1
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Youssef MM, Szot CW, Folz J, Collier LM, Kweon HK, DeFiglia SA, Ayad MF, Hussein LA, Abdel-Ghany MF, Hakansson K. Electron Capture vs Transfer Dissociation for Site Determination of Tryptic Peptide Tyrosine Sulfation: Direct Detection of Fibrinogen Sulfation Sites and Identification of Novel Isobaric Interferences. J Proteome Res 2024; 23:2386-2396. [PMID: 38900499 PMCID: PMC11231624 DOI: 10.1021/acs.jproteome.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tyrosine sulfation, an understudied but crucial post-translational modification, cannot be directly detected in conventional nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) due to the extreme sulfate lability. Here, we report the detection of sulfate-retaining fragments from LC-electron capture dissociation (ECD) and nanoLC-electron transfer higher energy collision dissociation (EThcD). Sulfopeptide candidates were identified by Proteome Discoverer and MSFragger analysis of nanoLC-HCD MS/MS data and added to inclusion lists for LC-ECD or nanoLC-EThcD MS/MS. When this approach failed, targeted LC-ECD with fixed m/z isolation windows was performed. For the plasma protein fibrinogen, the known pyroglutamylated sulfopeptide QFPTDYDEGQDDRPK from the beta chain N-terminus was identified despite a complete lack of sulfate-containing fragment ions. The peptide QVGVEHHVEIEYD from the gamma-B chain C-terminus was also identified as sulfated or phosphorylated. This sulfopeptide is not annotated in Uniprot but was previously reported. MSFragger further identified a cysteine-containing peptide from the middle of the gamma chain as sulfated and deamidated. NanoLC-EThcD and LC-ECD MS/MS confirmed the two former sulfopeptides via sulfate-retaining fragment ions, whereas an unexpected fragmentation pattern was observed for the third sulfopeptide candidate. Manual interpretation of the LC-ECD spectrum revealed two additional isobaric identifications: a trisulfide-linked cysteinyl-glycine or a carbamidomethyl-dithiothreiotol covalent adduct. Synthesis of such adducts confirmed the latter identity.
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Affiliation(s)
- Menatallah M Youssef
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Carson W Szot
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jeff Folz
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Luke M Collier
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Hye Kyong Kweon
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Miriam F Ayad
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Lobna A Hussein
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Maha F Abdel-Ghany
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Kristina Hakansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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2
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DeFiglia SA, Szot CW, Håkansson K. Negative-Ion Electron Capture Dissociation of MALDI-Generated Peptide Anions. Anal Chem 2024; 96:8800-8806. [PMID: 38742421 DOI: 10.1021/acs.analchem.4c01292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Negative-ion electron capture dissociation (niECD) is an anion MS/MS technique that provides fragmentation analogous to conventional ECD, including high peptide sequence coverage and retention of labile post-translational modifications (PTMs). niECD has been proposed to be the most efficient for salt-bridged zwitterionic precursor ion structures. Several important PTMs, e.g., sulfation and phosphorylation, are acidic and can, therefore, be challenging to characterize in the positive-ion mode. Furthermore, PTM-friendly techniques, such as ECD, require multiple precursor ion-positive charges. By contrast, singly charged ions, refractory to ECD, are most compatible with niECD. Because electrospray ionization (ESI) typically yields multiply charged ions, we sought to explore matrix-assisted laser desorption/ionization (MALDI) in combination with niECD. However, the requirement for zwitterionic gaseous structures may preclude efficient niECD of MALDI-generated anions. Unexpectedly, we found that niECD of anions from MALDI is not only possible but proceeds with similar or higher efficiency compared with ESI-generated anions. Matrix selection did not appear to have a major effect. With MALDI, niECD is demonstrated up to m/z ∼4300. For such larger analytes, multiple electron captures are observed, resulting in triply charged fragments from singly charged precursor ions. Such charge-increased fragments show improved detectability. Furthermore, significantly improved (∼20-fold signal-to-noise increase) niECD spectral quality is achieved with equivalent sample amounts from MALDI vs ESI. Overall, the reported combination with MALDI significantly boosts the analytical utility of niECD.
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Affiliation(s)
- Steven A DeFiglia
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Carson W Szot
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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3
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Wang N, Dixit SM, Lee T, DeFiglia SA, Ruotolo BT, Håkansson K. Salt-Bridged Peptide Anion Gaseous Structures Enable Efficient Negative Ion Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:784-792. [PMID: 38489759 DOI: 10.1021/jasms.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
We previously discovered that electron attachment to gaseous peptide anions can occur within a relatively narrow electron energy range. The resulting charge-increased radical ions undergo dissociation analogous to conventional cation electron capture/transfer dissociation (ECD/ETD), thus enabling a novel tandem mass spectrometry (MS/MS) technique that we termed negative ion electron capture dissociation (niECD). We proposed that gaseous zwitterionic structures are required for niECD with electron capture either occurring at or being directed by a positively charged site. Here, we further evaluate this zwitterion mechanism by performing niECD of peptides derivatized to alter their ability to form zwitterionic gaseous structures. Introduction of a fixed positive charge tag, a highly basic guanidino group, or a highly acidic sulfonate group to promote zwitterionic structures in singly charged anions, rescued the niECD ability of a peptide refractory to niECD in its unmodified form. We also performed a systematic study of five sets of synthetic peptides with decreasing zwitterion propensity and found that niECD efficiency decreased accordingly, further supporting the zwitterion mechanism. However, traveling-wave ion mobility-mass spectrometry experiments, performed to gain further insight into the gas-phase structures of peptides showing high niECD efficiency, exhibited an inverse correlation between the orientationally averaged collision cross sections and niECD efficiency. These results indicate that compact salt-bridged structures are also a requirement for effective niECD.
