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Rahman M, Marzullo BP, Lam PY, Barrow MP, Holman SW, Ray AD, O'Connor PB. Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS. Analyst 2024; 149:4687-4701. [PMID: 39101388 PMCID: PMC11382339 DOI: 10.1039/d4an00484a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Antisense oligonucleotides (ASOs) are crucial for biological applications as they bind to complementary RNA sequences, modulating protein expression. ASOs undergo synthetic modifications like phosphorothioate (PS) backbone and locked nucleic acid (LNA) to enhance stability and specificity. Tandem mass spectrometry (MS) techniques were employed to study gapmer ASOs, which feature a DNA chain within RNA segments at both termini, revealing enhanced cleavages with ultraviolet photodissociation (UVPD) and complementary fragment ions from collision-induced dissociation (CID) and electron detachment dissociation (EDD). 2DMS, a data-independent analysis technique, allowed for comprehensive coverage and identification of shared fragments across multiple precursor ions. EDD fragmentation efficiency correlated with precursor ion charge states, with higher charges facilitating dissociation due to intramolecular repulsions. An electron energy of 22.8 eV enabled electron capture and radical-based cleavage. Accumulating multiple scans and generating average spectra improved signal intensity, aided by denoising algorithms. Data analysis utilised a custom Python script capable of handling modifications and generating unique mass lists.
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Affiliation(s)
- Mohammed Rahman
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Bryan P Marzullo
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Pui Yiu Lam
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, AstraZeneca, SK10 2NA, UK
| | - Andrew D Ray
- New Modalities & Parental Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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2
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Girod M, Arquier D, Helms A, Juetten K, Brodbelt JS, Lemoine J, MacAleese L. Characterization of Phosphorylated Peptides by Electron-Activated and Ultraviolet Dissociation Mass Spectrometry: A Comparative Study with Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1040-1054. [PMID: 38626331 PMCID: PMC11382297 DOI: 10.1021/jasms.4c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Mass-spectrometry-based methods have made significant progress in the characterization of post-translational modifications (PTMs) in peptides and proteins; however, room remains to improve fragmentation methods. Ideal MS/MS methods are expected to simultaneously provide extensive sequence information and localization of PTM sites and retain labile PTM groups. This collection of criteria is difficult to meet, and the various activation methods available today offer different capabilities. In order to examine the specific case of phosphorylation on peptides, we investigate electron transfer dissociation (ETD), electron-activated dissociation (EAD), and 193 nm ultraviolet photodissociation (UVPD) and compare all three methods with classical collision-induced dissociation (CID). EAD and UVPD show extensive backbone fragmentation, comparable in scope to that of CID. These methods provide diverse backbone fragmentation, producing a/x, b/y, and c/z ions with substantial sequence coverages. EAD displays a high retention efficiency of the phosphate modification, attributed to its electron-mediated fragmentation mechanisms, as observed in ETD. UVPD offers reasonable retention efficiency, also allowing localization of the PTM site. EAD experiments were also performed in an LC-MS/MS workflow by analyzing phosphopeptides spiked in human plasma, and spectra allow accurate identification of the modified sites and discrimination of isomers. Based on the overall performance, EAD and 193 nm UVPD offer alternative options to CID and ETD for phosphoproteomics.
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Affiliation(s)
- Marion Girod
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Delphine Arquier
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle Juetten
- 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
| | - Jérôme Lemoine
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Luke MacAleese
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, F-69100 Villeurbanne, France
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3
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Carrick IJ, Fabijanczuk KC, Rong J, McLuckey SA. Tandem mass spectrometry using continuous-wave infrared multiphoton dissociation in an electrostatic linear ion trap. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9698. [PMID: 38356088 DOI: 10.1002/rcm.9698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/16/2024]
Abstract
RATIONALE The electrostatic linear ion trap (ELIT) can be operated as a multi-reflection time-of-flight (MR-TOF) or Fourier transform (FT) mass analyzer. It has been shown to be capable of performing high-resolution mass analysis and high-resolution ion isolations. Although it has been used in charge-detection mass spectrometry (CDMS), it has not been widely used as a conventional mass spectrometer for ensemble measurements of ions, or for tandem mass spectrometer. The advantages of tandem mass spectrometer with high-resolution ion isolations in the ELIT have thus not been fully exploited. METHODS A homebuilt ELIT was modified with BaF2 viewports to facilitate transmission of a laser beam at the turnaround point of the second ion mirror in the ELIT. Fragmentation that occurs at the turnaround point of these ion mirrors should result in minimal energy partitioning due to the low kinetic energy of ions at these points. The laser was allowed to irradiate ions for a period of many oscillations in the ELIT. RESULTS Due to the low energy absorption of gas-phase ions during each oscillation in the ELIT, fragmentation was found to occur over a range of oscillations in the ELIT generating a homogeneous ion beam. A mirror-switching pulse is shown to create time-varying perturbations in this beam that oscillate at the fragment ion characteristic frequencies and generate a time-domain signal. This was found to recover FT signal for protonated pYGGFL and pSGGFL precursor ions. CONCLUSIONS Fragmentation at the turnaround point of an ELIT by continuous-wave infrared multiphoton dissociation (cw-IRMPD) is demonstrated. In cases where laser power absorption is low and fragmentation occurs over many laps, a mirror-switching pulse may be used to recover varying time-domain signal. The combination of laser activation at the turnaround points and mirror-switching isolation allows for tandem MS in the ELIT.
