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Selective enrichment of N-terminal proline peptides via hydrazide chemistry for proteomics analysis. Anal Chim Acta 2020; 1142:48-55. [PMID: 33280703 DOI: 10.1016/j.aca.2020.10.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 11/20/2022]
Abstract
A challenge for shotgun proteomics is the identification of low abundance proteins, which is always hampered owing to the extreme complexity of protein digests and highly dynamic concentration range of proteins. To reduce the complexity of the peptide mixture, we developed a novel method to selectively enrich N-terminal proline peptides via hydrazide chemistry. This method consisted of ortho-phthalaldehyde (OPA) blocking of primary amines in peptides, reductive glutaraldehydation of N-terminal proline and solid phase hydrazide chemistry enrichment of aldehyde-modified N-terminal proline peptide. After enrichment, the number of detected peptides containing N-terminal proline increased from 1304 to 4039 and the ratio of N-terminal proline peptides jumped from 4.4% to 93.7%, showing good enrichment specificity towards N-terminal proline peptides. Besides, the ratio of identified peptides to proteins was decreased from 7.8 (29751/3811) to 1.5 (4347/2821), indicating that sample complexity was drastically reduced through this method. As a result, this novel approach for enriching N-terminal proline peptides is effective in identification of low abundance protein owing to the reduction of sample complexity.
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Cao T, Lv J, Zhang L, Yan G, Lu H. Selective Enrichment and Quantification of N-Terminal Glycine Peptides via Sortase A Mediated Ligation. Anal Chem 2018; 90:14303-14308. [DOI: 10.1021/acs.analchem.8b03562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Saraji M, Yousefi S. Hydrazide functionalized magnetic nanoparticles for specific extraction of N-terminal serine and threonine peptides. Biomed Chromatogr 2018; 32:e4305. [PMID: 29855045 DOI: 10.1002/bmc.4305] [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: 03/06/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 11/09/2022]
Abstract
In this study, we present hydrazide functionalized magnetic nanoparticles as a sorbent prepared by a new and facile method. Scanning electron microscope and Fourier transform infrared were used for characterizing the synthesized nanoparticles. The ability of the sorbent to extract N-terminal serine and threonine peptides was evaluated. The peptides were modified by oxidation of the hydroxyl group in the 1,2-amino alcohol structure before extraction. These aldehyde-forms of peptides were specifically bonded to the hydrazide groups of the sorbent. The formed hydrazone bonds were cleaved in the presence of hydroxylamine reagent. Finally, the oximated peptides were released and quantified with a high-performance liquid chromatography-diode array spectroscopy. The effects of experimental parameters including extraction time, elution time and elution volume on extraction efficiency were also investigated. The required time for the extraction process to reach equilibrium and elution time was only 8 h. The adsorption efficiency of the sorbent was 79 and 77% for peptides with N-terminal serine and threonine, respectively. The sorbent showed good specificity for extracting the peptides. In addition, the extraction efficiency of the sorbent remained constant in the presence of a non-N-terminal serine and threonine peptide as interference.
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Affiliation(s)
- Mohammad Saraji
- Isfahan University of Technology, Department of Chemistry, Isfahan, Iran
| | - Shila Yousefi
- Isfahan University of Technology, Department of Chemistry, Isfahan, Iran
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4
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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Huang J, Wang J, Li Q, Zhang Y, Zhang X. Enzyme and Chemical Assisted N-Terminal Blocked Peptides Analysis, ENCHANT, as a Selective Proteomics Approach Complementary to Conventional Shotgun Approach. J Proteome Res 2017; 17:212-221. [DOI: 10.1021/acs.jproteome.7b00521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jingnan Huang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Wang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qingqing Li
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
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Yao Y, Huang J, Cheng K, Pan Y, Qin H, Ye M, Zou H. Specific Enrichment of Peptides with N-Terminal Serine/Threonine by a Solid-Phase Capture-Release Approach for Efficient Proteomics Analysis. Anal Chem 2015; 87:11353-60. [DOI: 10.1021/acs.analchem.5b02711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yating Yao
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junfeng Huang
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Cheng
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanbo Pan
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongqiang Qin
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Mingliang Ye
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Hanfa Zou
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
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da Costa JP, Oliveira-Silva R, Daniel-da-Silva AL, Vitorino R. Bionanoconjugation for Proteomics applications — An overview. Biotechnol Adv 2014; 32:952-70. [DOI: 10.1016/j.biotechadv.2014.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/15/2014] [Accepted: 04/26/2014] [Indexed: 12/29/2022]
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8
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Zhao M, Xie Y, Deng C, Zhang X. Recent advances in the application of core–shell structured magnetic materials for the separation and enrichment of proteins and peptides. J Chromatogr A 2014; 1357:182-93. [DOI: 10.1016/j.chroma.2014.04.078] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/20/2014] [Accepted: 04/22/2014] [Indexed: 12/28/2022]
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Li Y, Zhang X, Deng C. Functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis. Chem Soc Rev 2013; 42:8517-39. [DOI: 10.1039/c3cs60156k] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Siegel D. Applications of reversible covalent chemistry in analytical sample preparation. Analyst 2012; 137:5457-82. [PMID: 23013801 DOI: 10.1039/c2an35697j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.
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Affiliation(s)
- David Siegel
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str 11, 12489 Berlin, Germany.
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11
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Prefractionation and separation by C8 stationary phase: Effective strategies for integral membrane proteins analysis. Talanta 2012; 88:567-72. [DOI: 10.1016/j.talanta.2011.11.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 11/10/2011] [Accepted: 11/13/2011] [Indexed: 11/18/2022]
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