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Bakels S, Daly S, Doğan B, Baerenfaenger M, Commandeur J, Rijs AM. Probing High-Order Transient Oligomers Using Ion Mobility Mass Spectrometry Coupled with Infrared Action Spectroscopy. Anal Chem 2024; 96. [PMID: 39150274 PMCID: PMC11359389 DOI: 10.1021/acs.analchem.4c02749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/23/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Understanding and controlling peptide aggregation are critical due to its neurotoxic implications. However, structural information about the key intermediates, the oligomers, is obscured by a cascade of coinciding events occurring at various time and energy scales, which results in complex and heterogeneous mixtures of oligomers. To address this challenge, we have developed the Photo-Synapt, a novel, multidimensional spectrometer that integrates ion mobility mass spectrometry with infrared (IR) action spectroscopy within a single experiment. By combining three different orthogonal analytical dimensions, we can select and isolate individual oligomers by mass, charge, size, and shape and provide a unique molecular fingerprint for each oligomer. The broad application of this technology is demonstrated by its application to oligosaccharide analysis from glycoproteins, which are challenging to analyze due to the minute differences between isomers. By integration of IR action spectroscopy with ion mobility mass spectrometry, this approach adds an analytical dimension that effectively addresses this limitation, offering a unique molecular fingerprint for each isomer.
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Affiliation(s)
- Sjors Bakels
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
- Centre
for Analytical Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Steven Daly
- MS
Vision, Spectrometry Vision B.V., Televisieweg 40, Almere 1322 AM, The Netherlands
| | - Berk Doğan
- MS
Vision, Spectrometry Vision B.V., Televisieweg 40, Almere 1322 AM, The Netherlands
| | - Melissa Baerenfaenger
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
- Centre
for Analytical Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jan Commandeur
- MS
Vision, Spectrometry Vision B.V., Televisieweg 40, Almere 1322 AM, The Netherlands
| | - Anouk M. Rijs
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
- Centre
for Analytical Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands
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2
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Li T, Zhang K, Liu R, Ren L, Li X, Li J, Liu W, Song Y. Direct infusion-multiple reaction monitoring cubed (DI-MRM 3) enables widely targeted bi-omics of Colla Corii Asini (Chinese name: Ejiao). Food Chem 2024; 447:138969. [PMID: 38507947 DOI: 10.1016/j.foodchem.2024.138969] [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: 10/18/2023] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
Food authenticity is extremely important and widely targeted bi-omics is a promising pipeline attributing to incorporating metabolomics and peptidomics. Colla Corii Asini (CCA, Ejiao) is one of the most popular tonic edible materials, with counterfeit and adulterated products being widespread. An attempt was devoted to develop a high-throughput and reliable DI-MRM3 program facilitating widely targeted bi-omics of CCA. Firstly, predictive MRM program captured metabolites and peptides in trypsin-digestive gelatins. After data alignment and structure annotation, primary parameters such as Q1 → Q3 → QLIT, CE, and EE were optimized for all 17 metabolites and 34 peptides by online ER-MS. Though a single run merely consumed 6.5 min, great selectivity was reached for each analyte. Statistical results showed that nine peptides contributed to distinguish CCA from other gelatins. After cross-validation with LC-MRM, DI-MRM3 was justified to be reproducible and high-throughput for widely targeted bi-omics of CCA, suggesting a meaningful tool for food authenticity.
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Affiliation(s)
- Ting Li
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ke Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Rui Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Luyao Ren
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaoyun Li
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jun Li
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Wenjing Liu
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China.
| | - Yuelin Song
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
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3
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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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4
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Brandner S, Habeck T, Lermyte F. New Insights into the Intrinsic Electron-Based Dissociation Behavior of Cytochrome c Oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1908-1916. [PMID: 37227392 DOI: 10.1021/jasms.3c00106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Between 2003 and 2017, four reports were published that demonstrated the intrinsic ability of the native iron-containing proteins cytochrome c and ferritin to undergo radical-based backbone fragmentation in the gas phase without the introduction of exogenous electrons. For cytochrome c in particular, this effect has so far only been reported to occur in the ion source, preventing the in-depth study of reactions occurring after gas-phase isolation of specific precursors. Here, we report the first observation of this intrinsic native electron capture dissociation behavior after quadrupole isolation of specific charge states of the cytochrome c dimer and trimer, providing direct experimental support for key aspects of the mechanism proposed 20 years ago. Furthermore, we provide evidence that, in contrast to some earlier proposals, these oligomeric states are formed in bulk solution rather than during the electrospray ionization process and that the observed fragmentation site preferences can be rationalized through the structure and interactions within these native oligomers rather than the monomer. We also show that the observed fragmentation pattern─and indeed, whether or not fragmentation occurs─is highly sensitive to the provenance and history of the protein samples, to the extent that samples can show distinct fragmentation behavior despite behaving identically in ion mobility experiments. This rather underexplored method therefore represents an exquisitely sensitive conformational probe and will hopefully receive more attention from the biomolecular mass spectrometry community in the future.