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Affiliation(s)
- Ian J Carrick
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Jiayue Rong
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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4
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Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
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Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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5
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Bashyal A, Hui JO, Flick T, Dykstra AB, Zhang Q, Campuzano IDG, Brodbelt JS. Differentiation of Aspartic and Isoaspartic Acid Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2023; 95:11510-11517. [PMID: 37458293 PMCID: PMC10588209 DOI: 10.1021/acs.analchem.3c02025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Spontaneous conversion of aspartic acid (Asp) to isoaspartic acid (isoAsp) is a ubiquitous modification that influences the structure and function of proteins. This modification of Asp impacts the stability of biotherapeutics and has been linked to the development of neurodegenerative diseases. We explored the use of 193 nm ultraviolet photodissociation (UVPD) to distinguish Asp and isoAsp in the protonated and deprotonated peptides. The differences in the relative abundances of several fragment ions uniquely generated by UVPD were used to differentiate isomeric peptide standards containing Asp or isoAsp. These fragment ions result from the cleavage of bonds N-terminal to Asp/isoAsp residues in addition to the side-chain losses from Asp/isoAsp or the losses of COOH, CO2, CO, or H2O from y-ions. Fragmentation of Asp-containing tryptic peptides using UVPD resulted in more enhanced w/w + 1/y - 1/x ions, while isoAsp-containing peptides yielded more enhanced y - 18/y - 45/y - 46 ions. UVPD was also used to identify an isomerized peptide from a tryptic digest of a monoclonal antibody. Moreover, UVPD of a protonated nontryptic peptide resulted in more enhanced y ions N- and C-terminal to isoAsp and differences in b/y ion ratios that were used to identify the isoAsp peptide.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - John O Hui
- Amgen Research, Molecular Analytics, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Tawnya Flick
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Andrew B Dykstra
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Qingchun Zhang
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Amgen Research, Molecular Analytics, Amgen Inc., Thousand Oaks, California 91320, 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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Theisen A, Wootton CA, Haris A, Morgan TE, Lam YPY, Barrow MP, O’Connor PB. Enhancing Biomolecule Analysis and 2DMS Experiments by Implementation of (Activated Ion) 193 nm UVPD on a FT-ICR Mass Spectrometer. Anal Chem 2022; 94:15631-15638. [DOI: 10.1021/acs.analchem.2c02354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Anisha Haris
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Tomos E. Morgan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Yuko P. Y. Lam
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark P. Barrow
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Peter B. O’Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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7
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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: 21] [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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8
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Edwards HM, Wu HT, Julian RR, Jackson GP. Differentiation of leucine and isoleucine residues in peptides using charge transfer dissociation mass spectrometry (CTD-MS). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9246. [PMID: 34927767 DOI: 10.1002/rcm.9246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
RATIONALE The function of a protein or the binding affinity of an antibody can be substantially altered by the replacement of leucine (Leu) with isoleucine (Ile), and vice versa, so the ability to identify the correct isomer using mass spectrometry can help resolve important biological questions. Tandem mass spectrometry approaches for Leu/Ile (Xle) discrimination have been developed, but they all have certain limitations. METHODS Four model peptides and two wild-type peptide sequences containing either Leu or Ile residues were subjected to charge transfer dissociation (CTD) mass spectrometry on a modified three-dimensional ion trap. The peptides were analyzed in both the 1+ and 2+ charge states, and the results were compared to conventional collision-induced dissociation spectra of the same peptides obtained using the same instrument. RESULTS CTD resulted in 100% sequence coverage for each of the studied peptides and provided a variety of side-chain cleavages, including d, w and v ions. Using CTD, reliable d and w ions of Xle residues were observed more than 80% of the time. When present, d ions are typically greater than 10% of the abundance of the corresponding a ions from which they derive, and w ions are typically more abundant than the z ions from which they derive. CONCLUSIONS CTD has the benefit of being applicable to both 1+ and 2+ precursor ions, and the overall performance is comparable to that of other high-energy activation techniques like hot electron capture dissociation and UV photodissociation. CTD does not require chemical modifications of the precursor peptides, nor does it require additional levels of isolation and fragmentation.
