1
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Chen J, Zhu M, Xiang F, Li J, Yang H, Mao Z. Research Progress on Microreactor Technology in Oxidation Reactions. CURR ORG CHEM 2021. [DOI: 10.2174/1385272825666210319092545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In recent years, the development of the chemical industry has been moving in a
green, safe and efficient direction. Oxidation reactions are one of the most important types of
reactions and have key applications in food, medicine, cosmetics, and petrochemicals. However,
the occurrence of the oxidation reaction is accompanied by a strong exothermic phenomenon,
and improper control can easily lead to safety problems and even explosions. The
realization of an environmentally friendly oxidation reaction is a key industrial milestone.
The unique structural characteristics of microreactors result in good mass and heat transfer
performance, precise control of the reaction temperature, reduced risk of explosion, improved
safety production and selectivity of products. These unique advantages of the microreactor
determine its significant application value in oxidation reactions. In this paper, the research
progress of several typical oxidation reactions, including alkane oxidation, alcohol oxidation,
aldosterone oxidation, aromatics oxidation and olefin oxidation combined with microreactors,
is reviewed systematically.
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Affiliation(s)
- Jian Chen
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070,China
| | - Mengjing Zhu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070,China
| | - Fuwei Xiang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070,China
| | - Junfeng Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070,China
| | - Hongjun Yang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070,China
| | - Zhipeng Mao
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070,China
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2
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Shen X, Sun L. Systematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics. Proteomics 2018; 18:e1700432. [PMID: 29577644 DOI: 10.1002/pmic.201700432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/02/2018] [Indexed: 11/08/2022]
Abstract
Immobilized trypsin (IM) has been recognized as an alternative to free trypsin (FT) for accelerating protein digestion 30 years ago. However, some questions of IM still need to be answered. How does the solid matrix of IM influence its preference for protein cleavage and how well can IM perform for deep bottom-up proteomics compared to FT? By analyzing Escherichia coli proteome samples digested with amine or carboxyl functionalized magnetic bead-based IM (IM-N or IM-C) or FT, it is observed that IM-N with the nearly neutral solid matrix, IM-C with the negatively charged solid matrix, and FT have similar cleavage preference considering the microenvironment surrounding the cleavage sites. IM-N (15 min) and FT (12 h) both approach 9000 protein identifications (IDs) from a mouse brain proteome. Compared to FT, IM-N has no bias in the digestion of proteins that are involved in various biological processes, are located in different components of cells, have diverse functions, and are expressed in varying abundance. A high-throughput bottom-up proteomics workflow comprising IM-N-based rapid protein cleavage and fast CZE-MS/MS enables the completion of protein sample preparation, CZE-MS/MS analysis, and data analysis in only 3 h, resulting in 1000 protein IDs from the mouse brain proteome.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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3
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Kecskemeti A, Gaspar A. Particle-based immobilized enzymatic reactors in microfluidic chips. Talanta 2018; 180:211-228. [DOI: 10.1016/j.talanta.2017.12.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
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4
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Liu B, Wu L, Zhou X, Wu H, Zheng B. Porous polydimethylsiloxane monolith for protein digestion. J Mater Chem B 2018; 6:824-829. [DOI: 10.1039/c7tb02738a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We developed a simple method to prepare interconnected porous PDMS monolith using glass microbubbles as the template.
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Affiliation(s)
- Baishu Liu
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Liang Wu
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Xiaohu Zhou
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Han Wu
- Department of Chemistry
- The Chinese University of Hong Kong
- China
| | - Bo Zheng
- Department of Chemistry
- The Chinese University of Hong Kong
- China
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5
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Yao Y, Bian Y, Dong M, Wang Y, Lv J, Chen L, Wang H, Mao J, Dong J, Ye M. SH2 Superbinder Modified Monolithic Capillary Column for the Sensitive Analysis of Protein Tyrosine Phosphorylation. J Proteome Res 2017; 17:243-251. [PMID: 29083189 DOI: 10.1021/acs.jproteome.7b00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this study, we present a method to specifically capture phosphotyrosine (pTyr) peptides from minute amount of sample for the sensitive analysis of protein tyrosine phosphorylation. We immobilized SH2 superbinder on a monolithic capillary column to construct a microreactor to enrich pTyr peptides. It was found that the synthetic pTyr peptide could be specifically enriched by the microreactor from the peptide mixture prepared by spiking of the synthetic pTyr peptide into the tryptic digests of α-casein and β-casein with molar ratios of 1:1000:1000. The microreactor was further applied to enrich pTyr peptides from pervanadate-treated HeLa cell digests for phosphoproteomics analysis, which resulted in the identification of 796 unique pTyr sites. In contrast, the conventional SH2 superbinder-based method identified 41 pTyr sites for the same sample, only 5.2% of the number achieved by the microreactor. Finally, this microreactor was also applied to analyze the pTyr in Shc1 complex, an immunopurified protein complex, which resulted in the identification of 15 pTyr sites. Together, this technique is best fitted to analyze the pTyr in minute amount of sample and will have broad application in fields where only a limited amount of sample is available.
