1
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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2
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Hellinger J, Brodbelt JS. Impact of Charge State on Characterization of Large Middle-Down Sized Peptides by Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1647-1656. [PMID: 39013103 DOI: 10.1021/jasms.3c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Fragmentation trends of large peptides were characterized by five activation methods, including HCD, ETD, EThcD, 213 nm UVPD, and 193 nm UVPD. Sequence coverages and scores were assessed based on charge site, peptide sequence, and peptide size. The effect of charge state and peptide size on sequence coverage was explored for a Glu-C digest of E. coli ribosomal proteins, and linear regression analysis of the collection of peptides indicated that HCD, ETD, and EThcD have a higher dependence charge state than 193 and 213 nm UV. Four model peptides, neuromedin, glucagon, galanin, and amyloid β, were characterized in greater detail based on charge site analysis and showed a charge state dependence on sequence coverage for collision and electron-based activation methods.
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Affiliation(s)
- Jessica Hellinger
- 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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3
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Jiang Y, Rex DAB, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Mayta ML, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry. ARXIV 2023:arXiv:2311.07791v1. [PMID: 38013887 PMCID: PMC10680866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department of Computational Biomedicine, Cedars Sinai Medical Center
| | - Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical Sciences Division, National Institute of Standards and Technology, NIST Charleston · Funded by NIST
| | - Germán L. Rosano
- Mass Spectrometry Unit, Institute of Molecular and Cellular Biology of Rosario, Rosario, Argentina · Funded by Grant PICT 2019-02971 (Agencia I+D+i)
| | - Norbert Volkmar
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California, USA
| | | | - Susan B. Egbert
- Department of Chemistry, University of Manitoba, Winnipeg, Cananda
| | - Simion Kreimer
- Smidt Heart Institute, Cedars Sinai Medical Center; Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center
| | - Emma H. Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Oliver M. Crook
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute · Funded by Grant BT/PR16456/BID/7/624/2016 (Department of Biotechnology, India); Grant Translational Research Program (TRP) at THSTI funded by DBT
| | - Muralidharan Vanuopadath
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam-690 525, Kerala, India · Funded by Department of Health Research, Indian Council of Medical Research, Government of India (File No.R.12014/31/2022-HR)
| | - Martín L. Mayta
- School of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martín 3103, Argentina; Molecular Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department of Chemistry, University of Washington · Funded by Summer Research Acceleration Fellowship, Department of Chemistry, University of Washington
| | - Nicholas M. Riley
- Department of Chemistry, University of Washington · Funded by National Institutes of Health Grant R00 GM147304
| | - Robert L. Moritz
- Institute for Systems biology, Seattle, WA, USA, 98109 · Funded by National Institutes of Health Grants R01GM087221, R24GM127667, U19AG023122, S10OD026936; National Science Foundation Award 1920268
| | - Jesse G. Meyer
- Department of Computational Biomedicine, Cedars Sinai Medical Center · Funded by National Institutes of Health Grant R21 AG074234; National Institutes of Health Grant R35 GM142502
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4
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Kolbowski L, Belsom A, Pérez-López AM, Ly T, Rappsilber J. Light-Induced Orthogonal Fragmentation of Crosslinked Peptides. JACS AU 2023; 3:2123-2130. [PMID: 37654600 PMCID: PMC10466327 DOI: 10.1021/jacsau.3c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Crosslinking mass spectrometry provides pivotal information on the structure and interaction of proteins. MS-cleavable crosslinkers are regarded as a cornerstone for the analysis of complex mixtures. Yet they fragment under similar conditions as peptides, leading to mixed fragmentation spectra of the crosslinker and peptide. This hampers selecting individual peptides for their independent identification. Here, we introduce orthogonal cleavage using ultraviolet photodissociation (UVPD) to increase crosslinker over peptide fragmentation. We designed and synthesized a crosslinker that can be cleaved at 213 nm in a commercial mass spectrometer configuration. In an analysis of crosslinked Escherichia coli lysate, the crosslinker-to-peptide fragment intensity ratio increases from nearly 1 for a conventionally cleavable crosslinker to 5 for the UVPD-cleavable crosslinker. This largely increased the sensitivity of selecting the individual peptides for MS3, even more so with an improved doublet detection algorithm. Data are available via ProteomeXchange with identifier PXD040267.
