1
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Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics. Metabolites 2023; 13:metabo13020155. [PMID: 36837774 PMCID: PMC9964739 DOI: 10.3390/metabo13020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The metabolomics and proteomics analysis of saliva, an excellent biofluid that is a rich source of biological compounds, allows for the safe and frequent screening of drugs, their metabolites, and molecular biomarkers of various diseases. One of the most frequently used analytical methods in saliva analysis is liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry. The low ionisation efficiency of some compounds and a complex matrix makes their identification by MS difficult. Furthermore, quantitative analysis by LC-MS frequently cannot be performed without isotopically labelled standards, which usually have to be specially synthesised. This review presented reports on qualitative and quantitative approaches in salivary metabolomics and proteomics. The purpose of this manuscript was to present the challenges, advances, and future prospects of mass spectrometry, both in the analysis of salivary metabolites and proteins. The presented review should appeal to those interested in the recent advances and trends in qualitative and quantitative mass spectrometry in salivary metabolomics and proteomics, which may facilitate a diagnostic accuracy, the evaluation of treatment efficacy, the early diagnosis of disease, and a forensic investigation of some unapproved drugs for any medical or dietary administration.
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2
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Kovács L. From Peptide Nucleic Acids to Supramolecular Structures of Nucleic Acid Derivatives. CHEM REC 2023; 23:e202200203. [PMID: 36251934 DOI: 10.1002/tcr.202200203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/20/2022] [Indexed: 01/24/2023]
Abstract
Nucleic acids play a pivotal role in life processes. The endeavours to shed light on the essential properties of these intriguing building blocks led us to the synthesis of different analogues and the investigation of their properties. First various peptide nucleic acid monomers and oligomers have been synthesized, using an Fmoc/acyl protecting group strategy, and their properties studied. The serendipitous discovery of a side reaction of coupling agents led us to the elaboration of a peptide sequencing method. The capricious behaviour of guanine derivatives spurred the determination of their substitution pattern using 13 C, 15 N NMR, and mass spectrometric methods. The properties of guanines initiated the logical transition to the study of supramolecular systems composed of purine analogues. Thus, xanthine and uracil derivatives have been obtained and their supramolecular self-assembly properties scrutinized in gas, solid, and liquid states and at solid-liquid interfaces.
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Affiliation(s)
- Lajos Kovács
- University of Szeged, Albert Szent-Györgyi Medical School, Department of Medicinal Chemistry, H-6720, Szeged, Dóm tér 8, Hungary
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3
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Grundke C, Kong C, Kampf CJ, Gupton BF, McQuade DT, Opatz T. Programmed Formation of HCN Oligomers through Organosulfur Catalysis. J Org Chem 2021; 86:10320-10329. [PMID: 34251206 DOI: 10.1021/acs.joc.1c01023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
An efficient, inexpensive, and reliable synthesis of diaminomaleonitrile (DAMN, 1) is described starting from readily available acetone cyanohydrin as the source of hydrogen cyanide (HCN). Diaminomaleonitrile (DAMN) is known to be an important intermediate in heterocyclic and medicinal chemistry as well as being a possible precursor for the origin of life's hypothesis within prebiotic chemistry. The mechanism of its formation through organosulfur catalysis has been investigated by electrospray ionization mass spectrometry (ESI-MS) using two newly synthesized cationic "marker" molecules as a tool that allows for sensitive detection. As a result, the proposed mechanism of a thiocyanate-mediated synthesis of the HCN tetramer DAMN starting from organic disulfides was confirmed.
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Affiliation(s)
- Caroline Grundke
- Department of Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Caleb Kong
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - B Frank Gupton
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - D Tyler McQuade
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia 23220, United States
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
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4
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Huang S, Palanisamy S, Yu X, Wang Y, Liu D, Gong W, Zhang X. α-Active Pyrylium Salt 2,4,5-Triphenylpyrylium for Improved Mass Spectrometry-Based Detection of Peptides. Anal Chem 2021; 93:11072-11080. [PMID: 34342978 DOI: 10.1021/acs.analchem.0c04809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyrylium salts are considered efficient chemical tags for amino groups. However, the apparent steric selectivity of pyrylium salts limits their application in the field of chemical labeling, especially during the labeling of sterically hindered compounds like amino acids, peptides, and proteins. Herein, we have investigated the effects of the α-substitution of pyrylium salts on their reactivity. We have also investigated the mechanism of nucleophilic reactions with pyrylium salts and further proposed that the reactivity of pyrylium salts mainly depends on the position and type of their substituents. A series of pyrylium salts were synthesized, and a highly active α-monosubstituted pyrylium salt, 2,4,5-triphenylpyrylium, was developed for efficient chemical labeling. All of the 15 amino acids studied were efficiently labeled under optimized reaction conditions. The 2,4,5-triphenylpyrylium salt was highly efficient in comparison to the previously reported 2,4,6-triphenylpyrylium salt developed for lysine-specific modifications. Furthermore, we successfully used 2,4,5-triphenylpyrylium salt for the hydrophobic labeling of peptides and protein hydrolysates. The most striking observation was that the ionization efficiency of short-chain multilabeled peptides in mixed samples, after derivatization, increased by up to 60 times. The increase in ionization efficiency gradually decreased with increasing peptide chain length. During the "soft" collision-induced dissociation (CID) process, the peptide was tagged at the N-terminus with 2,4,5-triphenylpyrylium, producing abundant a-type ions and b-type ions (Δ = 28), which eases the peptide resequencing process and assists in cracking the peptide codes. Moreover, 2,4,5-triphenylpyrylium has been utilized for the proteomic analysis of HeLa cell digests. In addition, 215 additional proteins were identified in the labeled products and the coverage of most proteins was improved.