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Affiliation(s)
- Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University , Zhengzhou, Henan 450052, China
| | - Mingming Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,Dalian Ocean University, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawen Lv
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lianfang Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023, China
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6
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Zhou C, Chen X, Du Z, Li G, Xiao X, Cai Z. A hybrid monolithic column based on boronate-functionalized graphene oxide nanosheets for online specific enrichment of glycoproteins. J Chromatogr A 2017; 1498:90-98. [DOI: 10.1016/j.chroma.2017.01.049] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 01/16/2017] [Accepted: 01/21/2017] [Indexed: 12/13/2022]
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7
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Development of an enzymatic reactor applying spontaneously adsorbed trypsin on the surface of a PDMS microfluidic device. Anal Bioanal Chem 2017; 409:3573-3585. [DOI: 10.1007/s00216-017-0295-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
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8
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Kecskemeti A, Gaspar A. Preparation and characterization of a packed bead immobilized trypsin reactor integrated into a PDMS microfluidic chip for rapid protein digestion. Talanta 2017; 166:275-283. [PMID: 28213235 DOI: 10.1016/j.talanta.2017.01.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 01/20/2023]
Abstract
This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i.e. measured mass ratio before the immobilization reaction) was determined. The amount of immobilized trypsin was 10-15μg trypsin for 1mg silica particle. Migration times of CZE peptide maps showed good repeatability and reproducibility (RSD%=0.02-0.31%). The IMER maintained its activity for 2 months, in this period it was used effectively for rapid proteolysis. Four proteins (myoglobin, lysozyme, hemoglobin and albumin) in a wide size range (15-70kDa) were digested to demonstrate the applicability of the reactor. Their CZE peptide maps were compared to peptide maps obtained from standard in-solution digestion of the four proteins. The number of peptide peaks correlated well with the theoretically expected peptide number in both cases, the peak patterns of the electropherograms were similar, however, digestion with the microchip IMER requires only <10s, while in-solution digestion takes 16h. LC-MS/MS peptide mapping was also carried out, the four proteins were identified with satisfying sequence coverages (29-50%), trypsin autolysis peptides were not detected. The protein content of human serum was digested with the IMER and with in-solution digestion.
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Affiliation(s)
- Adam Kecskemeti
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen 4032, Hungary
| | - Attila Gaspar
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen 4032, Hungary.
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9
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Moore S, Hess S, Jorgenson J. Characterization of an immobilized enzyme reactor for on-line protein digestion. J Chromatogr A 2016; 1476:1-8. [PMID: 27876348 PMCID: PMC5136339 DOI: 10.1016/j.chroma.2016.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/29/2016] [Accepted: 11/13/2016] [Indexed: 01/05/2023]
Abstract
Despite the developments for faster liquid chromatographic and mass spectral detection techniques, the standard in-solution protein digestion for proteomic analyses has remained relatively unchanged. The typical in-solution trypsin protein digestion is usually the slowest part of the workflow, albeit one of the most important. The development of a highly efficient immobilized enzyme reactor (IMER) with rapid performance for on-line protein digestion would greatly decrease the analysis time involved in a proteomic workflow. Presented here is the development of a silica based IMER for on-line protein digestion, which produced rapid digestions in the presence of organic mobile phase for both model proteins and a complex sample consisting of the insoluble portion of a yeast cell lysate. Protein sequence coverage and identifications evaluated between the IMER and in-solution digestions were comparable. Overall, for a yeast cell lysate with only a 10s volumetric residence time on-column, the IMER identified 507 proteins while the in-solution digestion identified 490. There were no significant differences observed based on identified protein's molecular weight or isoelectric point between the two digestion methods. Implementation of the IMER into the proteomic workflow provided similar protein identification results, automation for sample analysis, and reduced the analysis time by 15h.
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Affiliation(s)
- Stephanie Moore
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - Stephanie Hess
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - James Jorgenson
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States.
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10
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Hassing RJ, Goessens WH, Zeneyedpour L, Sultan S, van Kampen JJ, Verbon A, van Genderen PJ, Hays JP, Luider TM, Dekker LJ. Detection of amino acid substitutions in the GyrA protein of fluoroquinolone-resistant typhoidal Salmonella isolates using high-resolution mass spectrometry. Int J Antimicrob Agents 2016; 47:351-6. [PMID: 27132191 DOI: 10.1016/j.ijantimicag.2016.01.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/25/2016] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
Abstract
Infections with typhoidal Salmonella isolates that are resistant to fluoroquinolone antibiotics have become very common in several Asian countries. In the majority of these cases, resistance to fluoroquinolone-based antibiotics is associated with genetic mutations in the quinolone resistance-determining region (QRDR) of the bacterial DNA gyrase gene gyrA. The objective of this study was to detect these amino acid substitutions by high-resolution mass spectrometry instead of sequencing of the gyrA gene. A liquid chromatography-mass spectrometry (LC-MS) methodology was developed and evaluated for the detection of amino acid substitutions in the GyrA protein of 23 typhoidal Salmonella isolates. These isolates included typhoidal Salmonella that possessed different antibiotic sensitivities to fluoroquinolone antibiotics. The LC-MS methodology correctly identified peptide sequences associated with phenotypic QRDR mutations of the GyrA protein in all 23 phenotypically diverse typhoidal Salmonella isolates tested. In conclusion, a reliable and rapid LC-MS methodology has been developed that is able to identify GyrA QRDR mutations that are involved in the development of fluoroquinolone resistance in typhoidal Salmonella spp. Furthermore, this 'proof of principle' study indicates the potential usefulness of LC-MS in future detection of antibiotic resistance.
