1
|
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.
Collapse
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
| |
Collapse
|
2
|
Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
Collapse
Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Baba T, Rajabi K, Liu S, Ryumin P, Zhang Z, Pohl K, Causon J, Le Blanc JCY, Kurogochi M. Electron Impact Excitation of Ions from Organics on Singly Protonated Peptides with and without Post-Translational Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1723-1732. [PMID: 35948044 DOI: 10.1021/jasms.2c00146] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report on the dissociation of singly protonated peptides by electrons using electron-activated dissociation (EAD), which comprises electron impact excitation of ions from organics (EIEIO), electronic-excitation dissociation (EED), and electron ionization dissociation (EIoD). Various singly protonated peptides were dissociated using a recently reported fast EAD device. The dissociation can be induced through two pathways: (i) vibrational dissociation similar to collision-activated dissociation (CAD, or collision-induced dissociation, CID) by relaxation from a molecular electronic excited state to high vibrational states; and (ii) radical-induced dissociation where molecular electronic excitation is followed by homolytic cleavage. EAD is complementary to CAD as additional molecular information can be obtained; e.g., fragile PTM moieties, such as glycosylation and sulfation, can be localized. Simultaneously, the energetic production of radical z• fragments enables Leu and Ile discrimination, like in a hot ECD process. Using the fast EAD device, LC-EIEIO-time-of-flight mass spectrometry was applied to a tryptic monoclonal antibody digest containing short singly protonated peptides.
Collapse
Affiliation(s)
- Takashi Baba
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Khadijeh Rajabi
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Suya Liu
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Pavel Ryumin
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Zoe Zhang
- SCIEX, 1201 Radio Rd, Redwood City, California 94065, United States
| | - Kerstin Pohl
- SCIEX, 500 Old Connecticut Path, Framingham, Massachusetts 01701, United States
| | - Jason Causon
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | | | - Masaki Kurogochi
- The Noguchi Institute, 1-9-7, Kaga, Itabashi-ku, Tokyo 173-0003, Japan
| |
Collapse
|
6
|
Baba T, Ryumin P, Duchoslav E, Chen K, Chelur A, Loyd B, Chernushevich I. Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1964-1975. [PMID: 34080873 DOI: 10.1021/jasms.0c00425] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report the progress on an electron-activated dissociation (EAD) device coupled to a quadrupole TOF mass spectrometer (QqTOF MS) developed in our group. This device features a new electron beam optics design allowing up to 100 times stronger electron currents in the reaction cell. The electron beam current reached the space-charge limit of 0.5 μA at near-zero electron kinetic energies. These advances enable fast and efficient dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. Tunable electron energy provides access to different fragmentation regimes: ECD, hot ECD, and electron-impact excitation of ions from organics (EIEIO). The efficiency of the device was tested on a wide range of precursor charge states. The EAD device was installed in a QqTOF MS employing a novel trap-and-release strategy facilitating spatial mass focusing of ions at the center of the TOF accelerator. This technique increased the sensitivity 6-10 times and allows for the first time comprehensive structural lipidomics on an LC time scale. The system was evaluated for other compound classes such as intact proteins and glycopeptides. Application of hot ECD for the analysis of glycopeptides resulted in rich fragmentation with predominantly peptide backbone fragments; however, glycan fragments attributed to the ECD process were also observed. A standard small protein ubiquitin (8.6 kDa) was sequenced with 90% cleavage coverage at spectrum accumulation times of 100 ms and 98% at 800 ms. Comparable cleavage coverage for a medium-size protein (carbonic anhydrase: 29 kDa) could be achieved, albeit with longer accumulation times.
Collapse
Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Pavel Ryumin
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Eva Duchoslav
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Keqin Chen
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Anjali Chelur
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Bill Loyd
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | | |
Collapse
|
7
|
Commodore JJ, Cassady CJ. Electron transfer dissociation mass spectrometry of acidic phosphorylated peptides cationized with trivalent praseodymium. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1178-1188. [PMID: 30221809 PMCID: PMC6291000 DOI: 10.1002/jms.4291] [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: 06/21/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
The lanthanide ion praseodymium, Pr(III), was employed to study metallated ion formation and electron transfer dissociation (ETD) of 27 biological and model highly acidic phosphopeptides. All phosphopeptides investigated form metallated ions by electrospray ionization (ESI) that can be studied by ETD to yield abundant sequence information. The ions formed are [M + Pr - H]2+ , [M + Pr]3+ , and [M + Pr + H]4+ . All biological phosphopeptides with a chain length of seven or more residues generate [M + Pr]3+ . For biological phosphopeptides, [M + Pr]3+ undergoes more backbone cleavage by ETD than [M + Pr - H]2+ and, in some cases, full sequence coverage occurs. Acidic model phosphorylated hexa-peptides and octa-peptides, composed of alanine residues and one phosphorylated residue, form exclusively [M + Pr - H]2+ by ESI. Limited sequence information is obtained by ETD of [M + Pr - H]2+ with only metallated product ions being generated. For two biological phosphopeptides, [M + Pr + H]4+ is observed and may be due to the presence of at least one residue with a highly basic side chain that facilitates the addition of an extra proton. For the model phosphopeptides, more sequence coverage occurs when the phosphorylated residue is in the middle of the sequence than at either the N- or C-terminus. ETD of the metallated precursor ions formed by ESI generates exclusively metallated and nonmetallated c- and z-ions for the biological phosphopeptides, while metallated c-ions, z-ions, and a few y-ions form for the model phosphopeptides. Most of the product ions contain the phosphorylated residue indicating that the metal ion binds predominantly at the deprotonated phosphate group. The results of this study indicate that ETD is a promising tool for sequencing highly acidic phosphorylated peptides by metal adduction with Pr (III) and, by extension, all nonradioactive lanthanide metal ions.
Collapse
Affiliation(s)
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama, USA
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Jeanne Dit Fouque K, Moreno J, Hegemann JD, Zirah S, Rebuffat S, Fernandez-Lima F. Metal ions induced secondary structure rearrangements: mechanically interlocked lassovs.unthreaded branched-cyclic topoisomers. Analyst 2018; 143:2323-2333. [DOI: 10.1039/c8an00138c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change.