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Affiliation(s)
- Ning Wang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Teresa Lee
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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5
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Bashyal A, Brodbelt JS. Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation. MASS SPECTROMETRY REVIEWS 2024; 43:289-326. [PMID: 36165040 PMCID: PMC10040477 DOI: 10.1002/mas.21811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
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6
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Kweon HK, Kong AT, Hersberger KE, Huang S, Nesvizhskii AI, Wang Y, Hakansson K, Andrews PC. Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi. J Proteome Res 2024; 23:71-83. [PMID: 38112105 PMCID: PMC11218929 DOI: 10.1021/acs.jproteome.3c00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Tyrosine sulfation in the Golgi of secreted and membrane proteins is an important post-translational modification (PTM). However, its labile nature has limited analysis by mass spectrometry (MS), a major reason why no sulfoproteome studies have been previously reported. Here, we show that a phosphoproteomics experimental workflow, which includes serial enrichment followed by high resolution, high mass accuracy MS, and tandem MS (MS/MS) analysis, enables sulfopeptide coenrichment and identification via accurate precursor ion mass shift open MSFragger database search. This approach, supported by manual validation, allows the confident identification of sulfotyrosine-containing peptides in the presence of high levels of phosphorylated peptides, thus enabling these two sterically and ionically similar isobaric PTMs to be distinguished and annotated in a single proteomic analysis. We applied this approach to isolated interphase and mitotic rat liver Golgi membranes and identified 67 tyrosine sulfopeptides, corresponding to 26 different proteins. This work discovered 23 new sulfoproteins with functions related to, for example, Ca2+-binding, glycan biosynthesis, and exocytosis. In addition, we report the first preliminary evidence for crosstalk between sulfation and phosphorylation in the Golgi, with implications for functional control.
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Affiliation(s)
- Hye Kyong Kweon
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, United States
| | - Andy T Kong
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109-5602, United States
| | - Katherine E Hersberger
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Shijiao Huang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109-5602, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109-2218, United States
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1085, United States
| | - Kristina Hakansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Philip C Andrews
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109-2218, United States
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7
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Daly L, Byrne DP, Perkins S, Brownridge PJ, McDonnell E, Jones AR, Eyers PA, Eyers CE. Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides. J Proteome Res 2023; 22:3754-3772. [PMID: 37939282 PMCID: PMC10696596 DOI: 10.1021/acs.jproteome.3c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Protein tyrosine sulfation (sY) is a post-translational modification (PTM) catalyzed by Golgi-resident tyrosyl protein sulfo transferases (TPSTs). Information on sY in humans is currently limited to ∼50 proteins, with only a handful having verified sites of sulfation. As such, the contribution of sulfation to the regulation of biological processes remains poorly defined. Mass spectrometry (MS)-based proteomics is the method of choice for PTM analysis but has yet to be applied for systematic investigation of the "sulfome", primarily due to issues associated with discrimination of sY-containing from phosphotyrosine (pY)-containing peptides. In this study, we developed an MS-based workflow for sY-peptide characterization, incorporating optimized Zr4+ immobilized metal-ion affinity chromatography (IMAC) and TiO2 enrichment strategies. Extensive characterization of a panel of sY- and pY-peptides using an array of fragmentation regimes (CID, HCD, EThcD, ETciD, UVPD) highlighted differences in the generation of site-determining product ions and allowed us to develop a strategy for differentiating sulfated peptides from nominally isobaric phosphopeptides based on low collision energy-induced neutral loss. Application of our "sulfomics" workflow to a HEK-293 cell extracellular secretome facilitated identification of 21 new sulfotyrosine-containing proteins, several of which we validate enzymatically, and reveals new interplay between enzymes relevant to both protein and glycan sulfation.
