1
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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 DOI: 10.1021/jasms.4c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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2
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Zhu Y, Yun SD, Zhang T, Chang JY, Stover L, Laganowsky A. Native mass spectrometry of proteoliposomes containing integral and peripheral membrane proteins. Chem Sci 2023; 14:14243-14255. [PMID: 38098719 PMCID: PMC10718073 DOI: 10.1039/d3sc04938h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023] Open
Abstract
Cellular membranes are critical to the function of membrane proteins, whether they are associated (peripheral) or embedded (integral) within the bilayer. While detergents have contributed to our understanding of membrane protein structure and function, there remains challenges in characterizing protein-lipid interactions within the context of an intact membrane. Here, we developed a method to prepare proteoliposomes for native mass spectrometry (MS) studies. We first use native MS to detect the encapsulation of soluble proteins within liposomes. We then find the peripheral Gβ1γ2 complex associated with the membrane can be ejected and analyzed using native MS. Four different integral membrane proteins (AmtB, AqpZ, TRAAK, and TREK2), all of which have previously been characterized in detergent, eject from the proteoliposomes as intact complexes bound to lipids that have been shown to tightly associate in detergent, drawing a correlation between the two approaches. We also show the utility of more complex lipid environments, such as a brain polar lipid extract, and show TRAAK ejects from liposomes of this extract bound to lipids. These findings underscore the capability to eject protein complexes from membranes bound to both lipids and metal ions, and this approach will be instrumental in the identification of key protein-lipid interactions.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Sangho D Yun
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Lauren Stover
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
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3
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Zhu Y, Peng BJ, Kumar S, Stover L, Chang JY, Lyu J, Zhang T, Schrecke S, Azizov D, Russell DH, Fang L, Laganowsky A. Polyamine detergents tailored for native mass spectrometry studies of membrane proteins. Nat Commun 2023; 14:5676. [PMID: 37709761 PMCID: PMC10502129 DOI: 10.1038/s41467-023-41429-w] [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] [Received: 06/02/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
Native mass spectrometry (MS) is a powerful technique for interrogating membrane protein complexes and their interactions with other molecules. A key aspect of the technique is the ability to preserve native-like structures and noncovalent interactions, which can be challenging depending on the choice of detergent. Different strategies have been employed to reduce charge on protein complexes to minimize activation and preserve non-covalent interactions. Here, we report the synthesis of a class of polyamine detergents tailored for native MS studies of membrane proteins. These detergents, a series of spermine covalently attached to various alkyl tails, are exceptional charge-reducing molecules, exhibiting a ten-fold enhanced potency over spermine. Addition of polyamine detergents to proteins solubilized in maltoside detergents results in improved, charge-reduced native mass spectra and reduced dissociation of subunits. Polyamine detergents open new opportunities to investigate membrane proteins in different detergent environments that have thwarted previous native MS studies.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Bo-Ji Peng
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Djavdat Azizov
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lei Fang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
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4
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Juliano BR, Keating JW, Ruotolo BT. Infrared Photoactivation Enables Improved Native Top-Down Mass Spectrometry of Transmembrane Proteins. Anal Chem 2023; 95:13361-13367. [PMID: 37610409 PMCID: PMC11081007 DOI: 10.1021/acs.analchem.3c02788] [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: 08/24/2023]
Abstract
Membrane proteins are often challenging targets for native top-down mass spectrometry experimentation. The requisite use of membrane mimetics to solubilize such proteins necessitates the application of supplementary activation methods to liberate protein ions prior to sequencing, which typically limits the sequence coverage achieved. Recently, infrared photoactivation has emerged as an alternative to collisional activation for the liberation of membrane proteins from surfactant micelles. However, much remains unknown regarding the mechanism by which IR activation liberates membrane protein ions from such micelles, the extent to which such methods can improve membrane protein sequence coverage, and the degree to which such approaches can be extended to support native proteomics. Here, we describe experiments designed to evaluate and probe infrared photoactivation for membrane protein sequencing, proteoform identification, and native proteomics applications. Our data reveal that infrared photoactivation can dissociate micelles composed of a variety of detergent classes, without the need for a strong IR chromophore by leveraging the relatively weak association energies of such detergent clusters in the gas phase. Additionally, our data illustrate how IR photoactivation can be extended to include membrane mimetics beyond micelles and liberate proteins from nanodiscs, liposomes, and bicelles. Finally, our data quantify the improvements in membrane protein sequence coverage produced through the use of IR photoactivation, which typically leads to membrane protein sequence coverage values ranging from 40 to 60%.