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Affiliation(s)
- Shuai Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.,University of Chinese Academy of Science, Beijing 100039, P. R. China
| | - Sivakumar Palanisamy
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau, 999078P. R. China
| | - Yi Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.,University of Chinese Academy of Science, Beijing 100039, P. R. China
| | - Dan Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Weitao Gong
- State Key Laboratory of Fine Chemicals and School of Chemical Engineering, Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China
| | - Xiaozhe Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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5
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Hellhake S, Meckelmann SW, Empl MT, Rentmeister K, Wißdorf W, Steinberg P, Schmitz OJ, Benter T, Schebb NH. Non-targeted and targeted analysis of oxylipins in combination with charge-switch derivatization by ion mobility high-resolution mass spectrometry. Anal Bioanal Chem 2020; 412:5743-5757. [PMID: 32699965 PMCID: PMC7413910 DOI: 10.1007/s00216-020-02795-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/15/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Eicosanoids and other oxylipins play an important role in mediating inflammation as well as other biological processes. For the investigation of their biological role(s), comprehensive analytical methods are necessary, which are able to provide reliable identification and quantification of these compounds in biological matrices. Using charge-switch derivatization with AMPP (N-(4-aminomethylphenyl)pyridinium chloride) in combination with liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry (LC-IM-QTOF-MS), we developed a non-target approach to analyze oxylipins in plasma, serum, and cells. The developed workflow makes use of an ion mobility resolved fragmentation to pinpoint derivatized molecules based on the cleavage of AMPP, which yields two specific fragment ions. This allows a reliable identification of known and unknown eicosanoids and other oxylipins. We characterized the workflow using 52 different oxylipins and investigated their fragmentation patterns and ion mobilities. Limits of detection ranged between 0.2 and 10.0 nM (1.0-50 pg on column), which is comparable with other state-of-the-art methods using LC triple quadrupole (QqQ) MS. Moreover, we applied this strategy to analyze oxylipins in different biologically relevant matrices, as cultured cells, human plasma, and serum. Graphical abstract.
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Affiliation(s)
- Stefan Hellhake
- School of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Str. 20, 42119, Wuppertal, Germany
| | - Sven W Meckelmann
- Applied Analytical Chemistry & Teaching and Research Center for Separation, University of Duisburg-Essen, Universitätsstr. 5-7, 45141, Essen, Germany
| | - Michael T Empl
- Institute for Food Toxicology, University of Veterinary Medicine Hannover, Bünteweg 2, 30559, Hannover, Germany
| | - Kristina Rentmeister
- Applied Analytical Chemistry & Teaching and Research Center for Separation, University of Duisburg-Essen, Universitätsstr. 5-7, 45141, Essen, Germany
| | - Walter Wißdorf
- School of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Str. 20, 42119, Wuppertal, Germany
| | - Pablo Steinberg
- Institute for Food Toxicology, University of Veterinary Medicine Hannover, Bünteweg 2, 30559, Hannover, Germany
| | - Oliver J Schmitz
- Applied Analytical Chemistry & Teaching and Research Center for Separation, University of Duisburg-Essen, Universitätsstr. 5-7, 45141, Essen, Germany
| | - Thorsten Benter
- School of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Str. 20, 42119, Wuppertal, Germany
| | - Nils Helge Schebb
- School of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Str. 20, 42119, Wuppertal, Germany.
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6
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Polasky DA, Dixit SM, Keating MF, Gadkari VV, Andrews PC, Ruotolo BT. Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data. J Am Chem Soc 2020; 142:6750-6760. [DOI: 10.1021/jacs.0c01076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Michael F. Keating
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Philip C. Andrews
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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7
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Helal KY, Alamgir A, Berns EJ, Mrksich M. Traceless Immobilization of Analytes for High-Throughput Experiments with SAMDI Mass Spectrometry. J Am Chem Soc 2018; 140:8060-8063. [PMID: 29901996 PMCID: PMC6578359 DOI: 10.1021/jacs.8b02918] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Label-free assays, and particularly
those based on the combination
of mass spectroscopy with surface chemistries, enable high-throughput
experiments of a broad range of reactions. However, these methods
can still require the incorporation of functional groups that allow
immobilization of reactants and products to surfaces prior to analysis.
In this paper, we report a traceless method for attaching molecules
to a self-assembled monolayer for matrix-assisted laser desorption
and ionization (SAMDI) mass spectrometry. This method uses monolayers
that are functionalized with a 3-trifluoromethyl-3-phenyl-diazirine
group that liberates nitrogen when irradiated and gives a carbene
that inserts into a wide range of bonds to covalently immobilize molecules.
Analysis of the monolayer with SAMDI then reveals peaks for each of
the adducts formed from molecules in the sample. This method is applied
to characterize a P450 drug metabolizing enzyme and to monitor a Suzuki–Miyaura
coupling chemical reaction and is important because modification of
the substrates with a functional group would alter their activities.
This method will be important for high-throughput experiments in many
areas, including reaction discovery and optimization.
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Affiliation(s)
| | | | | | - Milan Mrksich
- Department of Cell and Molecular Biology , Northwestern University Feinberg School of Medicine , Chicago , Illinois 60611 , United States
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8
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Polasky DA, Lermyte F, Nshanian M, Sobott F, Andrews PC, Loo JA, Ruotolo BT. Fixed-Charge Trimethyl Pyrilium Modification for Enabling Enhanced Top-Down Mass Spectrometry Sequencing of Intact Protein Complexes. Anal Chem 2018; 90:2756-2764. [PMID: 29360341 PMCID: PMC6340295 DOI: 10.1021/acs.analchem.7b04806] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometry of intact proteins and protein complexes has the potential to provide a transformative level of information on biological systems, ranging from sequence and post-translational modification analysis to the structures of whole protein assemblies. This ambitious goal requires the efficient fragmentation of both intact proteins and the macromolecular, multicomponent machines they collaborate to create through noncovalent interactions. Improving technologies in an effort to achieve such fragmentation remains perhaps the greatest challenge facing current efforts to comprehensively analyze cellular protein composition and is essential to realizing the full potential of proteomics. In this work, we describe the use of a trimethyl pyrylium (TMP) fixed-charge covalent labeling strategy aimed at enhancing fragmentation for challenging intact proteins and intact protein complexes. Combining analysis of TMP-modified and unmodified protein complexes results in a greater diversity of regions within the protein that give rise to fragments, and results in an up to 2.5-fold increase in sequence coverage when compared to unmodified protein alone, for protein complexes up to 148 kDa. TMP modification offers a simple and powerful platform to expand the capabilities of existing mass spectrometric instrumentation for the complete characterization of intact protein assemblies.