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Affiliation(s)
- Robert-Jan Hassing
- Department of Internal Medicine and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Wil H Goessens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
| | - Lona Zeneyedpour
- Department of Neurology, Neuro-Oncology Laboratory, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Sadaf Sultan
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Jeroen J van Kampen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Perry J van Genderen
- Institute for Tropical Diseases, Havenziekenhuis, Haringvliet 72, 3011 TG Rotterdam, The Netherlands
| | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Neuro-Oncology Laboratory, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Lennard J Dekker
- Department of Neurology, Neuro-Oncology Laboratory, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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11
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Laurenti E, dos Santos Vianna Jr. A. Enzymatic microreactors in biocatalysis: history, features, and future perspectives. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/boca-2015-0008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractMicrofluidic reaction devices are a very promising technology for chemical and biochemical processes. In microreactors, the micro dimensions, coupled with a high surface area/volume ratio, permit rapid heat exchange and mass transfer, resulting in higher reaction yields and reaction rates than in conventional reactors. Moreover, the lower energy consumption and easier separation of products permit these systems to have a lower environmental impact compared to macroscale, conventional reactors. Due to these benefits, the use of microreactors is increasing in the biocatalysis field, both by using enzymes in solution and their immobilized counterparts. Following an introduction to the most common applications of microreactors in chemical processes, a broad overview will be given of the latest applications in biocatalytic processes performed in microreactors with free or immobilized enzymes. In particular, attention is given to the nature of the materials used as a support for the enzymes and the strategies employed for their immobilization. Mathematical and engineering aspects concerning fluid dynamics in microreactors were also taken into account as fundamental factors for the optimization of these systems.
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12
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Jiang S, Zhang Z, Li L. A one-step preparation method of monolithic enzyme reactor for highly efficient sample preparation coupled to mass spectrometry-based proteomics studies. J Chromatogr A 2015; 1412:75-81. [PMID: 26300481 DOI: 10.1016/j.chroma.2015.07.121] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 07/25/2015] [Accepted: 07/31/2015] [Indexed: 01/02/2023]
Abstract
Mass spectrometry (MS) coupled to sample preparation and separation techniques has become a primary tool for proteomics studies. However, due to sample complexity, it is often challenging to achieve fast and efficient sample preparation prior to MS analysis. In recent decades, monolithic materials have been developed not only as chromatographic media, but also as efficient solid supports for immobilizing multiple types of affinity reagents. Herein, the N-acryloxysuccinimide-co-acrylamide-co-N,N'-methylenebisacrylamide (NAS-AAm-Bis) monolith was fabricated within silanized 200 μm i.d. fused-silica capillaries and was used as an immobilized enzyme reactor (IMER). The column was conjugated with trypsin/Lys-C and Lys-N enzymes to allow enzymatic digestions to occur while protein mixture was loaded onto the IMER column followed by MS-based proteomics analysis. Similar MS signal and protein sequence coverage were observed using protein standard bovine serum albumin (BSA) compared to in-solution digestion. Furthermore, mouse serum, yeast, and human cell lysate samples were also subjected to enzymatic digestion by both IMER (in seconds to minutes) and conventional in solution digestion (overnight) for comparison in large-scale proteomics studies. Comparable protein identification results obtained by the two methods highlighted the potential of employing NAS-based IMER column for fast and highly efficient sample preparation for MS analysis in proteomics studies.
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Affiliation(s)
- Shan Jiang
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, United States
| | - Zichuan Zhang
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI 53705, United States; Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, United States.