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Affiliation(s)
- Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph W Keating
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. Angew Chem Int Ed Engl 2023; 62:e202305694. [PMID: 37329506 PMCID: PMC7615181 DOI: 10.1002/anie.202305694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 06/19/2023]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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6
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202305694. [PMID: 38516403 PMCID: PMC10953453 DOI: 10.1002/ange.202305694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 03/23/2024]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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7
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Smyrnakis A, Levin N, Kosmopoulou M, Jha A, Fort K, Makarov A, Papanastasiou D, Mohammed S. Characterization of an Omnitrap-Orbitrap Platform Equipped with Infrared Multiphoton Dissociation, Ultraviolet Photodissociation, and Electron Capture Dissociation for the Analysis of Peptides and Proteins. Anal Chem 2023; 95:12039-12046. [PMID: 37534599 PMCID: PMC10433246 DOI: 10.1021/acs.analchem.3c01899] [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] [Received: 05/03/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
We describe an instrument configuration based on the Orbitrap Exploris 480 mass spectrometer that has been coupled to an Omnitrap platform. The Omnitrap possesses three distinct ion-activation regions that can be used to perform resonant-based collision-induced dissociation, several forms of electron-associated fragmentation, and ultraviolet photodissociation. Each section can also be combined with infrared multiphoton dissociation. In this work, we demonstrate all these modes of operation in a range of peptides and proteins. The results show that this instrument configuration produces similar data to previous implementations of each activation technique and at similar efficiency levels. We demonstrate that this unique instrument configuration is extremely versatile for the investigation of polypeptides.
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Affiliation(s)
- Athanasios Smyrnakis
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Nikita Levin
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Pharmacology, University of Oxford, OX1 3QT Oxford, U.K.
| | - Mariangela Kosmopoulou
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Ajay Jha
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Pharmacology, University of Oxford, OX1 3QT Oxford, U.K.
| | - Kyle Fort
- Thermo
Fisher Scientific, 28199 Bremen, Germany
| | | | - Dimitris Papanastasiou
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Shabaz Mohammed
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Biochemistry, University of Oxford, OX1 3QU Oxford, U.K.
- Department
of Chemistry, University of Oxford, OX1 3TA Oxford, U.K.
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8
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Durbin KR, Robey MT, Voong LN, Fellers RT, Lutomski CA, El-Baba TJ, Robinson CV, Kelleher NL. ProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data. J Proteome Res 2023; 22:2660-2668. [PMID: 37436406 PMCID: PMC10407923 DOI: 10.1021/acs.jproteome.3c00171] [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] [Received: 03/22/2023] [Indexed: 07/13/2023]
Abstract
Native mass spectrometry has recently moved alongside traditional structural biology techniques in its ability to provide clear insights into the composition of protein complexes. However, to date, limited software tools are available for the comprehensive analysis of native mass spectrometry data on protein complexes, particularly for experiments aimed at elucidating the composition of an intact protein complex. Here, we introduce ProSight Native as a start-to-finish informatics platform for analyzing native protein and protein complex data. Combining mass determination via spectral deconvolution with a top-down database search and stoichiometry calculations, ProSight Native can determine the complete composition of protein complexes. To demonstrate its features, we used ProSight Native to successfully determine the composition of the homotetrameric membrane complex Aquaporin Z. We also revisited previously published spectra and were able to decipher the composition of a heterodimer complex bound with two noncovalently associated ligands. In addition to determining complex composition, we developed new tools in the software for validating native mass spectrometry fragment ions and mapping top-down fragmentation data onto three-dimensional protein structures. Taken together, ProSight Native will reduce the informatics burden on the growing field of native mass spectrometry, enabling the technology to further its reach.