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Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109
| | - Frederik Lermyte
- ♯ Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Michael Nshanian
- ‡ Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
| | - Frank Sobott
- ♯ Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- ° The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- + School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Phillip C. Andrews
- ‖ Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor MI, 48109
| | - Joseph A. Loo
- ‡ Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
- § Department of Biological Chemistry, David Geffen School of Medicine, and UCLA/DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109
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9
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Shen Y, Nemati R, Wang L, Yao X. Determining Linear Free Energy Relationships in Peptide Fragmentation Using Derivatization and Targeted Mass Spectrometry. Anal Chem 2018; 90:1587-1594. [DOI: 10.1021/acs.analchem.7b02191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yuanyuan Shen
- Department
of Chemistry and ‡Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Reza Nemati
- Department
of Chemistry and ‡Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lei Wang
- Department
of Chemistry and ‡Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Xudong Yao
- Department
of Chemistry and ‡Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, United States
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10
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Setner B, Wierzbicka M, Jerzykiewicz L, Lisowski M, Szewczuk Z. The unexpected racemization and hydrogen–deuterium exchange of the hydrogen at the α-carbon of proline analogs containing the 5-azoniaspiro[4.4]nonyl-group. Org Biomol Chem 2018; 16:825-831. [PMID: 29327743 DOI: 10.1039/c7ob02926h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present an unexpected racemization and the hydrogen–deuterium exchange (HDX) at the α-C atom of the proline derivative under basic aqueous conditions (1% water solution of triethylamine).
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Affiliation(s)
- B. Setner
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - M. Wierzbicka
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - L. Jerzykiewicz
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - M. Lisowski
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Z. Szewczuk
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
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11
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Peptide Sequencing Directly on Solid Surfaces Using MALDI Mass Spectrometry. Sci Rep 2017; 7:17811. [PMID: 29259225 PMCID: PMC5736625 DOI: 10.1038/s41598-017-18105-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/05/2017] [Indexed: 11/08/2022] Open
Abstract
There are an increasing variety of applications in which peptides are both synthesized and used attached to solid surfaces. This has created a need for high throughput sequence analysis directly on surfaces. However, common sequencing approaches that can be adapted to surface bound peptides lack the throughput often needed in library-based applications. Here we describe a simple approach for sequence analysis directly on solid surfaces that is both high speed and high throughput, utilizing equipment available in most protein analysis facilities. In this approach, surface bound peptides, selectively labeled at their N-termini with a positive charge-bearing group, are subjected to controlled degradation in ammonia gas, resulting in a set of fragments differing by a single amino acid that remain spatially confined on the surface they were bound to. These fragments can then be analyzed by MALDI mass spectrometry, and the peptide sequences read directly from the resulting spectra.
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12
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DeGraan-Weber N, Ward SA, Reilly JP. A Novel Triethylphosphonium Charge Tag on Peptides: Synthesis, Derivatization, and Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1889-1900. [PMID: 28560565 PMCID: PMC5709245 DOI: 10.1007/s13361-017-1694-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Charge tagging is a peptide derivatization process that commonly localizes a positive charge on the N-terminus. Upon low energy activation (e.g., collision-induced dissociation or post-source decay) of charge tagged peptides, relatively few fragment ions are produced due to the absence of mobile protons. In contrast, high energy fragmentation, such as 157 nm photodissociation, typically leads to a series of a-type ions. Disadvantages of existing charge tags are that they can produce mobile protons or that they are undesirably large and bulky. Here, we investigate a small triethylphosphonium charge tag with two different linkages: amide (158 Da) and amidine bonds (157 Da). Activation of peptides labeled with a triethylphosphonium charge tag through an amide bond can lead to loss of the charge tag and the production of protonated peptides. This enables low intensity fragment ions from both the protonated and charge tagged peptides to be observed. Triethylphosphonium charge tagged peptides linked through an amidine bond are more stable. Post-source decay and photodissociation yield product ions that primarily contain the charge tag. Certain amidine induced fragments are also observed. The previously reported tris(trimethoxyphenyl) phosphonium acetic acid N-hydroxysuccinimidyl ester charge tag shows a similar fragment ion distribution, but the mass of the triethylphosphonium tag label is 415 Da smaller. Graphical Abstract ᅟ.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Sarah A Ward
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA.
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13
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Setner B, Rudowska M, Kluczyk A, Stefanowicz P, Szewczuk Z. The 5-azoniaspiro[4.4]nonyl group for improved MS peptide analysis: A novel non-fragmenting ionization tag for mass spectrometric sensitive sequencing of peptides. Anal Chim Acta 2017; 986:71-81. [DOI: 10.1016/j.aca.2017.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 01/02/2023]
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14
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Kitanaka A, Juichi H, Nihashi Y, Miyashita M, Miyagawa H. A Facile Method for Preferential Modification of the N-Terminal Amino Group of Peptides Using Triazine-Based Coupling Reagents. ACTA ACUST UNITED AC 2017; 6:A0059. [PMID: 28785530 DOI: 10.5702/massspectrometry.a0059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/10/2017] [Indexed: 01/19/2023]
Abstract
It has been shown that chemical modification of the peptide N-terminus with a charged tag greatly affects the fragmentation process caused by collision-induced dissociation to obtain more interpretable product ion spectra. In this study, we examined the selective introduction of a charged tag, 4-(guanidinomethyl)benzoic acid (Gmb), into the peptide N-terminus. After optimization of the reaction conditions, we found that the most effective conversion in terms of the reaction rate and selectivity was achieved by reacting the peptide with the active ester of Gmb, prepared using 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMT-MM) at pH 7. This method is applicable to the introduction of various carboxylic acid-containing compounds into the N-terminus of peptides, which will be useful not only for improvement of MS/MS fragmentation but also for various biochemical studies of peptides and proteins.
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15
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Kuchibhotla B, Kola SR, Medicherla JV, Cherukuvada SV, Dhople VM, Nalam MR. Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1216-1226. [PMID: 28349438 DOI: 10.1007/s13361-017-1606-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/30/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. Graphical Abstract ᅟ.