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Affiliation(s)
- Leonard
A. Daly
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Dominic P. Byrne
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Simon Perkins
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Philip J. Brownridge
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Euan McDonnell
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Andrew R. Jones
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Patrick A. Eyers
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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8
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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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9
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Steckel A, Papp D, Uray K, Schlosser G. Collision-Induced Dissociation of Citrullinated Peptide Anions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1569-1575. [PMID: 37414397 PMCID: PMC10402709 DOI: 10.1021/jasms.3c00044] [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] [Received: 02/01/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 07/08/2023]
Abstract
Peptide identification by positive electrospray ionization (ES+) tandem mass spectrometry (MS/MS) is a well-established strategy in proteomics. Several research groups reported the usefulness of negative electrospray ionization (ES-) for gaining complementary structural information on peptides and their post-translational modifications (PTM) compared to ES+. Fragmentation of citrullinated peptides has not been previously explored in ES-. In this study, 9 peptides containing citrulline residues were investigated in ES- by stepwise collision energy-dependent measurements on a QTOF instrument and a Q-Orbitrap instrument. Our results of high resolution and mass accuracy show the favored citrulline-selective loss of HNCO from these peptide precursors and their fragments─similarly to that in ES+─along with y-NH3/z, c, c-NH3/b sequence ions. Loss of HNCO from citrullinated peptides in ES- and a proposed mechanism for the reaction have been described here for the first time. HNCO loss intensities from precursors were generally even higher than that in ES+. Interestingly, the most intense fragments corresponded to neutral losses from sequence ions while intact sequence ions were usually minor components of the spectra. High-intensity ions related to cleavages N-terminal to Asp and Glu residues that have been previously reported were also observed. On the other hand, a relatively high number of peaks were observed, possibly due to internal fragmentation and/or scrambling events. While (ES-) MS/MS spectra always require manual inspection and the annotation may be ambiguous, the favorable loss of HNCO and the preferable cleavage N-terminal to Asp residues can be used to differentiate between citrullinated/deamidated sequences.
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Affiliation(s)
- Arnold Steckel
- MTA-ELTE
Lendület Ion Mobility Mass Spectrometry Research Group, Department
of Analytical Chemistry, ELTE Eötvös
Loránd University, Budapest 1117, Hungary
| | - Dávid Papp
- MTA-ELTE
Lendület Ion Mobility Mass Spectrometry Research Group, Department
of Analytical Chemistry, ELTE Eötvös
Loránd University, Budapest 1117, Hungary
- Hevesy
György PhD School of Chemistry, ELTE
Eötvös Loránd University, Budapest 1117, Hungary
| | - Katalin Uray
- ELKH-ELTE
Research Group of Peptide Chemistry, ELTE
Eötvös Loránd University, Budapest 1117, Hungary
| | - Gitta Schlosser
- MTA-ELTE
Lendület Ion Mobility Mass Spectrometry Research Group, Department
of Analytical Chemistry, ELTE Eötvös
Loránd University, Budapest 1117, Hungary
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10
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Piovesana S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Zenezini Chiozzi R, Laganà A. The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry. Anal Chem 2022; 94:9234-9241. [PMID: 35714062 PMCID: PMC9260711 DOI: 10.1021/acs.analchem.1c05621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
Abstract
Site localization of protein sulfation by high-throughput proteomics remains challenging despite the technological improvements. In this study, sequence analysis and site localization of sulfation in tryptic peptides were determined under a conventional nano-liquid chromatography-mass spectrometry configuration. Tryptic sulfopeptide standards were used to study different fragmentation strategies, including collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), electron-transfer dissociation (ETD), electron-transfer/higher-energy collision dissociation (EThcD), and electron-transfer/collision-induced dissociation (ETciD), in the positive ionization mode. Sulfopeptides displayed only neutral loss of SO3 under CID, while the sequence could be determined for all other tested fragmentation techniques. Results were compared to the same sequences with phosphotyrosine, indicating important differences, as the sequence and modification localization could be studied by all fragmentation strategies. However, the use of metal adducts, especially potassium, provided valuable information for sulfopeptide localization in ETD and ETD-hybrid strategies by stabilizing the modification and increasing the charge state of sulfopeptides. In these conditions, both the sequence and localization could be obtained. In-source neutral loss of SO3 under EThcD provided diagnostic peaks suitable to distinguish the sulfopeptides from the nearly isobaric phosphopeptides. Further confirmation on the modification type was found in the negative ionization mode, where phosphopeptides always had the typical phosphate product ion corresponding to PO3-.
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Affiliation(s)
- Susy Piovesana
- Department
of Chemistry, University of Rome “La
Sapienza”, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Anna Laura Capriotti
- Department
of Chemistry, University of Rome “La
Sapienza”, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Chiara Cavaliere
- Department
of Chemistry, University of Rome “La
Sapienza”, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Andrea Cerrato
- Department
of Chemistry, University of Rome “La
Sapienza”, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Carmela Maria Montone
- Department
of Chemistry, University of Rome “La
Sapienza”, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Riccardo Zenezini Chiozzi
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Aldo Laganà
- Department
of Chemistry, University of Rome “La
Sapienza”, Piazzale Aldo Moro 5, Rome 00185, Italy
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11
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Lebedev AT, Vasileva ID, Samgina TY. FT-MS in the de novo top-down sequencing of natural nontryptic peptides. MASS SPECTROMETRY REVIEWS 2022; 41:284-313. [PMID: 33347655 DOI: 10.1002/mas.21678] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.