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Affiliation(s)
- Halle M Edwards
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, USA
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9
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Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics 2021; 18:795-807. [PMID: 34652972 DOI: 10.1080/14789450.2021.1994390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Protein phosphorylation is a primary mechanism of signal transduction in cellular systems. Isobaric tagging can be used to investigate alterations in phosphorylation events in sample multiplexing experiments where quantification extends across all conditions. As such, innovations in tandem mass tag methods can facilitate the expansion of the depth and breadth of phosphoproteomic analyses. AREAS COVERED This review discusses the current state of tandem mass tag-centric phosphoproteomics and highlights advances in reagent chemistry, instrumentation, data acquisition, and data analysis. We stress that approaches for phosphoproteomic investigations require high-specificity enrichment, sensitive detection, and accurate phosphorylation site localization. EXPERT OPINION Tandem mass tag-centric phosphoproteomics will continue to be an important conduit for our understanding of signal transduction in living organisms. We anticipate that progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in analytical strategies will be key to the discovery of biologically relevant findings from phosphoproteomics studies.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
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10
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Evaluating the Performance of 193 nm Ultraviolet Photodissociation for Tandem Mass Tag Labeled Peptides. ANALYTICA 2021. [DOI: 10.3390/analytica2040014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite the successful application of tandem mass tags (TMT) for peptide quantitation, missing reporter ions in higher energy collisional dissociation (HCD) spectra remains a challenge for consistent quantitation, especially for peptides with labile post-translational modifications. Ultraviolet photodissociation (UVPD) is an alternative ion activation method shown to provide superior coverage for sequencing of peptides and intact proteins. Here, we optimized and evaluated 193 nm UVPD for the characterization of TMT-labeled model peptides, HeLa proteome, and N-glycopeptides from model proteins. UVPD yielded the same TMT reporter ions as HCD, at m/z 126–131. Additionally, UVPD produced a wide range of fragments that yielded more complete characterization of glycopeptides and less frequent missing TMT reporter ion channels, whereas HCD yielded a strong tradeoff between characterization and quantitation of TMT-labeled glycopeptides. However, the lower fragmentation efficiency of UVPD yielded fewer peptide identifications than HCD. Overall, 193 nm UVPD is a valuable tool that provides an alternative to HCD for the quantitation of large and highly modified peptides with labile PTMs. Continued development of instrumentation specific to UVPD will yield greater fragmentation efficiency and fulfil the potential of UVPD to be an all-in-one spectrum ion activation method for broad use in the field of proteomics.
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11
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Watts E, Potts GK, Ready DB, George Thompson AM, Lee J, Escobar EE, Patterson MJ, Brodbelt JS. Characterization of HLA-A*02:01 MHC Immunopeptide Antigens Enhanced by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2021; 93:13134-13142. [PMID: 34553926 DOI: 10.1021/acs.analchem.1c01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying major histocompatibility complex (MHC) class I immunopeptide antigens represents a key step in the development of immune-based targeted therapeutics and vaccines. However, the complete characterization of these antigens by tandem mass spectrometry remains challenging due to their short sequence length, high degree of hydrophobicity, and/or lack of sufficiently basic amino acids. This study seeks to address the potential for 193 nm ultraviolet photodissociation (UVPD) to improve the analysis of MHC class I immunopeptides by offering enhanced characterization of these sequences in lower charge states and differentiation of prominent isomeric leucine and isoleucine residues in the HLA-A*02:01 motif. Although electron transfer dissociation-higher energy collisional dissociation (EThcD) offered some success in the differentiation of leucine and isoleucine, 193 nm UVPD was able to confirm the identity of nearly 60% of leucine and isoleucine residues in a synthetic peptide mixture. Furthermore, 193 nm UVPD led to significantly more peptide identifications and higher scoring metrics than EThcD for peptides obtained from immunoprecipitation of MHC class I immunopeptides from in vitro cell culture. Additionally, 193 nm UVPD represents a promising complementary technique to higher-energy collisional dissociation (HCD), in which 424 of the 2593 peptides identified by 193 nm UVPD were not identified by HCD in HLA-A*02:01-specific immunoprecipitation and 804 of the 3300 peptides identified by 193 nm UVPD were not identified by HCD for pan HLA-A, -B, and -C immunoprecipitation. These results highlight that 193 nm UVPD offers an option for the characterization of immunopeptides, including differentiation of leucine and isoleucine residues.
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Affiliation(s)
- Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | - Gregory K Potts
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Damien B Ready
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | | | - Janice Lee
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | | | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
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12
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LeBlanc BM, Moreno RY, Escobar EE, Venkat Ramani MK, Brodbelt JS, Zhang Y. What's all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry. RSC Chem Biol 2021; 2:1084-1095. [PMID: 34458825 PMCID: PMC8341212 DOI: 10.1039/d1cb00083g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and its phosphorylation state are critically important in regulating transcription in vivo. Early methods of identifying phosphorylation on the CTD heptad were plagued by issues of low specificity and ambiguous signals. However, advancements in the field of mass spectrometry (MS) have presented the opportunity to gain new insights into well-studied processes as well as explore new frontiers in transcription. By using MS, residues which are modified within the CTD heptad and across repeats are now able to be pinpointed. Likewise, identification of kinase and phosphatase specificity towards residues of the CTD has reached a new level of accuracy. Now, MS is being used to investigate the crosstalk between modified residues of the CTD and may be a critical technique for understanding how phosphorylation plays a role in the new LLPS model of transcription. Herein, we discuss the development of various MS techniques and evaluate their capabilities. By highlighting the pros and cons of each technique, we aim to provide future investigators with a comprehensive overview of how MS can be used to investigate the complexities of RNAP-II mediated transcription.