Collapse
Affiliation(s)
| | - Javier Moreno
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | | | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
| | | |
Collapse
|
10
|
Commodore JJ, Cassady CJ. Effects of acidic peptide size and sequence on trivalent praseodymium adduction and electron transfer dissociation mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:218-229. [PMID: 28170125 PMCID: PMC5407459 DOI: 10.1002/jms.3919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/31/2017] [Accepted: 02/02/2017] [Indexed: 05/05/2023]
Abstract
Using the lanthanide ion praseodymium, Pr(III), metallated ion formation and electron transfer dissociation (ETD) were studied for 25 biological and model acidic peptides. For chain lengths of seven or more residues, even highly acidic peptides that can be difficult to protonate by electrospray ionization will metallate and undergo abundant ETD fragmentation. Peptides composed of predominantly acidic residues form only the deprotonated ion, [M + Pr - H]2+ ; this ion yields near complete ETD sequence coverage for larger peptides. Peptides with a mixture of acidic and neutral residues generate [M + Pr]3+ , which cleaves between every residue for many peptides. Acidic peptides that contain at least one residue with a basic side chain also produce the protonated ion, [M + Pr + H]4+ ; this ion undergoes the most extensive sequence coverage by ETD. Primarily metallated and non-metallated c- and z-ions form for all peptides investigated. Metal adducted product ions are only present when at least half of the peptide sequence can be incorporated into the ion; this suggests that the metal ion simultaneously attaches to more than one acidic site. The only site consistently lacking dissociation is at the N-terminal side of a proline residue. Increasing peptide chain length generates more backbone cleavage for metal-peptide complexes with the same charge state. For acidic peptides with the same length, increasing the precursor ion charge state from 2+ to 3+ also leads to more cleavage. The results of this study indicate that highly acidic peptides can be sequenced by ETD of complexes formed with Pr(III). Copyright © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
| | - Carolyn J. Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487
| |
Collapse
|
11
|
Commodore JJ, Cassady CJ. The Effects of Trivalent Lanthanide Cationization on the Electron Transfer Dissociation of Acidic Fibrinopeptide B and its Analogs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1499-509. [PMID: 27294379 PMCID: PMC4974135 DOI: 10.1007/s13361-016-1428-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/22/2016] [Accepted: 05/23/2016] [Indexed: 05/08/2023]
Abstract
Electrospray ionization (ESI) on mixtures of acidic fibrinopeptide B and two peptide analogs with trivalent lanthanide salts generates [M + Met + H](4+), [M + Met](3+), and [M + Met -H](2+), where M = peptide and Met = metal (except radioactive promethium). These ions undergo extensive and highly efficient electron transfer dissociation (ETD) to form metallated and non-metallated c- and z-ions. All metal adducted product ions contain at least two acidic sites, which suggest attachment of the lanthanide cation at the side chains of one or more acidic residues. The three peptides undergo similar fragmentation. ETD on [M + Met + H](4+) leads to cleavage at every residue; the presence of both a metal ion and an extra proton is very effective in promoting sequence-informative fragmentation. Backbone dissociation of [M + Met](3+) is also extensive, although cleavage does not always occur between adjacent glutamic acid residues. For [M + Met - H ](2+), a more limited range of product ions form. All lanthanide metal peptide complexes display similar fragmentation except for europium (Eu). ETD on [M + Eu - H](2+) and [M + Eu](3+) yields a limited amount of peptide backbone cleavage; however, [M + Eu + H](4+) dissociates extensively with cleavage at every residue. With the exception of the results for Eu(III), metallated peptide ion formation by ESI, ETD fragmentation efficiencies, and product ion formation are unaffected by the identity of the lanthanide cation. Adduction with trivalent lanthanide metal ions is a promising tool for sequence analysis of acidic peptides by ETD. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
| | - Carolyn J Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA.
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, I-66100 Chieti, Italy
| | | | | | | | | | | | | |
Collapse
|
13
|
Chen X, Liu G, Elaine Wong YL, Deng L, Wang Z, Li W, Dominic Chan TW. Dissociation of trivalent metal ion (Al(3+), Ga(3+), In(3+) and Rh(3+))--peptide complexes under electron capture dissociation conditions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:705-710. [PMID: 26864523 DOI: 10.1002/rcm.7502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/24/2015] [Accepted: 12/24/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The electron capture dissociation (ECD) of proteins/peptides is affected by the nature of charge carrier. It has been reported that transition metal ions could tune the ECD pathway of peptides. To further explore the charge carrier effect of metal ions, ECD of peptides adducted with trivalent transition metal ions, including group IIIB (Al(3+), Ga(3+), and In(3+) ) and Rh(3+), were investigated and compared with that of the lanthanide ion (Ln(3+)). METHODS Bradykinin-derived peptides were used as model peptides to probe the dissociation pathways. The ECD experiments were performed on a Bruker APEX III 4.7T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. RESULTS Typical c-/z-ions with and without metal ions were observed in the ECD of peptides adducted with Group IIIB metal ions as charge carriers. Connection of non-metalated c-ions and metalated z-ions at the position of the serine residue indicated that serine is one of the binding sites of the metal ion on the model peptides. Typical slow heating ions, including metalated a-/b-ions and non-metalated y-ions, were generated in ECD of Rh(3+) -adducted peptides. CONCLUSIONS Based on the experimental results, it is proposed that (i) for Group IIIB metal ion-peptide complexes, the incoming electron is captured by the proton in the salt-bridge structures of precursor ions; (ii) for Rh(3+) -peptide complexes, the incoming electron is captured by the metal ion due to the formation of charge-solvated precursor ions formed through arginine residue-metal coordination. Our results indicate that the heterogeneity of precursor ions plays an important role for the ECD of metalated peptides.
Collapse
Affiliation(s)
- Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
- Shandong Academy of Sciences, Jinan, Shandong, P. R. China
| | - Guoqiang Liu
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - Y L Elaine Wong
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - Liulin Deng
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Washington, USA
| | - Ze Wang
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - Wan Li
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR
| |
Collapse
|
14
|
Asakawa D, Yamashita A, Kawai S, Takeuchi T, Wada Y. N-Cα Bond Cleavage of Zinc-Polyhistidine Complexes in Electron Transfer Dissociation Mediated by Zwitterion Formation: Experimental Evidence and Theoretical Analysis of the Utah-Washington Model. J Phys Chem B 2016; 120:891-901. [PMID: 26673038 DOI: 10.1021/acs.jpcb.5b11118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of gas-phase ions are widely used for peptide/protein sequencing by mass spectrometry. To understand the general mechanism of ECD/ETD of peptides, we focused on the ETD fragmentation of metal-peptide complexes in the absence of remote protons. Since Zn(2+) strongly binds to neutral histidine residues in peptides, Zn(2+)-polyhistidine complexation does not generate any remote protons. However, in the absence of remote protons, electron transfer to the Zn(2+)-polyhistidine complex induced the N-Cα bond cleavage. The formation pathway for the ETD products was investigated by density functional theory calculations. The calculations showed that the charge-reduced zinc-peptide radical, [M + Zn](•+), can exist in the low-energy zwitterionic amide π* states, which underwent homolytic N-Cα bond dissociation. The homolytic cleavage resulted in the donation of an electron from the N-Cα bond to the nitrogen atom, producing an iminoenol c' anion. The counterpart z(•) radical contained a radical site on the α-carbon atom. The iminoenol c' anion then abstracted a proton to presumably form the more stable amide c' fragment. The current experimental and computational joint study strongly suggested that the N-Cα bond cleavage occurred through the aminoketyl radical-anion formation for Zn(2+)-polyhistidine complexes in ETD.