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Affiliation(s)
- Sarah Brandner
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
| | - Tanja Habeck
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
| | - Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
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5
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Mao S, Jin W, Fu S, Liu K, Xu F, Wu L, Xu Y, Yang H, Liu H, Wang G, Liang Y. Strategies for mapping protein hydrolysate profiles and pharmacokinetics based on non-targeted proteomics combining skyline-aided quantitative techniques. Anal Chim Acta 2023; 1265:341272. [PMID: 37230566 DOI: 10.1016/j.aca.2023.341272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
Numerous works have been focused on the bioactivities of protein hydrolysates (PHs) and their application in food or drug formulations, but their composition and pharmacokinetics have never been addressed due to their complex constitutes, short half-life, extremely low concentrations and lack of authentic standards. The present study aims to develop systematic analytical strategy and technical platform with optimized sample preparation, separation and detection protocols for PHs. Lineal peptides (LPs), extraction of the spleen of healthy pigs or calves, were used as cases. First, solvents with polarity gradients were used to globally extract peptides of LP from biological matrix. Non-targeted proteomics based on a high-resolution MS system was used to establish a reliable qualitative analysis workflow for PHs. Based on the developed approach, 247 unique peptides were identified using NanoLC-Orbitrap-MS/MS, and then further verified on the MicroLC-Q-TOF/MS system. In the quantitative analysis workflow, Skyline software was used to predict and optimize the LC-MS/MS detection parameters of LPs followed by investigating the linearity and precision of the developed analytical assay. Note worthily, we innovatively prepared calibration curves by sequential dilution of LP solution to overcome the bottleneck of lacking authentic standards and complex PH composition. All the peptides exhibited good linearity and precision in biological matrix. The established qualitative and quantitative assays were successfully applied to study the distribution characteristics of LPs in mice, and would be conductive to systematically map the profile and pharmacokinetics of peptides in various PHs in vivo and in vitro.
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Affiliation(s)
- Shuying Mao
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Wei Jin
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Sisi Fu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Keanqi Liu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Feng Xu
- Hebei Zhitong Biopharmaceutical Co., Ltd, No. 1, Gucheng, Dingxing County, Hebei Province, 072656, PR China
| | - Linlin Wu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Yexin Xu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Huizhu Yang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Huafang Liu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China
| | - Guangji Wang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Yan Liang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
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6
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Schultz M, Parker SL, Fernando MT, Wellalage MM, Thomas DA. Diserinol Isophthalamide: A Novel Reagent for Complexation with Biomolecular Anions in Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:745-753. [PMID: 36975839 DOI: 10.1021/jasms.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transferring biomolecules from solution to vacuum facilitates a detailed analysis of molecular structure and dynamics by isolating molecules of interest from a complex environment. However, inherent in the ion desolvation process is the loss of solvent hydrogen bonding partners, which are critical for the stability of a condensed-phase structure. Thus, transfer of ions to vacuum can favor structural rearrangement, especially near solvent-accessible charge sites, which tend to adopt intramolecular hydrogen bonding motifs in the absence of solvent. Complexation of monoalkylammonium moieties (e.g., lysine side chains) with crown ethers such as 18-crown-6 can disfavor structural rearrangement of protonated sites, but no equivalent ligand has been investigated for deprotonated groups. Herein we describe diserinol isophthalamide (DIP), a novel reagent for the gas-phase complexation of anionic moieties within biomolecules. Complexation is observed to the C-terminus or side chains of the small model peptides GD, GE, GG, DF-OMe, VYV, YGGFL, and EYMPME in electrospray ionization mass spectrometry (ESI-MS) studies. In addition, complexation is observed with the phosphate and carboxylate moieities of phosphoserine and phosphotyrosine. DIP performs favorably in comparison to an existing anion recognition reagent, 1,1'-(1,2-phenylene)bis(3-phenylurea), that exhibits moderate carboxylate binding in organic solvent. This improved performance in ESI-MS experiments is attributed to reduced steric constraints to complexation with carboxylate groups of larger molecules. Overall, diserinol isophthalamide is an effective complexation reagent that can be applied in future work to study retention of solution-phase structure, investigate intrinsic molecular properties, and examine solvation effects.