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Affiliation(s)
- Albert T Lebedev
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Irina D Vasileva
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Y Samgina
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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12
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Gaunitz S, Tjernberg LO, Schedin-Weiss S. What Can N-glycomics and N-glycoproteomics of Cerebrospinal Fluid Tell Us about Alzheimer Disease? Biomolecules 2021; 11:858. [PMID: 34207636 PMCID: PMC8226827 DOI: 10.3390/biom11060858] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/18/2022] Open
Abstract
Proteomics-large-scale studies of proteins-has over the last decade gained an enormous interest for studies aimed at revealing proteins and pathways involved in disease. To fully understand biological and pathological processes it is crucial to also include post-translational modifications in the "omics". To this end, glycomics (identification and quantification of glycans enzymatically or chemically released from proteins) and glycoproteomics (identification and quantification of peptides/proteins with the glycans still attached) is gaining interest. The study of protein glycosylation requires a workflow that involves an array of sample preparation and analysis steps that needs to be carefully considered. Herein, we briefly touch upon important steps such as sample preparation and preconcentration, glycan release, glycan derivatization and quantification and advances in mass spectrometry that today are the work-horse for glycomics and glycoproteomics studies. Several proteins related to Alzheimer disease pathogenesis have altered protein glycosylation, and recent glycomics studies have shown differences in cerebrospinal fluid as well as in brain tissue in Alzheimer disease as compared to controls. In this review, we discuss these techniques and how they have been used to shed light on Alzheimer disease and to find glycan biomarkers in cerebrospinal fluid.
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Affiliation(s)
- Stefan Gaunitz
- Department of Clinical Chemistry, Karolinska University Hospital, 14186 Stockholm, Sweden;
| | - Lars O. Tjernberg
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17164 Solna, Sweden;
| | - Sophia Schedin-Weiss
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17164 Solna, Sweden;
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13
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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14
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Capriotti AL, Cerrato A, Laganà A, Montone CM, Piovesana S, Zenezini Chiozzi R, Cavaliere C. Development of a Sample-Preparation Workflow for Sulfopeptide Enrichment: From Target Analysis to Challenges in Shotgun Sulfoproteomics. Anal Chem 2020; 92:7964-7971. [DOI: 10.1021/acs.analchem.0c01342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, Netherlands
- Netherlands Proteomics CentrePadualaan 8Utrecht3584 CHNetherlands
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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15
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Asakawa D, Takahashi H, Sekiya S, Iwamoto S, Tanaka K. Sequencing of Sulfopeptides Using Negative-Ion Tandem Mass Spectrometry with Hydrogen Attachment/Abstraction Dissociation. Anal Chem 2019; 91:10549-10556. [DOI: 10.1021/acs.analchem.9b01568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hidenori Takahashi
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Sadanori Sekiya
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
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16
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Wang Q, Borotto NB, Håkansson K. Gas-Phase Hydrogen/Deuterium Scrambling in Negative-Ion Mode Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:855-863. [PMID: 30805882 PMCID: PMC6680243 DOI: 10.1007/s13361-019-02143-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/12/2019] [Accepted: 01/22/2019] [Indexed: 06/07/2023]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX MS) has become a powerful method to characterize protein conformational dynamics. Workflows typically utilize pepsin digestion prior to MS analysis to yield peptide level structural resolution. Tandem mass spectrometry (MS/MS) can potentially facilitate determination of site-specific deuteration to single-residue resolution. However, to be effective, MS/MS activation must minimize the occurrence of gas-phase intramolecular randomization of solution-generated deuterium labels. While significant work has focused on understanding this process in positive-ion mode, little is known about hydrogen/deuterium (H/D) scrambling processes in negative-ion mode. Here, we utilize selectively deuterated model peptides to investigate the extent of intramolecular H/D scrambling upon several negative-ion mode MS/MS techniques, including negative-ion collision-induced dissociation (nCID), electron detachment dissociation (EDD), negative-ion free radical-initiated peptide sequencing (nFRIPS), and negative-ion electron capture dissociation (niECD). H/D scrambling was extensive in deprotonated peptides upon nCID and nFRIPS. In fact, the energetics required to induce dissociation in nCID are sufficient to allow histidine C-2 and Cβ hydrogen atoms to participate in the scrambling process. EDD and niECD demonstrated moderate H/D scrambling with niECD being superior in terms of minimizing hydrogen migration, achieving ~ 30% scrambling levels for small c-type fragment ions. We believe the observed scrambling is likely due to activation during ionization and ion transport rather than during the niECD event itself.
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Affiliation(s)
- Qingyi Wang
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI, 48109-1055, USA
| | - Nicholas B Borotto
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI, 48109-1055, USA.
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI, 48109-1055, USA.