Collapse
Affiliation(s)
- Daiki Asakawa
- National Metrology Institute of Japan (NMIJ), Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba Central 2, Umezono 1-1-1, Tsukuba, Ibaraki, 305-8568, Japan
| | - Asuka Yamashita
- Department of Chemistry, Faculty of Science, Nara Women's University , Kitauoyanishi-machi, Nara, 630-8506, Japan
| | - Shikiho Kawai
- Department of Chemistry, Faculty of Science, Nara Women's University , Kitauoyanishi-machi, Nara, 630-8506, Japan
| | - Takae Takeuchi
- Department of Chemistry, Faculty of Science, Nara Women's University , Kitauoyanishi-machi, Nara, 630-8506, Japan
| | - Yoshinao Wada
- Department of Molecular Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health , Murodo-cho 840, Izumi, Osaka, 594-1101, Japan
| |
Collapse
|
15
|
Voinov VG, Hoffman PD, Bennett SE, Beckman JS, Barofsky DF. Electron Capture Dissociation of Sodium-Adducted Peptides on a Modified Quadrupole/Time-of-Flight Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2096-104. [PMID: 26266643 PMCID: PMC6726120 DOI: 10.1007/s13361-015-1230-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 05/02/2023]
Abstract
Electron capture dissociation (ECD), which generally preserves the position of labile post-translational modifications, can be a powerful method for de novo sequencing of proteins and peptides. In this report, ECD product-ion mass spectra of singly and doubly sodiated, nonphosphorylated, and phosphorylated peptides are presented and compared with the ECD mass spectra of their protonated counterparts. ECD of doubly charged, singly sodiated peptides yielded essentially the same sequence information as was produced by the corresponding doubly protonated peptides. The presence of several sodium binding sites on the polypeptide backbone, however, resulted in more complicated spectra. This situation is aggravated by the zwitterionic equilibrium of the free acid peptide precursors. The product-ion spectra of doubly and triply charged peptides possessing two sodium ions were further complicated by the existence of isomers created by the differential distribution of sodium binding sites. Triply charged, phosphorylated precursors containing one sodium, wherein the sodium is attached exclusively to the PO4 group, were found to be as useful for sequence analysis as the fully protonated species. Although sodium adducts are generally minimized during sample preparation, it appears that they can nonetheless provide useful sequence information. Additionally, they enable straightforward identification of a peptide's charge state, even on low-resolution instruments. The experiments were carried out using a radio frequency-free electromagnetostatic cell retrofitted into the collision-induced dissociation (CID) section of a hybrid quadrupole/time-of-flight tandem mass spectrometer. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Valery G Voinov
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA.
- Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia.
| | - Peter D Hoffman
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - Samuel E Bennett
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - Joseph S Beckman
- Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Douglas F Barofsky
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, 78712, USA
| | | | | |
Collapse
|
18
|
Sweet SMM, Cooper HJ. Electron capture dissociation in the analysis of protein phosphorylation. Expert Rev Proteomics 2014; 4:149-59. [PMID: 17425452 DOI: 10.1586/14789450.4.2.149] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein phosphorylation is a widespread and important post-translational modification. Despite recent advances in phosphoproteomic methods, phosphopeptide identification and site localization remain challenging. Electron capture dissociation has inherent advantages for phosphorylation analysis. The use of electron capture dissociation in this area to date is reviewed and future prospects are outlined.
Collapse
Affiliation(s)
- Steve M M Sweet
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, UK.
| | | |
Collapse
|
19
|
Zhou W, Håkansson K. Electron capture dissociation of divalent metal-adducted sulfated N-glycans released from bovine thyroid stimulating hormone. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1798-806. [PMID: 23982932 PMCID: PMC3867818 DOI: 10.1007/s13361-013-0700-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 07/03/2013] [Accepted: 07/06/2013] [Indexed: 05/04/2023]
Abstract
Sulfated N-glycans released from bovine thyroid stimulating hormone (bTSH) were ionized with the divalent metal cations Ca(2+), Mg(2+), and Co by electrospray ionization (ESI). These metal-adducted species were subjected to infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD) and the corresponding fragmentation patterns were compared. IRMPD generated extensive glycosidic and cross-ring cleavages, but most product ions suffered from sulfonate loss. Internal fragments were also observed, which complicated the spectra. ECD provided complementary structural information compared with IRMPD, and all observed product ions retained the sulfonate group, allowing sulfonate localization. To our knowledge, this work represents the first application of ECD towards metal-adducted sulfated N-glycans released from a glycoprotein. Due to the ability of IRMPD and ECD to provide complementary structural information, the combination of the two strategies is a promising and valuable tool for glycan structural characterization. The influence of different metal ions was also examined. Calcium adducts appeared to be the most promising species because of high sensitivity and ability to provide extensive structural information.
Collapse
Affiliation(s)
- Wen Zhou
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
20
|
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
| | | |
Collapse
|
21
|
Kalli A, Sweredoski MJ, Hess S. Data-Dependent Middle-Down Nano-Liquid Chromatography–Electron Capture Dissociation-Tandem Mass Spectrometry: An Application for the Analysis of Unfractionated Histones. Anal Chem 2013; 85:3501-7. [DOI: 10.1021/ac303103b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anastasia Kalli
- Proteome Exploration Laboratory,
Division of Biology,
Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Michael J. Sweredoski
- Proteome Exploration Laboratory,
Division of Biology,
Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Sonja Hess
- Proteome Exploration Laboratory,
Division of Biology,
Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
22
|
Cantel S, Brunel L, Ohara K, Enjalbal C, Martinez J, Vasseur JJ, Smietana M. An innovative strategy for sulfopeptides analysis using MALDI-TOF MS reflectron positive ion mode. Proteomics 2012; 12:2247-57. [DOI: 10.1002/pmic.201100525] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et 2; Montpellier France
| | - Luc Brunel
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et 2; Montpellier France
| | - Keiichiro Ohara
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et 2; Montpellier France
| | - Christine Enjalbal
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et 2; Montpellier France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et 2; Montpellier France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et 2; Montpellier France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et 2; Montpellier France
| |
Collapse
|
23
|
Mass Spectrometry-based Proteomics and Peptidomics for Systems Biology and Biomarker Discovery. ACTA ACUST UNITED AC 2012; 7:313-335. [PMID: 24504115 DOI: 10.1007/s11515-012-1218-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large datasets of proteins or peptides involved in various biological and disease progression processes producing testable hypothesis for complex biological questions. This review provides an introduction and insight to relevant topics in proteomics and peptidomics including biological material selection, sample preparation, separation techniques, peptide fragmentation, post-translation modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature and remaining challenges and emerging technologies for proteomics and peptidomics are presented.
Collapse
|
24
|
Hersberger KE, Håkansson K. Characterization of O-sulfopeptides by negative ion mode tandem mass spectrometry: superior performance of negative ion electron capture dissociation. Anal Chem 2012; 84:6370-7. [PMID: 22770115 DOI: 10.1021/ac301536r] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Positive ion mode collision-activated dissociation tandem mass spectrometry (CAD MS/MS) of O-sulfopeptides precludes determination of sulfonated sites due to facile proton-driven loss of the highly labile sulfonate groups. A previously proposed method for localizing peptide and protein O-sulfonation involves derivatization of nonsulfonated tyrosines followed by positive ion CAD MS/MS of the corresponding modified sulfopeptides for diagnostic sulfonate loss. This indirect method relies upon specific and complete derivatization of nonsulfonated tyrosines. Alternative MS/MS activation methods, including positive ion metastable atom-activated dissociation (MAD) and metal-assisted electron transfer dissociation (ETD) or electron capture dissociation (ECD) provide varying degrees of sulfonate retention. Sulfonate retention has also been reported following negative ion MAD and electron detachment dissociation (EDD), which also operates in negative ion mode in which sulfonate groups are less labile than in positive ion mode. However, an MS/MS activation technique that can effectively preserve sulfonate groups while providing extensive backbone fragmentation (translating to sequence information, including sulfonated sites) with little to no noninformative small molecule neutral loss has not previously been realized. Here, we report that negative ion CAD, EDD, and negative ETD (NETD) result in sulfonate retention mainly at higher charge states with varying degrees of fragmentation efficiency and sequence coverage. Similar to previous observations from CAD of sulfonated glycosaminoglycan anions, higher charge states translate to a higher probability of deprotonation at the sulfonate groups thus yielding charge-localized fragmentation without loss of the sulfonate groups. However, consequently, higher sulfonate retention comes at the price of lower sequence coverage in negative ion CAD. Fragmentation efficiency/sequence coverage averaged 19/6% and 33/20% in EDD and NETD, respectively, both of which are only applicable to multiply-charged anions. In contrast, the recently introduced negative ion ECD showed an average fragmentation efficiency of 69% and an average sequence coverage of 82% with complete sulfonate retention from singly- and doubly-deprotonated sulfopeptide anions.
