1
|
Sheng X, Tanaka M, Katagihara R, Hashimoto M, Nagaoka S, Matsui T. Novel Approach for Simultaneous Analysis of Peptide Metabolites from Orally Administered Glycinin in Rat Bloodstream by Coumarin-Tagged MALDI-MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14840-14848. [PMID: 34860514 DOI: 10.1021/acs.jafc.1c05791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The lack of an appropriate analytical approach characterizing metabolites from dietary proteins may prevent further studies that could clarify their health benefits. In this study, we attempted to establish a novel analytical assay of peptide metabolites from glycinin using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), in combination with the amine derivatization technique with coumarin (Cou). Cou (30 mmol/L) derivatization of peptides under rapid (30 min) and mild (25 °C, pH 8.5) conditions caused higher MS detection of the peptides as compared to nonderivatized peptides. In addition, an MS shift of the target by Cou derivatization (+202.0 m/z) can help to easily discriminate peptide metabolites in glycinin-administered blood, by comparing the MALDI-MS spectra of Cou-derivatized plasma with those of preadministered blood. After the oral administration of glycinin (100 mg/kg) to Sprague-Dawley rats, 15 di- to tetrapeptides were successfully characterized as glycinin-derived metabolites, demonstrating that the proposed Cou-tagged MALDI-MS is an appropriate characterization technique for peptide metabolites.
Collapse
Affiliation(s)
- Xiaojing Sheng
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mitsuru Tanaka
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Risa Katagihara
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Marika Hashimoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Satoshi Nagaoka
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Toshiro Matsui
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
2
|
N,N-Dimethylaminopyrene as a fluorescent affinity mass tag for ligand-binding mode analysis. Sci Rep 2020; 10:7311. [PMID: 32355254 PMCID: PMC7192892 DOI: 10.1038/s41598-020-64321-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Elucidation of the binding mode of protein–ligand interactions provides insights for the design of new pharmacological tools and drug leads. Specific labeling of target proteins with chemical probes, in which the ligands are conjugated with reacting and detecting groups, can establish the binding positions of ligands. Label-assisted laser desorption/ionization mass spectrometry (LA-LDI MS) is a promising detection method to selectively detect labeled molecules. However, previous LDI MS tags, such as nitrogen-substituted pyrenes, had problems with low sensitivity and stability. Here we show 6-N,N-dimethylaminopyrene (dmpy) as a versatile mass tag, which was detected at an amount of 0.1 fmol by LA-LDI MS and applicable for MS/MS analysis. By using ligand-dissociation-type dmpy probes and affinity purification with a polystyrene gel, we demonstrated that dmpy-labeled peptides were predominantly detected by MALDI MS. Our dmpy-probe-labeling method might be highly useful for determining the target biomacromolecules of various ligands and their binding sites.
Collapse
|
3
|
Patil MK, Kotresh MG, Inamdar SR. A combined solvatochromic shift and TDDFT study probing solute-solvent interactions of blue fluorescent Alexa Fluor 350 dye: Evaluation of ground and excited state dipole moments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 215:142-152. [PMID: 30822733 DOI: 10.1016/j.saa.2019.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Herein we report, the effect of solvents on absorption and fluorescence spectra of Alexa Fluor-350 labelled fluorescent dye examined both experimentally and computationally. The steady state absorption and fluorescence measurements are carried out in a series of solvents to explore their solvatochromism and to determine its dipole moments. To this end, different empirical solvatochromic models like Bilot-Kawaski, Lippert-Mataga, Bakhshiev, Kawaski-Chamma-Viallet and Reichardt models are assessed against Alexa Fluor 350 dye to determine the singlet excited and ground state dipole moments. Computational studies were carried out to optimize ground and excited geometries using density functional theory (DFT) and time dependent density functional theory (TD-DFT), respectively, in vacuum. Additionally, this study encompasses estimation of the electronic transition energies from the ground to first excited state of dye employing TD-DFT. Further, TD-DFT has been combined with integral equation formalism of the polarizable continuum model (IEF-PCM) to calculate various solute-solvent interaction potentials which are then compared with experimental values. The highest occupied molecular orbital energy (HOMO), lowest unoccupied molecular orbital energy (LUMO), the energy gap, chemical hardness (η), softness (σ), electronegativity (χ) and chemical potential (μ) were estimated. Mulliken atomic charge, natural population analysis (NPA) and molecular electrostatic potential (MEP) map are correlated using density functional theory. The experimentally obtained ground and excited state dipole moments are compared with the ones obtained from computational and the results are discussed. NBO analysis is carried out to investigate the intramolecular charge transfer interactions and stabilization energy within the studied molecule.