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17
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Jang I, Jeon A, Lim SG, Hong DK, Kim MS, Jo JH, Lee ST, Moon B, Oh HB. Free Radical-Initiated Peptide Sequencing Mass Spectrometry for Phosphopeptide Post-translational Modification Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:538-547. [PMID: 30414067 DOI: 10.1007/s13361-018-2100-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved. Analysis of the resulting peptide fragments revealed the extensive production of a-, c-, x-, and z-type fragments (with some minor b- and y-type fragments), suggesting that radical-driven peptide fragmentation was the primary mechanism involved in the FRIPS MS of phosphopeptides. Results of this study clearly indicate that FRIPS MS is a promising tool for the characterization of post-translational modifications such as phosphorylation. Graphical Abstract.
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Affiliation(s)
- Inae Jang
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Aeran Jeon
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Suk Gyu Lim
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Seoul National University, Seoul, 08826, Republic of Korea
| | - Duk Ki Hong
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Soo Kim
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Korea University, Seoul, 02841, Republic of Korea
| | - Jae Hyeong Jo
- Seoul Science High School, Seoul, 03066, Republic of Korea
- Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sang Tak Lee
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea.
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18
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Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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19
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Chen X, Wang Z, Wong YLE, Wu R, Zhang F, Chan TWD. Electron-ion reaction-based dissociation: A powerful ion activation method for the elucidation of natural product structures. MASS SPECTROMETRY REVIEWS 2018; 37:793-810. [PMID: 29603345 DOI: 10.1002/mas.21563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/12/2018] [Indexed: 05/16/2023]
Abstract
The structural elucidation of natural products (NPs) remains a challenge due to their structurally diversities and unpredictable functionalities, motifs, and scaffolds. Tandem mass spectrometry (MS/MS) is an effective method that assists the full elucidation of complicated NP structures. Ion activation methods play a key role in determining the fragmentation pathways and the structural information obtained from MS/MS. Electron-ion reaction-based dissociation (ExD) methods, including electron capture dissociation (ECD), electron transfer dissociation (ETD), electron-induced dissociation (EID), and electron detachment dissociation (EDD), can induce the breakage of specific chemical bonds and the generation of distinct fragment ions. This review article provides an overview of the mechanisms, instrumentation, and typical applications related to ExD MS/MS in the structural elucidation of NPs, primarly including lipids, oligosaccharides, glycoconjugates, metabolites, and pharmaceutical drugs. This work aims to reveal the capacity and potential of ExD mass spectrometry in analyzing NPs and consequently helping the NP communities to utilize the modern capabilities of MS/MS in the discovery and evaluation of novel NPs.
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Affiliation(s)
- Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Science), Shandong, P.R. China
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Ze Wang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Y-L Elaine Wong
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Ri Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Feng Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, P. R. China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
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20
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Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
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Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
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21
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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: 1.8] [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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22
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Hook V, Lietz CB, Podvin S, Cajka T, Fiehn O. Diversity of Neuropeptide Cell-Cell Signaling Molecules Generated by Proteolytic Processing Revealed by Neuropeptidomics Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:807-816. [PMID: 29667161 PMCID: PMC5946320 DOI: 10.1007/s13361-018-1914-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 05/23/2023]
Abstract
Neuropeptides are short peptides in the range of 3-40 residues that are secreted for cell-cell communication in neuroendocrine systems. In the nervous system, neuropeptides comprise the largest group of neurotransmitters. In the endocrine system, neuropeptides function as peptide hormones to coordinate intercellular signaling among target physiological systems. The diversity of neuropeptide functions is defined by their distinct primary sequences, peptide lengths, proteolytic processing of pro-neuropeptide precursors, and covalent modifications. Global, untargeted neuropeptidomics mass spectrometry is advantageous for defining the structural features of the thousands to tens of thousands of neuropeptides present in biological systems. Defining neuropeptide structures is the basis for defining the proteolytic processing pathways that convert pro-neuropeptides into active peptides. Neuropeptidomics has revealed that processing of pro-neuropeptides occurs at paired basic residues sites, and at non-basic residue sites. Processing results in neuropeptides with known functions and generates novel peptides representing intervening peptide domains flanked by dibasic residue processing sites, identified by neuropeptidomics. While very short peptide products of 2-4 residues are predicted from pro-neuropeptide dibasic processing sites, such peptides have not been readily identified; therefore, it will be logical to utilize metabolomics to identify very short peptides with neuropeptidomics in future studies. Proteolytic processing is accompanied by covalent post-translational modifications (PTMs) of neuropeptides comprising C-terminal amidation, N-terminal pyroglutamate, disulfide bonds, phosphorylation, sulfation, acetylation, glycosylation, and others. Neuropeptidomics can define PTM features of neuropeptides. In summary, neuropeptidomics for untargeted, global analyses of neuropeptides is essential for elucidation of proteases that generate diverse neuropeptides for cell-cell signaling. Graphical Abstract ᅟ.
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Affiliation(s)
- Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA.
