1
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Burton NR, Polasky DA, Shikwana F, Ofori S, Yan T, Geiszler DJ, Veiga Leprevost FD, Nesvizhskii AI, Backus KM. Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics. J Am Chem Soc 2023; 145:21303-21318. [PMID: 37738129 DOI: 10.1021/jacs.3c05797] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Mass spectrometry-based chemoproteomics has emerged as an enabling technology for functional biology and drug discovery. To address limitations of established chemoproteomics workflows, including cumbersome reagent synthesis and low throughput sample preparation, here, we established the silane-based cleavable isotopically labeled proteomics (sCIP) method. The sCIP method is enabled by a high yielding and scalable route to dialkoxydiphenylsilane fluorenylmethyloxycarbonyl (DADPS-Fmoc)-protected amino acid building blocks, which enable the facile synthesis of customizable, isotopically labeled, and chemically cleavable biotin capture reagents. sCIP is compatible with both MS1- and MS2-based quantitation, and the sCIP-MS2 method is distinguished by its click-assembled isobaric tags in which the reporter group is encoded in the sCIP capture reagent and balancer in the pan cysteine-reactive probe. The sCIP-MS2 workflow streamlines sample preparation with early stage isobaric labeling and sample pooling, allowing for high coverage and increased sample throughput via customized low cost six-plex sample multiplexing. When paired with a custom FragPipe data analysis workflow and applied to cysteine-reactive fragment screens, sCIP proteomics revealed established and unprecedented cysteine-ligand pairs, including the discovery that mitochondrial uncoupling agent FCCP acts as a covalent-reversible cysteine-reactive electrophile.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Flowreen Shikwana
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
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2
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Ispizua-Rodriguez X, Krishnamurti V, Carpio V, Barrett C, Prakash GKS. Copper-Catalyzed Synthesis of Difluoromethyl Alkynes from Terminal and Silyl Acetylenes. J Org Chem 2023; 88:1194-1199. [PMID: 36622772 DOI: 10.1021/acs.joc.2c02799] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
An efficient method for the direct C(sp)-H difluoromethylation of terminal alkynes and the desilylation-difluoromethylation of (trimethylsilyl)acetylenes is disclosed. The copper-catalyzed transformation provides access to a wide range of structurally diverse CF2H alkynes in good yields, utilizing a (difluoromethyl)zinc reagent and an organic oxidant. The difluoromethylation of important synthons and API's is showcased. The synthetic utility of these (difluoromethyl)alkynes is demonstrated by selected cycloaddition reactions. Additionally, a slight modification to the reaction conditions allowed the selective preparation of a 2-difluoromethylindole.
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Affiliation(s)
- Xanath Ispizua-Rodriguez
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1661, United States
| | - Vinayak Krishnamurti
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1661, United States
| | - Vanessa Carpio
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1661, United States
| | - Colby Barrett
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1661, United States
| | - G K Surya Prakash
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1661, United States
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3
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Yan T, Palmer AB, Geiszler DJ, Polasky DA, Boatner LM, Burton NR, Armenta E, Nesvizhskii AI, Backus KM. Enhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product Fragmentation. Anal Chem 2022; 94:3800-3810. [PMID: 35195394 DOI: 10.1021/acs.analchem.1c04402] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry-based chemoproteomics has enabled functional analysis and small molecule screening at thousands of cysteine residues in parallel. Widely adopted chemoproteomic sample preparation workflows rely on the use of pan cysteine-reactive probes such as iodoacetamide alkyne combined with biotinylation via copper-catalyzed azide-alkyne cycloaddition (CuAAC) or "click chemistry" for cysteine capture. Despite considerable advances in both sample preparation and analytical platforms, current techniques only sample a small fraction of all cysteines encoded in the human proteome. Extending the recently introduced labile mode of the MSFragger search engine, here we report an in-depth analysis of cysteine biotinylation via click chemistry (CBCC) reagent gas-phase fragmentation during MS/MS analysis. We find that CBCC conjugates produce both known and novel diagnostic fragments and peptide remainder ions. Among these species, we identified a candidate signature ion for CBCC peptides, the cyclic oxonium-biotin fragment ion that is generated upon fragmentation of the N(triazole)-C(alkyl) bond. Guided by our empirical comparison of fragmentation patterns of six CBCC reagent combinations, we achieved enhanced coverage of cysteine-labeled peptides. Implementation of labile searches afforded unique PSMs and provides a roadmap for the utility of such searches in enhancing chemoproteomic peptide coverage.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Andrew B Palmer