Collapse
Affiliation(s)
- Mallikarjun K Patil
- Laser Spectroscopy (DRDO/KU) Programme, UGC-CPEPA-Department of Physics, Karnatak University, Dharwad 580003, India
| | - M G Kotresh
- Department of Physics, Vijayanagara Sri Krishnadevaraya University, Bellary 583104, India
| | - Sanjeev R Inamdar
- Laser Spectroscopy (DRDO/KU) Programme, UGC-CPEPA-Department of Physics, Karnatak University, Dharwad 580003, India.
| |
Collapse
|
4
|
Oliveira E, Bértolo E, Núñez C, Pilla V, Santos HM, Fernández‐Lodeiro J, Fernández‐Lodeiro A, Djafari J, Capelo JL, Lodeiro C. Green and Red Fluorescent Dyes for Translational Applications in Imaging and Sensing Analytes: A Dual-Color Flag. ChemistryOpen 2018; 7:9-52. [PMID: 29318095 PMCID: PMC5754553 DOI: 10.1002/open.201700135] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 01/17/2023] Open
Abstract
Red and green are two of the most-preferred colors from the entire chromatic spectrum, and red and green dyes are widely used in biochemistry, immunohistochemistry, immune-staining, and nanochemistry applications. Selective dyes with green and red excitable chromophores can be used in biological environments, such as tissues and cells, and can be irradiated with visible light without cell damage. This critical review, covering a period of five years, provides an overview of the most-relevant results on the use of red and green fluorescent dyes in the fields of bio-, chemo- and nanoscience. The review focuses on fluorescent dyes containing chromophores such as fluorescein, rhodamine, cyanine, boron-dipyrromethene (BODIPY), 7-nitobenz-2-oxa-1,3-diazole-4-yl, naphthalimide, acridine orange, perylene diimides, coumarins, rosamine, Nile red, naphthalene diimide, distyrylpyridinium, benzophosphole P-oxide, benzoresorufins, and tetrapyrrolic macrocycles. Metal complexes and nanomaterials with these dyes are also discussed.
Collapse
Affiliation(s)
- Elisabete Oliveira
- BIOSCOPE GroupUCIBIO-LAQV-REQUIMTEDepartamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516LisboaPortugal
- Proteomass Scientific SocietyRua dos Inventores, Madan Park2829-516CaparicaPortugal
| | - Emilia Bértolo
- Biomolecular Research GroupSchool of Human and Life SciencesCanterbury Christ Church UniversityCanterburyCT1 1QUUK
| | - Cristina Núñez
- Research UnitHospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS)27003LugoSpain
| | - Viviane Pilla
- Instituto de FísicaUniversidade Federal de Uberlândia-UFUAv. João Naves de Ávila 2121Uberlândia, MG38400-902Brazil
| | - Hugo M. Santos
- BIOSCOPE GroupUCIBIO-LAQV-REQUIMTEDepartamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516LisboaPortugal
- Proteomass Scientific SocietyRua dos Inventores, Madan Park2829-516CaparicaPortugal
| | - Javier Fernández‐Lodeiro
- BIOSCOPE GroupUCIBIO-LAQV-REQUIMTEDepartamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516LisboaPortugal
- Proteomass Scientific SocietyRua dos Inventores, Madan Park2829-516CaparicaPortugal
| | - Adrian Fernández‐Lodeiro
- BIOSCOPE GroupUCIBIO-LAQV-REQUIMTEDepartamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516LisboaPortugal
- Proteomass Scientific SocietyRua dos Inventores, Madan Park2829-516CaparicaPortugal
| | - Jamila Djafari
- BIOSCOPE GroupUCIBIO-LAQV-REQUIMTEDepartamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516LisboaPortugal
- Proteomass Scientific SocietyRua dos Inventores, Madan Park2829-516CaparicaPortugal
| | - José Luis Capelo
- BIOSCOPE GroupUCIBIO-LAQV-REQUIMTEDepartamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516LisboaPortugal
- Proteomass Scientific SocietyRua dos Inventores, Madan Park2829-516CaparicaPortugal
| | - Carlos Lodeiro
- BIOSCOPE GroupUCIBIO-LAQV-REQUIMTEDepartamento de Química, Faculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516LisboaPortugal
- Proteomass Scientific SocietyRua dos Inventores, Madan Park2829-516CaparicaPortugal
| |
Collapse
|
5
|
Fluorescent Labeling of Protein Using Blue-Emitting 8-Amino-BODIPY Derivatives. J Fluoresc 2017; 27:2231-2238. [DOI: 10.1007/s10895-017-2164-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/10/2017] [Indexed: 01/27/2023]
|
6
|