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13
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Pepsin immobilization on an aldehyde-modified polymethacrylate monolith and its application for protein analysis. J Biosci Bioeng 2015; 119:505-10. [DOI: 10.1016/j.jbiosc.2014.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 12/16/2022]
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14
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Vlakh EG, Ponomareva EA, Tennikova TB. A multienzyme bioreactor based on a chitinase complex. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814050123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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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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16
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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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17
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Çelikbıçak Ö, Atakay M, Güler Ü, Salih B. A Trypsin Immobilized Sol-Gel for Protein Indentification in MALDI-MS Applications. ANAL LETT 2014. [DOI: 10.1080/00032719.2013.831423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Chen CC, Su WC, Huang BY, Chen YJ, Tai HC, Obena RP. Interaction modes and approaches to glycopeptide and glycoprotein enrichment. Analyst 2014; 139:688-704. [DOI: 10.1039/c3an01813j] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Kim JH, Inerowicz D, Hedrick V, Regnier F. Integrated Sample Preparation Methodology for Proteomics: Analysis of Native Proteins. Anal Chem 2013; 85:8039-45. [PMID: 23937592 DOI: 10.1021/ac401477w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jin-Hee Kim
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
| | - Dorota Inerowicz
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
| | - Vicki Hedrick
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
| | - Fred Regnier
- Department of Chemistry and ‡Bindley Bioscience Center at Discovery Park, Purdue University, West Lafayette, Indiana
47906, United States
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20
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Vlakh EG, Tennikova TB. Flow-through immobilized enzyme reactors based on monoliths: II. Kinetics study and application. J Sep Sci 2013; 36:1149-67. [DOI: 10.1002/jssc.201201090] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/17/2012] [Accepted: 12/17/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Evgenia G. Vlakh
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Tatiana B. Tennikova
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
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Vlakh EG, Tennikova TB. Flow-through immobilized enzyme reactors based on monoliths: I. Preparation of heterogeneous biocatalysts. J Sep Sci 2013; 36:110-27. [DOI: 10.1002/jssc.201200594] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/13/2012] [Accepted: 08/13/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Evgenia G. Vlakh
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Tatiana B. Tennikova
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
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22
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Jiao J, Miao A, Zhang X, Cai Y, Lu Y, Zhang Y, Lu H. Realization of on-tissue protein identification by highly efficient in situ digestion with graphene-immobilized trypsin for MALDI imaging analysis. Analyst 2013; 138:1645-8. [DOI: 10.1039/c3an36391k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Hwang HJ, Cho K, Kim JY, Kim YH, Oh HB. Protein Analysis Using a Combination of an Online Monolithic Trypsin Immobilized Enzyme Reactor and Collisionally-Activated Dissociation/Electron Transfer Dissociation Dual Tandem Mass Spectrometry. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.10.3233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Wang F, Wei X, Zhou H, Liu J, Figeys D, Zou H. Combination of online enzyme digestion with stable isotope labeling for high-throughput quantitative proteome analysis. Proteomics 2012; 12:3129-37. [DOI: 10.1002/pmic.201200162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/15/2012] [Accepted: 08/14/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Xiaoluan Wei
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Hu Zhou
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jing Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
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25
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Zhang Z, Wang F, Xu B, Qin H, Ye M, Zou H. Preparation of capillary hybrid monolithic column with sulfonate strong cation exchanger for proteome analysis. J Chromatogr A 2012; 1256:136-43. [DOI: 10.1016/j.chroma.2012.07.071] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/16/2022]
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26
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Jiang H, Yuan H, Liang Y, Xia S, Zhao Q, Wu Q, Zhang L, Liang Z, Zhang Y. A hydrophilic immobilized trypsin reactor with N-vinyl-2-pyrrolidinone modified polymer microparticles as matrix for highly efficient protein digestion with low peptide residue. J Chromatogr A 2012; 1246:111-6. [DOI: 10.1016/j.chroma.2012.03.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 02/12/2012] [Accepted: 03/04/2012] [Indexed: 11/26/2022]
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27
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Chen Y, Wang K, Yang H, Liu Y, Yao S, Chen B, Nie L, Xu G. Synthesis of sulfo/vinyl biphasic silica hybrid monolithic capillary column and its application to on-column preconcentration for capillary electrochromatography. J Chromatogr A 2012; 1233:91-9. [DOI: 10.1016/j.chroma.2012.01.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/10/2012] [Accepted: 01/11/2012] [Indexed: 10/14/2022]
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28
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Zhou Z, Yang Y, Zhang J, Zhang Z, Bai Y, Liao Y, Liu H. Ion-exchange-membrane-based enzyme micro-reactor coupled online with liquid chromatography–mass spectrometry for protein analysis. Anal Bioanal Chem 2012; 403:239-46. [DOI: 10.1007/s00216-012-5812-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 01/31/2012] [Accepted: 01/31/2012] [Indexed: 11/28/2022]
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29
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Sun L, Li Y, Yang P, Zhu G, Dovichi NJ. High efficiency and quantitatively reproducible protein digestion by trypsin-immobilized magnetic microspheres. J Chromatogr A 2012; 1220:68-74. [PMID: 22176736 PMCID: PMC3253205 DOI: 10.1016/j.chroma.2011.11.050] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/18/2011] [Accepted: 11/23/2011] [Indexed: 11/22/2022]
Abstract