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Affiliation(s)
- Blase M LeBlanc
- Department of Molecular Biosciences, University of Texas Austin USA
| | - R Yvette Moreno
- Department of Molecular Biosciences, University of Texas Austin USA
| | | | | | | | - Yan Zhang
- Department of Molecular Biosciences, University of Texas Austin USA
- Institute of Cellular and Molecular Biology, University of Texas Austin USA
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13
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Escobar EE, Venkat Ramani MK, Zhang Y, Brodbelt JS. Evaluating Spatiotemporal Dynamics of Phosphorylation of RNA Polymerase II Carboxy-Terminal Domain by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2021; 143:8488-8498. [PMID: 34053220 DOI: 10.1021/jacs.1c03321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The critical role of site-specific phosphorylation in eukaryotic transcription has motivated efforts to decipher the complex phosphorylation patterns exhibited by the carboxyl-terminal domain (CTD) of RNA polymerase II. Phosphorylation remains a challenging post-translational modification to characterize by mass spectrometry owing to the labile phosphate ester linkage and low stoichiometric prevalence, two features that complicate analysis by high-throughput MS/MS methods. Identifying phosphorylation sites represents one significant hurdle in decrypting the CTD phosphorylation, a problem exaggerated by a large number of potential phosphorylation sites. An even greater obstacle is decoding the dynamic phosphorylation pattern along the length of the periodic CTD sequence. Ultraviolet photodissociation (UVPD) is a high-energy ion activation method that provides ample backbone cleavages of peptides while preserving labile post-translational modifications that facilitate their confident localization. Herein, we report a quantitative parallel reaction monitoring (PRM) method developed to monitor spatiotemporal changes in site-specific Ser5 phosphorylation of the CTD by cyclin-dependent kinase 7 (CDK7) using UVPD for sequence identification, phosphosite localization, and differentiation of phosphopeptide isomers. We capitalize on the series of phospho-retaining fragment ions produced by UVPD to create unique transition lists that are pivotal for distinguishing the array of phosphopeptides generated from the CTD.
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14
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Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics 2021; 21:e2000140. [PMID: 33455035 DOI: 10.1002/pmic.202000140] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
Eukaryotic protein phosphorylation modulates nearly every major biological process. Phosphorylation regulates protein activity, mediates cellular signal transduction, and manipulates cellular structure. Consequently, the dysregulation of kinase and phosphatase pathways has been linked to a multitude of diseases. Mass spectrometry-based proteomic techniques are increasingly used for the global interrogation of perturbations in phosphorylation-based cellular signaling. Strategies for studying phosphoproteomes require high-specificity enrichment, sensitive detection, and accurate localization of phosphorylation sites with advanced LC-MS/MS techniques and downstream informatics. Sample multiplexing with isobaric tags has also been integral to recent advancements in throughput and sensitivity for phosphoproteomic studies. Each of these facets of phosphoproteomics analysis present distinct challenges and thus opportunities for improvement and innovation. Here, we review current methodologies, explore persistent challenges, and discuss the outlook for isobaric tag-based quantitative phosphoproteomic analysis.
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Affiliation(s)
- Joao A Paulo
- Harvard Medical School, Boston, Massachusetts, USA
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15
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Sun B, Liu Z, Fang X, Wang X, Lai C, Liu L, Xiao C, Jiang Y, Wang F. Improving the performance of proteomic analysis via VAILase cleavage and 193-nm ultraviolet photodissociation. Anal Chim Acta 2021; 1155:338340. [PMID: 33766312 DOI: 10.1016/j.aca.2021.338340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/27/2021] [Accepted: 02/16/2021] [Indexed: 10/22/2022]
Abstract
Further improving the proteomic identification coverage and reliability is still challenging in the mass spectrometry (MS)-based proteomics. Herein, we combine VAILase and trypsin digestion with 193-nm ultraviolet photodissociation (UVPD) and higher-energy collision dissociation (HCD) to improve the performance of bottom-up proteomics. As VAILase exhibits high complementarity to trypsin, the proteome sequence coverage is improved obviously whether with HCD or 193-nm UVPD. The high diversity of fragment ion types produced by UVPD contributes to the improvements of identification reliability for both trypsin- and VAILase-digested peptides with an average XCorr score improvement of 10%.