Yoneda K, Hu Y, Kita M, Kigoshi H. 6-Amidopyrene as a label-assisted laser desorption/ionization (LA-LDI) enhancing tag: development of photoaffinity pyrene derivative. Sci Rep 2015; 5:17853. [PMID: 26667050 PMCID: PMC4678867 DOI: 10.1038/srep17853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/06/2015] [Indexed: 02/02/2023] Open
Abstract
Pyrene-conjugated compounds are detected by label-assisted laser desorption/ionization mass spectrometry (LA-LDI MS) without matrixes. We found that 6-amidopyrene derivatives were highly detectable by the LDI MS instrument equipped with a 355 nm laser. In a certain case of a 6-amidopyrene derivative, a molecular ion peak [M]+• and a characteristic fragment ion peak [M–42]+• were detected in an amount of only 10 fmol. The latter peak, corresponding to the 6-aminopyrene fragment, might be generated in situ by the removal of ketene (CH2=C=O) from the parent molecule. A photoaffinity amidopyrene derivative of an antitumor macrolide aplyronine A (ApA–PaP) was synthesized, which showed potent cytotoxicity and actin-depolymerizing activity. In an LDI MS analysis of the MeOH- and water-adducts of ApA–PaP, oxime N–O bonds as well as amidopyrene N-acetyl moieties were preferentially cleaved, and their internal structures were confirmed by MS/MS analysis. Amidopyrene moiety might enhance fragmentation and stabilize the cleaved fragments by intramolecular or intermolecular weak interactions including hydrogen bonding. Our chemical probe methods might contribute to a detailed analysis of binding modes between various ligands and target biomacromolecules that include multiple and weak interactions.
Collapse
Affiliation(s)
- Kozo Yoneda
- Graduate School of Pure and Applied Sciences, University of Tsukuba
| | - Yaping Hu
- Graduate School of Pure and Applied Sciences, University of Tsukuba
| | - Masaki Kita
- Graduate School of Pure and Applied Sciences, University of Tsukuba.,PRESTO, JST, 1-1-1 Tennodai, Tsukuba 305-8571, Japan
| | - Hideo Kigoshi
- Graduate School of Pure and Applied Sciences, University of Tsukuba
| |
Collapse
|
7
|
Hayashida O, Harada Y, Kojima M. Synthesis of coumarin-appended cyclophanes and evaluation of their complexation with myoglobin. J INCL PHENOM MACRO 2015. [DOI: 10.1007/s10847-015-0546-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
8
|
Red Emitting Coumarins: Insights of Photophysical Properties with DFT Methods. J Fluoresc 2015; 25:1117-26. [DOI: 10.1007/s10895-015-1602-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/15/2015] [Indexed: 12/26/2022]
|
9
|
Qiao X, Qin X, She D, Wang R, Zhang X, Zhang L, Zhang Y. Mass spectrometry-based tag and its application to high efficient peptide analysis – A review. Talanta 2014; 126:91-102. [DOI: 10.1016/j.talanta.2014.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/27/2014] [Accepted: 03/10/2014] [Indexed: 12/16/2022]
|
10
|
Taniguchi K, Kuyama H, Kajihara S, Tanaka K. MALDI mass spectrometry-based sequence analysis of arginine-containing glycopeptides: improved fragmentation of glycan and peptide chains by modifying arginine residue. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:951-960. [PMID: 23893643 DOI: 10.1002/jms.3241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/20/2013] [Accepted: 05/27/2013] [Indexed: 06/02/2023]
Abstract
This paper describes an improved method for the sequence analysis of Arg-containing glycopeptide by MALDI mass spectrometry (MS). The method uses amino group derivatization (4-aza-6-(2,6-dimethyl-1-piperidinyl)-5-oxohexanoic acid N-succinimidyl ester) and removal (carboxypeptidase B) or modification (peptidylarginine deiminase 4) of the arginine residue of the peptide. The derivatization attaches a basic tertiary amine moiety onto the peptides, and the enzymatic treatment removes or modifies the arginine residue. Fragmentation of the resulting glycopeptide under low-energy collision-induced dissociation yielded a simplified ion series of both the glycan and the peptide that can facilitate their sequencing. The feasibility of the method was studied using α1 -acid glycoprotein-derived N-linked glycopeptides, and glycan and peptide in each glycopeptide were successfully sequenced by MALDI tandem MS (MS/MS).