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Affiliation(s)
- Madeline Schultz
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah L Parker
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Maleesha T Fernando
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Miyuru M Wellalage
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel A Thomas
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
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7
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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8
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Depraz Depland A, Stroganova I, Wootton CA, Rijs AM. Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:193-204. [PMID: 36633834 PMCID: PMC9896548 DOI: 10.1021/jasms.2c00253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.
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Affiliation(s)
- Agathe Depraz Depland
- Division
of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life
Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Iuliia Stroganova
- Division
of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life
Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | | | - Anouk M. Rijs
- Division
of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life
Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
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9
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Sipe SN, Jeanne Dit Fouque K, Garabedian A, Leng F, Fernandez-Lima F, Brodbelt JS. Exploring the Conformations and Binding Location of HMGA2·DNA Complexes Using Ion Mobility Spectrometry and 193 nm Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1092-1102. [PMID: 35687872 PMCID: PMC9274541 DOI: 10.1021/jasms.2c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Although it is widely accepted that protein function is largely dependent on its structure, intrinsically disordered proteins (IDPs) lack defined structure but are essential in proper cellular processes. Mammalian high mobility group proteins (HMGA) are one such example of IDPs that perform a number of crucial nuclear activities and have been highly studied due to their involvement in the proliferation of a variety of disease and cancers. Traditional structural characterization methods have had limited success in understanding HMGA proteins and their ability to coordinate to DNA. Ion mobility spectrometry and mass spectrometry provide insights into the diversity and heterogeneity of structures adopted by IDPs and are employed here to interrogate HMGA2 in its unbound states and bound to two DNA hairpins. The broad distribution of collision cross sections observed for the apo-protein are restricted when HMGA2 is bound to DNA, suggesting that increased protein organization is promoted in the holo-form. Ultraviolet photodissociation was utilized to probe the changes in structures for the compact and elongated structures of HMGA2 by analyzing backbone cleavage propensities and solvent accessibility based on charge-site analysis, which revealed a spectrum of conformational possibilities. Namely, preferential binding of the DNA hairpins with the second of three AT-hooks of HMGA2 is suggested based on the suppression of backbone fragmentation and distribution of DNA-containing protein fragments.
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Affiliation(s)
- Sarah N Sipe
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712 United States
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10
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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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11
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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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12
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Liu FC, Ridgeway ME, Park MA, Bleiholder C. Tandem-trapped ion mobility spectrometry/mass spectrometry ( tTIMS/MS): a promising analytical method for investigating heterogenous samples. Analyst 2022; 147:2317-2337. [PMID: 35521797 PMCID: PMC9914546 DOI: 10.1039/d2an00335j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ion mobility spectrometry/mass spectrometry (IMS/MS) is widely used to study various levels of protein structure. Here, we review the current state of affairs in tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS). Two different tTIMS/MS instruments are discussed in detail: the first tTIMS/MS instrument, constructed from coaxially aligning two TIMS devices; and an orthogonal tTIMS/MS configuration that comprises an ion trap for irradiation of ions with UV photons. We discuss the various workflows the two tTIMS/MS setups offer and how these can be used to study primary, tertiary, and quaternary structures of protein systems. We also discuss, from a more fundamental perspective, the processes that lead to denaturation of protein systems in tTIMS/MS and how to soften the measurement so that biologically meaningful structures can be characterised with tTIMS/MS. We emphasize the concepts underlying tTIMS/MS to underscore the opportunities tandem-ion mobility spectrometry methods offer for investigating heterogeneous samples.