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Nikolas R Burton
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ernest Armenta
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
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4
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Calle B, Bineva-Todd G, Marchesi A, Flynn H, Ghirardello M, Tastan OY, Roustan C, Choi J, Galan MC, Schumann B, Malaker SA. Benefits of Chemical Sugar Modifications Introduced by Click Chemistry for Glycoproteomic Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2366-2375. [PMID: 33871988 PMCID: PMC7611619 DOI: 10.1021/jasms.1c00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Mucin-type O-glycosylation is among the most complex post-translational modifications. Despite mediating many physiological processes, O-glycosylation remains understudied compared to other modifications, simply because the right analytical tools are lacking. In particular, analysis of intact O-glycopeptides by mass spectrometry is challenging for several reasons; O-glycosylation lacks a consensus motif, glycopeptides have low charge density which impairs ETD fragmentation, and the glycan structures modifying the peptides are unpredictable. Recently, we introduced chemically modified monosaccharide analogues that allowed selective tracking and characterization of mucin-type O-glycans after bioorthogonal derivatization with biotin-based enrichment handles. In doing so, we realized that the chemical modifications used in these studies have additional benefits that allow for improved analysis by tandem mass spectrometry. In this work, we built on this discovery by generating a series of new GalNAc analogue glycopeptides. We characterized the mass spectrometric signatures of these modified glycopeptides and their signature residues left by bioorthogonal reporter reagents. Our data indicate that chemical methods for glycopeptide profiling offer opportunities to optimize attributes such as increased charge state, higher charge density, and predictable fragmentation behavior.
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Affiliation(s)
- Beatriz Calle
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
| | - Andrea Marchesi
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Mattia Ghirardello
- School of Chemistry, Cantock’s Close, University of Bristol, BS8 1TS, United Kingdom
| | - Omur Y. Tastan
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Junwon Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - M. Carmen Galan
- School of Chemistry, Cantock’s Close, University of Bristol, BS8 1TS, United Kingdom
| | - Benjamin Schumann
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, CT 06511, United States
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5
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Ai Y, Zhao P, FNU PIJ, Chen H. Absolute Quantitation of Tryptophan-Containing Peptides and Amyloid β-Peptide Fragments by Coulometric Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1771-1779. [PMID: 34101439 PMCID: PMC8925997 DOI: 10.1021/jasms.1c00121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Isotope-labeled internal standards are routinely used for mass spectrometry (MS)-based absolute quantitation. However, syntheses of isotope-labeled peptides are time-consuming and costly. To tackle this issue, we recently developed a coulometric mass spectrometric (CMS) approach for absolute quantitation without the use of standards, based on the electrochemical oxidation of cysteine or tyrosine-containing peptides followed by mass spectrometric measurement of the oxidation yield. To further expand the utility of this method, herein we present the CMS method for absolute quantitation of peptides based on tryptophan electrochemical oxidation. Several tryptophan-containing peptides, such as WGG, WQPPRARI, WAGGDASGE, RTRPLWVRME, and KVPRNQDWL, were successfully quantified with a quantification error ranging from -4.5 to +4.3%. Furthermore, this quantitation approach is also applicable to protein, in which protein can be digested and a surrogate peptide can be selected for quantification to reflect the amount of the parent protein, as exemplified by CMS analysis of peptide GITWK from cytochrome c. The CMS result agreed well with the traditional isotope dilution method, with only a small difference of 3.5%. In addition, CMS was used to successfully quantify amyloid beta (Aβ) peptide fragments (up to 28 amino acid residues) based on tyrosine oxidation. The validity of the CMS method for peptide and protein absolute quantitation without using isotope-labeled peptide standards would greatly facilitate proteomics research.