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Affiliation(s)
- Bhanuramanand Kuchibhotla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Sankara Rao Kola
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Jagannadham V Medicherla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Swamy V Cherukuvada
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Vishnu M Dhople
- Department of Functional Genomics, University Medicine Greifswald, Interface Institute Genetics & Functional Genomics, D-17475, Greifswald, Germany
| | - Madhusudhana Rao Nalam
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
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16
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Topolyan AP, Strizhevskaya DA, Slyundina MS, Belyaeva MA, Ivanova OM, Korshun VA, Ustinov AV, Mikhura IV, Formanovsky AA, Borisov RS. Tris(2,6-dimethoxyphenyl)methyl carbenium ion as a charge derivatization agent for the analysis of primary amines by MALDI mass spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1134/s106193481614015x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Waliczek M, Kijewska M, Rudowska M, Setner B, Stefanowicz P, Szewczuk Z. Peptides Labeled with Pyridinium Salts for Sensitive Detection and Sequencing by Electrospray Tandem Mass Spectrometry. Sci Rep 2016; 6:37720. [PMID: 27892962 PMCID: PMC5125270 DOI: 10.1038/srep37720] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/28/2016] [Indexed: 01/02/2023] Open
Abstract
Mass spectrometric analysis of trace amounts of peptides may be problematic due to the insufficient ionization efficiency resulting in limited sensitivity. One of the possible ways to overcome this problem is the application of ionization enhancers. Herein we developed new ionization markers based on 2,4,6-triphenylpyridinium and 2,4,6-trimethylpyridinium salts. Using of inexpensive and commercially available pyrylium salt allows selective derivatization of primary amino groups, especially those sterically unhindered, such as ε-amino group of lysine. The 2,4,6-triphenylpyridinium modified peptides generate in MS/MS experiments an abundant protonated 2,4,6-triphenylpyridinium ion. This fragment is a promising reporter ion for the multiple reactions monitoring (MRM) analysis. In addition, the fixed positive charge of the pyridinium group enhances the ionization efficiency. Other advantages of the proposed ionization enhancers are the simplicity of derivatization of peptides and the possibility of convenient incorporation of isotopic labels into derivatized peptides.
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Affiliation(s)
- Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Monika Kijewska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Magdalena Rudowska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Bartosz Setner
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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18
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Baghdady YZ, Schug KA. Review of in situ derivatization techniques for enhanced bioanalysis using liquid chromatography with mass spectrometry. J Sep Sci 2015; 39:102-14. [DOI: 10.1002/jssc.201501003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/02/2015] [Accepted: 10/02/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Yehia Z. Baghdady
- Department of Chemistry and Biochemistry; The University of Texas at Arlington; Arlington TX USA
| | - Kevin A. Schug
- Department of Chemistry and Biochemistry; The University of Texas at Arlington; Arlington TX USA
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19
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Medzihradszky KF, Chalkley RJ. Lessons in de novo peptide sequencing by tandem mass spectrometry. MASS SPECTROMETRY REVIEWS 2015; 34:43-63. [PMID: 25667941 PMCID: PMC4367481 DOI: 10.1002/mas.21406] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are "translated" into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general.
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Abstract
Enriched by a decade of remarkable developments, matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has witnessed a phenomenal expansion. Initially introduced for the mapping of peptides and intact proteins from mammalian tissue sections, MALDI IMS applications now extend to a wide range of molecules including peptides, lipids, metabolites and xenobiotics. Technology and methodology are quickly evolving to push the limits of the technique forward. Within a short period of time, numerous protocols and concepts have been developed and introduced in tissue section preparation, nonexhaustively including in situ tissue chemistries and solvent-free matrix depositions. Considering the past progress and current capabilities, this Review aims to cover the different aspects and challenges of tissue section preparation for MALDI IMS.
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21
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Setner B, Rudowska M, Klem E, Cebrat M, Szewczuk Z. Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:995-1001. [PMID: 25303389 DOI: 10.1002/jms.3410] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/28/2014] [Accepted: 06/06/2014] [Indexed: 06/04/2023]
Abstract
Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1-azabicyclo[2.2.2]octane (ABCO) or 1,4-diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI-MS) and longer retention times on the reverse-phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision-induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a- and b-type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision-induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI-MS/MS sequencing of peptides.
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Affiliation(s)
- Bartosz Setner
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
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22
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Bąchor R, Rudowska M, Kluczyk A, Stefanowicz P, Szewczuk Z. Hydrogen-deuterium exchange of α-carbon protons and fragmentation pathways in N-methylated glycine and alanine-containing peptides derivatized by quaternary ammonium salts. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:529-536. [PMID: 24913405 DOI: 10.1002/jms.3371] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/19/2014] [Accepted: 04/03/2014] [Indexed: 06/03/2023]
Abstract
Recently, we developed a selective and efficient method of hydrogen-deuterium exchange (HDX) at the α-carbon (α-C) of sarcosine residue (N-methylglycine) in model peptides [Bąchor et al. J. Mass Spectrom. 2014, 49, 43]. Here, we report the influence of quaternary ammonium (QA) group on HDX at the α-C of sarcosine and N-methylalanine in peptides. The obtained results suggest a significant acceleration of the HDX in sarcosine residue caused by the presence of QA. The effect depends on the distance between the sarcosine residue and QA moiety. The deuterons, introduced at α-C, are resistant to the back-exchange in acidic aqueous solution. The collision induced dissociation of the deuterium-labeled analogs of QA-tagged oligosarcosine peptides without mobile hydrogen revealed the mobilization of the hydrogens localized at α-C of sarcosine residue.