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Affiliation(s)
- Fanny C Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA.
| | | | | | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, USA
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13
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
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14
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Zhou M, Jiao L, Xu S, Xu Y, Du M, Zhang X, Kong X. A novel method for photon unfolding spectroscopy of protein ions in the gas phase. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:043003. [PMID: 35489914 DOI: 10.1063/5.0080040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
In this study, a new experimental method for photon unfolding spectroscopy of protein ions based on a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer was developed. The method of short-time Fourier transform has been applied here to obtain decay curves of target ions trapped in the cell of the FT ICR mass spectrometer. Based on the decay constants, the collision cross sections (CCSs) of target ions were calculated using the energetic hard-sphere model. By combining a tunable laser to the FT ICR mass spectrometer, the changes of CCSs of the target ions were recorded as a function of the wavelengths; thus, the photon isomerization spectrum was obtained. As one example, the photon isomerization spectrum of [Cyt c + 13H]13+ was recorded as the decay constants relative to the applied wavelengths of the laser in the 410-480 nm range. The spectrum shows a maximum at 426 nm, where an unfolded structure induced by a 4 s irradiation can be deduced. The strong peak at 426 nm was also observed for another ion of [Cyt c + 15H]15+, although some difference at 410 nm between the two spectra was found at the same time. This novel method can be expanded to ultraviolet or infrared region, making the experimental study of wavelength-dependent photon-induced structural variation of a variety of organic or biological molecules possible.
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Affiliation(s)
- Min Zhou
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Luyang Jiao
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Shiyin Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Yicheng Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Mengying Du
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Xianyi Zhang
- School of Physics and Electronic Information, Anhui Normal University, Wuhu 241000, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
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15
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Zhang K, Gong X, Wang Q, Tu P, Li J, Song Y. Rapid tryptic peptide mapping of human serum albumin using DI-MS/MS ALL. RSC Adv 2022; 12:9868-9882. [PMID: 35424948 PMCID: PMC8963265 DOI: 10.1039/d1ra08717g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/13/2022] [Indexed: 11/27/2022] Open
Abstract
In recent decades, proteinic drugs, in particular monoclonal antibodies, are taking the leading role of small molecule drugs, and peptide mapping relying on liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an emerging approach to substitute the role of a ligand-binding assay for the quality control of the proteinic drugs. However, such LC-MS/MS approaches extensively suffer from time-intensive measurements, leading to a limited throughput. To achieve accelerated measurements, here, the potential of DI-MS/MSALL towards tryptic peptide mapping was evaluated through comparing with well-defined LC-MS/MS means, and human serum albumin (HSA) was employed as the representative protein for applicability illustration. Among the 55 tryptic peptides theoretically suggested by Skyline software, 47 were successfully captured by DI-MS/MSALL through acquiring the desired MS2 spectra, in comparison to 51 detected by LC-MS/MS. DI-MS/MSALL measurements merely took 5 min, which was dramatically superior to the LC-MS/MS assay. Noteworthily, different from fruitful multi-charged MS1 signals for LC-MS/MS, most quasi-molecular ions received lower charged states. DI-MS/MSALL also possessed advantages such as lower solvent consumption and facile instrumentation; however, more sample was consumed. In conclusion, DI-MS/MSALL is eligible to act as an alternative analytical tool for LC-MS/MS towards the peptide mapping of proteinic drugs, particularly when a heavy measurement workload. DI-MS/MSALL records MS2 spectrum at each 1 Da mass window through gas phase ion fractionation theory, and is eligible to act as an alternative analytical tool for LC-MS/MS towards the peptide mapping of proteinic drugs.![]()
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Affiliation(s)
- Ke Zhang
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine Beijing 100029 China
| | - Xingcheng Gong
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine Beijing 100029 China
| | - Qian Wang
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine Beijing 100029 China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine Beijing 100029 China
| | - Jun Li
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine Beijing 100029 China
| | - Yuelin Song
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine Beijing 100029 China
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16
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Marlton SJP, Trevitt A. Laser Photodissocation, Action Spectroscopy and Mass Spectrometry Unite to Detect and Separate Isomers. Chem Commun (Camb) 2022; 58:9451-9467. [DOI: 10.1039/d2cc02101c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The separation and detection of isomers remains a challenge for many areas of mass spectrometry. This article highlights laser photodissociation and ion mobility strategies that have been deployed to tackle...