Aldehyde- and NHS-activated magnetic microspheres were used to immobilize trypsin (CHO-trypsin and NHS-trypsin), and their performance for protein digestion was evaluated by reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry using an LTQ Orbitrap Velos instrument. NHS-trypsin provided greater sequence coverage and identified more peptides for the digestion of bovine serum albumin. A 1-min digestion at room temperature using the immobilized trypsin also identified more peptides (96±6 vs. 48±1) and produced higher sequence coverage (90±2% vs. 75±2%) than traditional free trypsin digestion for 12h at 37 °C. Analysis of 15 nM (0.001 mg/mL) BSA digested by NHS-trypsin in 1 min at room temperature consistently yielded one detected peptide; 150 nM BSA generated 22 peptides. Peptide intensity and protein spectral count were used to evaluate the run-to-run digestion reproducibility of NHS-trypsin with a three-protein-mixture. Three high intensity peptides for each protein generated intensity ratios from 0.70 to 1.09 and spectral count ratios from 0.78 to 1.18. Finally, RAW 264.7 cell lysates were digested by NHS-trypsin for 10 min and 30 min at room temperature, 604 and 697 protein groups, respectively, were identified by RPLC-ESI-MS/MS, with a peptide false discovery rate of less than 1%. Digestion by solution phase trypsin for 12h at 37 °C resulted in identification of 878 protein groups.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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30
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Chen Y, Wu M, Wang K, Chen B, Yao S, Zou H, Nie L. Vinyl functionalized silica hybrid monolith-based trypsin microreactor for on line digestion and separation via thiol-ene “click” strategy. J Chromatogr A 2011; 1218:7982-8. [DOI: 10.1016/j.chroma.2011.09.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 10/17/2022]
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31
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Rozenbrand J, van Bennekom WP. Silica-based and organic monolithic capillary columns for LC: recent trends in proteomics. J Sep Sci 2011; 34:1934-44. [PMID: 21710526 DOI: 10.1002/jssc.201100294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/03/2011] [Accepted: 05/03/2011] [Indexed: 11/10/2022]
Abstract
The use of monolithic liquid chromatography (LC) columns for proteomics, covering the scientific literature from 2004 to the beginning of 2011, is reviewed. Attention is paid to recent developments in column technology and materials, focusing on silica-based and organic (polystyrene and methacrylate) monolithic capillary columns for proteomics. The applicability of these columns is illustrated by examples of the analysis of (complex) protein digests and proteins conveniently summarized in tables. Furthermore, characteristics of column materials are compared and future trends and prospects are presented.
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Affiliation(s)
- Johan Rozenbrand
- Biomolecular Analysis, Faculty of Science, Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
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32
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Tian R, Hoa XD, Lambert JP, Pezacki JP, Veres T, Figeys D. Development of a multiplexed microfluidic proteomic reactor and its application for studying protein-protein interactions. Anal Chem 2011; 83:4095-102. [PMID: 21520965 DOI: 10.1021/ac200194d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometry-based proteomics techniques have been very successful for the identification and study of protein-protein interactions. Typically, immunopurification of protein complexes is conducted, followed by protein separation by gel electrophoresis and in-gel protein digestion, and finally, mass spectrometry is performed to identify the interacting partners. However, the manual processing of the samples is time-consuming and error-prone. Here, we developed a polymer-based microfluidic proteomic reactor aimed at the parallel analysis of minute amounts of protein samples obtained from immunoprecipitation. The design of the proteomic reactor allows for the simultaneous processing of multiple samples on the same devices. Each proteomic reactor on the device consists of SCX beads packed and restricted into a 1 cm microchannel by two integrated pillar frits. The device is fabricated using a combination of low-cost hard cyclic olefin copolymer thermoplastic and elastomeric thermoplastic materials (styrene/(ethylene/butylenes)/styrene) using rapid hot-embossing replication techniques with a polymer-based stamp. Three immunopurified protein samples are simultaneously captured, reduced, alkylated, and digested on the device within 2-3 h instead of the days required for the conventional protein-protein interaction studies. The limit of detection of the microfluidic proteomic reactor was shown to be lower than 2 ng of protein. Furthermore, the application of the microfluidic proteomic reactor was demonstrated for the simultaneous processing of the interactome of the histone variant Htz1 in wild-type yeast and in a swr1Δ yeast strain compared to an untagged control using a novel three-channel microfluidic proteomic reactor.
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Affiliation(s)
- Ruijun Tian
- Ottawa Institute of Systems Biology, National Research Council, Boucherville, QC, Canada J4B 6Y4
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33
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34
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Liu Y, Wang H, Liu Q, Qu H, Liu B, Yang P. Improvement of proteolytic efficiency towards low-level proteins by an antifouling surface of alumina gel in a microchannel. LAB ON A CHIP 2010; 10:2887-2893. [PMID: 20927474 DOI: 10.1039/c0lc00016g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A microfluidic reactor has been developed for rapid enhancement of protein digestion by constructing an alumina network within a poly(ethylene terephthalate) (PET) microchannel. Trypsin is stably immobilized in a sol-gel network on the PET channel surface after pretreatment, which produces a protein-resistant interface to reduce memory effects, as characterized by X-ray fluorescence spectrometry and electroosmotic flow. The gel-derived network within a microchannel provides a large surface-to-volume ratio stationary phase for highly efficient proteolysis of proteins existing both at a low level and in complex extracts. The maximum reaction rate of the encapsulated trypsin reactor, measured by kinetic analysis, is much faster than in bulk solution. Due to the microscopic confinement effect, high levels of enzyme entrapment and the biocompatible microenvironment provided by the alumina gel network, the low-level proteins can be efficiently digested using such a microreactor within a very short residence time of a few seconds. The on-chip microreactor is further applied to the identification of a mixture of proteins extracted from normal mouse liver cytoplasm sample via integration with 2D-LC-ESI-MS/MS to show its potential application for large-scale protein identification.