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Affiliation(s)
- Remigiusz Bąchor
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wroclaw, Poland
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23
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Ho MY, Shieh YT, Liao CL, Chen YH, Cheng CC. Functional Dihydro-1H-Imidazole Derivatives for MALDI Signal Enhancement of a Lysine-Specific Chemical Modification. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200900144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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24
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Rudowska M, Wieczorek R, Kluczyk A, Stefanowicz P, Szewczuk Z. Gas-phase fragmentation of oligoproline peptide ions lacking easily mobilizable protons. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:846-856. [PMID: 23609183 PMCID: PMC3650240 DOI: 10.1007/s13361-013-0585-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/17/2012] [Accepted: 12/31/2012] [Indexed: 06/02/2023]
Abstract
The fragmentation of peptides containing quaternary ammonium group, but lacking easily mobilizable protons, was examined with the aid of deuterium-labeled analogs and quantum-chemical modeling. The fragmentation of oligoproline containing quaternary ammonium group involves the mobilization of hydrogens localized at α- and γ- or δ-carbon atoms in the pyrrolidine ring of proline. The study of the dissociation pattern highlights the unusual proline residue behavior during MS/MS experiments of peptides.
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Affiliation(s)
| | | | - Alicja Kluczyk
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
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25
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Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
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26
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An M, Zou X, Wang Q, Zhao X, Wu J, Xu LM, Shen HY, Xiao X, He D, Ji J. High-confidence de novo peptide sequencing using positive charge derivatization and tandem MS spectra merging. Anal Chem 2013; 85:4530-7. [PMID: 23536960 DOI: 10.1021/ac4001699] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
De novo peptide sequencing holds great promise in discovering new protein sequences and modifications but has often been hindered by low success rate of mass spectra interpretation, mainly due to the diversity of fragment ion types and insufficient information for each ion series. Here, we describe a novel methodology that combines highly efficient on-tip charge derivatization and tandem MS spectra merging, which greatly boosts the performance of interpretation. TMPP-Ac-OSu (succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide) was used to derivatize peptides at N-termini on tips to reduce mass spectra complexity. Then, a novel approach of spectra merging was adopted to combine the benefits of collision-induced dissociation (CID) and electron transfer dissociation (ETD) fragmentation. We applied this methodology to rat C6 glioma cells and the Cyprinus carpio and searched the resulting peptide sequences against the protein database. Then, we achieved thousands of high-confidence peptide sequences, a level that conventional de novo sequencing methods could not reach. Next, we identified dozens of novel peptide sequences by homology searching of sequences that were fully backbone covered but unmatched during the database search. Furthermore, we randomly chose 34 sequences discovered in rat C6 cells and verified them. Finally, we conclude that this novel methodology that combines on-tip positive charge derivatization and tandem MS spectra merging will greatly facilitate the discovery of novel proteins and the proteome analysis of nonmodel organisms.
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Affiliation(s)
- Mingrui An
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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27
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2D gels still have a niche in proteomics. J Proteomics 2013; 88:4-13. [PMID: 23353020 DOI: 10.1016/j.jprot.2013.01.010] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 01/26/2023]
Abstract
With the rapid advance of MS-based proteomics one might think that 2D gel-based proteomics is dead. This is far from the truth. Current research has shown that there are still a number of places in the field of protein and molecular biology where 2D gels still play a leading role. The aim of this review is to highlight some of these applications. Examples from our own research as well as from other published works are used to illustrate the 2D gel driven research in the areas of: 1) de novo sequencing and protein identification from organisms with no or incomplete genome sequences available; 2) alternative detection methods for modification specific proteomics; 3) identification of protein isoforms and modified proteins. With an example of the glycoprotein TIMP-1 protein we illustrate the unique properties of 2D gels for the separation and characterisation of multiply modified proteins. We also show that careful analysis of experimental and theoretical protein mass and pI can lead to the identification of unanticipated protein variants modified by for example proteolytic cleavage. Together this shows that there is an important niche for 2D gel-based proteomics, which compliments traditional LC-MS techniques for specific protein research purposes.
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28
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Gao X, Wu H, Lee KC, Liu H, Zhao Y, Cai Z, Jiang Y. Stable Isotope N-Phosphorylation Labeling for Peptide de Novo Sequencing and Protein Quantification Based on Organic Phosphorus Chemistry. Anal Chem 2012; 84:10236-44. [DOI: 10.1021/ac301939v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xiang Gao
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Hanzhi Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
| | - Kim-Chung Lee
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
| | - Hongxia Liu
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yufen Zhao
- Department of Chemistry and The
Key Laboratory for Chemical Biology of Fujian Province, College of
Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People’s Republic of China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yuyang Jiang
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
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29
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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.
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Affiliation(s)
- Yi He
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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30
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Zimnicka M, Moss CL, Chung TW, Hui R, Tureček F. Tunable charge tags for electron-based methods of peptide sequencing: design and applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:608-620. [PMID: 21952752 DOI: 10.1007/s13361-011-0184-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 05/31/2023]
Abstract
Charge tags using basic auxiliary functional groups 6-aminoquinolinylcarboxamido, 4-aminopyrimidyl-1-methylcarboxamido, 2-aminobenzoimidazolyl-1-methylcarboxamido, and the fixed-charge 4-(dimethylamino)pyridyl-1-carboxamido moiety are evaluated as to their properties in electron transfer dissociation mass spectra of arginine C-terminated peptides. The neutral tags have proton affinities that are competitive with those of amino acid residues in peptides. Charge reduction by electron transfer from fluoranthene anion-radicals results in peptide backbone dissociations that improve sequence coverage by providing extensive series of N-terminal c-type fragments without impeding the formation of C-terminal z fragments. Comparison of ETD mass spectra of free and tagged peptides allows one to resolve ambiguities in fragment ion assignment through mass shifts of c ions. Simple chemical procedures are reported for N-terminal tagging of Arg-containing tryptic peptides.