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17
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Liu FC, Ridgeway ME, Winfred JSRV, Polfer NC, Lee J, Theisen A, Wootton CA, Park MA, Bleiholder C. Tandem-trapped ion mobility spectrometry/mass spectrometry coupled with ultraviolet photodissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9192. [PMID: 34498312 PMCID: PMC9195479 DOI: 10.1002/rcm.9192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 05/05/2023]
Abstract
RATIONALE Tandem-ion mobility spectrometry/mass spectrometry methods have recently gained traction for the structural characterization of proteins and protein complexes. However, ion activation techniques currently coupled with tandem-ion mobility spectrometry/mass spectrometry methods are limited in their ability to characterize structures of proteins and protein complexes. METHODS Here, we describe the coupling of the separation capabilities of tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS) with the dissociation capabilities of ultraviolet photodissociation (UVPD) for protein structure analysis. RESULTS We establish the feasibility of dissociating intact proteins by UV irradiation at 213 nm between the two TIMS devices in tTIMS/MS and at pressure conditions compatible with ion mobility spectrometry (2-3 mbar). We validate that the fragments produced by UVPD under these conditions result from a radical-based mechanism in accordance with prior literature on UVPD. The data suggest stabilization of fragment ions produced from UVPD by collisional cooling due to the elevated pressures used here ("UVnoD2"), which otherwise do not survive to detection. The data account for a sequence coverage for the protein ubiquitin comparable to recent reports, demonstrating the analytical utility of our instrument in mobility-separating fragment ions produced from UVPD. CONCLUSIONS The data demonstrate that UVPD carried out at elevated pressures of 2-3 mbar yields extensive fragment ions rich in information about the protein and that their exhaustive analysis requires IMS separation post-UVPD. Therefore, because UVPD and tTIMS/MS each have been shown to be valuable techniques on their own merit in proteomics, our contribution here underscores the potential of combining tTIMS/MS with UVPD for structural proteomics.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4389, USA
| | - Mark E. Ridgeway
- Bruker Daltonics, Inc., 40 Manning Rd., Billerica, MA 01821, USA
| | | | - Nicolas C. Polfer
- Athénée de Luxembourg, 24 boulevard Pierre Dupont, L-1430 Luxembourg, Grand-Duchy of Luxembourg
| | - Jusung Lee
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4389, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., 40 Manning Rd., Billerica, MA 01821, USA
- Correspondence to: ,
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4389, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4389, USA
- Correspondence to: ,
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18
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Zhang K, Shi Y, Du M, Xu Y, Wang Y, Kong X. Versatile Double-Beam Confocal Laser System Combined with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Photodissociation Mass Spectrometry and Spectroscopy. Anal Chem 2021; 93:9056-9063. [PMID: 34165954 DOI: 10.1021/acs.analchem.1c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Both infrared multiphoton dissociation (IRMPD) and ultraviolet photodissociation (UVPD) play important roles in tandem mass spectrometry and the action spectroscopy of organic and biological molecules. A flexible combination of the two methods may provide researchers with more versatile and powerful ion activation/dissociation choices for structural characterization and spectroscopic studies. Here, we report the integration of two tunable lasers with a Fourier transform ion cyclotron resonance mass spectrometer in a confocal mode, which offers multiple capabilities for photon activation/dissociation experiments. The two overlapped beams can be introduced into the cell individually, sequentially, or simultaneously, providing highly flexible and diverse activation schemes. The setup can also measure the UVPD or IRMPD action spectra of fragment ions generated by previous photon dissociation processes. In addition, the multistage tandem-in-time mass spectrometry performance up to MS4, including three different activation methods in a single cell, has also been demonstrated.
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Affiliation(s)
- Kailin Zhang
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China.,School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Yingying Shi
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Mengying Du
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Yicheng Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Yan Wang
- School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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19
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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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20
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Allison TM, Barran P, Benesch JLP, Cianferani S, Degiacomi MT, Gabelica V, Grandori R, Marklund EG, Menneteau T, Migas LG, Politis A, Sharon M, Sobott F, Thalassinos K. Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data. Anal Chem 2020; 92:10881-10890. [PMID: 32649184 DOI: 10.1021/acs.analchem.9b05792] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The past few years have seen a dramatic increase in applications of native mass and ion mobility spectrometry, especially for the study of proteins and protein complexes. This increase has been catalyzed by the availability of commercial instrumentation capable of carrying out such analyses. As in most fields, however, the software to process the data generated from new instrumentation lags behind. Recently, a number of research groups have started addressing this by developing software, but further improvements are still required in order to realize the full potential of the data sets generated. In this perspective, we describe practical aspects as well as challenges in processing native mass spectrometry (MS) and ion mobility-MS data sets and provide a brief overview of currently available tools. We then set out our vision of future developments that would bring the community together and lead to the development of a common platform to expedite future computational developments, provide standardized processing approaches, and serve as a location for the deposition of data for this emerging field. This perspective has been written by members of the European Cooperation in Science and Technology Action on Native MS and Related Methods for Structural Biology (EU COST Action BM1403) as an introduction to the software tools available in this area. It is intended to serve as an overview for newcomers and to stimulate discussions in the community on further developments in this field, rather than being an in-depth review. Our complementary perspective (http://dx.doi.org/10.1021/acs.analchem.9b05791) focuses on computational approaches used in this field.