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Affiliation(s)
- Yun Liu
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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35
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Aarnisalo AA, Green KM, O'Malley J, Makary C, Adams J, Merchant SN, Evans JE. A method for MS(E) differential proteomic analysis of archival formalin-fixed celloidin-embedded human inner ear tissue. Hear Res 2010; 270:15-20. [PMID: 20708670 DOI: 10.1016/j.heares.2010.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 07/29/2010] [Accepted: 08/04/2010] [Indexed: 10/19/2022]
Abstract
Proteomic analysis of cadaveric formalin-fixed, celloidin-embedded (FFCE) temporal bone tissue has the potential to provide new insights into inner ear disorders. We have developed a liquid chromatography-mass spectrometry (LC-MS) method for tissue sections embedded with celloidin. Q-TOF (Quadrupole-time of flight mass spectrometry) MS(E) (mass spectrometry where E represents collision energy) and Identity(E)™ were used in conjunction with nano-UPLC (capillary ultrahigh pressure liquid chromatography) for robust identification and quantification of a large number of proteins. Formalin-fixed paraffin-embedded (FFPE) mouse liver sections were used to evaluate formalin de-cross-linking by five different methods. Unfixed fresh mouse liver tissue was used as a control. Five different methods for preparation of FFPE tissue for MS analysis were compared, as well as four methods for celloidin removal with FFCE mouse liver tissue. The methods judged best were applied to FFCE 20 μm sections of mouse inner ear samples, and FFCE 20 μm human inner ear and human otic capsule bone sections. Three of the five-tissue extraction methods worked equally in detecting peptides and proteins from FFPE mouse liver tissue. The modified Liquid Tissue kit protocol was chosen for further studies. Four different celloidin removal methods were compared and the acetone removal method was chosen for further analysis. These two methods were applied to the analysis of FFCE inner ear and otic capsule sections. Proteins from all major cellular components were detected in the FFCE archival human temporal bone sections. This newly developed technique enables the use of FFCE tissues for proteomic studies.
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Affiliation(s)
- Antti A Aarnisalo
- Massachusetts Eye & Ear Infirmary, Harvard Medical School, Boston, MA, USA.
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36
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Krenkova J, Lacher NA, Svec F. Highly efficient enzyme reactors containing trypsin and endoproteinase LysC immobilized on porous polymer monolith coupled to MS suitable for analysis of antibodies. Anal Chem 2010; 81:2004-12. [PMID: 19186936 DOI: 10.1021/ac8026564] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capillary enzymatic microreactors containing trypsin and endoproteinase LysC immobilized on a porous polymer monolith have been prepared and used for the characterization and identification of proteins such as cytochrome c, bovine serum albumin, and high-molecular weight human immunoglobulin G. The hydrophilicity of diol functionalities originating from the hydrolyzed poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith was not sufficient to avoid adsorption of hydrophobic albumin in a highly aqueous mobile phase. Therefore, this monolith was first hydrophilized via photografting of poly(ethylene glycol) methacrylate followed by photografting of a 4-vinyl-2,2-dimethylazlactone to provide the pore surface with reactive functionalities required for immobilization. This new approach reduced the undesired nonspecific adsorption of proteins and peptides and facilitated control of both the enzyme immobilization and protein digestion processes. The enzymatic reactors were coupled off-line with MALDI/TOF MS and/or on-line with ESI/TOF MS. Experimental conditions for digestion were optimized using cytochrome c and bovine serum albumin as model proteins. The optimized reactors were then integrated into a multidimensional system comprised of a monolithic capillary enzyme reactor, an in-line nanoLC separation of peptides using a poly(lauryl methacrylate-co-ethylene dimethacrylate) monolithic column, and ESI/TOF MS. With the use of this system, immunoglobulin G was digested at room temperature in 6 min to an extent similar to that achieved with soluble enzyme at 37 degrees C after 24 h.
