51
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Sun L, Zhu G, Yan X, Mou S, Dovichi NJ. Uncovering immobilized trypsin digestion features from large-scale proteome data generated by high-resolution mass spectrometry. J Chromatogr A 2014; 1337:40-7. [PMID: 24636566 PMCID: PMC4000775 DOI: 10.1016/j.chroma.2014.02.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 12/21/2022]
Abstract
Immobilized trypsin produces very fast protein digestion, which is attractive for application to high throughput bottom-up proteomics. While there is a rich literature on the preparation of immobilized trypsin, there are very few studies that investigate its application to complex proteomic samples. In this work, we compared solution-phase trypsin with trypsin immobilized on magnetic microspheres for digestion of two complex proteomes, Escherichia coli and the MCF7 cell line. The digests were separated by HPLC, and detected with a Q-Exactive mass spectrometer, which generated high resolution and high quality parent- and fragment-ion mass spectra. The data were analyzed using MaxQuant. We make several conclusions about the features of immobilized trypsin digestion of complex proteomes. First, both immobilized and solution-phase trypsin generate peptides that sample the same protein pool. Second, immobilized trypsin can digest complex proteomes two orders of magnitude faster than solution-phase trypsin while retaining similar numbers of protein identifications and proteome depth. Digestion using immobilized trypsin for 5-min produces a similar number of missed cleavages as solution-based trypsin digestion for 4-h; digestion using immobilized trypsin for 20-min produces a similar number of missed cleavages as solution-based trypsin digestion for 12-h. Third, immobilized trypsin produces quantitatively reproducible digestion of complex proteomes. Finally, there is small but measurable loss of peptide due to non-specific adsorption to the immobilization matrix. This adsorption generates a bias against detection of basic peptides.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Si Mou
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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52
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Yan Y, Sun X, Deng C, Li Y, Zhang X. Metal Oxide Affinity Chromatography Platform–Polydopamine Coupled Functional Two-Dimensional Titania Graphene Nanohybrid for Phosphoproteome Research. Anal Chem 2014; 86:4327-32. [DOI: 10.1021/ac500047p] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yinghua Yan
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Xueni Sun
- Pharmaceutical
Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Chunhui Deng
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Yan Li
- Pharmaceutical
Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xiangmin Zhang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
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53
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An ultra-fast and highly efficient multiple proteases digestion strategy using graphene-oxide-based immobilized protease reagents. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5082-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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54
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Development of continuous microwave-assisted protein digestion with immobilized enzyme. Biochem Biophys Res Commun 2014; 445:491-6. [DOI: 10.1016/j.bbrc.2014.02.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 02/06/2014] [Indexed: 11/17/2022]
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55
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Fan C, Shi Z, Pan Y, Song Z, Zhang W, Zhao X, Tian F, Peng B, Qin W, Cai Y, Qian X. Dual Matrix-Based Immobilized Trypsin for Complementary Proteolytic Digestion and Fast Proteomics Analysis with Higher Protein Sequence Coverage. Anal Chem 2014; 86:1452-8. [DOI: 10.1021/ac402696b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Chao Fan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Graduate School of Anhui Medical University, Hefei, Chian
| | - Zhaomei Shi
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Graduate School of Anhui Medical University, Hefei, Chian
| | - Yiting Pan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Zifeng Song
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Wanjun Zhang
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xinyuan Zhao
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Fang Tian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Bo Peng
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Weijie Qin
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yun Cai
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xiaohong Qian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
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56
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Safdar M, Sproß J, Jänis J. Microscale immobilized enzyme reactors in proteomics: Latest developments. J Chromatogr A 2014; 1324:1-10. [DOI: 10.1016/j.chroma.2013.11.045] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 11/18/2013] [Accepted: 11/24/2013] [Indexed: 01/10/2023]
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57
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WANG L, ZANG XH, WANG C, WANG Z. Research Developments for Applications of Graphene in Sample Preparation. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(13)60705-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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58
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Yin Z, Zhao W, Tian M, Zhang Q, Guo L, Yang L. A capillary electrophoresis-based immobilized enzyme reactor using graphene oxide as a support via layer by layer electrostatic assembly. Analyst 2014; 139:1973-9. [DOI: 10.1039/c3an02241b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Using graphene oxide as an enzyme support, we developed a novel CE-based microreactor via layer-by-layer electrostatic assembly, which can be used for accurate on-line analysis and characterization of peptides and proteins.