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Affiliation(s)
- Magdalena Zimnicka
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA 98195-1700, USA
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31
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Enjalbert Q, Simon R, Salvador A, Antoine R, Redon S, Ayhan MM, Darbour F, Chambert S, Bretonnière Y, Dugourd P, Lemoine J. Photo-SRM: laser-induced dissociation improves detection selectivity of Selected Reaction Monitoring mode. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3375-3381. [PMID: 22002689 DOI: 10.1002/rcm.5232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Selected Reaction Monitoring (SRM) carried out on triple-quadrupole mass spectrometers coupled to liquid chromatography has been a reference method to develop quantitative analysis of small molecules in biological or environmental matrices for years and is currently emerging as a promising tool in clinical proteomic. However, sensitive assays in complex matrices are often hampered by the presence of co-eluted compounds that share redundant transitions with the target species. On-the-fly better selection of the precursor ion by high-field asymmetric waveform ion mobility spectrometry (FAIMS) or increased quadrupole resolution is one way to escape from interferences. In the present work we document the potential interest of substituting classical gas-collision activation mode by laser-induced dissociation in the visible wavelength range to improve the specificity of the fragmentation step. Optimization of the laser beam pathway across the different quadrupoles to ensure high photo-dissociation yield in Q2 without detectable fragmentation in Q1 was assessed with sucrose tagged with a push-pull chromophore. Next, the proof of concept that photo-SRM ensures more specific detection than does conventional collision-induced dissociation (CID)-based SRM was carried out with oxytocin peptide. Oxytocin was derivatized by the thiol-reactive QSY® 7 C(5)-maleimide quencher on cysteine residues to shift its absorption property into the visible range. Photo-SRM chromatograms of tagged oxytocin spiked in whole human plasma digest showed better detection specificity and sensitivity than CID, that resulted in extended calibration curve linearity. We anticipate that photo-SRM might significantly improve the limit of quantification of classical SRM-based assays targeting cysteine-containing peptides.
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Nawrocki A, Thorup-Kristensen K, Jensen ON. Quantitative proteomics by 2DE and MALDI MS/MS uncover the effects of organic and conventional cropping methods on vegetable products. J Proteomics 2011; 74:2810-25. [DOI: 10.1016/j.jprot.2011.06.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 06/18/2011] [Accepted: 06/21/2011] [Indexed: 01/16/2023]
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33
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Xu F, Zou L, Liu Y, Zhang Z, Ong CN. Enhancement of the capabilities of liquid chromatography-mass spectrometry with derivatization: general principles and applications. MASS SPECTROMETRY REVIEWS 2011; 30:1143-1172. [PMID: 21557289 DOI: 10.1002/mas.20316] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/12/2010] [Accepted: 07/12/2010] [Indexed: 05/30/2023]
Abstract
The integration of liquid chromatography-mass spectrometry (LC-MS) with derivatization is a relatively new and unique strategy that could add value and could enhance the capabilities of LC-MS-based technologies. The derivatization process could be carried out in various analytical steps, for example, sampling, storage, sample preparation, HPLC separation, and MS detection. This review presents an overview of derivatization-based LC-MS strategy over the past 10 years and covers both the general principles and applications in the fields of pharmaceutical and biomedical analysis, biomarker and metabolomic research, environmental analysis, and food-safety evaluation. The underlying mechanisms and theories for derivative reagent selection are summarized and highlighted to guide future studies.
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Affiliation(s)
- Fengguo Xu
- Department of Epidemiology and Public Health, National University of Singapore, 16 Medical Drive, Singapore 117600, Singapore
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34
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Miyashita M, Hanai Y, Awane H, Yoshikawa T, Miyagawa H. Improving peptide fragmentation by N-terminal derivatization with high proton affinity. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1130-1140. [PMID: 21488112 DOI: 10.1002/rcm.4962] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
An improved method of de novo peptide sequencing based on mass spectrometry using novel N-terminal derivatization reagents with high proton affinity has been developed. The introduction of a positively charged group into the N-terminal amino group of a peptide is known to enhance the relative intensity of b-ions in product ion spectra, allowing the easy interpretation of the spectra. However, the physicochemical properties of charge derivatization reagents required for efficient fragmentation remain unclear. In this study, we prepared several derivatization reagents with high proton affinity, which are thought to be appropriate for peptide fragmentation under low-energy collision-induced dissociation (CID) conditions, and examined their usefulness in de novo peptide sequencing. Comparison of the effects on fragmentation among three derivatization reagents having a guanidino or an amidino moiety, which differ in proton affinity, clearly indicated that there was an optimal proton affinity for efficient fragmentation of peptides. Among reagents tested in this study, derivatization with 4-amidinobenzoic acid brought about the most effective fragmentation. This derivatization approach will offer a novel de novo peptide sequencing method under low-energy CID conditions.
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Affiliation(s)
- Masahiro Miyashita
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan. ‐u.ac.jp
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35
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Chen X, Khairallah GN, O’Hair RA, Williams SJ. Fixed-charge labels for simplified reaction analysis: 5-hydroxy-1,2,3-triazoles as byproducts of a copper(I)-catalyzed click reaction. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.03.094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Cydzik M, Rudowska M, Stefanowicz P, Szewczuk Z. Derivatization of peptides as quaternary ammonium salts for sensitive detection by ESI-MS. J Pept Sci 2011; 17:445-53. [PMID: 21351320 DOI: 10.1002/psc.1342] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 10/19/2010] [Accepted: 11/11/2010] [Indexed: 01/19/2023]
Abstract
A series of model peptides in the form of quaternary ammonium salts at the N-terminus was efficiently prepared by the solid-phase synthesis. Tandem mass spectrometric analysis of the peptide quaternary ammonium derivatives was shown to provide sequence confirmation and enhanced detection. We designed the 2-(1,4-diazabicyclo[2.2.2] octylammonium)acetyl quaternary ammonium group which does not suffer from neutral losses during MS/MS experiments. The presented quaternization of 1,4-diazabicyclo[2.2.2]octane (DABCO) by iodoacetylated peptides is relatively easy and compatible with standard solid-phase peptide synthesis. This methodology offers a novel sensitive approach to analyze peptides and other compounds.