Collapse
Affiliation(s)
- Katherine E Hersberger
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
| | | |
Collapse
|
25
|
Brunet C, Antoine R, Dugourd P, Canon F, Giuliani A, Nahon L. Formation and fragmentation of radical peptide anions: insights from vacuum ultra violet spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:274-281. [PMID: 22083590 DOI: 10.1007/s13361-011-0285-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 05/31/2023]
Abstract
We have studied the photodissociation of gas-phase deprotonated caerulein anions by vacuum ultraviolet (VUV) photons in the 4.5 to 20 eV range, as provided by the DESIRS beamline at the synchrotron radiation facility SOLEIL (France). Caerulein is a sulphated peptide with three aromatic residues and nine amide bonds. Electron loss is found to be the major relaxation channel at every photon energy. However, an increase in the fragmentation efficiency (neutral losses and peptide backbone cleavages) as a function of the energy is also observed. The oxidized ions, generated by electron photodetachment were further isolated and activated by collision (CID) in a MS(3) scheme. The branching ratios of the different fragments observed by CID as a function of the initial VUV photon energy are found to be independent of the initial photon energy. Thus, there is no memory effect of the initial excitation energy on the fragmentation channels of the oxidized species on the time scale of our tandem MS experiment. We also report photofragment yields as a function of photon energy for doubly deprotonated caerulein ions, for both closed-shell ([M-2H](2-)) non-radical ions and open-shell ([M-3H](2-•)) radical ions. These latter ions are generated by electron photodetachment from [M-3H](3-) precursor ions. The detachment yield increases monotonically with the energy with the appearance of several absorption bands. Spectra for radical and non-radical ions are quite similar in terms of observed bands; however, the VUV fragmentation yield is enhanced by the presence of a radical in caerulein peptides.
Collapse
|
26
|
Chen X, Fung YME, Chan WYK, Wong PS, Yeung HS, Chan TWD. Transition metal ions: charge carriers that mediate the electron capture dissociation pathways of peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2232-2245. [PMID: 21952786 DOI: 10.1007/s13361-011-0246-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/31/2011] [Accepted: 09/04/2011] [Indexed: 05/31/2023]
Abstract
Electron capture dissociation (ECD) of model peptides adducted with first row divalent transition metal ions, including Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+), were investigated. Model peptides with general sequence of ZGGGXGGGZ were used as probes to unveil the ECD mechanism of metalated peptides, where X is either V or W; and Z is either R or N. Peptides metalated with different divalent transition metal ions were found to generate different ECD tandem mass spectra. ECD spectra of peptides metalated by Mn(2+) and Zn(2+) were similar to those generated by ECD of peptides adducted with alkaline earth metal ions. Series of c-/z-type fragment ions with and without metal ions were observed. ECD of Fe(2+), Co(2+), and Ni(2+) adducted peptides yielded abundant metalated a-/y-type fragment ions; whereas ECD of Cu(2+) adducted peptides generated predominantly metalated b-/y-type fragment ions. From the present experimental results, it was postulated that electronic configuration of metal ions is an important factor in determining the ECD behavior of the metalated peptides. Due presumably to the stability of the electronic configuration, metal ions with fully-filled (i.e., Zn(2+)) and half filled (i.e., Mn(2+)) d-orbitals might not capture the incoming electron. Dissociation of the metal ions adducted peptides would proceed through the usual ECD channel(s) via "hot-hydrogen" or "superbase" intermediates, to form series of c-/z(•)- fragments. For other transition metal ions studied, reduction of the metal ions might occur preferentially. The energy liberated by the metal ion reduction would provide enough internal energy to generate the "slow-heating" type of fragment ions, i.e., metalated a-/y- fragments and metalated b-/y- fragments.
Collapse
Affiliation(s)
- Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | | | | | | | | | | |
Collapse
|
27
|
Watson HM, Vincent JB, Cassady CJ. Effects of transition metal ion coordination on the collision-induced dissociation of polyalanines. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1099-1107. [PMID: 22124980 DOI: 10.1002/jms.1992] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transition metal-polyalanine complexes were analyzed in a high-capacity quadrupole ion trap after electrospray ionization. Polyalanines have no polar amino acid side chains to coordinate metal ions, thus allowing the effects metal ion interaction with the peptide backbone to be explored. Positive mode mass spectra produced from peptides mixed with salts of the first row transition metals Cr(III), Fe(II), Fe(III), Co(II), Ni(II), Cu(I), and Cu(II) yield singly and doubly charged metallated ions. These precursor ions undergo collision-induced dissociation (CID) to give almost exclusively metallated N-terminal product ions whose types and relative abundances depend on the identity of the transition metal. For example, Cr(III)-cationized peptides yield CID spectra that are complex and have several neutral losses, whereas Fe(III)-cationized peptides dissociate to give intense non-metallated products. The addition of Cu(II) shows the most promise for sequencing. Spectra obtained from the CID of singly and doubly charged Cu-heptaalanine ions, [M + Cu - H](+) and [M + Cu](2+) , are complimentary and together provide cleavage at every residue and no neutral losses. (This contrasts with [M + H](+) of heptaalanine, where CID does not provide backbone ions to sequence the first three residues.) Transition metal cationization produces abundant metallated a-ions by CID, unlike protonated peptides that produce primarily b- and y-ions. The prominence of metallated a-ions is interesting because they do not always form from b-ions. Tandem mass spectrometry on metallated (Met = metal) a- and b-ions indicate that [b(n) + Met - H](2+) lose CO to form [a(n) + Met - H](2+), mimicking protonated structures. In contrast, [a(n) + Met - H](2+) eliminate an amino acid residue to form [a(n-1) + Met - H](2+), which may be useful in sequencing.
Collapse
Affiliation(s)
- Heather M Watson
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL, USA
| | | | | |
Collapse
|
28
|
Kim JS, Song SU, Kim HJ. Simultaneous identification of tyrosine phosphorylation and sulfation sites utilizing tyrosine-specific bromination. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1916-1925. [PMID: 21952757 DOI: 10.1007/s13361-011-0214-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 07/06/2011] [Accepted: 07/06/2011] [Indexed: 05/31/2023]
Abstract
Tyrosine phosphorylation and sulfation play many key roles in the cell. Isobaric phosphotyrosine and sulfotyrosine residues in peptides were determined by mass spectrometry using phosphatase or sulfatase to remove the phosphate or the sulfate group. Unique Br signature was introduced to the resulting tyrosine residues by incubation with 32% HBr at -20 °C for 20 min. MS/MS analysis of the brominated peptide enabled unambiguous determination of the phosphotyrosine and the sulfotyrosine sites. When phosphotyrosine and sulfotyrosine as well as free tyrosine were present in the same peptide, they could be determined simultaneously using either phosphatase or sulfatase following acetylation of the free tyrosine.
