electron-based fragmentation methods have revolutionized biomolecular mass spectrometry, in particular native and top-down protein analysis. Here, we report the use of a new electromagnetostatic cell to perform electron capture dissociation (ECD) within a quadrupole/ion mobility/time-of-flight mass spectrometer. This cell was installed between the ion mobility and time-of-flight regions of the instrument, and fragmentation was fast enough to be compatible with mobility separation. The instrument was already fitted with electron transfer dissociation (ETD) between the quadrupole and mobility regions prior to modification. We show excellent fragmentation efficiency for denatured peptides and proteins without the need to trap ions in the gas phase. Additionally, we demonstrate native top-down backbone fragmentation of noncovalent protein complexes, leading to comparable sequence coverage to what was achieved using the instrument's existing ETD capabilities. Limited collisional ion activation of the hemoglobin tetramer before ECD was reflected in the observed fragmentation pattern, and complementary ion mobility measurements prior to ECD provided orthogonal evidence of monomer unfolding within this complex. The approach demonstrated here provides a powerful platform for both top-down proteomics and mass spectrometry-based structural biology studies.
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Affiliation(s)
- Jonathan P Williams
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Lindsay J Morrison
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Joseph S Beckman
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Valery G Voinov
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Frederik Lermyte
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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30
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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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31
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Gomes FP, Yates JR. Recent trends of capillary electrophoresis-mass spectrometry in proteomics research. MASS SPECTROMETRY REVIEWS 2019; 38:445-460. [PMID: 31407381 PMCID: PMC6800771 DOI: 10.1002/mas.21599] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis-mass spectrometry (CE-MS) in the past few years. This review provides highlights of recent advances in CE-MS for proteomics research, including a short introduction to top-down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE-MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1-16, 2019.
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Affiliation(s)
| | - John R. Yates
- Correspondent author: , Phone number: (858) 784-8862, Departments of Molecular Medicine and Neurobiology, 10550 North Torrey Pines Road, SR302B, The Scripps Research Institute, La Jolla, CA 92037
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32
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Illes-Toth E, Cooper HJ. Probing the Fundamentals of Native Liquid Extraction Surface Analysis Mass Spectrometry of Proteins: Can Proteins Refold during Extraction? Anal Chem 2019; 91:12246-12254. [PMID: 31490666 PMCID: PMC7006963 DOI: 10.1021/acs.analchem.9b02075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Native ambient mass spectrometry has the potential for simultaneous analysis of native protein structure and spatial distribution within thin tissue sections. Notwithstanding sensitivity, this information can, in principle, be obtained for any protein present with no requirement for a priori knowledge of protein identity. To date, native ambient mass spectrometry has primarily made use of the liquid extraction surface analysis (LESA) sampling technique. Here, we address a fundamental question: Are the protein structures observed following native liquid extraction surface analysis representative of the protein structures within the substrate, or does the extraction process facilitate refolding (or unfolding)? Specifically, our aim was to determine whether protein-ligand complexes observed following LESA are indicative of complexes present in the substrate, or an artifact of the sampling process. The systems investigated were myoglobin and its noncovalently bound heme cofactor, and the Zn-binding protein carbonic anhydrase and its binding with ethoxzolamide. Charge state distributions, drift time profiles, and collision cross sections were determined by liquid extraction surface analysis ion mobility mass spectrometry of native and denatured proteins and compared with those obtained by direct infusion electrospray. The results show that it was not possible to refold denatured proteins with concomitant ligand binding (neither heme, zinc, nor ethoxzolamide) simply by use of native-like LESA solvents. That is, protein-ligand complexes were only observed by LESA MS when present in the substrate.
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Affiliation(s)
- Eva Illes-Toth
- School of Biosciences , University of Birmingham , Birmingham , B15 2TT , U.K
| | - Helen J Cooper
- School of Biosciences , University of Birmingham , Birmingham , B15 2TT , U.K
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