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Affiliation(s)
- Marzena Cydzik
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
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37
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Chung TW, Moss CL, Zimnicka M, Johnson RS, Moritz RL, Tureček F. Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:13-30. [PMID: 21472540 DOI: 10.1007/s13361-010-0012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/26/2010] [Accepted: 10/11/2010] [Indexed: 05/30/2023]
Abstract
Pyridiniummethylcarbonyl moieties that were previously designed on the basis of electronic structure analysis are now utilized as fixed-charge tags with tunable electronic properties to be used for N-terminal peptide derivatization and sequencing by electron-transfer dissociation. Dipeptides AK and KA were derivatized at the peptide N-terminus with 4-dimethylaminopyridinium-N-acetyl (DMAP-ac) and pyridinium-N-acetyl (pyrid-ac) tags of increasing intrinsic recombination energies. Upon the capture of a free electron or electron transfer from fluoranthene anions, (DMAP-ac-AK+H)(2+), (DMAP-ac-KA+H)(2+), (pyrid-ac-AK+H)(2+) and (pyrid-ac-KA+H)(2+) ions, as well as underivatized (AK+2H)(2+), completely dissociated. The fixed-charge tags steered the dissociation upon electron transfer to form abundant backbone N-C(α) bond cleavages, whereas the underivatized peptide mainly underwent H-atom and side-chain losses. Precursor ion structures for the tagged peptides were analyzed by an exhaustive conformational search combined with B3LYP/6-31+G(d,p) geometry optimization and single-point energy calculations in order to select the global energy minima. Structures, relative energies, transition states, ion-molecule complexes, and dissociation products were identified for several charge-reduced species from the tagged peptides. The electronic properties of the charge tags and their interactions with the peptide moieties are discussed. Electrospray ionization and electron-transfer dissociation of larger peptides are illustrated with a DMAP-tagged pentapeptide.
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Affiliation(s)
- Thomas W Chung
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA 98195-1700, USA
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Tran BQ, Hernandez C, Waridel P, Potts A, Barblan J, Lisacek F, Quadroni M. Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides. J Proteome Res 2010; 10:800-11. [DOI: 10.1021/pr100951t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bao Quoc Tran
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Celine Hernandez
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Patrice Waridel
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Alexandra Potts
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Jachen Barblan
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Frederique Lisacek
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
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39
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Xiang B, Macisaac S, Lardizabal K, Li B. In-gel protein N- and C-termini identification and its application for transgenic protein characterization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3447-55. [PMID: 21072801 DOI: 10.1002/rcm.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A new method for the determination of N- and C-termini of a protein isolated in a polyacrylamide gel is introduced. In-gel partial protein hydrolysis by hydrochloric acid is used to generate N- and C-terminal peptides for identification. This new method is complementary to existing techniques. The application of the in-gel protein termini identification technique to the characterization of the transgenic protein diacylglycerol acyltransferase (UrDGAT2A) purified from soybean seeds is also reported here. Both N- and C-termini of UrDGAT2A were successfully identified and the N-terminus was found to be blocked by acetylation. The analysis results of UrDGAT2A and two commercial proteins (bovine serum albumin (BSA) and alcohol dehydrogenase) are used to demonstrate the effectiveness of the method in identifying actual N- and C-termini, terminal truncation and blocking.
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Affiliation(s)
- Bosong Xiang
- Monsanto Company, 800 N. Lindbergh Blvd., St. Louis, MO 63167, USA.
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40
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García-Murria MJ, Valero ML, Sánchez del Pino MM. Simple chemical tools to expand the range of proteomics applications. J Proteomics 2010; 74:137-50. [PMID: 21074642 DOI: 10.1016/j.jprot.2010.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/08/2010] [Accepted: 11/03/2010] [Indexed: 12/26/2022]
Abstract
Proteomics is an expanding technology with potential applications in many research fields. Even though many research groups do not have direct access to its main analytical technique, mass spectrometry, they can interact with proteomics core facilities to incorporate this technology into their projects. Protein identification is the analysis most frequently performed in core facilities and is, probably, the most robust procedure. Here we discuss a few chemical reactions that are easily implemented within the conventional protein identification workflow. Chemical modification of proteins with N-hydroxysuccinimide esters, 4-sulfophenyl isothiocyanate, O-methylisourea or through β-elimination/Michael addition can be easily performed in any laboratory. The reactions are quite specific with almost no side reactions. These chemical tools increase considerably the number of applications and have been applied to characterize protein-protein interactions, to determine the N-terminal residues of proteins, to identify proteins with non-sequenced genomes or to locate phosphorylated and O-glycosylated.
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Affiliation(s)
- María Jesús García-Murria
- Laboratorio de Proteómica, Centro de Investigación Príncipe Felipe, Avda, Autopista del Saler 16, 46012 Valencia, Spain
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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.
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Affiliation(s)
- Giovanni Chiappetta
- USR 3149 CNRS/ESPCI ParisTech, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, Paris, France.
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Hayama T, Sakaguchi Y, Yoshida H, Itoyama M, Todoroki K, Yamaguchi M, Nohta H. Fluorous derivatization combined with liquid chromatography/tandem mass spectrometry: a method for the selective and sensitive determination of sialic acids in biological samples. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2868-2874. [PMID: 20857447 DOI: 10.1002/rcm.4710] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We have developed a novel method for selective and sensitive analysis of sialic acids (N-acetylneuraminic, N-glycolylneuraminic, and 2-keto-3-deoxy-D-glycero-D-galactonononic acid) utilizing liquid chromatography/tandem mass spectrometry (LC/MS/MS) combined with a fluorous derivatization technique. In this method, the carboxylic groups in the sialic acids are derivatized via amidation with heptadecafluoroundecylamine, a commercially available perfluoroalkylamine reagent. This reaction proceeds rapidly and readily at room temperature in the presence of a condensation reagent. Subsequently, the derivatives are retained specifically on an LC column with a perfluoroalkyl stationary phase by means of a fluorophilic or 'fluorous' interaction, and detected by positive electrospray ionization MS/MS. The detection limits of the examined sialic acids are in the range of 60-750 amol on column. We show that the proposed method can be used to analyze trace amounts of sialic acids in biological samples.