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Affiliation(s)
| | | | - Lilien N. Voong
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
| | - Ryan T. Fellers
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
- Northwestern
University, Evanston, Illinois 60208, United States
| | - Corinne A. Lutomski
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Tarick J. El-Baba
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Neil L. Kelleher
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
- Northwestern
University, Evanston, Illinois 60208, United States
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9
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Santos-Fernandez M, Jeanne Dit Fouque K, Fernandez-Lima F. Integration of Trapped Ion Mobility Spectrometry and Ultraviolet Photodissociation in a Quadrupolar Ion Trap Mass Spectrometer. Anal Chem 2023; 95:8417-8422. [PMID: 37220214 PMCID: PMC10877586 DOI: 10.1021/acs.analchem.3c01220] [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: 05/25/2023]
Abstract
There is a growing demand for lower-cost, benchtop analytical instruments with complementary separation capabilities for the screening and characterization of biological samples. In this study, we report on the custom integration of trapped ion mobility spectrometry and ultraviolet photodissociation capabilities in a commercial Paul quadrupolar ion trap multistage mass spectrometer (TIMS-QIT-MSn UVPD platform). A gated TIMS operation allowed for the accumulation of ion mobility separated ion in the QIT, followed by a mass analysis (MS1 scan) or m/z isolation, followed by selected collision induced dissociation (CID) or ultraviolet photodissociation (UVPD) and a mass analysis (MS2 scan). The analytical potential of this platform for the analysis of complex and labile biological samples is illustrated for the case of positional isomers with varying PTM location of the histone H4 tryptic peptide 4-17 singly and doubly acetylated and the histone H3.1 tail (1-50) singly trimethylated. For all cases, a baseline ion mobility precursor molecular ion preseparation was obtained. The tandem CID and UVPD MS2 allowed for effective sequence confirmation as well as the identification of reporter fragment ions associated with the PTM location; a higher sequence coverage was obtained using UVPD when compared to CID. Different from previous IMS-MS implementation, the novel TIMS-QIT-MSn UVPD platform offers a lower-cost alternative for the structural characterization of biological molecules that can be widely disseminated in clinical laboratories.
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Affiliation(s)
- Miguel Santos-Fernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL, 33199, USA
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10
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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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11
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Miller SA, Fouque KJD, Ridgeway ME, Park MA, Fernandez-Lima F. Trapped Ion Mobility Spectrometry, Ultraviolet Photodissociation, and Time-of-Flight Mass Spectrometry for Gas-Phase Peptide Isobars/Isomers/Conformers Discrimination. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1267-1275. [PMID: 35658468 PMCID: PMC9262853 DOI: 10.1021/jasms.2c00091] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Trapped ion mobility spectrometry (TIMS) when coupled with mass spectrometry (MS) offers great advantages for the separation of isobaric, isomeric, and/or conformeric species. In the present work, we report the advantages of coupling TIMS with a low-cost, ultraviolet photodissociation (UVPD) linear ion trap operated at few mbars prior to time-of-flight (ToF) MS analysis for the effective characterization of isobaric, isomeric, and/or conformeric species based on mobility-selected fragmentation patterns. These three traditional challenges to MS-based separations are illustrated for the case of biologically relevant model systems: H3.1 histone tail PTM isobars (K4Me3/K18Ac), lanthipeptide regioisomers (overlapping/nonoverlapping ring patterns), and a model peptide conformer (angiotensin I). The sequential nature of the TIMS operation allows for effective synchronization with the ToF MS scans, in addition to parallel operation between the TIMS and the UVPD trap. Inspection of the mobility-selected UVPD MS spectra showed that for all three cases considered, unique fragmentation patterns (fingerprints) were observed per mobility band. Different from other IMS-UVPD implementations, the higher resolution of the TIMS device allowed for high mobility resolving power (R > 100) and effective mobility separation. The mobility selected UVPD MS provided high sequence coverage (>85%) with a fragmentation efficiency up to ∼40%.
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Affiliation(s)
- Samuel A. Miller
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
| | | | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, MA 01821, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
- Corresponding Author: Francisco Fernandez-Lima,
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12
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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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13
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Giska F, Mariappan M, Bhattacharyya M, Gupta K. Deciphering the molecular organization of GET pathway chaperones through native mass spectrometry. Biophys J 2022; 121:1289-1298. [PMID: 35189106 PMCID: PMC9034188 DOI: 10.1016/j.bpj.2022.02.026] [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] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 02/15/2022] [Indexed: 11/02/2022] Open
Abstract
Get3/4/5 chaperone complex is responsible for targeting C-terminal tail-anchored membrane proteins to the endoplasmic reticulum. Despite the availability of several crystal structures of independent proteins and partial structures of subcomplexes, different models of oligomeric states and structural organization have been proposed for the protein complexes involved. Here, using native mass spectrometry (Native-MS), coupled with intact dissociation, we show that Get4/5 exclusively forms a tetramer using both Get5/5 and a novel Get4/4 dimerization interface. Addition of Get3 to this leads to a hexameric (Get3)2-(Get4)2-(Get5)2 complex with closed-ring cyclic architecture. We further validate our claims through molecular modeling and mutational abrogation of the proposed interfaces. Native-MS has become a principal tool to determine the state of oligomeric organization of proteins. The work demonstrates that for multiprotein complexes, native-MS, coupled with molecular modeling and mutational perturbation, can provide an alternative route to render a detailed view of both the oligomeric states as well as the molecular interfaces involved. This is especially useful for large multiprotein complexes with large unstructured domains that make it recalcitrant to conventional structure determination approaches.