Collapse
Affiliation(s)
- Kenichi Taniguchi
- Koichi Tanaka Laboratory of Advanced Science and Technology (KTLAST), Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
| | | | | | | |
Collapse
|
11
|
He Y, Parthasarathi R, Raghavachari K, Reilly JP. Photodissociation of charge tagged peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1182-1190. [PMID: 22532332 DOI: 10.1007/s13361-012-0379-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 02/29/2012] [Accepted: 03/16/2012] [Indexed: 05/31/2023]
Abstract
Tris(2,4,6-trimethoxyphenyl) phosphonium acetyl (TMPP-Ac) was previously introduced to improve the mass spectrometric sequence analysis of peptides by fixing a permanent charge at the N-termini. However, peptides containing arginine residues did not fragment efficiently after TMPP-Ac modification. In this work, we combine charge derivatization with photodissociation. The fragmentation of TMPP-derivatized peptides is greatly improved and a series of N-terminal fragments is generated with complete sequence information. Arginine has a special effect on the fragmentation of the TMPP tagged peptides when it is the N-terminal peptide residue. Theoretical and experimental results suggest that this is due to hydrogen transfer from the charged N-terminus to the hydrogen-deficient peptide sequence.
Collapse
Affiliation(s)
- Yi He
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | | | | |
Collapse
|
12
|
Kim JS, Song JS, Kim Y, Park SB, Kim HJ. De novo analysis of protein N-terminal sequence utilizing MALDI signal enhancing derivatization with Br signature. Anal Bioanal Chem 2011; 402:1911-9. [PMID: 22200925 DOI: 10.1007/s00216-011-5642-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/29/2011] [Accepted: 12/06/2011] [Indexed: 11/24/2022]
Abstract
De novo analysis of protein N-terminal sequence is important for identification of N-terminal proteolytic processing such as N-terminal methionine or signal peptide removal, or for the genome annotation of uncharacterized proteins. We introduce a de novo sequencing method of protein N terminus utilizing matrix-assisted laser desorption/ionization (MALDI) signal enhancing picolinamidination with bromine isotopic tag incorporated to the N terminus. The doublet signature of bromine in the tandem mass (MS/MS) spectrum distinguished N-terminal ion series from C-terminal ion series, facilitating de novo N-terminal sequencing of protein. The dual advantage of MALDI signal enhancement by the basic picolinamidine and b-ion selection aided by Br signature is demonstrated using a variety of peptides. The N-terminal sequences of myoglobin and hemoglobin as model proteins were determined by incorporating the Br tag to the N terminus of the proteins and obtaining a series of b-ions with Br signature by MS/MS analysis after chymotryptic digestion of the tagged proteins. The N-terminal peptide was selected for MS/MS analysis from the chymotryptic digest based on the Br signature in the mass spectrum. Identification of phosphorylation site as well as N-terminal sequencing of a phosphopeptide was straightforward.
Collapse
Affiliation(s)
- Jong-Seo Kim
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea.
| | | | | | | | | |
Collapse
|
13
|
Chiappetta G, Ndiaye S, Demey E, Haddad I, Marino G, Amoresano A, Vinh J. Dansyl-peptides matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) and tandem mass spectrometric (MS/MS) features improve the liquid chromatography/MALDI-MS/MS analysis of the proteome. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3021-3032. [PMID: 20872635 DOI: 10.1002/rcm.4734] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Peptide tagging is a useful tool to improve matrix-assisted laser desorption/ionization tandem mass spectrometric (MALDI-MS/MS) analysis. We present a new application of the use of the dansyl chloride (DNS-Cl). DNS-Cl is a specific primary amine reagent widely used in protein biochemistry. It adds a fluorescent dimethylaminonaphthalene moiety to the molecule. The evaluation of MALDI-MS and MS/MS analyses of dansylated peptides shows that dansylation raises the ionization efficiency of the most hydrophilic species compared with the most hydrophobic ones. Consequently, higher Mascot scores and protein sequence coverage are obtained by combining MS and MS/MS data of native and tagged samples. The N-terminal DNS-Cl sulfonation improves the peptide fragmentation and promotes the generation of b-fragments allowing better peptide sequencing. In addition, we set up a labeling protocol based on the microwave chemistry. Peptide dansylation proved to be a rapid and cheap method to improve the performance of liquid chromatography (LC)/MALDI-MS/MS analysis at the proteomic scale in terms of peptide detection and sequence coverage.