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Affiliation(s)
- Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiang Fang
- National Institute of Metrology, Beijing, 100013, China
| | - Xiaolei Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, 116023, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Liu
- School of Life Sciences, Anhui University, 230601, Hefei, Anhui, China
| | - Chunlei Xiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, 116023, China.
| | - You Jiang
- National Institute of Metrology, Beijing, 100013, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Mehaffey MR, Ahn YC, Rivera DD, Thomas PW, Cheng Z, Crowder MW, Pratt RF, Fast W, Brodbelt JS. Elusive structural changes of New Delhi metallo-β-lactamase revealed by ultraviolet photodissociation mass spectrometry. Chem Sci 2020; 11:8999-9010. [PMID: 34123154 PMCID: PMC8163344 DOI: 10.1039/d0sc02503h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We use mass spectrometry (MS), under denaturing and non-denaturing solution conditions, along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation. Mapping changes in the abundances and distributions of fragment ions enables sensitive detection of structural alterations throughout the protein. Binding of three covalent inhibitors was characterized: a pentafluorphenyl ester, an O-aryloxycarbonyl hydroxamate, and ebselen. The first two inhibitors modify Lys211 and maintain dizinc binding, although the pentafluorophenyl ester is not selective (Lys214 and Lys216 are also modified). Ebselen reacts with the sole Cys (Cys208) and ejects Zn2 from the active site. For each inhibitor, native UVPD-MS enabled simultaneous detection of the closing of a substrate-binding beta-hairpin loop, identification of covalently-modified residue(s), reporting of the metalation state of the enzyme, and in the case of ebselen, observation of the induction of partial disorder in the C-terminus of the protein. Owing to the ability of native UVPD-MS to track structural changes and metalation state with high sensitivity, we further used this method to evaluate the impact of mutations found in NDM clinical variants. Changes introduced by NDM-4 (M154L) and NDM-6 (A233V) are revealed to propagate through separate networks of interactions to direct zinc ligands, and the combination of these two mutations in NDM-15 (M154L, A233V) results in additive as well as additional structural changes. Insight from UVPD-MS helps to elucidate how distant mutations impact zinc affinity in the evolution of this antibiotic resistance determinant. UVPD-MS is a powerful tool capable of simultaneous reporting of ligand binding, conformational changes and metalation state of NDM, revealing structural aspects of ligand recognition and clinical variants that have proven difficult to probe. We use mass spectrometry (MS) along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation.![]()
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Dann D Rivera
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Pei W Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - R F Pratt
- Department of Chemistry, Wesleyan University Middletown CT 06459 USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
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17
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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: 160] [Impact Index Per Article: 32.0] [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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18
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Maitre P, Scuderi D, Corinti D, Chiavarino B, Crestoni ME, Fornarini S. Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications. Chem Rev 2019; 120:3261-3295. [PMID: 31809038 DOI: 10.1021/acs.chemrev.9b00395] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.
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Affiliation(s)
- Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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19
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Mukherjee S, Fang M, Kok WM, Kapp EA, Thombare VJ, Huguet R, Hutton CA, Reid GE, Roberts BR. Establishing Signature Fragments for Identification and Sequencing of Dityrosine Cross-Linked Peptides Using Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2019; 91:12129-12133. [DOI: 10.1021/acs.analchem.9b02986] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Soumya Mukherjee
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mengxuan Fang
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - W. Mei Kok
- University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
| | - Eugene A. Kapp
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Varsha J. Thombare
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Craig A. Hutton
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Gavin E. Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Blaine R. Roberts
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
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20
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Bailey LS, Alves M, Galy N, Patrick AL, Polfer NC. Mechanistic insights into intramolecular phosphate group transfer during collision induced dissociation of phosphopeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:449-458. [PMID: 30860300 DOI: 10.1002/jms.4351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/22/2019] [Accepted: 03/04/2019] [Indexed: 05/28/2023]
Abstract
We report on the rearrangement chemistry of model phosphorylated peptides during collision-induced dissociation (CID), where intramolecular phosphate group transfers are observed from donor to acceptor residues. Such "scrambling" could result in inaccurate modification localization, potentially leading to misidentifications. Systematic studies presented herein provide mechanistic insights for the unusually high phosphate group rearrangements presented some time ago by Reid and coworkers (Proteomics 2013, 13 [6], 964-973). It is postulated here that a basic residue like histidine can play a key role in mediating the phosphate group transfer by deprotonating the serine acceptor site. The proposed mechanism is consistent with the observation that fast collisional activation by collision-cell CID and higher-energy collisional dissociation (HCD) can shut down rearrangement chemistry. Additionally, the rearrangement chemistry is highly dependent on the charge state of the peptide, mirroring previous studies that less rearrangement is observed under mobile proton conditions.