Collapse
Affiliation(s)
- Jong-Seo Kim
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea.
| | | | | |
Collapse
|
29
|
Cook SL, Jackson GP. Metastable atom-activated dissociation mass spectrometry of phosphorylated and sulfonated peptides in negative ion mode. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1088-99. [PMID: 21953050 DOI: 10.1007/s13361-011-0123-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/02/2011] [Accepted: 03/03/2011] [Indexed: 05/16/2023]
Abstract
The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were C(α) - C peptide backbone cleavages and neutral losses of CO(2), H(2)O, and [CO(2) + H(2)O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.
Collapse
Affiliation(s)
- Shannon L Cook
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701-2979, USA
| | | |
Collapse
|
30
|
Ganisl B, Valovka T, Hartl M, Taucher M, Bister K, Breuker K. Electron detachment dissociation for top-down mass spectrometry of acidic proteins. Chemistry 2011; 17:4460-9. [PMID: 21433149 PMCID: PMC3120980 DOI: 10.1002/chem.201003709] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 02/01/2023]
Abstract
Electron detachment dissociation (EDD) is an emerging mass spectrometry (MS) technique for the primary structure analysis of peptides, carbohydrates, and oligonucleotides. Herein, we explore the potential of EDD for sequencing of proteins of up to 147 amino acid residues by using top-down MS. Sequence coverage ranged from 72% for Melittin, which lacks carboxylic acid functionalities, to 19% for an acidic 147-residue protein, to 12% for Ferredoxin, which showed unusual backbone fragmentation next to cysteine residues. A limiting factor for protein sequencing by EDD is the facile loss of small molecules from amino acid side chains, in particular CO(2). Based on the types of fragments observed and fragmentation patterns found, we propose detailed mechanisms for protein backbone cleavage and side chain dissociation in EDD. The insights from this study should further the development of EDD for top-down MS of acidic proteins.
Collapse
Affiliation(s)
- Barbara Ganisl
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnrain 52a, 6020 Innsbruck (Austria), Fax: (+43) 512-507-2892 E-mail:
| | - Taras Valovka
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckPeter-Mayr-Strasse 1a, 6020 Innsbruck (Austria)
| | - Markus Hartl
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckPeter-Mayr-Strasse 1a, 6020 Innsbruck (Austria)
| | - Monika Taucher
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnrain 52a, 6020 Innsbruck (Austria), Fax: (+43) 512-507-2892 E-mail:
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckPeter-Mayr-Strasse 1a, 6020 Innsbruck (Austria)
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnrain 52a, 6020 Innsbruck (Austria), Fax: (+43) 512-507-2892 E-mail:
| |
Collapse
|
31
|
Sargaeva NP, Lin C, O’Connor PB. Unusual fragmentation of β-linked peptides by ExD tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:480-91. [PMID: 21472566 PMCID: PMC4361814 DOI: 10.1007/s13361-010-0049-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 11/18/2010] [Accepted: 11/18/2010] [Indexed: 05/11/2023]
Abstract
Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β(3)-type amino acid that has an additional methylene group in the backbone, forming a C(α)-C(β) bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a C(α)-C(β) bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N-C(β) and C(α)-C(β) bond cleavages were rare, providing few c and z• type fragments, which was attributed to the instability of the C(β) radical. Instead, the electron capture resulted primarily in the formation of a• and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.
Collapse
Affiliation(s)
- Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| |
Collapse
|
32
|
Chen X, Chan WYK, Wong PS, Yeung HS, Chan TWD. Formation of peptide radical cations (m+·) in electron capture dissociation of peptides adducted with group IIB metal ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:233-244. [PMID: 21472583 DOI: 10.1007/s13361-010-0035-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 05/30/2023]
Abstract
Peptides adducted with different divalent Group IIB metal ions (Zn(2+), Cd(2+), and Hg(2+)) were found to give very different ECD mass spectra. ECD of Zn(2+) adducted peptides gave series of c-/z-type fragment ions with and without metal ions. ECD of Cd(2+) and Hg(2+) adducted model peptides gave mostly a-type fragment ions with M(+•) and fragment ions corresponding to losses of neutral side chain from M(+•). No detectable a-ions could be observed in ECD spectra of Zn(2+) adducted peptides. We rationalized the present findings by invoking both proton-electron recombination and metal-ion reduction processes. As previously postulated, divalent metal-ions adducted peptides could adopt several forms, including (a) [M + Cat](2+), (b) [(M + Cat - H) + H](2+), and (c) [(M + Cat - 2H) + 2H](2+). The relative population of these precursor ions depends largely on the acidity of the metal-ion peptide complexes. Peptides adducted with divalent metal-ions of small ionic radii (i.e., Zn(2+)) would form predominantly species (b) and (c); whereas peptides adducted with metal ions of larger ionic radii (i.e., Hg(2+)) would adopt predominantly species (a). Species (b) and (c) are believed to be essential for proton-electron recombination process to give c-/z-type fragments via the labile ketylamino radical intermediates. Species (c) is particularly important for the formation of non-metalated c-/z-type fragments. Without any mobile protons, species (a) are believed to undergo metal ion reduction and subsequently induce spontaneous electron transfer from the peptide moiety to the charge-reduced metal ions. Depending on the exothermicity of the electron transfer reaction, the peptide radical cations might be formed with substantial internal energy and might undergo further dissociation to give structural related fragment ions.
Collapse
Affiliation(s)
- Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, SAR, China
| | | | | | | | | |
Collapse
|
33
|
Carlton DD, Schug KA. A review on the interrogation of peptide–metal interactions using electrospray ionization-mass spectrometry. Anal Chim Acta 2011; 686:19-39. [DOI: 10.1016/j.aca.2010.11.050] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/24/2010] [Accepted: 11/25/2010] [Indexed: 11/27/2022]
|
34
|
Taucher M, Breuker K. Top-down mass spectrometry for sequencing of larger (up to 61 nt) RNA by CAD and EDD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:918-929. [PMID: 20363646 DOI: 10.1016/j.jasms.2010.02.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 02/18/2010] [Accepted: 02/18/2010] [Indexed: 05/29/2023]
Abstract
We have studied the effect of solution additives on hydrolysis and charge state distribution in ESI MS of RNA. Lower and higher charge state ions can be electrosprayed from solutions containing 25 mM piperidine/25 mM imidazole and 1% vol. triethylamine, respectively, with base-catalyzed hydrolysis rates that are sufficiently slow to perform MS/MS experiments. These lower and higher charge state ions are suitable as precursors for CAD and EDD, respectively. We demonstrate nearly complete sequence coverage for 61 nt RNA dissociated by CAD, and 34 nt RNA dissociated by EDD, and suggest a mechanism for backbone fragmentation in EDD of RNA.