Collapse
Affiliation(s)
- Giovanni Chiappetta
- USR 3149 CNRS/ESPCI ParisTech, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, Paris, France.
| | | | | | | | | | | | | |
Collapse
|
14
|
Peš O, Preisler J. Off-line coupling of microcolumn separations to desorption mass spectrometry. J Chromatogr A 2010; 1217:3966-77. [DOI: 10.1016/j.chroma.2010.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 01/13/2023]
|
15
|
Kita M, Ohno O, Han C, Uemura D. Bioactive secondary metabolites from symbiotic marine dinoflagellates: symbiodinolide and durinskiols. CHEM REC 2010; 10:57-69. [DOI: 10.1002/tcr.200900007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
16
|
Applications of chemical tagging approaches in combination with 2DE and mass spectrometry. Methods Mol Biol 2009; 519:83-101. [PMID: 19381578 DOI: 10.1007/978-1-59745-281-6_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Chemical modification reactions play an important role in various protocols for mass-spectrometry-based proteome analysis; this applies to both gel-based and gel-free proteomics workflows. In combination with two-dimensional gel electrophoresis (2DE), the addition of "tags" by means of chemical reactions serves several purposes. Potential benefits include increased sensitivity or sequence coverage for peptide mass fingerprinting and improved peptide fragmentation for de novo sequencing studies. Tagging strategies can also be used to obtain complementary quantitative information in addition to densitometry, and they may be employed for the study of post-translational modifications. In combination with the unique advantages of 2DE as a separation technique, such approaches provide a powerful toolbox for proteomic research. In this review, relevant examples from recent literature will be given to illustrate the capabilities of chemical tagging approaches, and methodological requirements will be discussed.
Collapse
|
17
|
Madsen JA, Brodbelt JS. Simplifying Fragmentation Patterns of Multiply Charged Peptides by N-Terminal Derivatization and Electron Transfer Collision Activated Dissociation. Anal Chem 2009; 81:3645-53. [DOI: 10.1021/ac9000942] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James A. Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
| |
Collapse
|
18
|
Kuyama H, Sonomura K, Shima K, Nishimura O, Tsunasawa S. An improved method for de novo sequencing of arginine-containing, Nalpha-tris(2,4,6-trimethoxyphenyl)phosphonium-acetylated peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:2063-2072. [PMID: 18521828 DOI: 10.1002/rcm.3587] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An improved method for de novo sequencing of arginine-containing peptides modified with succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-Ac-OSu) is reported. A tagging reagent, TMPP-Ac-OSu, was introduced to improve the sequence analysis of peptides owing to the simplified fragmentation pattern. However, peptides containing arginine residues did not fragment efficiently even after TMPP-Ac modification at their N-termini. This report describes how fragmentation efficiency of TMPP-Ac-modified arginine-containing peptides was significantly improved by modifying the guanidino group on the side chain of arginine with acetylacetone.
Collapse
Affiliation(s)
- Hiroki Kuyama
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan.
| | | | | | | | | |
Collapse
|
19
|
Kuyama H, Shima K, Sonomura K, Yamaguchi M, Ando E, Nishimura O, Tsunasawa S. A simple and highly successful C-terminal sequence analysis of proteins by mass spectrometry. Proteomics 2008; 8:1539-50. [DOI: 10.1002/pmic.200701044] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
20
|
Rizzarelli P, Puglisi C. Structural characterization of synthetic poly(ester amide) from sebacic acid and 4-amino-1-butanol by matrix-assisted laser desorption ionization time-of-flight/time-of-flight tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:739-754. [PMID: 18278818 DOI: 10.1002/rcm.3417] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS) was employed to analyze a poly(ester amide) sample (PEA-Bu) from the melt condensation of sebacic acid and 4-amino-1-butanol. In particular, we investigated the fragmentation pathways, the ester/amide bond sequences and the structure of species derived from side reactions during the synthesis. MALDI-TOF/TOF-MS/MS analysis was performed on cyclic species and linear oligomers terminated by dicarboxyl groups, carboxyl and hydroxyl groups and diamino alcohol groups. The sodium adducts of these oligomers were selected as precursor ions. Different end groups do not influence the fragmentation of sodiated poly(ester amide) oligomers and similar series of product ions were observed in the MALDI-TOF/TOF-MS/MS spectra. According to the structures of the most abundant product ions identified, the main cleavages proceed through a beta-hydrogen-transfer rearrangement, leading to the selective scission of the --O--CH2-- bonds. Abundant product ions originating from --CH2--CH2-- (beta-gamma) bond cleavage in the sebacate moiety were also detected. Their formation should be promoted by the presence of an alpha,beta-unsaturated ester or amide end group. MALDI-TOF/TOF-MS/MS provided structural information concerning the ester/amide sequences in the polymer chains. In the MALDI-TOF/TOF-MS/MS spectra acquired, using argon as the collision gas, of cyclic species and linear oligomers terminated by diamino alcohol groups, product ions in the low-mass range, undetected in the mass spectra acquired using air as the collision gas, proved to be diagnostic and made it possible to establish the presence of random sequences of ester and amide bonds in the poly(ester amide) sample. Furthermore, MALDI-TOF/TOF-MS/MS provided useful information to clarify the structures of precursor ions derived from side reactions during the synthesis.