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Affiliation(s)
- Lars Kolbowski
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
| | - Adam Belsom
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
| | - Ana M. Pérez-López
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
| | - Tony Ly
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
| | - Juri Rappsilber
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
- Si-M/″Der
Simulierte Mensch″, a Science Framework of Technische Universität
Berlin and Charité - Universitätsmedizin Berlin, 10623 Berlin, Germany
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5
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Lanzillotti M, Brodbelt JS. Comparison of Top-Down Protein Fragmentation Induced by 213 and 193 nm UVPD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:279-285. [PMID: 36594540 DOI: 10.1021/jasms.2c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The growing interest in advancing tandem mass spectrometry strategies for top-down proteomics has motivated efforts to optimize ion activation strategies for intact proteins, including the comparison of 193 and 213 nm wavelengths for ultraviolet photodissociation (UVPD). The present study focuses on the performance and outcomes of UVPD for five proteins, ubiquitin, cytochrome C, frataxin, myoglobin, and carbonic anhydrase, with an emphasis on evaluating the similarities and differences in fragmentation promoted by UVPD using 193 nm versus 213 nm photons. Mass spectra were collected as a function of the number of laser pulses, and precursor depletion levels were monitored and controlled to provide consistent energy deposition between 213 and 193 nm UVPD. Fragment ions were confirmed on the basis of their isotopic distributions in m/z space to preserve both charge state and abundance information and were classified on the basis of ion type and frequency. A large portion of the total fragment ion abundance was attributable to preferential cleavages, particularly ones adjacent to proline residues. These cleavages were examined on the basis of the backbone site and abundances, revealing that a and y-2 ions N-terminal to proline residues appeared at disproportionately high abundances in 213 nm UVPD spectra as compared to 193 nm UVPD spectra, highlighting one notable difference in the top-down spectra. We theorize that these fragments are formed more efficiently in 213 nm UVPD than in 193 nm UVPD due to increased absorption of 213 nm photons at the proline amide bond.
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Affiliation(s)
- Michael Lanzillotti
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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6
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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: 27] [Impact Index Per Article: 9.0] [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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7
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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: 0.8] [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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8
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Pandeswari PB, Chary RN, Kamalanathan AS, Prabhakar S, Sabareesh V. Mimicking LysC Proteolysis by 'Arginine-Modification-cum-Trypsin digestion': Comparison of Bottom-Up & Middle-Down Proteomic Approaches by ESI-QTOF-MS. Protein Pept Lett 2021; 28:1379-1390. [PMID: 34587878 DOI: 10.2174/0929866528666210929163307] [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: 02/23/2021] [Revised: 07/04/2021] [Accepted: 08/09/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Middle-down (MD) proteomics is an emerging approach for reliable identification of post- translational modifications and isoforms, as this approach focuses on proteolytic peptides containing > 25 - 30 amino acid residues (a.a.r.), which are longer than typical tryptic peptides. Such longer peptides can be obtained by AspN, GluC, LysC proteases. Additionally, some special proteases were developed specifically to effect MD approach, e.g., OmpT, Sap9, etc. However, these proteases are expensive. Herein we report a cost-effective strategy, 'arginine modification-cum trypsin digestion', which can produce longer tryptic peptides resembling LysC peptides derived from proteins. OBJECTIVE To obtain proteolytic peptides that resemble LysC peptides, by using 'trypsin', which is an less expensive protease. METHODS This strategy is based on the simple principle that trypsin cannot act at the C-termini of those arginines in proteins, whose sidechain guanidine groups are modified by 1,2-cyclohexanedione or phenylglyoxal. RESULTS As a proof of concept, we demonstrate this strategy on four models: β-casein (bovine), β- lactoglobulin (bovine), ovalbumin (chick) and transferrin (human), by electrospray ionization-mass spectrometry (ESI-MS) involving hybrid quadrupole time-of-flight. From the ESI-MS of these models, we obtained several arginine modified tryptic peptides, whose lengths are in the range, 30 - 60 a.a.r. The collision-induced dissociation MS/MS characteristics of some of the arginine modified longer tryptic peptides are compared with the unmodified standard tryptic peptides. CONCLUSION The strategy followed in this proof-of-concept study, not only helps in obtaining longer tryptic peptides that mimic LysC proteolytic peptides, but also facilitates in enhancing the probability of missed cleavages by the trypsin. Hence, this method aids in evading the possibility of obtaining very short peptides that are < 5 - 10 a.a.r. Therefore, this is indeed an cost-effective alternative/substitute for LysC proteolysis and in turn, for those MD proteomic studies that utilize LysC. Additionally, this methodology can be fruitful for mass spectrometry based de novo protein and peptide sequencing.