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Affiliation(s)
- Jana Krenkova
- The Molecular Foundry, E. O. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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37
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Kim J, Kim BC, Lopez-Ferrer D, Petritis K, Smith RD. Nanobiocatalysis for protein digestion in proteomic analysis. Proteomics 2010; 10:687-99. [PMID: 19953546 DOI: 10.1002/pmic.200900519] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The process of protein digestion is a critical step for successful protein identification in bottom-up proteomic analyses. To substitute the present practice of in-solution protein digestion, which is long, tedious, and difficult to automate, many efforts have been dedicated for the development of a rapid, recyclable and automated digestion system. Recent advances of nanobiocatalytic approaches have improved the performance of protein digestion by using various nanomaterials such as nanoporous materials, magnetic nanoparticles, and polymer nanofibers. Especially, the unprecedented success of trypsin stabilization in the form of trypsin-coated nanofibers, showing no activity decrease under repeated uses for 1 year and retaining good resistance to proteolysis, has demonstrated its great potential to be employed in the development of automated, high-throughput, and on-line digestion systems. This review discusses recent developments of nanobiocatalytic approaches for the improved performance of protein digestion in speed, detection sensitivity, recyclability, and trypsin stability. In addition, we also introduce approaches for protein digestion under unconventional energy input for protein denaturation and the development of microfluidic enzyme reactors that can benefit from recent successes of these nanobiocatalytic approaches.
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Affiliation(s)
- Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Anam-dong, Seongbuk-gu, Seoul, Republic of Korea.
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38
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Tao D, Zhang L, Shan Y, Liang Z, Zhang Y. Recent advances in micro-scale and nano-scale high-performance liquid-phase chromatography for proteome research. Anal Bioanal Chem 2010; 399:229-41. [PMID: 20683586 DOI: 10.1007/s00216-010-3946-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/18/2010] [Accepted: 06/20/2010] [Indexed: 10/25/2022]
Abstract
High-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS-MS) is regarded as one of the most powerful techniques for separation and identification of proteins. Recently, much effort has been made to improve the separation capacity, detection sensitivity, and analysis throughput of micro- and nano-HPLC, by increasing column length, reducing column internal diameter, and using integrated techniques. Development of HPLC columns has also been rapid, as a result of the use of submicrometer packing materials and monolithic columns. All these innovations result in clearly improved performance of micro- and nano-HPLC for proteome research.
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Affiliation(s)
- Dingyin Tao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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39
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Zhang X, Liu B, Zhang L, Zou H, Cao J, Gao M, Tang J, Liu Y, Yang P, Zhang Y. Recent advances in proteolysis and peptide/protein separation by chromatographic strategies. Sci China Chem 2010; 53:685-694. [PMID: 32214996 PMCID: PMC7089403 DOI: 10.1007/s11426-010-0135-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 01/28/2010] [Indexed: 11/05/2022]
Abstract
This review gives a broad glance on the progress of recent advances on proteolysis and peptide/protein separation by chromatographic strategies in the past ten years, covering the main research in these areas especially in China. The reviewed research focused on enzymatic micro-reactors and peptide separation in bottom-up approaches, and protein and peptide separation in top-down approaches. The new enzymatic micro-reactor is able to accelerate proteolytic reaction rate from conventionally a couple of hours to a few seconds, and the multiple dimensional chromatographic-separation with various models or arrays could sufficiently separate the proteomic mixture. These advances have significantly promoted the research of protein/peptide separation and identification in proteomics.
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Affiliation(s)
- XiangMin Zhang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - BaoHong Liu
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - LiHua Zhang
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - HanFa Zou
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Jing Cao
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - MingXia Gao
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - Jia Tang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - Yun Liu
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - PengYuan Yang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - YuKui Zhang
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
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40
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Ren L, Liu Y, Dong M, Liu Z. Synthesis of hydrophilic boronate affinity monolithic capillary for specific capture of glycoproteins by capillary liquid chromatography. J Chromatogr A 2009; 1216:8421-5. [PMID: 19850296 DOI: 10.1016/j.chroma.2009.10.014] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 09/30/2009] [Accepted: 10/06/2009] [Indexed: 11/29/2022]
Abstract
Boronate affinity chromatography is an important tool for specific isolation of cis-diol-containing compounds such as glycoproteins, RNA and carbohydrates. Boronate functionalized monolithic capillaries have been recently developed for specific capture of cis-diol-containing small biomolecules, but the apparent hydrophobicity of the columns prevents them from specific capture of glycoproteins. In this paper, a hydrophilic boronate affinity monolithic capillary was prepared by in situ free radical polymerization, using 4-vinylphenylboronic acid (VPBA) and N, N'-methylenebisacrylamide (MBAA) as functional monomer and cross-linker, respectively. The prepared poly(VPBA-co-MBAA) monolithic capillary exhibited uniform open channel network and high density of accessible boronic acid. Due to the utilization of hydrophilic cross-linker, the prepared column was hydrophilic, allowing for specific capture of glycoproteins.