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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
| | - Justin L P Benesch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Matteo T Degiacomi
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom.,Department of Physics, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Valerie 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
- Division of Biosciences, Institute of Structural and Molecular Biology, University College of London, Gower Street, London WC1E 6BT, United Kingdom.,Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
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21
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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22
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23
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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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24
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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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25
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Yan B, Taylor AJ, Bunch J. Cryo-LESA Mass Spectrometry-a Step Towards Truly Native Surface Sampling of Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1179-1189. [PMID: 30927181 DOI: 10.1007/s13361-019-02178-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/12/2019] [Accepted: 03/03/2019] [Indexed: 06/09/2023]
Abstract
Liquid extraction surface analysis (LESA) is a powerful method for measuring proteins from surfaces. In this work, we present development and initial testing of a cryo-platform for LESA mass spectrometry of proteins. We explore the use of native sampling solutions for probing proteins directly from frozen surfaces. Our initial results from analysis of ubiquitin and hemoglobin standards showed that protein and protein complex refolding or unfolding occurs during the liquid solvent extraction stage of routine room temperature LESA. However, by employing the cryo-sampling method, the refolding or unfolding of protein ubiquitin can be dramatically reduced, while for the protein complex of hemoglobin, its native structures can be better preserved compared with room temperature sampling. This indicates that a truly native LESA sampling method of proteins is feasible. We also present detection of proteins directly from a frozen tissue section. Interestingly, slight conformational differences are observed from different regions of the frozen tissue surface. Further development of this strategy should be considered as a method for preserving, maintaining, and studying proteins in their native states, directly from tissue. Graphical Abstract.
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Affiliation(s)
- Bin Yan
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Adam J Taylor
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
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26
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Sipe SN, Brodbelt JS. Impact of charge state on 193 nm ultraviolet photodissociation of protein complexes. Phys Chem Chem Phys 2019; 21:9265-9276. [PMID: 31016301 DOI: 10.1039/c9cp01144g] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
As applications in mass spectrometry continue to expand into the field of structural biology, there have been an increasing number of studies on noncovalent biological assemblies. Ensuring that protein complexes maintain native-like conformations and architectures during the transition from solution to the gas phase is a key aim. Probing composition and arrangement of subunits of multi-charged complexes via tandem mass spectrometry (MS/MS) may lead to protein unfolding and the redistribution of charges on the constituent subunits, leading to asymmetric charge partitioning and ejection of a high-charged monomer. Additionally, the overall dissociation efficiency of many ion activation methods is often suppressed for low charge states, hindering the effectiveness of MS/MS for complexes that have low charge density. Ultraviolet photodissociation (UVPD) of proteins using 193 nm photons is a high-energy alternative to collisional activation and demonstrates little to no charge state dependence. Here the symmetry of charge partitioning upon UVPD is evaluated for an array of multimeric protein complexes as a function of initial charge state. The results demonstrate that high laser energies (3 mJ) for UVPD induces more symmetric charge partitioning and ejection of low-charged, presumably compact monomers than higher-energy collisional dissociation (HCD).