Collapse
Affiliation(s)
- Paola Rizzarelli
- Institute of Chemistry and Technology of Polymers, National Council of Research, V. le A. Doria 6, 95125 Catania, Italy.
| | | |
Collapse
|
21
|
Wilson JJ, Brodbelt JS. MS/MS simplification by 355 nm ultraviolet photodissociation of chromophore-derivatized peptides in a quadrupole ion trap. Anal Chem 2007; 79:7883-92. [PMID: 17845006 DOI: 10.1021/ac071241t] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet photodissociation (UVPD) of chromophore-modified peptides enhances the capabilities for de novo sequencing in a quadrupole ion trap mass spectrometer. Attachment of UV chromophores allows efficient photoactivation of not only the precursor ions but also any fragments that retain the chromophore functionality. For doubly protonated peptides, UVPD leads to a vast reduction in MS/MS complexity. The array of b and y ions typically seen upon collisionally activated dissociation is reduced to a single series of either y or b ions by UVPD depending on the location of the chromophore (i.e., N- or C-terminus). The sulfonation reagent Alexa Fluor 350 (AF350) provided the best overall results for the singly and doubly charged peptides by UVPD. The nonsulfonated analogue of AF350, 7-amino-4-methylcoumarin-3-acetic acid, also led to simplified spectra for doubly charged, but not singly charged, peptides by UVPD. Dinitrophenyl-peptides also yielded simplified spectra by UVPD albeit with a small amount of internal fragments accompanying the series of diagnostic y ions. The success of this MS/MS simplification process stems from extensive secondary fragmentation of any chromophore-containing fragments upon exposure to subsequent laser pulses. Energy-variable UVPD reveals that the abundances of non-chromophore-containing y fragment ions increase linearly with laser pulse energy, suggesting secondary dissociation of these species is insignificant. The abundances of chromophore-containing a/b fragment ions follow a quadratic trend due to the extensive secondary fragmentation at higher laser energies or multiple pulses.
Collapse
Affiliation(s)
- Jeffrey J Wilson
- Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
| | | |
Collapse
|
22
|
Chen W, Lee PJ, Shion H, Ellor N, Gebler JC. Improving de Novo Sequencing of Peptides Using a Charged Tag and C-Terminal Digestion. Anal Chem 2007; 79:1583-90. [PMID: 17297959 DOI: 10.1021/ac061670b] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An improved method for peptide de novo sequencing by MALDI mass spectrometry is presented. The method couples a charge derivatization reaction with C-terminal digestion to modify tryptic peptides. The charge derivatization attaches a fixed charge group onto the N-termini of peptides, and the enzymatic digestion after the derivatization step removes C-terminal basic amino acid residues such as arginine and lysine. The fragmentation of the modified peptide(s) under low-energy CID conditions (MALDI Q-TOF mass spectrometer) yields a simplified yet complete ion series of the peptide sequence. The validity of the method is demonstrated by the results from several model protein digests, where peptide sequences were correctly deduced either manually or through an automated sequencing program.
Collapse
Affiliation(s)
- Weibin Chen
- Life Sciences R and D, Waters Corporation, Milford, Massachusetts 01757, USA.
| | | | | | | | | |
Collapse
|
23
|
Leitner A, Lindner W. Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics. Proteomics 2007; 6:5418-34. [PMID: 16972287 DOI: 10.1002/pmic.200600255] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As proteomics matures from a purely descriptive to a function-oriented discipline of the life sciences, there is strong demand for novel methodologies that increase the depth of information that can be obtained from proteomic studies. MS has long played a central role for protein identification and characterization, often in combination with dedicated chemical modification reactions. Today, chemistry is helping to advance the field of proteomics in numerous ways. In this review, we focus on those methodologies that have a significant impact for the large-scale study of proteins and peptides. This includes approaches that allow the introduction of affinity tags for the enrichment of subclasses of peptides or proteins and strategies for in vitro stable isotope labeling for quantification purposes, among others. Particular attention is given to the study of PTMs where recent advancements have been promising, but many interesting targets are not yet being addressed.