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Affiliation(s)
- Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Mélanie Alves
- Département de chimie, UFR 926, Sorbonne Université, Paris, France
| | - Nicolas Galy
- Département de chimie, Université Paul Sabatier, Toulouse, France
| | - Amanda L Patrick
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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21
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Liu Z, Wang R, Liu J, Sun R, Wang F. Global Quantification of Intact Proteins via Chemical Isotope Labeling and Mass Spectrometry. J Proteome Res 2019; 18:2185-2194. [PMID: 30990045 DOI: 10.1021/acs.jproteome.9b00071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although thousands of intact proteins have been feasibly identified in recent years, global quantification of intact proteins is still challenging. Herein, we develop a high-throughput strategy for global intact protein quantification based on chemical isotope labeling. The isotope incorporation efficiency is as high as 99.2% for complex intact protein samples extracted from HeLa cells. Further, the pTop 2.0 software is developed for automated quantification of intact proteoforms in a high-throughput manner. The high quantification accuracy and reproducibility of this strategy have been demonstrated for both standard and complex cellular protein samples. A total of 2283 intact proteoforms originated from 660 protein accessions are successfully quantified under anaerobic and aerobic conditions and the differentially expressed proteins are observed to be involved in the important biological processes such as stress response.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , 116023 , China
| | - Ruimin Wang
- Institute of Computing Technology , Chinese Academy of Sciences , Beijing , 100190 , China
| | - Jing Liu
- College of Pharmacy , Dalian Medical University , Dalian , 116044 , China
| | - Ruixiang Sun
- Institute of Computing Technology , Chinese Academy of Sciences , Beijing , 100190 , China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , 116023 , China
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22
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Needham EJ, Parker BL, Burykin T, James DE, Humphrey SJ. Illuminating the dark phosphoproteome. Sci Signal 2019; 12:12/565/eaau8645. [PMID: 30670635 DOI: 10.1126/scisignal.aau8645] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein phosphorylation is a major regulator of protein function and biological outcomes. This was first recognized through functional biochemical experiments, and in the past decade, major technological advances in mass spectrometry have enabled the study of protein phosphorylation on a global scale. This rapidly growing field of phosphoproteomics has revealed that more than 100,000 distinct phosphorylation events occur in human cells, which likely affect the function of every protein. Phosphoproteomics has improved the understanding of the function of even the most well-characterized protein kinases by revealing new downstream substrates and biology. However, current biochemical and bioinformatic approaches have only identified kinases for less than 5% of the phosphoproteome, and functional assignments of phosphosites are almost negligible. Notably, our understanding of the relationship between kinases and their substrates follows a power law distribution, with almost 90% of phosphorylation sites currently assigned to the top 20% of kinases. In addition, more than 150 kinases do not have a single known substrate. Despite a small group of kinases dominating biomedical research, the number of substrates assigned to a kinase does not correlate with disease relevance as determined by pathogenic human mutation prevalence and mouse model phenotypes. Improving our understanding of the substrates targeted by all kinases and functionally annotating the phosphoproteome will be broadly beneficial. Advances in phosphoproteomics technologies, combined with functional screening approaches, should make it feasible to illuminate the connectivity and functionality of the entire phosphoproteome, providing enormous opportunities for discovering new biology, therapeutic targets, and possibly diagnostics.
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Affiliation(s)
- Elise J Needham
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Timur Burykin
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia. .,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Sean J Humphrey
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia. .,Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
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23
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Affiliation(s)
- Clement
M. Potel
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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24
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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: 3.7] [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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25
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Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
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26
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Chouinard CD, Nagy G, Webb IK, Shi T, Baker ES, Prost SA, Liu T, Ibrahim YM, Smith RD. Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry. Anal Chem 2018; 90:10889-10896. [PMID: 30118596 PMCID: PMC6211290 DOI: 10.1021/acs.analchem.8b02397] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphoproteomics greatly augments proteomics and holds tremendous potential for insights into the modulation of biological systems for various disease states. However, numerous challenges hinder conventional methods in terms of measurement sensitivity, throughput, quantification, and capabilities for confident phosphopeptide and phosphosite identification. In this work, we report the first example of integrating structures for lossless ion manipulations ion mobility-mass spectrometry (SLIM IM-MS) with online reversed-phase liquid chromatography (LC) to evaluate its potential for addressing the aforementioned challenges. A mixture of 51 heavy-labeled phosphopeptides was analyzed with a SLIM IM module having integrated ion accumulation and long-path separation regions. The SLIM IM-MS provided limits of detection as low as 50-100 pM (50-100 amol/μL) for several phosphopeptides, with the potential for significant further improvements. In addition, conventionally problematic phosphopeptide isomers could be resolved following an 18 m SLIM IM separation. The 2-D LC-IM peak capacity was estimated as ∼9000 for a 90 min LC separation coupled to an 18 m SLIM IM separation, considerably higher than LC alone and providing a basis for both improved identification and quantification, with additional gains projected with the future use of longer path SLIM IM separations. Thus, LC-SLIM IM-MS offers great potential for improving the sensitivity, separation, and throughput of phosphoproteomics analyses.