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Christopher B Lietz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Tomas Cajka
- West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA
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23
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Schaller-Duke RM, Bogala MR, Cassady CJ. Electron Transfer Dissociation and Collision-Induced Dissociation of Underivatized Metallated Oligosaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1021-1035. [PMID: 29492773 PMCID: PMC5943087 DOI: 10.1007/s13361-018-1906-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/25/2018] [Accepted: 01/25/2018] [Indexed: 05/04/2023]
Abstract
Electron transfer dissociation (ETD) and collision-induced dissociation (CID) were used to investigate underivatized, metal-cationized oligosaccharides formed via electrospray ionization (ESI). Reducing and non-reducing sugars were studied including the tetrasaccharides maltotetraose, 3α,4β,3α-galactotetraose, stachyose, nystose, and a heptasaccharide, maltoheptaose. Univalent alkali, divalent alkaline earth, divalent and trivalent transition metal ions, and a boron group trivalent metal ion were adducted to the non-permethylated oligosaccharides. ESI generated [M + Met]+, [M + 2Met]2+, [M + Met]2+, [M + Met - H]+, and [M + Met - 2H]+ most intensely along with low intensity nitrate adducts, depending on the metal and sugar ionized. The ability of these metal ions to produce oligosaccharide adduct ions by ESI had the general trend: Ca(II) > Mg(II) > Ni(II) > Co(II) > Zn(II) > Cu(II) > Na(I) > K(I) > Al(III) ≈ Fe(III) ≈ Cr(III). Although trivalent metals were utilized, no triply charged ions were formed. Metal cations allowed for high ESI signal intensity without permethylation. ETD and CID on [M + Met]2+ produced various glycosidic and cross-ring cleavages, with ETD producing more cross-ring and internal ions, which are useful for structural analysis. Product ion intensities varied based on glycosidic-bond linkage and identity of monosaccharide sub-unit, and metal adducts. ETD and CID showed high fragmentation efficiency, often with complete precursor dissociation, depending on the identity of the adducted metal ion. Loss of water was occasionally observed, but elimination of small neutral molecules was not prevalent. For both ETD and CID, [M + Co]2+ produced the most uniform structurally informative dissociation with all oligosaccharides studied. The ETD and CID spectra were complementary. Graphical Abstract ᅟ.
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Affiliation(s)
- Ranelle M Schaller-Duke
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Mallikharjuna R Bogala
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Carolyn J Cassady
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA.
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24
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Chen G, Zhang Y, Trinidad JC, Dann C. Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:455-462. [PMID: 29313205 DOI: 10.1007/s13361-017-1854-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/15/2017] [Accepted: 11/18/2017] [Indexed: 06/07/2023]
Abstract
Sulfotyrosine and phosphotyrosine are two post-translational modifications present in higher eukaryotes. A simple and direct mass spectrometry method to distinguish between these modifications is crucial to advance our understanding of the sulfoproteome. While sulfation and phosphorylation are nominally isobaric, the accurate mass of the sulfuryl moiety is 9.6 mDa less than the phosphoryl moiety. Based on this difference, we have used an Orbitrap Fusion Lumos mass spectrometer to characterize, resolve, and distinguish between sulfotyrosine and phosphotyrosine modifications using a set of model peptides. Multiple fragmentation techniques, namely HCD, CID, ETD, ETciD, and EThcD, have been used to compare the different fragmentation behaviors between peptides modified with these species. Sulfotyrosine undergoes neutral loss using HCD and CID, but the sulfuryl moiety is largely stable under ETD. In contrast, phosphotyrosine is stable during fragmentation using all these methods. This differential stability provides a mechanism to distinguish sulfopeptides from phosphopeptides. Based on the rigorous characterization presented herein, this work serves as a model for accurate identification of phosphotyrosine and, more challenging, sulfotyrosine, in complex proteomic samples. Graphical Abstract ᅟ.
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Affiliation(s)
- Guangming Chen
- Department of Chemistry and Interdisciplinary Graduate Program in Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Yixiang Zhang
- Department of Chemistry and Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, IN, 47405, USA
| | - Jonathan C Trinidad
- Department of Chemistry and Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, IN, 47405, USA.
| | - Charles Dann
- Department of Chemistry and Interdisciplinary Graduate Program in Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
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25
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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: 2.2] [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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26
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Anderson LC, Håkansson M, Walse B, Nilsson CL. Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1796-1804. [PMID: 28681360 PMCID: PMC5556139 DOI: 10.1007/s13361-017-1705-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/16/2023]
Abstract
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a ~45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. Graphical Abstract ᅟ.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Carol L Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX, 77555-1074, USA.
- Institute of Clinical Sciences-Lund, Lund University, SE-221 85, Lund, Sweden.