Collapse
Affiliation(s)
- Alexander Leitner
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Vienna, Austria.
| | | |
Collapse
|
24
|
Abstract
Liquid chromatography-matrix-assisted laser desorption/ionization mass spectrometry represents a sensitive, hyphenated MS- and MS/MS-technique with a broad range of applications in all areas ofproteome analysis. Whereas a number of interface types have been developed for coupling MALDI MS and liquid chromatography, in this chapter selected on-line and off-line types and techniques will be discussed with respect to their individual properties and performance. The technique is especially attractive in off-line mode where LC-separation and MS analyses are decoupled and each step can be performed at its individual optimum. Different speed of chromatographic separation and achievement of S/N criteria in MS or MS/MS mode can be optimized independently by individual adjustment of specific operating parameters. This flexibility makes LC-MALDI MS attractive for the analysis of peptide mixtures from low to medium complexity. Using sequential MS analysis of parallel LC runs (multiplexing), even highly complex samples can be handled. Quantitation at the MS and MS/MS level can be accomplished by a variety of labeling techniques, where the predominant formation of singly charged ions in MALDI alleviates the assignment of isotopomers. After discussing the level of complementarity between LC-MALDI and LC-ESI MS, selected applications of LC-MALDI MS are presented. Examples of membrane protein analysis applying 1D SDS PAGE are discussed in detail as well as applications in protein interaction analysis. These application examples clearly show that in all respects LC-MALDI MS and MS/MS are flexible and sensitive techniques which can be adapted to a wide range of different workflows.
Collapse
|
25
|
Nordhoff E, Lehrach H. Identification and characterization of DNA-binding proteins by mass spectrometry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2006; 104:111-95. [PMID: 17290821 DOI: 10.1007/10_2006_037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.
Collapse
Affiliation(s)
- Eckhard Nordhoff
- Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
| | | |
Collapse
|
26
|
Samyn B, Sergeant K, Carpentier S, Debyser G, Panis B, Swennen R, Van Beeumen J. Functional Proteome Analysis of the Banana Plant (Musa spp.) Using de Novo Sequence Analysis of Derivatized Peptides. J Proteome Res 2006; 6:70-80. [PMID: 17203950 DOI: 10.1021/pr0601943] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the use of chemical derivatization with MALDI-MS/MS analysis for de novo sequence analysis. Using three frequently used homology-based search algorithms, we were able to identify more than 40 proteins from banana, a nonmodel plant with unsequenced genome. Furthermore, this approach allowed the identification of different isoforms. We also observed that the identification score obtained varied according to the position of the peptide sequences in the query using the MS-Blast algorithm.
Collapse
Affiliation(s)
- Bart Samyn
- Department of Biochemistry, Physiology and Microbiology, Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.
| | | | | | | | | | | | | |
Collapse
|
27
|
Alley WR, Mechref Y, Klouckova I, Novotny MV. Improved Collision-Induced Dissociation Analysis of Peptides by Matrix-Assisted Laser Desorption/Ionization Tandem Time-of-Flight Mass Spectrometry through 3-Sulfobenzoic Acid Succinimidyl Ester Labeling. J Proteome Res 2006; 6:124-32. [PMID: 17203956 DOI: 10.1021/pr0602747] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The sulfonation reagent, a succinimidyl ester of 3-sulfobenzoic acid, has been synthesized for effective peptide sequencing. It is capable of incorporating an additional mobile proton into the peptide backbone, thus, facilitating efficient collision-induced dissociation. This reagent is easily and inexpensively prepared in short time. Tandem mass spectra of the guanidinated and reagent-sulfonated peptides consist mainly of the y-ion series with higher intensities than those observed for solely guanidinated peptides. These enhanced tandem MS attributes significantly improved MASCOT total-ion scores, thus, allowing more confident peptide sequencing. This derivatization was also very effective for the analysis of tryptic digest of human blood serum proteins separated by two-dimensional gel electrophoresis. When used in LC-MALDI/MS/MS format, this type of derivatization does not adversely affect chromatographic efficiencies.