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Affiliation(s)
- Christopher D. Chouinard
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ian K. Webb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin S. Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Spencer A. Prost
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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27
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Greer SM, Sidoli S, Coradin M, Schack Jespersen M, Schwämmle V, Jensen ON, Garcia BA, Brodbelt JS. Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy. Anal Chem 2018; 90:10425-10433. [PMID: 30063333 PMCID: PMC6383154 DOI: 10.1021/acs.analchem.8b02320] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ability to map combinatorial patterns of post-translational modifications (PTMs) of proteins remains challenging for traditional bottom-up mass spectrometry workflows. There are also hurdles associated with top-down approaches related to limited data analysis options for heavily modified proteoforms. These shortcomings have accelerated interest in middle-down MS methods that focus on analysis of large peptides generated by specific proteases in conjunction with validated bioinformatics strategies to allow quantification of isomeric histoforms. Mapping multiple PTMs simultaneously requires the ability to obtain high sequence coverage to allow confident localization of the modifications, and 193 nm ultraviolet photodissociation (UVPD) has been shown to cause extensive fragmentation for large peptides and proteins. Histones are an ideal system to test the ability of UVPD to characterize multiple modifications, as the combinations of PTMs are the underpinning of the biological significance of histones and at the same time create an imposing challenge for characterization. The present study focuses on applying 193 nm UVPD to the identification and localization of PTMs on histones by UVPD and comparison to a popular alternative, electron-transfer dissociation (ETD), via a high-throughput middle-down LC/MS/MS strategy. Histone Coder and IsoScale, bioinformatics tools for verification of PTM assignments and quantification of histone peptides, were adapted for UVPD data and applied in the present study. In total, over 300 modified forms were identified, and the distributions of PTMs were quantified between UVPD and ETD. Significant differences in patterns of PTMs were found for histones from HeLa cells prior to and after treatment with a deacetylase inhibitor. Additional fragment ion types generated by UVPD proved essential for extensive characterization of the most heavily modified forms (>5 PTMs).
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Affiliation(s)
- Sylvester M Greer
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Mariel Coradin
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Malena Schack Jespersen
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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28
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Mehaffey MR, Sanders JD, Holden DD, Nilsson CL, Brodbelt JS. Multistage Ultraviolet Photodissociation Mass Spectrometry To Characterize Single Amino Acid Variants of Human Mitochondrial BCAT2. Anal Chem 2018; 90:9904-9911. [PMID: 30016590 PMCID: PMC6323636 DOI: 10.1021/acs.analchem.8b02099] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Unraveling disease mechanisms requires a comprehensive understanding of how the interplay between higher-order structure and protein-ligand interactions impacts the function of a given protein. Recent advances in native mass spectrometry (MS) involving multimodal or higher-energy activation methods have allowed direct interrogation of intact protein complexes in the gas phase, allowing analysis of both composition and subunit connectivity. We report a multistage approach combining collisional activation and 193 nm ultraviolet photodissociation (UVPD) to characterize single amino acid variants of the human mitochondrial enzyme branched-chain amino acid transferase 2 (BCAT2), a protein implicated in chemotherapeutic resistance in glioblastoma tumors. Native electrospray ionization confirms that both proteins exist as homodimers. Front-end collisional activation disassembles the dimers into monomeric subunits that are further interrogated using UVPD to yield high sequence coverage of the mutated region. Additionally, holo (ligand-bound) fragment ions resulting from photodissociation reveal that the mutation causes destabilization of the interactions with a bound cofactor. This study demonstrates the unique advantages of implementing UVPD in a multistage MS approach for analyzing intact protein assemblies.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Dustin D. Holden
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Carol L. Nilsson
- Institute of Experimental Medical Sciences, Lund University, SE-221, Lund Sweden
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29
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Borotto NB, Ileka KM, Tom CATMB, Martin BR, Håkansson K. Free Radical Initiated Peptide Sequencing for Direct Site Localization of Sulfation and Phosphorylation with Negative Ion Mode Mass Spectrometry. Anal Chem 2018; 90:9682-9686. [PMID: 30063332 DOI: 10.1021/acs.analchem.8b02707] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tandem mass spectrometry (MS/MS) is the primary method for discovering, identifying, and localizing post-translational modifications (PTMs) in proteins. However, conventional positive ion mode collision induced dissociation (CID)-based MS/MS often fails to yield site-specific information for labile and acidic modifications due to low ionization efficiency in positive ion mode and/or preferential PTM loss. While a number of alternative methods have been developed to address this issue, most require specialized instrumentation or indirect detection. In this work, we present an amine-reactive TEMPO-based free radical initiated peptide sequencing (FRIPS) approach for negative ion mode analysis of phosphorylated and sulfated peptides. FRIPS-based fragmentation generates sequence informative ions for both phosphorylated and sulfated peptides with no significant PTM loss. Furthermore, FRIPS is compared to positive ion mode CID, electron transfer dissociation (ETD), as well as negative ion mode electron capture dissociation (niECD) and CID, both in terms of sequence coverage and fragmentation efficiency for phospho- and sulfo-peptides. Because FRIPS-based fragmentation has no particular instrumentation requirements and shows limited PTM loss, we propose this approach as a promising alternative to current techniques for analysis of labile and acidic PTMs.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Kevin M Ileka
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Christina A T M B Tom
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brent R Martin
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Kristina Håkansson
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
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30
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Cammarata MB, Macias LA, Rosenberg J, Bolufer A, Brodbelt JS. Expanding the Scope of Cross-Link Identifications by Incorporating Collisional Activated Dissociation and Ultraviolet Photodissociation Methods. Anal Chem 2018; 90:6385-6389. [PMID: 29722964 PMCID: PMC6040644 DOI: 10.1021/acs.analchem.7b04009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
With the advent of new cross-linking chemistries, analytical technologies, and search algorithms, cross-linking has become an increasingly popular strategy for evaluating tertiary and quaternary structures of proteins. Collisional activated dissociation remains the primary MS/MS method for identifications of peptide cross-links in high throughput workflows. Ultraviolet photodissociation (UVPD) at 193 nm has emerged as an alternative ion activation method well-suited for characterization of peptides and has been found in some cases to identify different peptides or provide distinctive sequence information than obtained by collisional activation methods. Complementary high energy collision dissociation (HCD) and UVPD were used in the present study to characterize protein cross-linking for bovine serum albumin, hemoglobin, and E. coli ribosome. Cross-links identified by HCD and UVPD using bis(sulfosuccinimidyl)suberate (BS3), a homobifunctional amine-to-amine cross-linker, and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM), a heterofunctional amine-to-carboxylic acid cross-linker, were evaluated in the present study. While more unique BS3 cross-links were identified by HCD, UVPD, and HCD provided a complementary panel of DMTMM cross-links which extended the degree of structural insight obtained for the proteins.