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Affiliation(s)
- Fabian Giska
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut
| | - Malaiyalam Mariappan
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut
| | | | - Kallol Gupta
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut.
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14
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Webb IK. Recent technological developments for native mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140732. [PMID: 34653668 DOI: 10.1016/j.bbapap.2021.140732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022]
Abstract
Native mass spectrometry (MS), the analysis of proteins and protein complexes from solutions that stabilize native solution structures, is a rapidly expanding area. There is strong evidence supporting the retention of proteins' native folds in the absence of solvent under the experimental timescales of MS experiments. Therefore, instrumentation has been developed to use gas-phase native-like protein ions to exploit the speed, sensitivity, and selectivity of mass spectrometry approaches to solve emerging problems in structural biology. This article reviews some of the recent advances and applications in gas-phase instrumentation for structural proteomics.
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Affiliation(s)
- Ian K Webb
- Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, United States of America; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America.
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16
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Macias LA, Sipe SN, Santos IC, Bashyal A, Mehaffey MR, Brodbelt JS. Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2860-2873. [PMID: 34714071 PMCID: PMC8639798 DOI: 10.1021/jasms.1c00269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Analysis of native-like protein structures in the gas phase via native mass spectrometry and auxiliary techniques has become a powerful tool for structural biology applications. In combination with ultraviolet photodissociation (UVPD), native top-down mass spectrometry informs backbone flexibility, topology, hydrogen bonding networks, and conformational changes in protein structure. Although it is known that the primary structure affects dissociation of peptides and proteins in the gas phase, its effect on the types and locations of backbone cleavages promoted by UVPD and concomitant influence on structural characterization of native-like proteins is not well understood. Here, trends in the fragmentation of native-like proteins were evaluated by tracking the propensity of 10 fragment types (a, a+1, b, c, x, x+1, y, y-1, Y, and z) in relation to primary structure in a native-top down UVPD data set encompassing >9600 fragment ions. Differing fragmentation trends are reported for the production of distinct fragment types, attributed to a combination of both direct dissociation pathways from excited electronic states and those surmised to involve intramolecular vibrational energy redistribution after internal conversion. The latter pathways were systematically evaluated to evince the role of proton mobility in the generation of "CID-like" fragments through UVPD, providing pertinent insight into the characterization of native-like proteins. Fragmentation trends presented here are envisioned to enhance analysis of the protein higher-order structure or augment scoring algorithms in the high-throughput analysis of intact proteins.
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sarah N Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês C Santos
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- 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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17
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Pepi LE, Leach FE, Klein DR, Brodbelt JS, Amster IJ. Investigation of the Experimental Parameters of Ultraviolet Photodissociation for the Structural Characterization of Chondroitin Sulfate Glycosaminoglycan Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1759-1770. [PMID: 34096288 PMCID: PMC8377745 DOI: 10.1021/jasms.1c00119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides that participate in a broad range of biological functions. Their incomplete biosynthesis pathway leads to nonuniform chains and complex mixtures. For this reason, the characterization of GAGs has been a difficult hurdle for the analytical community. Recently, ultraviolet photodissociation (UVPD) has emerged as a useful tool for determining sites of modification within a GAG chain. Here, we investigate the ability for UVPD to distinguish chondroitin sulfate epimers and the effects of UVPD experimental parameters on fragmentation efficiency. Chondroitin sulfate A (CS-A) and chondroitin sulfate B (CS-B), commonly referred to as dermatan sulfate (DS), differ only in C-5 uronic acid stereochemistry. This uronic acid difference can influence GAG-protein binding and therefore can alter the specific biological function of a GAG chain. Prior tandem mass spectrometry methods investigated for the elucidation of GAG structures also have difficulty differentiating 4-O from 6-O sulfation in chondroitin sulfate GAGs. Preliminary data using UVPD to characterize GAGs showed a promising ability to characterize 4-O sulfation in CS-A GAGs. Here, we look in depth at the capability of UVPD to distinguish chondroitin sulfate C-5 diastereomers and the role of key experimental parameters in making this distinction. Results using a 193 nm excimer laser and a 213 nm solid-state laser are compared for this study. The effect of precursor ionization state, the number of laser pulses (193 or 213 nm UVPD), and the use of the low-pressure versus high-pressure trap are investigated.
