1
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Zhao B, Reilly CP, Reilly JP. ETD-Cleavable Linker for Confident Cross-linked Peptide Identifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1631-1642. [PMID: 31098958 DOI: 10.1007/s13361-019-02227-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Peptide cross-links formed using the homobifunctional-linker diethyl suberthioimidate (DEST) are shown to be ETD-cleavable. DEST has a spacer arm consisting of a 6-carbon alkyl chain and it cleaves at the amidino groups created upon reaction with primary amines. In ETD MS2 spectra, DEST cross-links can be recognized based on mass pairs consisting of peptide-NH2• and peptide+linker+NH3 ions, and backbone cleavages are more equally distributed over the two constituent peptides compared with collisional activation. Dead ends that are often challenging to distinguish from cross-links are diagnosed by intense reporter ions. ETD mass pairs can be used in MS3 experiments to confirm cross-link identifications. These features provide a simple but reliable approach to identify cross-links that should facilitate studies of protein complexes.
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Affiliation(s)
- Bingqing Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Colin P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
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2
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Protein profiling and pseudo-parallel reaction monitoring to monitor a fusion-associated conformational change in hemagglutinin. Anal Bioanal Chem 2019; 411:4987-4998. [PMID: 31254054 DOI: 10.1007/s00216-019-01921-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/22/2022]
Abstract
Influenza infection requires viral escape from early endosomes into the cytosol, which is enabled by an acid-induced irreversible conformational transformation in the viral protein hemagglutinin. Despite the direct relationship between this conformational change and infectivity, label-free methods for characterizing this and other protein conformational changes in biological mixtures are limited. While the chemical reactivity of the protein backbone and side-chain residues is a proxy for protein conformation, coupling this reactivity to quantitative mass spectrometry is a challenge in complex environments. Herein, we evaluate whether electrophilic amidination coupled with pseudo-parallel reaction monitoring is an effective label-free approach to detect the fusion-associated conformational transformation in recombinant hemagglutinin (rHA). We identified rHA peptides that are differentially amidinated between the pre- and post-fusion states, and validated that this difference relies upon the fusion-associated conformational switch. We further demonstrate that we can distinguish the fusion profile in a matrix of digested cellular lysate. This fusion assay can be used to evaluate fusion competence for modified HA. Graphical abstract.
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3
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Witkowska E, Kubik K, Krosnicka J, Grabowska K, Niescioruk A, Wilenska B, Misicka A. Microwave-assisted guanidinylation in solid phase peptide synthesis: comparison of various reagents. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.09.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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4
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Cammarata M, Lin KY, Pruet J, Liu HW, Brodbelt J. Probing the Unfolding of Myoglobin and Domain C of PARP-1 with Covalent Labeling and Top-Down Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2014; 86:2534-42. [DOI: 10.1021/ac4036235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Michael Cammarata
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Ke-Yi Lin
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Jeff Pruet
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Jennifer Brodbelt
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
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5
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Lauber MA, Rappsilber J, Reilly JP. Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry. Mol Cell Proteomics 2012; 11:1965-76. [PMID: 23033476 PMCID: PMC3518124 DOI: 10.1074/mcp.m112.019562] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 09/19/2012] [Indexed: 11/23/2022] Open
Abstract
Ribosomal protein S1 has been shown to be a significant effector of prokaryotic translation. The protein is in fact capable of efficiently initiating translation, regardless of the presence of a Shine-Dalgarno sequence in mRNA. Structural insights into this process have remained elusive, as S1 is recalcitrant to traditional techniques of structural analysis, such as x-ray crystallography. Through the application of protein cross-linking and high resolution mass spectrometry, we have detailed the ribosomal binding site of S1 and have observed evidence of its dynamics. Our results support a previous hypothesis that S1 acts as the mRNA catching arm of the prokaryotic ribosome. We also demonstrate that in solution the major domains of the 30S subunit are remarkably flexible, capable of moving 30-50Å with respect to one another.