Collapse
Affiliation(s)
- Monika Taucher
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innsbruck, Austria
| | | |
Collapse
|
35
|
Kalli A, Håkansson K. Electron capture dissociation of highly charged proteolytic peptides from Lys N, Lys C and Glu C digestion. MOLECULAR BIOSYSTEMS 2010; 6:1668-81. [DOI: 10.1039/c003834b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
36
|
Improved detection of intact tyrosine sulfate-containing peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in linear negative ion mode. Int J Biochem Cell Biol 2009; 42:174-9. [PMID: 19857600 DOI: 10.1016/j.biocel.2009.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 09/28/2009] [Accepted: 10/14/2009] [Indexed: 12/15/2022]
Abstract
Sulfation of tyrosine residues is a common post-translational modification, but detecting and quantitating this modification poses challenges due to lability of the sulfate group. The goal of our studies was to determine how best to detect and to assess the stoichiometry of this modification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). Sulfated and nonsulfated forms of peptides-hirudin(55-65), caerulein, and cholecystokinin octapeptide and phosphorylated and nonphosphorylated pp60-c-src (521-533)-were analyzed using several matrices: sinapinic acid (SA), 2,5-dihydroxybenzoic acid (DBA), and cyano-4-hydroxycinnamic acid (CHCA). Intact sulfated peptides were difficult to detect using positive ion mode; peptides were observed as desulfated ions. Phosphorylated peptide was stable and was detected in positive and negative ion modes. Detection of sulfated peptides improved with: (1) Analysis in negative ion mode, (2) Decreased laser power, (3) Matrix selection: DBA>/=SA>CHCA. In negative ion mode, desorption/ionization of sulfated peptide was equivalent or more efficient than nonsulfated peptide, depending on conditions of analysis. Examination of a tryptic digest of alpha(2)-antiplasmin detected the single site of sulfation in negative ion mode but not in positive ion mode. We conclude that improved detection of sulfated peptides can be achieved in negative ion mode. Dual analysis in positive and negative ion modes serves as a potential means of identifying peptides with labile modifications such as sulfation and distinguishing them from phosphorylation.
Collapse
|
37
|
Jensen CS, Holm AIS, Zettergren H, Overgaard JB, Hvelplund P, Nielsen SB. On the charge partitioning between c and z fragments formed after electron-capture induced dissociation of charge-tagged Lys-Lys and Ala-Lys dipeptide dications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1881-1889. [PMID: 19651526 DOI: 10.1016/j.jasms.2009.06.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 06/21/2009] [Accepted: 06/22/2009] [Indexed: 05/28/2023]
Abstract
Here we report on the charge partition between c and z fragments formed after femtosecond collisional electron-transfer from Cs atoms to charge-tagged peptide dications. Peptides chosen for study were Ala-Lys (AK) and Lys-Lys (KK) where one or both of the lysine epsilon-amino groups were trimethylated to provide one or two fixed charges. For peptides with only one charge tag, the other charge was obtained by protonation of an amino group. In some experiments the ammonium group was tagged by 18-crown-6-ether (CE). Since recombination energies decrease in the order: MeNH3+ > NMe4+ > MeNH3+(CE) > NMe4+(CE), it is possible to change the probability for the transferred electron to end up at either the N-terminal or the C-terminal residue by CE attachment. We find, however, that the individual recombination energies have little influence on the relative ratio between the yield of c and z ions as long as there are no mobile protons that can be transferred between the two fragments. Our results can be accounted for by the Utah-Washington model where the electron is captured into an amide pi* orbital that weakens the N-C(alpha) bond and causes its breakage, followed by proton, electron, or hydrogen transfer between the c and z fragments that stay together as an ion-molecule complex for some time. The data are also in accordance with the notion that an amide group competes with the charged groups for the electron. Electron capture by charged groups results in loss of small neutrals such as hydrogen and ammonia.
Collapse
|
38
|
Feketeová L, Ryzhov V, O'Hair RAJ. Comparison of collision- versus electron-induced dissociation of Pt(II) ternary complexes of histidine- and methionine-containing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3133-3143. [PMID: 19714712 DOI: 10.1002/rcm.4234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Incubation of the histidine-containing peptides (GH, HG, GGH, GHG, HGG) and methionine-containing peptides (GM, MG, GGM, GMG, MGG) with the platinum complexes [Pt(terpy)Cl](+) (A) and [Pt(dien)Cl](+) (B) followed by electrospray ionisation (ESI) led to a number of singly and doubly charged ternary platinum peptide complexes, including [Pt(L)M](2+) and [Pt(L)M-H](+) (where L = the ligand terpy or dien; M is a peptide). Each of the [Pt(L)M](2+) complexes was subjected to electron capture dissociation (ECD), collision-induced dissociation (CID) and electron-induced dissociation (EID), while each of the [Pt(L)M-H](+) complexes was subjected to CID and EID. Results from ECD suggest that the free electron is captured by the metal ion thus weakening the bonds to its ligands. In the case of the ligand terpy, which binds more strongly than dien, this weakening leads to the loss of the peptide. The minor products in the ECD spectra of [Pt(terpy)M](2+) complexes do show fragmentation along the peptide backbone, but the ions observed are of the a-, b-, and y-type. For the complexes with methionine-containing peptides, a marker ion, [Pt(L)SCH(3)](+), was found which is indicative of binding of Pt to the methionine side chain. For the histidine-containing peptides, an ion containing platinum, the auxiliary ligand, and the histidine imine was observed in many instances, thus indicating the binding of the histidine side chain to the metal, but other modes of Pt coordination (N-terminus) were also found to be competitive. These findings are consistent with a recent finding (Sze et al. J. Biol. Inorg. Chem. 2009; 14: 163) that Pt occupies the methionine-rich copper(I)-binding site rather than histidine-rich copper(II)-binding site in the CopC protein.
Collapse
Affiliation(s)
- Linda Feketeová
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
| | | | | |
Collapse
|
39
|
Turecek F, Jones JW, Holm AIS, Panja S, Nielsen SB, Hvelplund P. Transition metals as electron traps. I. Structures, energetics, electron capture, and electron-transfer-induced dissociations of ternary copper-peptide complexes in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:707-724. [PMID: 19132713 DOI: 10.1002/jms.1546] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Electron-induced dissociations of gas-phase ternary copper-2,2'-bipyridine complexes of Gly-Gly-Gly and Gly-Gly-Leu were studied on a time scale ranging from 130 ns to several milliseconds using a combination of charge-reversal ((+)CR(-)) and electron-capture-induced dissociation (ECID) measured on a beam instrument and electron capture dissociation (ECD) measured in a Penning trap. Charge-reduced intermediates were observed on the short time scale in the (+)CR(-) and ECID experiments but not in ECD. Ion dissociations following electron transfer or capture mostly occurred by competitive bpy or peptide ligand loss, whereas peptide backbone fragmentations were suppressed in the presence of the ligated metal ion. Extensive electron structure theory calculations using density functional theory and large basis sets provided optimized structures and energies for the precursor ions, charge-reduced intermediates, and dissociation products. The Cu complexes underwent substantial structure changes upon electron capture. Cu was calculated to be pentacoordinated in the most stable singly charged complexes of the [Cu(peptide-H)bpy](+*) type where it carried a approximately +1 atomic charge. Cu coordination in charge-reduced [Cu(peptide-H)bpy] intermediates depended on the spin state. The themodynamically more stable singlet states had tricoordinated Cu, whereas triplet states had a tetracoordinated Cu. Cu was tricoordinated in stable [Cu(peptide-H)bpy](-*) products of electron transfer. [Cu(peptide)bpy](2+*) complexes contained the peptide ligand in a zwitterionic form while Cu was tetracoordinated. Upon electron capture, Cu was tri- or tetracoordinated in the [Cu(peptide)bpy](+) charge-reduced analogs and the peptide ligands underwent prototropic isomerization to canonical forms. The role of excited singlet and triplet electronic states is assessed.