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Affiliation(s)
- P Boomathi Pandeswari
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu - 632014. India
| | - R Nagarjuna Chary
- Centre for Mass Spectrometry, Department of Analytical & Structural Chemistry, CSIR - Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana - 500007. India
| | - A S Kamalanathan
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu - 632014. India
| | - Sripadi Prabhakar
- Centre for Mass Spectrometry, Department of Analytical & Structural Chemistry, CSIR - Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana - 500007. India
| | - Varatharajan Sabareesh
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu - 632014. India
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9
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Becher S, Wang H, Leeming MG, Donald WA, Heiles S. Influence of protein ion charge state on 213 nm top-down UVPD. Analyst 2021; 146:3977-3987. [PMID: 34009215 DOI: 10.1039/d1an00571e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultraviolet photodissociation (UVPD) is a powerful and rapidly developing method in top-down proteomics. Sequence coverages can exceed those obtained with collision- and electron-induced fragmentation methods. Because of the recent interest in UVPD, factors that influence protein fragmentation and sequence coverage are actively debated in the literature. Here, we performed top-down 213 nm UVPD experiments on a 7 T Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for the model proteins ubiquitin, myoglobin and cytochrome c that were electrosprayed from native, denaturing and supercharging solutions in order to investigate the effect of protein charge states on UVPD fragments. By performing UVPD in ultrahigh vacuum, factors associated with collisional cooling and any ion activation during transfer between mass analyzers can be largely eliminated. Sequence coverage increased from <10% for low charge states to >60% for high charge states for all three proteins. This trend is influenced by the overall charge state, i.e., charges per number of amino acid residues, and to a lesser degree by associated structural changes of protein ions of different charge states based on comparisons to published collision-cross section measurements. To rationalize this finding, and correlate sequence ion formation and identity with the number and location of protons, UVPD results were compared to protonation sites predicted based on electrostatic modelling. Assuming confined protonation sites, these results indicate the presence of two general fragmentation types; i.e., charge remote and charge directed. For moderately high protein charge states, fragment ions mostly originate in regions between likely protonation sites (charge remote), whereas sequence ions of highly charge protein ions occur either near backbone amide protonation sites at low-basicity residues (charge directed) or at charge remote sites (i.e., high-basicity residues). Overall, our results suggest that top-down 213 UVPD performance in the zero-pressure limit depends strongly on protein charge states and protonation sites can influence the location of backbone cleavages.
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Affiliation(s)
- Simon Becher
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
| | - Huixin Wang
- Mark Wainwright Analytical Centre, University of New South Wales, New South Wales, Australia
| | - Michael G Leeming
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
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10
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Modzel M, Wollenberg DTW, Trelle MB, Larsen MR, Jørgensen TJD. Ultraviolet Photodissociation of Protonated Peptides and Proteins Can Proceed with H/D Scrambling. Anal Chem 2021; 93:691-696. [PMID: 33295747 DOI: 10.1021/acs.analchem.0c02957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet photodissociation (UVPD) has recently been introduced as an ion activation method for the determination of single-residue deuterium levels in H/D exchange tandem mass spectrometry experiments. In this regard, it is crucial to know which fragment ion types can be utilized for this purpose. UVPD yields rich product ion spectra where all possible backbone fragment ion types (a/x, b/y, and c/z) are typically observed. Here we provide a detailed investigation of the level of H/D scrambling for all fragment ion types upon UVPD of the peptide scrambling probe P1 (HHHHHHIIKIIK) using an Orbitrap tribrid mass spectrometer equipped with a solid-state 213 nm UV laser. The most abundant UVPD-generated fragment ions (i.e., b/y ions) exhibit extensive H/D scrambling. Similarly, a/x and c/z ions have also undergone H/D scrambling due to UV-induced heating of the precursor ion population. Therefore, dominant b/y ions upon UVPD of protonated peptides are a strong indicator for the occurrence of extensive H/D scrambling of the precursor ion population. In contrast to peptide P1, UV-irradiation of ubiquitin did not induce H/D scrambling in the nonfragmented precursor ion population. However, the UVPD-generated b2 and a4 ions from ubiquitin exhibit extensive H/D scrambling. To minimize H/D scrambling, short UV-irradiation time and high gas pressures are recommended.
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Affiliation(s)
- Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.,Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Daniel T Weltz Wollenberg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.,Novozymes A/S, Krogshøjvej 36, Bagsværd 2880, Denmark
| | - Morten Beck Trelle
- Department of Clinical Biochemistry, Svendborg Hospital, Baagøes Allé 15, SVB Building 17.01, 5700 Svendborg, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
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