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Affiliation(s)
- Matthew A. Lauber
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Juri Rappsilber
- §Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, UK and Institut für Biotechnologie, Technische Universität Berlin, 13353 Berlin, Germany
| | - James P. Reilly
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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6
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Jaffee EG, Lauber MA, Running WE, Reilly JP. In Vitro and In Vivo Chemical Labeling of Ribosomal Proteins: A Quantitative Comparison. Anal Chem 2012; 84:9355-61. [DOI: 10.1021/ac302115m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ethan G. Jaffee
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
| | - Matthew A. Lauber
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
| | - William E. Running
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
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7
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Running WE, Ni P, Kao CC, Reilly JP. Chemical reactivity of brome mosaic virus capsid protein. J Mol Biol 2012; 423:79-95. [PMID: 22750573 DOI: 10.1016/j.jmb.2012.06.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 06/01/2012] [Accepted: 06/20/2012] [Indexed: 12/12/2022]
Abstract
Viral particles are biological machines that have evolved to package, protect, and deliver the viral genome into the host via regulated conformational changes of virions. We have developed a procedure to modify lysine residues with S-methylthioacetimidate across the pH range from 5.5 to 8.5. Lysine residues that are not completely modified are involved in tertiary or quaternary structural interactions, and their extent of modification can be quantified as a function of pH. This procedure was applied to the pH-dependent structural transitions of brome mosaic virus (BMV). As the reaction pH increases from 5.5 to 8.5, the average number of modified lysine residues in the BMV capsid protein increases from 6 to 12, correlating well with the known pH-dependent swelling behavior of BMV virions. The extent of reaction of each of the capsid protein's lysine residues has been quantified at eight pH values using coupled liquid chromatography-tandem mass spectrometry. Each lysine can be assigned to one of three structural classes identified by inspection of the BMV virion crystal structure. Several lysine residues display reactivity that indicates their involvement in dynamic interactions that are not obvious in the crystal structure. The influence of several capsid protein mutants on the pH-dependent structural transition of BMV has also been investigated. Mutant H75Q exhibits an altered swelling transition accompanying solution pH increases. The H75Q capsids show increased reactivity at lysine residues 64 and 130, residues distal from the dimer interface occupied by H75, across the entire pH range.
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Affiliation(s)
- W E Running
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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8
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Chang FMJ, Lauber MA, Running WE, Reilly JP, Giedroc DP. Ratiometric pulse-chase amidination mass spectrometry as a probe of biomolecular complex formation. Anal Chem 2011; 83:9092-9. [PMID: 22007758 DOI: 10.1021/ac202154r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Selective chemical modification of protein side chains coupled with mass spectrometry is often most informative when used to compare residue-specific reactivities in a number of functional states or macromolecular complexes. Herein, we develop ratiometric pulse-chase amidination mass spectrometry (rPAm-MS) as a site-specific probe of lysine reactivities at equilibrium using the Cu(I)-sensing repressor CsoR from Bacillus subtilis as a model system. CsoR in various allosteric states was reacted with S-methyl thioacetimidate (SMTA) for pulse time, t, and chased with excess of S-methyl thiopropionimidate (SMTP) (Δ = 14 amu), quenched and digested with chymotrypsin or Glu-C protease, and peptides were quantified by high-resolution matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and/or liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). We show that the reactivities of individual lysines from peptides containing up to three Lys residues are readily quantified using this method. New insights into operator DNA binding and the Cu(I)-mediated structural transition in the tetrameric copper sensor CsoR are also obtained.
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Affiliation(s)
- Feng-Ming James Chang
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405-7102, USA
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9
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Lauber MA, Reilly JP. Structural analysis of a prokaryotic ribosome using a novel amidinating cross-linker and mass spectrometry. J Proteome Res 2011; 10:3604-16. [PMID: 21618984 DOI: 10.1021/pr200260n] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of the Escherichia coli ribosome, a 2.5 MDa ribonucleoprotein complex containing more than 50 proteins, was probed using the novel amidinating cross-linker diethyl suberthioimidate (DEST) and mass spectrometry. Peptide cross-links derived from this complex structure were identified at high confidence (FDR 0.8%) from precursor mass measurements and collision-induced dissociation (CID) fragmentation spectra. The acquired cross-linking data were found to be in excellent agreement with the crystal structure of the E. coli ribosome. DEST cross-links are particularly amenable to strong cation exchange (SCX) chromatography, facilitating a large-scale analysis. SCX enrichment and fractionation were shown to increase the number of cross-link spectra matches in our analysis 10-fold. Evidence is presented that these techniques can be used to study complex interactomes.
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Affiliation(s)
- Matthew A Lauber
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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10
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Xu Y, Falk IN, Hallen MA, Fitzgerald MC. Mass Spectrometry- and Lysine Amidination-Based Protocol for Thermodynamic Analysis of Protein Folding and Ligand Binding Interactions. Anal Chem 2011; 83:3555-62. [DOI: 10.1021/ac200211t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ying Xu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Irene N. Falk
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Mark A. Hallen
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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11
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Lauber MA, Reilly JP. Novel amidinating cross-linker for facilitating analyses of protein structures and interactions. Anal Chem 2011; 82:7736-43. [PMID: 20795639 DOI: 10.1021/ac101586z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel bifunctional thioimidate cross-linking reagent (diethyl suberthioimidate) that modifies amines without sacrificing their native basicity is developed. Intermolecular cross-linking of neurotensin and intramolecular cross-linking of cytochrome c under physiological conditions is investigated with this reagent. Because it does not perturb the electrostatic properties of a protein, it is unlikely to lead to artifactual conclusions about native protein structure. The interpeptide cross-links formed with this reagent are easily separated from other tryptic fragments using strong cation exchange chromatography, and they have a readily identified mass spectrometric signature. The use of this novel amidinating protein cross-linking reagent holds great promise for efficient, large-scale structural analysis of complex systems.