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Affiliation(s)
- Michael B Cammarata
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Luis A Macias
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Jake Rosenberg
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Alexander Bolufer
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
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31
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Elucidating the various multi-phosphorylation statuses of protein functional regions by 193-nm ultraviolet photodissociation. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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32
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Greer SM, Bern M, Becker C, Brodbelt JS. Extending Proteome Coverage by Combining MS/MS Methods and a Modified Bioinformatics Platform Adapted for Database Searching of Positive and Negative Polarity 193 nm Ultraviolet Photodissociation Mass Spectra. J Proteome Res 2018; 17:1340-1347. [DOI: 10.1021/acs.jproteome.7b00673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Marshall Bern
- Protein
Metrics,
Inc., San Carlos, California 94070, United States
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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33
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Halim MA, MacAleese L, Lemoine J, Antoine R, Dugourd P, Girod M. Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:270-283. [PMID: 28980177 DOI: 10.1007/s13361-017-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Luke MacAleese
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| | - Rodolphe Antoine
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France.
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
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34
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Sanders JD, Greer SM, Brodbelt JS. Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down Proteomics. Anal Chem 2017; 89:11772-11778. [DOI: 10.1021/acs.analchem.7b03396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sylvester M. Greer
- 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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35
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McClory PJ, Håkansson K. Corona Discharge Suppression in Negative Ion Mode Nanoelectrospray Ionization via Trifluoroethanol Addition. Anal Chem 2017; 89:10188-10193. [PMID: 28841300 PMCID: PMC5642034 DOI: 10.1021/acs.analchem.7b01225] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Negative ion mode nanoelectrospray ionization (nESI) is often utilized to analyze acidic compounds, from small molecules to proteins, with mass spectrometry (MS). Under high aqueous solvent conditions, corona discharge is commonly observed at emitter tips, resulting in low ion abundances and reduced nESI needle lifetimes. We have successfully reduced corona discharge in negative ion mode by trace addition of trifluoroethanol (TFE) to aqueous samples. The addition of as little as 0.2% TFE increases aqueous spray stability not only in nESI direct infusion, but also in nanoflow liquid chromatography (nLC)/MS experiments. Negative ion mode spray stability with 0.2% TFE is approximately 6× higher than for strictly aqueous samples. Upon addition of 0.2% TFE to the mobile phase of nLC/MS experiments, tryptic peptide identifications increased from 93 to 111 peptides, resulting in an average protein sequence coverage increase of 18%.
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Affiliation(s)
- Phillip J. McClory
- Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109-1055
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Ave., Ann Arbor, MI 48109-1055
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36
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Riley NM, Hebert AS, Dürnberger G, Stanek F, Mechtler K, Westphall MS, Coon JJ. Phosphoproteomics with Activated Ion Electron Transfer Dissociation. Anal Chem 2017; 89:6367-6376. [PMID: 28383256 PMCID: PMC5555596 DOI: 10.1021/acs.analchem.7b00212] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in α-casein, an ∼23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander S. Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gerhard Dürnberger
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- GMI, Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Florian Stanek
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Michael S. Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
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37
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Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, LeDuc RD, Parker WR, Thomas PM, Kelleher NL, Brodbelt JS. High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer. J Proteome Res 2017; 16:2072-2079. [PMID: 28412815 DOI: 10.1021/acs.jproteome.7b00043] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale. However, utilization of UVPD for high-throughput top-down analysis to date has been limited by bioinformatics. Here we detected 153 proteins and 489 proteoforms using UVPD and 271 proteins and 982 proteoforms using higher energy collisional dissociation (HCD) in a comparative analysis of HeLa whole-cell lysate by qualitative top-down proteomics. Of the total detected proteoforms, 286 overlapped between the UVPD and HCD data sets, with 68% of proteoforms having C scores greater than 40 for UVPD and 63% for HCD. The average sequence coverage (28 ± 20% for UVPD versus 17 ± 8% for HCD, p < 0.0001) was found to be higher for UVPD than HCD and with a trend toward improvement in q value for the UVPD data set. This study demonstrates the complementarity of UVPD and HCD for more extensive protein profiling and proteoform characterization.
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Affiliation(s)
- Timothy P Cleland
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Alexandra J VanNispen
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - W Ryan Parker
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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38
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- 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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