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Affiliation(s)
- Sarah N Sipe
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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27
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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28
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Theisen A, Black R, Corinti D, Brown JM, Bellina B, Barran PE. Initial Protein Unfolding Events in Ubiquitin, Cytochrome c and Myoglobin Are Revealed with the Use of 213 nm UVPD Coupled to IM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:24-33. [PMID: 29949061 PMCID: PMC6318241 DOI: 10.1007/s13361-018-1992-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 05/11/2023]
Abstract
The initial stages of protein unfolding may reflect the stability of the entire fold and can also reveal which parts of a protein can be perturbed, without restructuring the rest. In this work, we couple UVPD with activated ion mobility mass spectrometry to measure how three model proteins start to unfold. Ubiquitin, cytochrome c and myoglobin ions produced via nESI from salty solutions are subjected to UV irradiation pre-mobility separation; experiments are conducted with a range of source conditions which alter the conformation of the precursor ion as shown by the drift time profiles. For all three proteins, the compact structures result in less fragmentation than more extended structures which emerge following progressive in-source activation. Cleavage sites are found to differ between conformational ensembles, for example, for the dominant charge state of cytochrome c [M + 7H]7+, cleavage at Phe10, Thr19 and Val20 was only observed in activating conditions whilst cleavage at Ala43 is dramatically enhanced. Mapping the photo-cleaved fragments onto crystallographic structures provides insight into the local structural changes that occur as protein unfolding progresses, which is coupled to global restructuring observed in the drift time profiles. Graphical Abstract.
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Affiliation(s)
- Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Rachelle Black
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", 00185, Rome, Italy
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - 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, UK
| | - 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, UK.
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30
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Attard TJ, Carter MD, Fang M, Johnson RC, Reid GE. Structural Characterization and Absolute Quantification of Microcystin Peptides Using Collision-Induced and Ultraviolet Photo-Dissociation Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1812-1825. [PMID: 29845563 PMCID: PMC6088756 DOI: 10.1007/s13361-018-1981-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/21/2018] [Accepted: 04/25/2018] [Indexed: 05/23/2023]
Abstract
Microcystin (MC) peptides produced by cyanobacteria pose a hepatotoxic threat to human health upon ingestion from contaminated drinking water. While rapid MC identification and quantification in contaminated body fluids or tissue samples is important for patient treatment and outcomes, conventional immunoassay-based measurement strategies typically lack the specificity required for unambiguous determination of specific MC variants, whose toxicity can significantly vary depending on their structures. Furthermore, the unambiguous identification and accurate quantitation of MC variants using tandem mass spectrometry (MS/MS)-based methods can be limited due to a current lack of appropriate stable isotope-labeled internal standards. To address these limitations, we have systematically examined here the sequence and charge state dependence to the formation and absolute abundance of both "global" and "variant-specific" product ions from representative MC-LR, MC-YR, MC-RR, and MC-LA peptides, using higher-energy collisional dissociation (HCD)-MS/MS, ion-trap collision-induced dissociation (CID)-MS/MS and CID-MS3, and 193 nm ultraviolet photodissociation (UPVD)-MS/MS. HCD-MS/MS was found to provide the greatest detection sensitivity for both global and variant-specific product ions in each of the MC variants, except for MC-YR where a variant-specific product uniquely formed via UPVD-MS/MS was observed with the greatest absolute abundance. A simple methodology for the preparation and characterization of 18O-stable isotope-labeled MC reference materials for use as internal standards was also developed. Finally, we have demonstrated the applicability of the methods developed herein for absolute quantification of MC-LR present in human urine samples, using capillary scale liquid chromatography coupled with ultra-high resolution / accurate mass spectrometry and HCD-MS/MS. Graphical abstract ᅟ.
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Affiliation(s)
- Troy J Attard
- School of Chemistry, The University of Melbourne, Melbourne, VIC, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa D Carter
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mengxuan Fang
- School of Chemistry, The University of Melbourne, Melbourne, VIC, Australia
| | - Rudolph C Johnson
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Melbourne, VIC, Australia.
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC, Australia.