Collapse
Affiliation(s)
- William R Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | | | | | | |
Collapse
|
28
|
Cindrić M, Cepo T, Skrlin A, Vuletić M, Bindila L. Accelerated on-column lysine derivatization and cysteine methylation by imidazole reaction in a deuterated environment for enhanced product ion analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:694-702. [PMID: 16444798 DOI: 10.1002/rcm.2359] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The combination of separation techniques and mass spectrometry (MS) for peptide investigation allows superior sensitivity of detection and richer fragmentation data than available by direct MS analysis of a complex mixture. In this regard, liquid chromatography (LC) coupled to electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) MS have evolved as versatile analytical tools in proteomics. Very often, however, the product ion mass spectrum is either incomplete or overfilled with ions, thus making sequence analysis difficult. Here we report overall ion intensity improvement of C-terminal lysine-containing peptides from Lys-C digest by on-column derivatization of lysines with 2-methoxy-4,5-dihydro-1H-imidazole. The method is simple, fast and exhibits 100% efficiency of the reaction. Additionally, post-source decay carried out on derivatized peptides gave rise almost exclusively to y-series ion formation, at 100% sequence coverage and high intensity. The novelty of the method resides in the side reaction of this derivatization process, namely the methylation of cysteines. This facilitates the estimation of the disulfide bridge position in a protein and the fragmentation of cysteine-containing peptide fragments. Additionally, by using this derivatization procedure, the loss of peptides, their degradation and/or oxidation, usually occurring in digest alkylation procedures, is greatly minimized. The new on-column derivatization protocol is designed to be carried out on C18 Spin Tubes or Cleanup C18 Pipette Tips. We observed that use of buffered D2O solvent prevented unwanted oxidation and degradation reactions with respect to the stationary phase. This may be due to the fact that a deuteron is less polar than a proton, and thus the bonded silica stationary phase saturated with deuterons does not affect the reaction between epsilon-amino or cysteine thiol groups and 2-methoxy-4,5-dihydro-1H-imidazole. Complete tagging of the peptides by on-column reaction could be obtained when using D2O, as compared to water-based reaction. Methylation of cysteine residues was enhanced when beta-mercaptoethanol was added in the reactant solution.
Collapse
Affiliation(s)
- Mario Cindrić
- Pliva - Research & Development Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia.
| | | | | | | | | |
Collapse
|
29
|
Rizzarelli P, Puglisi C, Montaudo G. Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectra of poly(butylene adipate). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:1683-94. [PMID: 16645991 DOI: 10.1002/rcm.2483] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS) was employed to analyze four poly(butylene adipate) (PBAd) oligomers and to investigate their fragmentation pathways as a continuation of our work on the MALDI-TOF/TOF-MS/MS study of synthetic polymers. MALDI-TOF/TOF-MS/MS analysis was performed on oligomers terminated by carboxyl and hydroxyl groups, methyl adipate and hydroxyl groups, dihydroxyl groups, and dicarboxyl groups. The sodium adducts of these oligomers were selected as precursor ions. Different end groups do not influence the fragmentation of sodiated polyester oligomers and similar series of product ions were observed in all the MALDI-TOF/TOF-MS/MS spectra. According to the structures of the most abundant product ions identified in the present work, three fragmentation pathways have been proposed to occur most frequently in PBAd: beta-hydrogen-transfer rearrangement, leading to the selective cleavage of the --O--CH(2)-- bonds; --CH(2)--CH(2)-- (beta--beta) bond cleavage in the adipate moiety; and ester bond scission.
Collapse
Affiliation(s)
- Paola Rizzarelli
- Istituto di Chimica e Tecnologia dei Polimeri, Consiglio Nazionale delle Ricerche, V. le A. Doria 6, 95125 Catania, Italy.
| | | | | |
Collapse
|
30
|
Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1390-401. [PMID: 16237664 DOI: 10.1002/jms.811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
|
31
|
Rizzarelli P, Puglisi C, Montaudo G. Sequence determination in aliphatic poly(ester amide)s by matrix-assisted laser desorption/ionization time-of-flight and time-of-flight/time-of-flight tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:2407-18. [PMID: 16078301 DOI: 10.1002/rcm.2075] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Poly(ester amide)s from dimethyl sebacate or sebacic acid and 2-aminoethanol or 4-amino-1-butanol were characterized by post-source decay matrix-assisted laser desorption/ionization time-of-flight (PSD-MALDI-TOF) and time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS). Sodiated oligomers were selected as precursor ions for dissociation studies. PSD analysis was performed on dimethyl sebacate, dicarboxylic, carboxylic and amino alcohol, and diamino alcohol terminated oligomers. PSD-MALDI-TOF mass spectra yielded information on the fragmentation mechanisms of the poly(ester amide) chains, showing that the main cleavages proceed through a beta-hydrogen transfer rearrangement. MALDI-TOF/TOF-MS/MS provided structural information concerning ester/amide sequences in the polymer chains. As expected, together with the ions appearing in the PSD-MALDI mass spectrum, several new abundant fragment ions in the low-mass range are present in MALDI-TOF/TOF-MS/MS spectra. These new product ions proved to be diagnostic and made it possible to establish the presence of random sequences of ester and amide bonds in the poly(ester amide)s samples.
Collapse
Affiliation(s)
- Paola Rizzarelli
- Istituto di Chimica e Tecnologia dei Polimeri, Consiglio Nazionale delle Ricerche, V.le A. Doria 6, 95125 Catania, Italy.
| | | | | |
Collapse
|
32
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|