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Affiliation(s)
| | | | | | - Hao Chen
- Corresponding Author: Hao Chen - Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA 07102
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6
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Xu C, Zheng Q, Zhao P, Paterson J, Chen H. A New Quantification Method Using Electrochemical Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:685-693. [PMID: 30604392 DOI: 10.1007/s13361-018-2116-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 11/19/2018] [Accepted: 11/25/2018] [Indexed: 06/09/2023]
Abstract
Mass spectrometry-based quantification method has advanced rapidly. In general, the methods for accurate quantification rely on the use of authentic target compounds or isotope-labeled compounds as standards, which might be not available or difficult to synthesize. To tackle this grand challenge, this paper presents a novel approach, based on electrochemistry (EC) combined with mass spectrometry (MS). In this approach, a target compound is allowed to undergo electrochemical oxidation and then subject to MS analysis. The oxidation current recorded from electrochemistry (EC) measurement provides information about the amount of the oxidized analyte, based on the Faraday's Law. On the other hand, the oxidation reaction yield can be determined from the analyte MS signal changes upon electrolysis. Therefore, the total amount of analyte can be determined. In combination with liquid chromatography (LC), the method can be applicable to mixture analysis. The striking strength of such a method for quantitation is that neither standard compound nor calibration curve is required. Various analyte molecules such as dopamine, norepinephrine, and rutin as well as peptide glutathione in low quantity were successfully quantified using our method with the quantification error ranging from - 2.6 to + 4.6%. Analyte in a complicated matrix (e.g., uric acid in urine) was also accurately measured. Graphical Abstract.
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Affiliation(s)
- Chang Xu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Pengyi Zhao
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Joseph Paterson
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA.
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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7
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Setner B, Stefanowicz P, Szewczuk Z. Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:115-123. [PMID: 29087004 DOI: 10.1002/jms.4040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/11/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry-based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium-based isobaric tag for relative and absolute quantification of peptides (QAS-iTRAQ 2-plex). Upon collisional activation, the new stable benzylic-type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS-iTRAQ 2-plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides.
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Affiliation(s)
- Bartosz Setner
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław, 50-383, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław, 50-383, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław, 50-383, Poland
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8
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Setner B, Szewczuk Z. New ionization tags based on the structure of the 5-azoniaspiro[4.4]nonyl tag for a sensitive peptide sequencing by mass spectrometry. Anal Bioanal Chem 2017; 410:1311-1321. [PMID: 29214541 PMCID: PMC5775984 DOI: 10.1007/s00216-017-0771-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 11/08/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
Abstract
Quaternary ammonium salts (QAS), both linear and bicyclic, are often utilized to improve the mass spectrometry (MS) analysis of peptides by fixing a permanent positive charge on the analyzed molecule. However, during collision-induced dissociation (CID) experiments, QAS undergo unwanted side reactions-Hofmann elimination as well as a tertiary amine loss- rendering the data interpretation complicated. In this work, we present 2-thia- and 2-oxa-5-azoniaspiro[4.4]nonyl groups as heterocyclic derivatives of the highly stable ionization group, 5-azoniaspiro[4.4]nonyl, for a sensitive peptide analysis by MS. Due to the permanent positive charge, labeled peptides are characterized by enhanced ionization efficiency during electrospray mass spectrometry (ESI-MS) conditions. Moreover, interpretation of the CID fragmentation of labeled peptides is facilitated since a series of generated fragmentation ions enable a complete sequence coverage. Introduction of a heteroatom into the 5-azoniaspiro[4.4]nonyl scaffold allows for liberation of a stable reporter ion which could be used in selected reaction monitoring (SRM)-targeted quantification experiments. Additionally, we synthesized a deuterated analog of the tag for LC-SRM-targeted quantitative analysis. The obtained results indicate the general usefulness of the proposed heterocyclic quaternary ammonium ionization tag for sequencing and quantification of peptides. Graphical abstract New reagents based on the structure of the 5-azoniaspiro[4.4]nonyl tag for peptide analysis by tandem mass spectrometry.
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Affiliation(s)
- Bartosz Setner
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50383, Wrocław, Poland.