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31
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Talbert LE, Julian RR. Directed-Backbone Dissociation Following Bond-Specific Carbon-Sulfur UVPD at 213 nm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1760-1767. [PMID: 29623659 PMCID: PMC6087500 DOI: 10.1007/s13361-018-1934-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 05/22/2023]
Abstract
Ultraviolet photodissociation or UVPD is an increasingly popular option for tandem-mass spectrometry experiments. UVPD can be carried out at many wavelengths, and it is important to understand how the results will be impacted by this choice. Here, we explore the utility of 213 nm photons for initiating bond-selective fragmentation. It is found that bonds previously determined to be labile at 266 nm, including carbon-iodine and sulfur-sulfur bonds, can also be cleaved with high selectivity at 213 nm. In addition, many carbon-sulfur bonds that are not subject to direct dissociation at 266 nm can be selectively fragmented at 213 nm. This capability can be used to site-specifically create alaninyl radicals that direct backbone dissociation at the radical site, creating diagnostic d-ions. Furthermore, the additional carbon-sulfur bond fragmentation capability leads to signature triplets for fragmentation of disulfide bonds. Absorption of amide bonds can enhance dissociation of nearby labile carbon-sulfur bonds and can be used for stochastic backbone fragmentation typical of UVPD experiments at shorter wavelengths. Several potential applications of the bond-selective fragmentation chemistry observed at 213 nm are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Lance E Talbert
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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32
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Mistarz UH, Bellina B, Jensen PF, Brown JM, Barran PE, Rand KD. UV Photodissociation Mass Spectrometry Accurately Localize Sites of Backbone Deuteration in Peptides. Anal Chem 2017; 90:1077-1080. [DOI: 10.1021/acs.analchem.7b04683] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ulrik H. Mistarz
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bruno Bellina
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Pernille F. Jensen
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jeffery M. Brown
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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33
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Chandler SA, Benesch JL. Mass spectrometry beyond the native state. Curr Opin Chem Biol 2017; 42:130-137. [PMID: 29288996 DOI: 10.1016/j.cbpa.2017.11.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022]
Abstract
Native mass spectrometry allows the study of proteins by probing in vacuum the interactions they form in solution. It is a uniquely useful approach for structural biology and biophysics due to the high resolution of separation it affords, allowing the concomitant interrogation of multiple protein components with high mass accuracy. At its most basic, native mass spectrometry reports the mass of intact proteins and the assemblies they form in solution. However, the opportunities for more detailed characterisation are extensive, enabled by the exquisite control of ion motion that is possible in vacuum. Here we describe recent developments in mass spectrometry approaches to the structural interrogation of proteins both in, and beyond, their native state.
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Affiliation(s)
- Shane A Chandler
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Justin Lp Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
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34
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Hale OJ, Cramer R. Collision-induced dissociation of doubly-charged barium-cationized lipids generated from liquid samples by atmospheric pressure matrix-assisted laser desorption/ionization provides structurally diagnostic product ions. Anal Bioanal Chem 2017; 410:1435-1444. [DOI: 10.1007/s00216-017-0788-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/14/2017] [Accepted: 11/24/2017] [Indexed: 01/13/2023]
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35
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Greisch JF, Chmela J, Harding ME, Wunderlich D, Schäfer B, Ruben M, Klopper W, Schooss D, Kappes MM. Correlation of the structural information obtained for europium-chelate ensembles from gas-phase photoluminescence and ion-mobility spectroscopy with density-functional computations and ligand-field theory. Phys Chem Chem Phys 2017; 19:6105-6112. [PMID: 28191564 DOI: 10.1039/c6cp04656h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a combined investigation of europium(iii)9-oxo-phenalen-1-one (PLN) coordination complexes, [Eu(PLN)4AE]+ with AE = Mg, Ca, and Sr, using gas-phase photoluminescence, trapped ion-mobility spectrometry and density-functional computations. In order to sort out the structural impact of the alkali earth dications on the photoluminescence spectra, the experimental data are compared to the predicted ligand-field splittings as well as to the collision cross-sections for different isomers of [Eu(PLN)4AE]+. The best fitting interpretation is that one isomer family predominantly contributes to the recorded luminescence. The present work demonstrates the complexity of the coordination patterns of multicenter lanthanoid chelates involved in dynamical equilibria and the pertinence of using isolation techniques to elucidate their photophysical properties.
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Affiliation(s)
- Jean-François Greisch
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Jiří Chmela
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Michael E Harding
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Dirk Wunderlich
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany.
| | - Bernhard Schäfer
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Mario Ruben
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. and Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), CNRS-Université de Strasbourg, Rue du Loess 23, BP 43, 67034 Strasbourg Cedex 2, France
| | - Wim Klopper
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. and Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Detlef Schooss
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. and Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. and Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
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36
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Egorov D, Hoekstra R, Schlathölter T. A comparative VUV absorption mass-spectroscopy study on protonated peptides of different size. Phys Chem Chem Phys 2017; 19:20608-20618. [DOI: 10.1039/c7cp03203j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The response of gas-phase peptides upon vacuum ultraviolet absorption depends strongly on the peptide size.
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Affiliation(s)
- D. Egorov
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
| | - R. Hoekstra
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
| | - T. Schlathölter
- Zernike Institute for Advanced Materials
- University of Groningen
- 9747AG Groningen
- The Netherlands
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