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Affiliation(s)
- Matthew A Lauber
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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12
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Running WE, Reilly JP. Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH. Proteomics 2010; 10:3669-87. [DOI: 10.1002/pmic.201000342] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Lauber MA, Running WE, Reilly JP. B. subtilis ribosomal proteins: structural homology and post-translational modifications. J Proteome Res 2009; 8:4193-206. [PMID: 19653700 DOI: 10.1021/pr801114k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identification of these proteins and facilitated the unambiguous assignment of post-translational modifications, including the methylation of S7, L11, and L16 and the N-terminal acetylation of S9. In addition, the high degree of structural homology between B. subtilis and other eubacterial ribosomal proteins was demonstrated through chemical labeling with S-methylthioacetimidate. One striking difference from previous characterizations of bacterial ribosomal proteins is that dozens of protein masses were found to be in error and not easily accounted for by post-translational modifications. This, in turn, led us to discover an inordinate number of sequencing errors in the reference genome of B. subtilis 168. We have found that these errors have been corrected in a recently revised version of the genome.
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Affiliation(s)
- Matthew A Lauber
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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14
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Liu X, Reilly JP. Correlating the Chemical Modification of Escherichia coli Ribosomal Proteins with Crystal Structure Data. J Proteome Res 2009; 8:4466-78. [DOI: 10.1021/pr9002382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaohui Liu
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
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15
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Mendoza VL, Vachet RW. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. MASS SPECTROMETRY REVIEWS 2009; 28:785-815. [PMID: 19016300 PMCID: PMC2768138 DOI: 10.1002/mas.20203] [Citation(s) in RCA: 270] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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16
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Fitzgerald MC, West GM. Painting proteins with covalent labels: what's in the picture? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1193-1206. [PMID: 19269190 DOI: 10.1016/j.jasms.2009.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/06/2009] [Accepted: 02/09/2009] [Indexed: 05/27/2023]
Abstract
Knowledge about the structural and biophysical properties of proteins when they are free in solution and/or in complexes with other molecules is essential for understanding the biological processes that proteins regulate. Such knowledge is also important to drug discovery efforts, particularly those focused on the development of therapeutic agents with protein targets. In the last decade a variety of different covalent labeling techniques have been used in combination with mass spectrometry to probe the solution-phase structures and biophysical properties of proteins and protein-ligand complexes. Highlighted here are five different mass spectrometry-based covalent labeling strategies including: continuous hydrogen/deuterium (H/D) exchange labeling, hydroxyl radical-mediated footprinting, SUPREX (stability of unpurified proteins from rates of H/D exchange), PLIMSTEX (protein-ligand interaction by mass spectrometry, titration, and H/D exchange), and SPROX (stability of proteins from rates of oxidation). The basic experimental protocols used in each of the above-cited methods are summarized along with the kind of biophysical information they generate. Also discussed are the relative strengths and weaknesses of the different methods for probing the wide range of conformational states that proteins and protein-ligand complexes can adopt when they are in solution.
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Affiliation(s)
- Michael C Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708-0346, USA.
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17
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Running WE, Reilly JP. Ribosomal Proteins of Deinococcus radiodurans: Their Solvent Accessibility and Reactivity. J Proteome Res 2009; 8:1228-46. [DOI: 10.1021/pr800544y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William E. Running
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
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18
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Kim JS, Kim JH, Kim HJ. Matrix-assisted laser desorption/ionization signal enhancement of peptides by picolinamidination of amino groups. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:495-502. [PMID: 18205249 DOI: 10.1002/rcm.3392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Picolinamidination of amino groups in peptides was carried out using ethyl picolinimidate tetrafluoroborate synthesized from picolinamide and triethyloxonium tetrafluoroborate. The N-terminal amino group as well as the epsilon-amino group of lysine were derivatized. The matrix-assisted laser desorption/ionization (MALDI) signal of a peptide was enhanced 20-35-fold upon picolinamidination depending on the number of amino groups derivatized. The signal enhancement effect is much higher than that of acetamidination or guanidination previously reported. Improved protein identification by mass mapping of the derivatized peptides was demonstrated.
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Affiliation(s)
- Jong-Seo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea 151-747
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