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50383, Wrocław, Poland
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9
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Yang L, Chumsae C, Kaplan JB, Moulton KR, Wang D, Lee DH, Zhou ZS. Detection of Alkynes via Click Chemistry with a Brominated Coumarin Azide by Simultaneous Fluorescence and Isotopic Signatures in Mass Spectrometry. Bioconjug Chem 2017; 28:2302-2309. [DOI: 10.1021/acs.bioconjchem.7b00354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lihua Yang
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Chris Chumsae
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Jenifer B. Kaplan
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Kevin Ryan Moulton
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Dongdong Wang
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - David H. Lee
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Zhaohui Sunny Zhou
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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10
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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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11
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El-Kashef N, Gomes I, Mercer-Chalmers-Bender K, Schneider PM, Rothschild MA, Juebner M. Comparative proteome analysis for identification of differentially abundant proteins in SIDS. Int J Legal Med 2017; 131:1597-1613. [DOI: 10.1007/s00414-017-1632-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 07/04/2017] [Indexed: 12/01/2022]
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12
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A facile synthetic approach to 3-halo-4-substituted-1,5-dihydro-4H-1,2,4-triazoline-5-thiones based on retro-Michael addition. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6491-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Liu JM, Sweredoski MJ, Hess S. Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap-High-Energy Collision Induced Dissociation MS(3) Scan. Anal Chem 2016; 88:7471-5. [PMID: 27377715 DOI: 10.1021/acs.analchem.6b01067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The use of tandem mass tags (TMT) as an isobaric labeling strategy is a powerful method for quantitative proteomics, yet its accuracy has traditionally suffered from interference. This interference can be largely overcome by selecting MS(2) fragment precursor ions for high-energy collision induced dissociation (HCD) MS(3) analysis in an Orbitrap scan. While this approach minimizes the interference effect, sensitivity suffers due to the high AGC targets and long acquisition times associated with MS(3) Orbitrap detection. We investigated whether acquiring the MS(3) scan in a linear ion trap with its lower AGC target would increase overall quantification levels with a minimal effect on precision and accuracy. Trypsin-digested proteins from Saccharomyces cerevisiae were tagged with 6-plex TMT reagents. The sample was subjected to replicate analyses using either the Orbitrap or the linear ion trap for the HCD MS(3) scan. HCD MS(3) detection in the linear ion trap vs Orbitrap increased protein identification by 66% with minor loss in precision and accuracy. Thus, the use of a linear ion trap-HCD MS(3) scan during a 6-plex TMT experiment can improve overall identification levels while maintaining the power of multiplexed quantitative analysis.
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Affiliation(s)
- Jane M Liu
- Department of Chemistry, Pomona College , Claremont, California 91711, United States.,Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology , Pasadena, California 91125, United States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology , Pasadena, California 91125, United States
| | - Sonja Hess
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology , Pasadena, California 91125, United States
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14
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Topolyan AP, Strizhevskaya DA, Belyaeva MA, Brylev VA, Ustinov AV, Formanovsky AA, Korshun VA. A triphenylcyclopropenylium mass tag: synthesis and application to ultrasensitive LC/MS analysis of amines. Analyst 2016; 141:3289-95. [DOI: 10.1039/c5an02642c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Thiol adducts of triphenylcyclopropenylium undergo efficient heterolytic dissociation in electrospray (ESI) or laser desorption ionization (LDI) mass spectrometry giving rise to a prominent signal of an aromatic C3Ph3+ cation.
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Affiliation(s)
- Artyom P. Topolyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
| | | | - Maria A. Belyaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
| | - Vladimir A. Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
- Lumiprobe Corp
- Hallandale Beach
| | | | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
- Gause Institute of New Antibiotics
- 119021 Moscow
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15
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Braun CR, Bird GH, Wuhr M, Erickson BK, Rad R, Walensky LD, Gygi SP, Haas W. Generation of multiple reporter ions from a single isobaric reagent increases multiplexing capacity for quantitative proteomics. Anal Chem 2015; 87:9855-63. [PMID: 26308379 PMCID: PMC4890644 DOI: 10.1021/acs.analchem.5b02307] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Isobaric labeling strategies for mass spectrometry-based proteomics enable multiplexed simultaneous quantification of samples and therefore substantially increase the sample throughput in proteomics. However, despite these benefits, current limits to multiplexing capacity are prohibitive for large sample sizes and impose limitations on experimental design. Here, we introduce a novel mechanism for increasing the multiplexing density of isobaric reagents. We present Combinatorial Isobaric Mass Tags (CMTs), an isobaric labeling architecture with the unique ability to generate multiple series of reporter ions simultaneously. We demonstrate that utilization of multiple reporter ion series improves multiplexing capacity of CMT with respect to a commercially available isobaric labeling reagent with preserved quantitative accuracy and depth of coverage in complex mixtures. We provide a blueprint for the realization of 16-plex reagents with 1 Da spacing between reporter ions and up to 28-plex at 6 mDa spacing using only 5 heavy isotopes per reagent. We anticipate that this improvement in multiplexing capacity will further advance the application of quantitative proteomics, particularly in high-throughput screening assays.