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27
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Nišavić M, Hozić A, Hameršak Z, Radić M, Butorac A, Duvnjak M, Cindrić M. High-Efficiency Microflow and Nanoflow Negative Electrospray Ionization of Peptides Induced by Gas-Phase Proton Transfer Reactions. Anal Chem 2017; 89:4847-4854. [DOI: 10.1021/acs.analchem.6b04466] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marija Nišavić
- Vinča
Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Amela Hozić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Zdenko Hameršak
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Martina Radić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Ana Butorac
- BIOCentre, Central
Lab Services, Zagreb, Croatia
| | - Marija Duvnjak
- Faculty
of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Mario Cindrić
- Ruđer Bošković
Institute, Bijenička cesta 54, Zagreb, Croatia
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28
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Robinson MR, Brodbelt JS. Integrating Weak Anion Exchange and Ultraviolet Photodissociation Mass Spectrometry with Strategic Modulation of Peptide Basicity for the Enrichment of Sulfopeptides. Anal Chem 2016; 88:11037-11045. [PMID: 27768275 DOI: 10.1021/acs.analchem.6b02899] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Tyrosine sulfation is an important post-translational modification but remains difficult to detect in biological samples owing to its low stoichiometric abundance and the lack of effective enrichment methods. In the present study, weak anion exchange (WAX) is evaluated for the enrichment of sulfopeptides that have been modified via carbamylation to convert all primary amines to less basic carbamates. The decrease in basicity enhanced the binding of carbamylated sulfopeptides to WAX resin relative to nonsulfated peptides. Upon elution and electrospray ionization in the negative mode, ultraviolet photodissociation (UVPD) was applied for peptide sequencing. Application of the method to a tryptic digest of bovine coagulation factor V resulted in identification of sulfation on tyrosine 1513.
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Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, The University of Texas , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas , Austin, Texas 78712, United States
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29
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Riley NM, Bern M, Westphall MS, Coon JJ. Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation. J Proteome Res 2016; 15:2768-76. [PMID: 27402189 DOI: 10.1021/acs.jproteome.6b00319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Negative electron-transfer dissociation (NETD) has emerged as a premier tool for peptide anion analysis, offering access to acidic post-translational modifications and regions of the proteome that are intractable with traditional positive-mode approaches. Whole-proteome scale characterization is now possible with NETD, but proper informatic tools are needed to capitalize on advances in instrumentation. Currently only one database search algorithm (OMSSA) can process NETD data. Here we implement NETD search capabilities into the Byonic platform to improve the sensitivity of negative-mode data analyses, and we benchmark these improvements using 90 min LC-MS/MS analyses of tryptic peptides from human embryonic stem cells. With this new algorithm for searching NETD data, we improved the number of successfully identified spectra by as much as 80% and identified 8665 unique peptides, 24 639 peptide spectral matches, and 1338 proteins in activated-ion NETD analyses, more than doubling identifications from previous negative-mode characterizations of the human proteome. Furthermore, we reanalyzed our recently published large-scale, multienzyme negative-mode yeast proteome data, improving peptide and peptide spectral match identifications and considerably increasing protein sequence coverage. In all, we show that new informatics tools, in combination with recent advances in data acquisition, can significantly improve proteome characterization in negative-mode approaches.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Marshall Bern
- Protein Metrics, Inc. , San Carlos, California 94070, United States
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Genome Center of Wisconsin, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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30
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Paciotti R, Coletti C, Re N, Scuderi D, Chiavarino B, Fornarini S, Crestoni ME. Serine O-sulfation probed by IRMPD spectroscopy. Phys Chem Chem Phys 2016; 17:25891-904. [PMID: 26027702 DOI: 10.1039/c5cp01409c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sulfation of amino acids is a frequent post-translational modification. It is highly labile, though, and characterizing it by mass spectrometry, an otherwise powerful and widely exploited tool in analytical proteomics, is a challenge. The presently reported study is aimed at revealing the O-sulfation of l-serine and elucidating the effects of protonation and deprotonation on the structure and stability of the ensuing ionic species, [sSer + H](+) and [sSer - H](-). These ions are obtained as gaseous, isolated species by electrospray ionization, trapped in a Paul ion-trap, and sampled by IR multiple photon dissociation (IRMPD) spectroscopy in either the 750-1900 cm(-1) fingerprint range, or the 2900 and 3700 cm(-1) range encompassing the N-H and O-H stretching modes. The recorded IRMPD spectra present diagnostic signatures of the sulfate modification which are missing in the spectra of the native serine ions, [Ser + H](+) and [Ser - H](-). The experimental IRMPD features have been interpreted by comparison with the linear IR spectra of the lowest energy structures that are likely candidates for the sampled ions, calculated at the M06-2X/6-311+G(d,p) level of theory. Evidence is gathered that the most stable conformations of [sSer + H](+) are stabilized by hydrogen bonding interactions between the protonated amino group and both the carbonyl and sulfate oxygens. [sSer - H](-) ions possess a negatively charged sulfate group involved in either a S=O···HN or a S=O···HO hydrogen bond. The experimental IRMPD spectra are consistent with the presence of multiple low-lying structures in a thermally equilibrated population of several species particularly in the case of [sSer - H](-) ions, where the high structural flexibility combined with the presence of a negative charge favors the co-existence of several different H-bonding motifs.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
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31
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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32