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Affiliation(s)
- Zhengri Yin
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Wenwen Zhao
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Miaomiao Tian
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Qian Zhang
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Liping Guo
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
| | - Li Yang
- Faculty of Chemistry
- Northeast Normal University
- Changchun, P. R. China
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59
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60
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Yan Y, Zheng Z, Deng C, Li Y, Zhang X, Yang P. Hydrophilic Polydopamine-Coated Graphene for Metal Ion Immobilization as a Novel Immobilized Metal Ion Affinity Chromatography Platform for Phosphoproteome Analysis. Anal Chem 2013; 85:8483-7. [DOI: 10.1021/ac401668e] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yinghua Yan
- Department of Chemistry and
Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Zhifang Zheng
- Department of Chemistry and
Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry and
Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yan Li
- Pharmaceutical Analysis Department,
School of Pharmacy, Fudan University, Shanghai
201203, China
| | - Xiangmin Zhang
- Department of Chemistry and
Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry and
Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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61
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Bao H, Zhang L, Chen G. Immobilization of trypsin via graphene oxide-silica composite for efficient microchip proteolysis. J Chromatogr A 2013; 1310:74-81. [PMID: 23998335 DOI: 10.1016/j.chroma.2013.08.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 08/01/2013] [Accepted: 08/12/2013] [Indexed: 11/15/2022]
Abstract
In this report, trypsin was covalently immobilized in the graphene oxide (GO)-silica composite coating on the channel wall of poly(methyl methacrylate) (PMMA) microchips to fabricate microfluidic bioreactors for highly efficient proteolysis. A mixture solution containing GO nanosheets and silica gel was injected into the channels to form coating. 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide and N-hydroxysuccinimide were used as carboxyl activating agents to crosslink the primary amino groups of trypsin to the carboxyl groups of the entrapped GO sheets in the composite to realize covalent immobilization. The feasibility and performance of the novel GO-based microfluidic bioreactors were demonstrated by the digestion of hemoglobin (HEM), cytochrome c (Cyt-c), myoglobin (MYO), and ovalbumin (OVA) and the digestion time was significantly reduced to 5s. The obtained digests were identified by MALDI-TOF MS with the sequence coverages of 95%, 76%, 69%, and 55% for HEM, Cyt-c, MYO, and OVA, respectively. The suitability of the prepared bioreactors to complex proteins was demonstrated by digesting human serum.
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Affiliation(s)
- Huimin Bao
- School of Pharmacy, Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
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62
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Wang W, Ma R, Wu Q, Wang C, Wang Z. Magnetic microsphere-confined graphene for the extraction of polycyclic aromatic hydrocarbons from environmental water samples coupled with high performance liquid chromatography–fluorescence analysis. J Chromatogr A 2013; 1293:20-7. [DOI: 10.1016/j.chroma.2013.03.071] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/27/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
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63
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Agrawal GK, Timperio AM, Zolla L, Bansal V, Shukla R, Rakwal R. Biomarker discovery and applications for foods and beverages: proteomics to nanoproteomics. J Proteomics 2013; 93:74-92. [PMID: 23619387 DOI: 10.1016/j.jprot.2013.04.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/17/2013] [Accepted: 04/01/2013] [Indexed: 12/18/2022]
Abstract
Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal.
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64
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Tian MM, Chen DX, Sun YL, Yang YW, Jia Q. Pillararene-functionalized Fe3O4 nanoparticles as magnetic solid-phase extraction adsorbent for pesticide residue analysis in beverage samples. RSC Adv 2013. [DOI: 10.1039/c3ra43752c] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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65
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LI Z, HOU M, BAI S, WANG C, WANG Z. Extraction of Imide Fungicides in Water and Juice Samples Using Magnetic Graphene Nanoparticles as Adsorbent Followed by Their Determination with Gas Chromatography and Electron Capture Detection. ANAL SCI 2013; 29:325-31. [DOI: 10.2116/analsci.29.325] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhi LI
- Department of Chemistry, College of Science, Agricultural University of Hebei
| | - Mengying HOU
- Department of Chemistry, College of Science, Agricultural University of Hebei
| | - Shasha BAI
- College of Food Science & Technology, Agricultural University of Hebei
| | - Chun WANG
- Department of Chemistry, College of Science, Agricultural University of Hebei
| | - Zhi WANG
- Department of Chemistry, College of Science, Agricultural University of Hebei
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66
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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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