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Affiliation(s)
- Craig R. Braun
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Gregory H. Bird
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana–Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Martin Wuhr
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Brian K. Erickson
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Ramin Rad
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Loren D. Walensky
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana–Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts 02129, United States
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16
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Andia AA, Miner MR, Woerpel KA. Copper(I)-Catalyzed Oxidation of Alkenes Using Molecular Oxygen and Hydroxylamines: Synthesis and Reactivity of α-Oxygenated Ketones. Org Lett 2015; 17:2704-7. [DOI: 10.1021/acs.orglett.5b01120] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander A. Andia
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Matthew R. Miner
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - K. A. Woerpel
- Department of Chemistry, New York University, New York, New York 10003, United States
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17
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Yeom J, Kang MJ, Shin D, Song HK, Lee C, Lee JE. MTRAQ-based quantitative analysis combined with peptide fractionation based on cysteinyl peptide enrichment. Anal Biochem 2015; 477:41-9. [PMID: 25766576 DOI: 10.1016/j.ab.2015.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/27/2015] [Accepted: 03/04/2015] [Indexed: 01/23/2023]
Abstract
In the present study, the fractionation scheme for cysteinyl peptide enrichment (CPE) was combined with the mass differential tags for relative and absolute quantification (mTRAQ) method to reduce sample complexity and increase proteome coverage. Cysteine residues of the proteins were first alkylated using iodoacetyl PEG2-biotin instead of other conventional alkylating agents such as iodoacetamide. After trypsin digestion, amine groups were labeled with mTRAQ, and these labeled peptides were fractionated according to the presence or absence of cysteine residues using avidin-biotin affinity chromatography. With these approaches, we were able to divide the peptides into the two fractions with more than 90% fractionation efficiency for standard protein and MCF7 cell lysate. When the fractionation strategy was applied to colorectal cancer tissue samples, we were able to obtain quantitative information that was consistent with the previous study based on mTRAQ quantification, implying that the cysteine-based fractionation method does not affect mTRAQ quantification. We expect that the mTRAQ-based quantitative analysis combined with peptide fractionation through the CPE strategy would allow for deep-down analysis of proteome samples and ultimately for increasing proteome coverage with simultaneous quantification for biomarker discovery.
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Affiliation(s)
- Jeonghun Yeom
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Republic of Korea
| | - Min Jung Kang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea; Department of Life Sciences, Korea University, Seoul 136-701, Republic of Korea
| | - Dongyun Shin
- College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul 136-701, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea.