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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33
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Riley NM, Rush MJP, Rose CM, Richards AL, Kwiecien NW, Bailey DJ, Hebert AS, Westphall MS, Coon JJ. The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD). Mol Cell Proteomics 2015; 14:2644-60. [PMID: 26193884 DOI: 10.1074/mcp.m115.049726] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 01/15/2023] Open
Abstract
The field of proteomics almost uniformly relies on peptide cation analysis, leading to an underrepresentation of acidic portions of proteomes, including relevant acidic posttranslational modifications. Despite the many benefits negative mode proteomics can offer, peptide anion analysis remains in its infancy due mainly to challenges with high-pH reversed-phase separations and a lack of robust fragmentation methods suitable for peptide anion characterization. Here, we report the first implementation of activated ion negative electron transfer dissociation (AI-NETD) on the chromatographic timescale, generating 7,601 unique peptide identifications from Saccharomyces cerevisiae in single-shot nLC-MS/MS analyses of tryptic peptides-a greater than 5-fold increase over previous results with NETD alone. These improvements translate to identification of 1,106 proteins, making this work the first negative mode study to identify more than 1,000 proteins in any system. We then compare the performance of AI-NETD for analysis of peptides generated by five proteases (trypsin, LysC, GluC, chymotrypsin, and AspN) for negative mode analyses, identifying as many as 5,356 peptides (1,045 proteins) with LysC and 4,213 peptides (857 proteins) with GluC in yeast-characterizing 1,359 proteins in total. Finally, we present the first deep-sequencing approach for negative mode proteomics, leveraging offline low-pH reversed-phase fractionation prior to online high-pH separations and peptide fragmentation with AI-NETD. With this platform, we identified 3,467 proteins in yeast with trypsin alone and characterized a total of 3,730 proteins using multiple proteases, or nearly 83% of the expressed yeast proteome. This work represents the most extensive negative mode proteomics study to date, establishing AI-NETD as a robust tool for large-scale peptide anion characterization and making the negative mode approach a more viable platform for future proteomic studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Joshua J Coon
- From the ‡Department of Chemistry, §Genome Center, and ¶Department of Biomolecular Chemistry University of Wisconsin, Madison, Wisconsin, 53706
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34
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Donohoe GC, Khakinejad M, Valentine SJ. Ion mobility spectrometry-hydrogen deuterium exchange mass spectrometry of anions: part 1. Peptides to proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:564-576. [PMID: 25510931 DOI: 10.1007/s13361-014-1045-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/28/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.
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Affiliation(s)
- Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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35
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Robinson MR, Moore KL, Brodbelt JS. Direct identification of tyrosine sulfation by using ultraviolet photodissociation mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1461-71. [PMID: 24845354 PMCID: PMC4108549 DOI: 10.1007/s13361-014-0910-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/30/2014] [Accepted: 04/05/2014] [Indexed: 05/25/2023]
Abstract
Sulfation is a common post-translational modification of tyrosine residues in eukaryotes; however, detection using traditional liquid chromatography-mass spectrometry (LC-MS) methods is challenging based on poor ionization efficiency in the positive ion mode and facile neutral loss upon collisional activation. In the present study, 193 nm ultraviolet photodissociation (UVPD) is applied to sulfopeptide anions to generate diagnostic sequence ions, which do not undergo appreciable neutral loss of sulfate even using higher energy photoirradiation parameters. At the same time, neutral loss of SO₃ is observed from the precursor and charge-reduced precursor ions, a spectral feature that is useful for differentiating tyrosine sulfation from the nominally isobaric tyrosine phosphorylation. LC-MS detection limits for UVPD analysis in the negative mode were determined to be around 100 fmol for three sulfated peptides, caerulein, cionin, and leu-enkephalin. The LC-UVPD-MS method was applied for analysis of bovine fibrinogen, and its key sulfated peptide was confidently identified.
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Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, 78712, USA
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36
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Patrick AL, Stedwell CN, Polfer NC. Differentiating sulfopeptide and phosphopeptide ions via resonant infrared photodissociation. Anal Chem 2014; 86:5547-52. [PMID: 24823797 DOI: 10.1021/ac500992f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The post-translational modifications sulfation and phosphorylation pose special challenges to mass spectral analysis due to their isobaric nature and their lability in the gas phase, as both types of peptides dissociate through similar channels upon collisional activation. Here, we present resonant infrared photodissociation based on diagnostic sulfate and phosphate OH stretches, as a means to differentiate sulfated from phosphorylated peptides within the framework of a mass spectrometry platform. The approach is demonstrated for a number of tyrosine-containing peptides, ranging from dipeptides (YG, pYG, and sYG) over tripeptides (GYR, GpYR, and GsYR), to more biologically relevant enkephalin peptides (YGGFL, pYGGFL, and sYGGFL). In all cases, the diagnostic ranges for sulfate OH stretches are established as 3580-3600 cm(-1) and can thus be distinguished from other characteristic hydrogen stretches, such as carboxylic acid OH, alcohol OH, and phosphate OH stretches.
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Affiliation(s)
- Amanda L Patrick
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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37
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Kailemia MJ, Ruhaak LR, Lebrilla CB, Amster IJ. Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal Chem 2014; 86:196-212. [PMID: 24313268 PMCID: PMC3924431 DOI: 10.1021/ac403969n] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - L. Renee Ruhaak
- Department of Chemistry, University of California at Davis, Davis, CA 95616
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