Collapse
Affiliation(s)
- Frantisek Turecek
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA 98195-1700, USA.
| | | | | | | | | | | |
Collapse
|
40
|
Wolff JJ, Laremore TN, Leach FE, Linhardt RJ, Amster IJ. Electron capture dissociation, electron detachment dissociation and infrared multiphoton dissociation of sucrose octasulfate. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:275-81. [PMID: 19423912 PMCID: PMC3951291 DOI: 10.1255/ejms.951] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The structural analysis of sulfated carbohydrates such as glycosaminoglycans (GAGs) has been a long- standing challenge for the field of mass spectrometry. The dissociation of sulfated carbohydrates by collisionally- activated dissociation (CAD) or infrared multiphoton dissociation (IRMPD), which activate ions via vibrational excitation, typically result in few cleavages and abundant SO(3) loss for highly sulfated GAGs such as heparin and heparan sulfate, hampering efforts to determine sites of modification. The recent application of electron activation techniques, specifically electron capture dissociation (ECD) and electron detachment dissociation (EDD), provides a marked improvement for the mass spectrometry characterization of GAGs. In this work, we compare ECD, EDD and IRMPD for the dissociation of the highly sulfated carbohydrate sucrose octasulfate (SOS). Both positive and negative multiply-charged ions are investigated. ECD, EDD and IRMPD of SOS produce abundant and reproducible fragmentation. The product ions produced by ECD are quite different than those produced by IRMPD of SOS positive ions, suggesting different dissociation mechanisms as a result of electronic versus vibrational excitation. The product ions produced by EDD and IRMPD of SOS negative ions also differ from each other. Evidence for SO(3) rearrangement exists in the negative ion IRMPD data, complicating the assignment of product ions.
Collapse
Affiliation(s)
- Jeremy J. Wolff
- Department of Chemistry, University of Georgia, Athens, GA 30602
| | - Tatiana N. Laremore
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180
| | | | - Robert J. Linhardt
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180
| | | |
Collapse
|
41
|
Li X, Cournoyer JJ, Lin C, O’Connor PB. The effect of fixed charge modifications on electron capture dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1514-26. [PMID: 18657441 PMCID: PMC3116146 DOI: 10.1016/j.jasms.2008.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 05/20/2008] [Accepted: 06/20/2008] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation (ECD) studies of two modified amyloid beta peptides (20-29 and 25-35) were performed to investigate the role of H* radicals in the ECD of peptide ions and the free-radical cascade (FRC) mechanism. 2,4,6-Trimethylpyridinium (TMP) was used as the fixed charge tag, which is postulated to both trap the originally formed radical upon electron capture and inhibit the H* generation. It was found that both the number and locations of the fixed charge groups influenced the backbone and side-chain cleavages of these peptides in ECD. In general, the frequency and extent of backbone cleavages decreased and those of side-chain cleavages increased with the addition of fixed charge tags. A singly labeled peptide with the tag group farther away from the protonated site experienced a smaller abundance decrease in backbone cleavage fragments than the one with the tag group closer to the protonated site. Despite the nonprotonated nature of all charge carriers in doubly labeled peptide ions, several c and z* ions were still observed in their ECD spectra. Thus, although H* transfer may be important for the NC(alpha) bond cleavage, there also exist other pathways, which would require a radical migration via H* abstraction through space or via an amide superbase mechanism. Finally, internal fragment ions were observed in the ECD of these linear peptides, indicating that the important role of the FRC in backbone cleavages is not limited to the ECD of cyclic peptides.
Collapse
Affiliation(s)
- Xiaojuan Li
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Jason J. Cournoyer
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| |
Collapse
|
42
|
James PF, Perugini MA, O'Hair RAJ. Electron capture dissociation of complexes of diacylglycerophosphocholine and divalent metal ions: competition between charge reduction and radical induced phospholipid fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:978-986. [PMID: 18455426 DOI: 10.1016/j.jasms.2008.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/14/2008] [Accepted: 03/19/2008] [Indexed: 05/26/2023]
Abstract
Divalent metal complexes of phosphocholines, [Metal(II)(L)(n)](2+) (where Metal=Cu(2+), Co(2+), Mg(2+), and Ca(2+), L=1,2-dihexanoyl-sn-glycero-3-phosphocholine [6:0/6:0GPCho] and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine [16:0/18:1GPCho] and n=2-5), were formed upon electrospray ionization mass spectrometry (ESI/MS) of 8 mM solution of phosphocholine (L) with 4 mM metal salt (Metal). The electron capture dissociation (ECD) reactions of these [Metal(II)(L)(n)](2+) complexes were examined via Fourier-transform ion-cyclotron resonance mass spectrometry. A rich and complex chemistry was observed, including charge reduction and fragmentation involving losses of a methyl radical, trimethylamine, and the acyl chains. The predominant reaction channel was dependent on the size (n) of the complex, the metal and ligand used, and the size of the acyl chain. Thus charge reduction dominates the ECD spectra of the larger phosphocholine, 16:0/18:1GPCho, but is largely absent in the smaller 6:0/6:0GPCho. For complexes of 16:0/18:1GPCho, n=4-5, fragmentation from the head group mainly occurs via loss of the methyl radical and trimethylamine. At n=3, the relative abundance of fragments due to loss of acyl chain radicals increases. The abundances of ions arising from these radical losses increase further for the n=2 complexes, thereby providing information on the composition and position of the 16:0 and 18:1 acyl groups. Thus ECD of metal complexes provides structurally useful information on the phosphocholine, including the nature of the head group, the acyl chains, and the positions of the acyl chains.
Collapse
Affiliation(s)
- Patrick F James
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | | | | |
Collapse
|
43
|
Chen X, Hao C. Where Does the Electron Go? Electron Distribution and Reactivity of Peptide Cation Radicals Formed by Electron Transfer in the Gas phase. J Am Chem Soc 2008; 130:8818-33. [DOI: 10.1021/ja8019005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaohong Chen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - Changtong Hao
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| |
Collapse
|
44
|
Kalli A, Håkansson K. Comparison of the Electron Capture Dissociation Fragmentation Behavior of Doubly and Triply Protonated Peptides from Trypsin, Glu-C, and Chymotrypsin Digestion. J Proteome Res 2008; 7:2834-44. [DOI: 10.1021/pr800038y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Anastasia Kalli
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
| |
Collapse
|
45
|
Liu H, Yoo HJ, Håkansson K. Characterization of phosphate-containing metabolites by calcium adduction and electron capture dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:799-808. [PMID: 18417357 DOI: 10.1016/j.jasms.2008.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 03/13/2008] [Accepted: 03/14/2008] [Indexed: 05/26/2023]
Abstract
Several phosphate-containing metabolites, including nicotinamide adenine dinucleotide (NAD), nicotinamide adenine dinucleotide phosphate (NADP), adenosine 5'-diphosphate ribose (ADP-r), adenosine 5'-triphosphate (ATP), and guanosine 5'-triphosphate (GTP), have been characterized with electron capture dissociation (ECD) and sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) tandem mass spectrometry (MS/MS) in positive-ion mode. Calcium complexation was used to successfully produce abundant doubly charged cationic precursor ions with or without hydration. This approach enabled application of ECD to acidic metabolites for the first time. Fragmentation pathways observed in ECD and SORI-CAD of calcium-adducted phosphate-containing metabolites were complementary. Unique fragmentation was observed in ECD compared to SORI-CAD MS/MS, including ribose cross-ring cleavage for NAD and NADP, and generation of hydrated product ions, including cross-ring fragments, for hydrated ATP and GTP. A combination of ECD and CAD appears promising for maximizing structural information about metabolites.