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Affiliation(s)
- Lauren E Pepi
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Franklin E Leach
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department of Environmental Health Sciences, University of Georgia, Athens, Georgia 30602, United States
| | - Dustin R Klein
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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18
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Cohn W, Huguet R, Zabrouskov V, Whitelegge J. Dissociation Strategies to Maximize Coverage of α-Helical Domains in Top-Down Mass Spectrometry of Integral Membrane Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1380-1387. [PMID: 33956438 DOI: 10.1021/jasms.1c00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transmembrane α-helical domains of membrane proteins tend to remain structured in the gas phase, presenting a challenge for efficient electron capture/transfer dissociation during top-down dissociation mass spectrometry (MS) experiments. In this study, we compare results from different dissociation modes on a modern Orbitrap platform applied to a model integral membrane protein containing two transmembrane helices, the c-subunit of the Fo domain of the chloroplast ATP synthase. Using commercially available options, we compare collisionally activated dissociation (CAD) with the related variant higher-energy collisional dissociation (HCD) and with electron transfer dissociation (ETD). HCD performed better than CAD and ETD. A combined method utilizing both ETD and HCD (EThcD) demonstrates significant synergy over HCD or ETD alone, representing a robust option analogous to activated ion electron capture dissociation, whereby an infrared laser was used to heat the protein ion alongside electron bombardment. Ultraviolet photodissociation at 213 nm displays at least three backbone dissociation mechanisms and covered nearly 100% of backbone bonds, suggesting significant potential for this technique.
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Affiliation(s)
- Whitaker Cohn
- The Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90024, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95054, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95054, United States
| | - Julian Whitelegge
- The Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90024, United States
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19
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Snyder DT, Lin YF, Somogyi A, Wysocki V. Tandem surface-induced dissociation of protein complexes on an ultrahigh resolution platform. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 461:116503. [PMID: 33889055 PMCID: PMC8057730 DOI: 10.1016/j.ijms.2020.116503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We describe instrumentation for conducting tandem surface-induced dissociation (tSID) of native protein complexes on an ultrahigh resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The two stages of SID are accomplished with split lenses replacing the entrance lenses of the quadrupole mass filter (stage 1, referred to herein as SID-Q) and the collision cell (stage 2, Q-SID). After SID-Q, the scattered projectile ions and subcomplexes formed in transit traverse the 20 mm pre-filter prior to the mass-selecting quadrupole, providing preliminary insights into the SID fragmentation kinetics of noncovalent protein complexes. The isolated SID fragments (subcomplexes) are then fragmented by SID in the collision cell entrance lens (Q-SID), generating subcomplexes of subcomplexes. We show that the ultrahigh resolution of the FT-ICR can be used for deconvolving species overlapping in m/z, which are particularly prominent in tandem SID spectra due to the combination of symmetric charge partitioning and narrow product ion charge state distributions. Various protein complex topologies are explored, including homotetramers, homopentamers, a homohexamer, and a heterohexamer.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
| | - Yu-Fu Lin
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH, USA 43210
| | - Arpad Somogyi
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
| | - Vicki Wysocki
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH, USA 43210
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20
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Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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21
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Stiving AQ, Harvey SR, Jones BJ, Bellina B, Brown JM, Barran PE, Wysocki VH. Coupling 193 nm Ultraviolet Photodissociation and Ion Mobility for Sequence Characterization of Conformationally-Selected Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2313-2320. [PMID: 32959654 PMCID: PMC8127984 DOI: 10.1021/jasms.0c00259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ultraviolet photodissociation (UVPD) has emerged as a useful technique for characterizing peptide, protein, and protein complex primary and secondary structure. 193 nm UVPD, specifically, enables extensive covalent fragmentation of the peptide backbone without the requirement of a specific side chain chromophore and with no precursor charge state dependence. We have modified a commercial quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometer to include 193 nm UVPD following ion mobility. Ion mobility (IM) is a gas-phase separation technique that enables separation of ions by their size, shape, and charge, providing an orthogonal dimension of separation to mass analysis. Following instrument modifications, we characterized the performance of, and information that could be generated from, this new setup using the model peptides substance P, melittin, and insulin chain B. These experiments show extensive fragmentation across the peptide backbone and a variety of ion types as expected from 193 nm UVPD. Additionally, y-2 ions (along with complementary a+2 and b+2 ions) N-terminal to proline were observed. Combining the IM separation and mobility gating capabilities with UVPD, we demonstrate the ability to accomplish both mass- and mobility-selection of bradykinin des-Arg9 and des-Arg1 peptides followed by complete sequence characterization by UVPD. The new capabilities of this modified instrument demonstrate the utility of combining IM with UVPD because isobaric species cannot be independently selected with a traditional quadrupole alone.
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Affiliation(s)
- Alyssa Q Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | | | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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22
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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