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18
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Yoon HJ, Seo J, Shin SK. Multi-functional MBIT for peptide tandem mass spectrometry. MASS SPECTROMETRY REVIEWS 2015; 34:209-218. [PMID: 24872020 DOI: 10.1002/mas.21435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 11/20/2013] [Accepted: 03/26/2014] [Indexed: 06/03/2023]
Abstract
Isobaric tags have been widely used for the identification and quantification of proteins in mass spectrometry-based proteomics. The mass-balanced, (1) H/(2) H isotope-coded dipeptide tag (MBIT) is a multifunctional isobaric tag based on N-acetyl-Ala-Ala dipeptide containing an amine-reactive linker that conjugates the tag to the primary amines of proteolytic peptides. MBITs provide a pair of isotope-coded quantitation signals separated by 3 Da, which enables 2-plex quantification and identification of proteins in the 15-250 fmol range. Various MBITs diversified at the N-acetyl group or at the side chain of the first alanine provide a pair of bs ions as low-mass quantitation signals in a distinct mass window. Thus, a combination of different MBITs allows multiplex quantification of proteins in a single liquid chromatography-mass spectrometry experiment. Unlike other isobaric tags, MBITs also offer a pair of ys ions as high-mass quantitation signals in a noise-free region, facilitating protein quantification in quadrupole ion trap mass spectrometers. Uniquely, bS ions, forming N-protonated oxazolone, undergo unimolecular dissociation and generate the secondary low-mass quantitation signals, aS ions. The yield of aS ions derived from bS ions can be used to measure the temperature of bS ions, which enables a reproducible acquisition of the peptide tandem mass spectra. Thus, MBITs enable multiplexed quantitation of proteins and the concurrent measurement of ion temperature using bS and aS signal ions as well as the isobaric protein quantitation in resonance-type ion trap using yS (complement of bS ) signal ions. This review provides an overview of MBITs with a focus on the multi-functionality that has been successfully demonstrated in the peptide tandem mass spectrometry.
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Affiliation(s)
- Hye-Joo Yoon
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
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19
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Pan Y, Ye M, Zheng H, Cheng K, Sun Z, Liu F, Liu J, Wang K, Qin H, Zou H. Trypsin-Catalyzed N-Terminal Labeling of Peptides with Stable Isotope-Coded Affinity Tags for Proteome Analysis. Anal Chem 2014; 86:1170-7. [DOI: 10.1021/ac403060d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanbo Pan
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Zheng
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Sun
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjie Liu
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keyun Wang
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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20
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Zhou Y, Shan Y, Wu Q, Zhang S, Zhang L, Zhang Y. Mass defect-based pseudo-isobaric dimethyl labeling for proteome quantification. Anal Chem 2013; 85:10658-63. [PMID: 24180428 DOI: 10.1021/ac402834w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Discovering differentially expressed proteins in various biological samples requires proteome quantification methods with accuracy, precision, and wide dynamic range. This study describes a mass defect-based pseudo-isobaric dimethyl labeling (pIDL) method based on the subtle mass defect differences between (12)C/(13)C and (1)H/(2)H. Lys-C protein digests were labeled with CD2O/(13)CD2O and reduced with NaCNBD3/NaCNBH3 as heavy and light isotopologues, respectively. The fragment ion pairs with mass differences of 5.84 mDa were resolved by high-resolution tandem mass spectrometry (MS/MS) and used for quantification. The pIDL method described here resulted in highly accurate and precise quantification results with approximately 100-fold dynamic range. Furthermore, the pIDL method was extended to 4-plex proteome quantification and applied to the quantitative analysis of proteomes from Hca-P and Hca-F, two mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates.
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Affiliation(s)
- Yuan Zhou
- National Chromatographic Research and Analysis Center, Key Lab of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, China
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21
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Peptide conjugation via CuAAC 'click' chemistry. Molecules 2013; 18:13148-74. [PMID: 24284482 PMCID: PMC6270195 DOI: 10.3390/molecules181113148] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 01/14/2023] Open
Abstract
The copper (I)-catalyzed alkyne azide 1,3-dipolar cycloaddition (CuAAC) or ‘click’ reaction, is a highly versatile reaction that can be performed under a variety of reaction conditions including various solvents, a wide pH and temperature range, and using different copper sources, with or without additional ligands or reducing agents. This reaction is highly selective and can be performed in the presence of other functional moieties. The flexibility and selectivity has resulted in growing interest in the application of CuAAC in various fields. In this review, we briefly describe the importance of the structural folding of peptides and proteins and how the 1,4-disubstituted triazole product of the CuAAC reaction is a suitable isoster for an amide bond. However the major focus of the review is the application of this reaction to produce peptide conjugates for tagging and targeting purpose, linkers for multifunctional biomacromolecules, and reporter ions for peptide and protein analysis.