Collapse
Affiliation(s)
- Haichuan Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | | | | |
Collapse
|
46
|
Devakumar A, O'Dell DK, Walker JM, Reilly JP. Structural analysis of leukotriene C4 isomers using collisional activation and 157 nm photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:14-26. [PMID: 18024058 DOI: 10.1016/j.jasms.2007.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 10/01/2007] [Accepted: 10/02/2007] [Indexed: 05/25/2023]
Abstract
The fragmentation of 5-hydroxy-6-glutathionyl-7,9,11,14-eicosatetraenoic acid [leukotriene C4 or LTC4 (5, 6)] and its isomeric counterpart LTC4 (14, 15) were studied by low and high-energy collisional induced dissociation (CID) and 157 nm photofragmentation. For singly charged protonated LTC4 precursors, photodissociation significantly enhances the signal intensities of informative fragment ions that are very important to distinguish the two LTC4 isomers and generates a few additional fragment ions that are not usually observed in CID experiments. The ion trap enables MSn experiments on the fragment ions generated by photodissociation. Photofragmentation is found to be suitable for the structural identification and isomeric differentiation of cysteinyl leukotrienes and is more informative than low or high-energy CID. We describe for the first time the structural characterization of the LTC4 (14, 15) isomer by mass spectrometry using CID and 157 nm light activation methods.
Collapse
Affiliation(s)
- Arugadoss Devakumar
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | | | | | | |
Collapse
|
47
|
Chamot-Rooke J, van der Rest G, Dalleu A, Bay S, Lemoine J. The combination of electron capture dissociation and fixed charge derivatization increases sequence coverage for O-glycosylated and O-phosphorylated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1405-13. [PMID: 17560119 DOI: 10.1016/j.jasms.2007.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 04/10/2007] [Accepted: 04/11/2007] [Indexed: 05/15/2023]
Abstract
Electron capture dissociation (ECD) has become an alternative method to collision-activated dissociation (CAD) to avoid gas-phase cleavage of post-translational modifications carried by side chains from the peptide backbone. Nonetheless, as illustrated herein by the study of O-glycosylated and O-phosphorylated peptides, the extent of ECD fragmentations may be insufficient to cover the entire peptide sequence and to localize accurately these modifications. The present work demonstrates that the derivatization of peptides at their N-terminus by a phosphonium group improves dramatically and systematically the sequence coverage deduced from the ECD spectrum for both O-glycosylated and O-phosphorylated peptides compared with their native counterparts. The exclusive presence of N-terminal fragments (c-type ions) in the ECD spectra of doubly charged molecular cations simplifies peptide sequence interpretation. Thus, the combination of ECD and fixed charge derivatization appears as an efficient analytical tool for the extensive sequencing of peptides bearing labile groups.
Collapse
Affiliation(s)
- Julia Chamot-Rooke
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, Palaiseau, France.
| | | | | | | | | |
Collapse
|
48
|
Leib RD, Donald WA, Bush MF, O'Brien JT, Williams ER. Nonergodicity in electron capture dissociation investigated using hydrated ion nanocalorimetry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1217-31. [PMID: 17521917 PMCID: PMC2034202 DOI: 10.1016/j.jasms.2007.03.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 03/29/2007] [Accepted: 03/29/2007] [Indexed: 05/02/2023]
Abstract
Hydrated divalent magnesium and calcium clusters are used as nanocalorimeters to measure the internal energy deposited into size-selected clusters upon capture of a thermally generated electron. The infrared radiation emitted from the cell and vacuum chamber surfaces as well as from the heated cathode results in some activation of these clusters, but this activation is minimal. No measurable excitation due to inelastic collisions occurs with the low-energy electrons used under these conditions. Two different dissociation pathways are observed for the divalent clusters that capture an electron: loss of water molecules (Pathway I) and loss of an H atom and water molecules (Pathway II). For Ca(H(2)O)(n)(2+), Pathway I occurs exclusively for n >or= 30 whereas Pathway II occurs exclusively for n <or= 22 with a sharp transition in the branching ratio for these two processes that occurs for n approximately 24. The number of water molecules lost by both pathways increases with increasing cluster size reaching a broad maximum between n = 23 and 32, and then decreases for larger clusters. From the number of water molecules that are lost from the reduced cluster, the average and maximum possible internal energy is determined to be approximately 4.4 and 5.2 eV, respectively, for Ca(H(2)O)(30)(2+). This value is approximately the same as the calculated ionization energies of M(H(2)O)(n)(+), M = Mg and Ca, for large n indicating that the vast majority of the recombination energy is partitioned into internal modes of the ion and that the dissociation of these ions is statistical. For smaller clusters, estimates of the dissociation energies for the loss of H and of water molecules are obtained from theory. For Mg(H(2)O)(n)(2+), n = 4-6, the average internal energy deposition is estimated to be 4.2-4.6 eV. The maximum possible energy deposited into the n = 5 cluster is <7.1 eV, which is significantly less than the calculated recombination energy for this cluster. There does not appear to be a significant trend in the internal energy deposition with cluster size whereas the recombination energy is calculated to increase significantly for clusters with fewer than 10 water molecules. These, and other results, indicate that the dissociation of these smaller clusters is nonergodic.
Collapse
Affiliation(s)
- Ryan D Leib
- Department of Chemistry, University of California-Berkeley, Berkeley, California 94720-1460, USA
| | | | | | | | | |
Collapse
|
49
|
Liu H, Håkansson K, Lee JY, Sherman DH. Collision-activated dissociation, infrared multiphoton dissociation, and electron capture dissociation of the Bacillus anthracis siderophore petrobactin and its metal ion complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:842-9. [PMID: 17331739 DOI: 10.1016/j.jasms.2007.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 01/08/2007] [Accepted: 01/09/2007] [Indexed: 05/14/2023]
Abstract
Siderophores are high-affinity iron-chelating ligands produced by microorganisms to scavenge vital Fe(3+) from the environment. Thus, siderophores constitute potential therapeutic targets and their structural determination is important for exploiting their therapeutic value. Here, the virulence-associated siderophore petrobactin from Bacillus anthracis was characterized with electron capture dissociation (ECD). Fragmentation of doubly protonated petrobactin was investigated and compared to sustained off-resonance irradiation collision-activated dissociation (SORI CAD) and infrared multiphoton dissociation (IRMPD) of both the singly and doubly protonated species. These experiments demonstrate that ECD provides additional information (complementary bond cleavages) on the structure of petrobactin compared to both SORI CAD and IRMPD. Furthermore, complexes of petrobactin with divalent (Ca(2+), Fe(2+), and Co(2+)) and trivalent (Fe(3+) and Ga(3+)) metal cations were also subjected to SORI CAD and ECD. Again, most structural information was obtained from the ECD spectra. However, significant differences were found in both SORI CAD and ECD of metal complexes, dependent on the nature of the metal ion. Intriguingly, unique behavior, consistent with a recently proposed solution-phase structure, was observed for the highly preferred Fe(3+)-petrobactin complex.
Collapse
Affiliation(s)
- Haichuan Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | | | | | | |
Collapse
|