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Affiliation(s)
- Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
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Simon ES, Papoulias PG, Andrews PC. Gas-phase fragmentation characteristics of benzyl-aminated lysyl-containing tryptic peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1624-1632. [PMID: 20471281 PMCID: PMC2927711 DOI: 10.1016/j.jasms.2010.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 04/08/2010] [Accepted: 04/13/2010] [Indexed: 05/29/2023]
Abstract
The fragmentation characteristics of peptides derivatized at the side-chain epsilon-amino group of lysyl residues via reductive amination with benzaldehyde have been examined using collision-induced dissociation (CID) tandem mass spectrometry. The resulting MS/MS spectra exhibit peaks representing product ions formed from two independent fragmentation pathways. One pathway results in backbone fragmentation and commonly observed sequence ion peaks. The other pathway corresponds to the unsymmetrical, heterolytic cleavage of the C(zeta)-N(epsilon) bond that links the benzyl derivative to the side-chain lysyl residue. This results in the elimination of the derivative as a benzylic or tropylium carbocation and a (n - 1)(+)-charged peptide product (where n is the precursor ion charge state). The frequency of occurrence of the elimination pathway increases with increasing charge of the precursor ion. For the benzyl-modified tryptic peptides analyzed in this study, peaks representing products from both of these pathways are observed in the MS/MS spectra of doubly-charged precursor ions, but the carbocation elimination pathway occurs almost exclusively for triply-charged precursor ions. The experimental evidence presented herein, combined with molecular orbital calculations, suggests that the elimination pathway is a charge-directed reaction contingent upon protonation of the secondary epsilon-amino group of the benzyl-derivatized lysyl side chain. If the secondary epsilon-amine is protonated, the elimination of the carbocation is observed. If the precursor is not protonated at the secondary epsilon-amine, backbone fragmentation persists. The application of appropriately substituted benzyl analogs may allow for selective control over the relative abundance of product ions generated from the two pathways.
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Affiliation(s)
- Eric S Simon
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Song HW, Yue GH, Lu Y, Yang PY, Wang HH. Sequence Pattern Correlation of Amino Acid in Collision-induced Dissociation Electrospray Ionization Mass Spectrometry. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20020200511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal (18)O labeling, MS(n) of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.
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Affiliation(s)
- Joerg Seidler
- Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
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46
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An M, Dai J, Wang Q, Tong Y, Ji J. Efficient and clean charge derivatization of peptides for analysis by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1869-1874. [PMID: 20533316 DOI: 10.1002/rcm.4589] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Charge derivatization with succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-Ac-OSu) has great potential in several aspects of proteomics, such as peptide de novo sequencing, PTM analysis, etc. However, the excess reagent and its side products greatly limited its scope of use. Here, we report an improved method to perform charge derivatization of peptides by TMPP-Ac-OSu without interference from the excess reagent and corresponding side products. Briefly, the protein was first separated on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) or coagulated with the gel. The protein in-gel was then incubated with a high concentration of reagent, followed by extensive washing. Afterwards, the protein was in-gel digested with trypsin according to the routine protocol. The mainly resultant peptides were attached with one positive tag on the N-termini or Lys-epsilon-NH(2). The process has been successfully applied to 2-DE resolved protein spots. Compared to the native proteins, the derivatized counterparts have higher rates of PMF identification and more straightforward tandem mass spectra. This promising method should pave the way for the practical use of charge derivatization in proteomics.
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Affiliation(s)
- Mingrui An
- The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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47
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Koszinowski K. Oxidation State, Aggregation, and Heterolytic Dissociation of Allyl Indium Reagents. J Am Chem Soc 2010; 132:6032-40. [DOI: 10.1021/ja908101j] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Konrad Koszinowski
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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48
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Franck J, Ayed ME, Wisztorski M, Salzet M, Fournier I. On tissue protein identification improvement by N-terminal peptide derivatization. Methods Mol Biol 2010; 656:323-338. [PMID: 20680600 DOI: 10.1007/978-1-60761-746-4_19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Identification of potential markers of a physiological stage (e.g., pathology) discovered using MALDI-MSI is an important step in the understanding of signaling pathways or for providing sets of diagnosis and prognosis markers for clinical applications. Classically, identification can be achieved by extraction from a piece of tissue and proteomics strategies. However, this induces loss of information especially for low-abundance proteins or proteins localized to a specific region of the tissue. In this respect, identification directly at the tissue level is an attractive alternative. Because the molecular charge states in MALDI are low, on tissue identification is possible using bottom-up MALDI-MSI strategies. Enzymatic digestion using an enzyme such as trypsin can be performed at the micro-scale level to generate peptide collections while avoiding these peptides to be delocalized. It is, therefore, possible to image proteins through the molecular images of their digested peptides. These peptides can also be used to retrieve information on protein sequences by performing MS/MS, although databank interrogation or de novo sequencing using MS/MS spectra does not always lead to a successful or confident identification because on tissue complexities render PMF data problematic. Identification can be improved by increasing MS/MS spectra quality and simplifying their interpretation. This can be achieved by derivatization of peptides. In fact, derivatization of peptides leads to increases in fragmentation yields and orients fragmentations toward a specific series of fragment ions. In this respect, N-terminal chemical derivatization has proven to be particularly efficient. N-terminal chemical derivatization of tryptic peptides has been developed to be performed at the tissue level after on tissue digestion. Specific focus is given to 4-sulfophenyl isothiocyanate (4-SPITC), 3-sulfobenzoic acid NHS ester (3-SBASE), and (N-succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) derivatizations. This provides a complete strategy for protein identification in a bottom-up MALDI-MSI approach and opens the way for novel biomarker identification.
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Affiliation(s)
- Julien Franck
- Laboratoire de Neuroimmunologie et Neurochimie Evolutives, FRE CNRS 3249, MALDI Imaging Team, Université Lille Nord de France, Université Lille 1, Villeneuve d'Ascq, France
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49
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Than CTL, Ferguson GA, Raghavachari K. Quaternary Amine-Induced Peptide Degradation via Cyclization. J Phys Chem A 2009; 114:481-5. [DOI: 10.1021/jp906646n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Franck J, El Ayed M, Wisztorski M, Salzet M, Fournier I. On-Tissue N-Terminal Peptide Derivatizations for Enhancing Protein Identification in MALDI Mass Spectrometric Imaging Strategies. Anal Chem 2009; 81:8305-17. [DOI: 10.1021/ac901043n] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Franck
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. El Ayed
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. Wisztorski
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. Salzet
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - I. Fournier
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
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