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22
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Seo J, Suh MS, Yoon HJ, Shin SK. N-Acylated Dipeptide Tags Enable Precise Measurement of Ion Temperature in Peptide Fragmentation. J Phys Chem B 2012; 116:13982-90. [DOI: 10.1021/jp308697v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jongcheol Seo
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
| | - Min-Soo Suh
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
| | - Hye-Joo Yoon
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
| | - Seung Koo Shin
- Bio-Nanotechnology Center, Department
of Chemistry, Pohang University of Science and Technology, San 31
Hyoja-dong Nam-gu, Pohang, 790-784, Korea
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23
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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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24
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McAlister GC, Huttlin EL, Haas W, Ting L, Jedrychowski MP, Rogers JC, Kuhn K, Pike I, Grothe RA, Blethrow JD, Gygi SP. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal Chem 2012; 84:7469-78. [PMID: 22880955 DOI: 10.1021/ac301572t] [Citation(s) in RCA: 451] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantitative mass spectrometry methods offer near-comprehensive proteome coverage; however, these methods still suffer with regards to sample throughput. Multiplex quantitation via isobaric chemical tags (e.g., TMT and iTRAQ) provides an avenue for mass spectrometry-based proteome quantitation experiments to move away from simple binary comparisons and toward greater parallelization. Herein, we demonstrate a straightforward method for immediately expanding the throughput of the TMT isobaric reagents from 6-plex to 8-plex. This method is based upon our ability to resolve the isotopic shift that results from substituting a (15)N for a (13)C. In an accommodation to the preferred fragmentation pathways of ETD, the TMT-127 and -129 reagents were recently modified such that a (13)C was exchanged for a (15)N. As a result of this substitution, the new TMT reporter ions are 6.32 mDa lighter. Even though the mass difference between these reporter ion isotopologues is incredibly small, modern high-resolution and mass accuracy analyzers can resolve these ions. On the basis of our ability to resolve and accurately measure the relative intensity of these isobaric reporter ions, we demonstrate that we are able to quantify across eight samples simultaneously by combining the (13)C- and (15)N-containing reporter ions. Considering the structure of the TMT reporter ion, we believe this work serves as a blueprint for expanding the multiplexing capacity of the TMT reagents to at least 10-plex and possibly up to 18-plex.
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Affiliation(s)
- Graeme C McAlister
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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25
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Isobaric tagging approaches in quantitative proteomics: the ups and downs. Anal Bioanal Chem 2012; 404:1029-37. [DOI: 10.1007/s00216-012-6012-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/24/2012] [Accepted: 04/02/2012] [Indexed: 12/27/2022]
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26
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Evans C, Noirel J, Ow SY, Salim M, Pereira-Medrano AG, Couto N, Pandhal J, Smith D, Pham TK, Karunakaran E, Zou X, Biggs CA, Wright PC. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012; 404:1011-27. [PMID: 22451173 DOI: 10.1007/s00216-012-5918-6] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 01/09/2023]
Abstract
The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.
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Affiliation(s)
- Caroline Evans
- The ChELSI Institute, Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
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27
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Sohn CH, Agnew HD, Lee JE, Sweredoski MJ, Graham RL, Smith GT, Hess S, Czerwieniec G, Loo JA, Heath JR, Deshaies RJ, Beauchamp JL. Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions. Anal Chem 2012; 84:2662-9. [PMID: 22339618 PMCID: PMC3310289 DOI: 10.1021/ac202637n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein-protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell-permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enrichment of cross-linked peptides are performed for cross-linked ubiquitin digests mixed with yeast cell lysates. Cross-linked peptides are detected and identified by collision induced dissociation (CID) and ETD with linear quadrupole ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) and LTQ-Orbitrap mass spectrometers. The application of CXLs to more complex systems (e.g., in vivo cross-linking) is illustrated by Western blot detection of Cul1 complexes including known binders, Cand1 and Skp2, in HEK 293 cells, confirming good water solubility and cell-permeability.
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Affiliation(s)
- Chang Ho Sohn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Heather D. Agnew
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - J. Eugene Lee
- Division of Biology, California Institute of Technology, Pasadena, CA 91125
| | - Michael J. Sweredoski
- The Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Robert L.J. Graham
- The Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Geoffrey T. Smith
- The Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Sonja Hess
- The Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Gregg Czerwieniec
- Molecular Instrumentation Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095
| | - James R. Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | | | - J. L. Beauchamp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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