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Affiliation(s)
- Lianbing Ren
- Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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41
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Gao M, Zhang P, Hong G, Guan X, Yan G, Deng C, Zhang X. Novel monolithic enzymatic microreactor based on single-enzyme nanoparticles for highly efficient proteolysis and its application in multidimensional liquid chromatography. J Chromatogr A 2009; 1216:7472-7. [DOI: 10.1016/j.chroma.2009.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 04/25/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022]
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42
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Ma J, Liu J, Sun L, Gao L, Liang Z, Zhang L, Zhang Y. Online Integration of Multiple Sample Pretreatment Steps Involving Denaturation, Reduction, and Digestion with Microflow Reversed-Phase Liquid Chromatography−Electrospray Ionization Tandem Mass Spectrometry for High-Throughput Proteome Profiling. Anal Chem 2009; 81:6534-40. [DOI: 10.1021/ac900971w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junfeng Ma
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinxiang Liu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liangliang Sun
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liang Gao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
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43
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Feng S, Yang N, Pennathur S, Goodison S, Lubman DM. Enrichment of glycoproteins using nanoscale chelating concanavalin A monolithic capillary chromatography. Anal Chem 2009; 81:3776-83. [PMID: 19366252 PMCID: PMC2759973 DOI: 10.1021/ac900085k] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Immobilized lectin chromatography can be employed for glycoprotein enrichment, but commonly used columns have limitations of yield and resolution. To improve efficiency and to make the technique applicable to minimal sample material, we have developed a nanoscale chelating Concanavalin A (Con A) monolithic capillary prepared using GMA-EDMA (glycidyl methacrylate-co-ethylene dimethacrylate) as polymeric support. Con A was immobilized on Cu(II)-charged iminodiacetic acid (IDA) regenerable sorbents by forming a IDA:Cu(II):Con A sandwich affinity structure that has high column capacity, as well as stability. When compared with conventional Con A lectin chromatography, the monolithic capillary enabled the better reproducible detection of over double the number of unique N-glycoproteins in human urine samples. Utility for analysis of minimal biological samples was confirmed by the successful elucidation of glycoprotein profiles in mouse urine samples at the microliter scale. The improved efficiency of the nanoscale monolithic capillary will impact the analysis of glycoproteins in complex biological samples, especially where only limited material may be available.
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Affiliation(s)
- Shun Feng
- Department of Surgery, The University of Michigan Medical Center, Ann Arbor, MI 48109
| | - Na Yang
- Department of Surgery, The University of Michigan Medical Center, Ann Arbor, MI 48109
| | - Subramaniam Pennathur
- Department of Internal Medicine, Division of Nephrology, The University of Michigan, Ann Arbor, MI 48109
| | - Steve Goodison
- Department of Surgery, The University of Florida, Jacksonville, FL 32009
| | - David M. Lubman
- Department of Surgery, The University of Michigan Medical Center, Ann Arbor, MI 48109
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109
- Comprehensive Cancer Center, The University of Michigan Medical Center, Ann Arbor, MI 48109
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Ren L, Liu Z, Dong M, Ye M, Zou H. Synthesis and characterization of a new boronate affinity monolithic capillary for specific capture of cis-diol-containing compounds. J Chromatogr A 2009; 1216:4768-74. [PMID: 19419728 DOI: 10.1016/j.chroma.2009.04.036] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 03/27/2009] [Accepted: 04/14/2009] [Indexed: 10/20/2022]
Abstract
Boronate affinity chromatography (BAC) is an important tool for specific capture and separation of cis-diol-containing compounds such as glycoproteins, RNA and carbohydrates. Only a few reports on monolithic column-based BAC have appeared. In this paper, boronate functionalized monolithic capillary column was synthesized by in situ free radical polymerization for the first time. The prepared column was first characterized in terms of morphology, pore properties, capacity and retention mechanisms. The column exhibited uniform open channel network and high capture capacity. Systematical investigation on the retention mechanism revealed that multiple intermolecular interactions occur between the analytes and the boronate affinity monolith, including boronate affinity, reversed-phase, cation-exchange and hydrogen bonding interactions, depending on the conditions used. In addition, the presence of Lewis base such as fluoride ion in the mobile phase was found to be favorable to the complexation between cis-diol-containing compounds with the boronic acid ligand under less basic conditions. On the basis of these fundamental investigations, the prepared monolithic column was then applied to the capture of adenosine and flavin adenine dinucleotide. The investigations in this study provide sound understanding not only on how to manipulate the separation selectivity through selection of appropriate mobile phase composition on the currently prepared columns but also on how to design next-generation columns with desired properties and functions.
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Affiliation(s)
- Lianbing Ren
- Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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45
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Hickey AM, Ngamsom B, Wiles C, Greenway GM, Watts P, Littlechild JA. A microreactor for the study of biotransformations by a cross-linked γ-lactamase enzyme. Biotechnol J 2009; 4:510-6. [PMID: 19291707 DOI: 10.1002/biot.200800302] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Krenkova J, Svec F. Less common applications of monoliths: IV. Recent developments in immobilized enzyme reactors for proteomics and biotechnology. J Sep Sci 2009; 32:706-18. [PMID: 19194973 PMCID: PMC2766777 DOI: 10.1002/jssc.200800641] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Use of monolithic supports for enzyme immobilization has rapidly expanded since we published the preceding paper in the series of articles concerned with this topic almost three years ago. Many groups worldwide have realized the benefits of applying monoliths as support structures and used a variety of techniques to immobilize many different enzymes. Although some of these new developments are just refinements of the methods developed previously, some notable new approaches have also been reported. This review summarizes the literature published since 2006 and demonstrates the broad variability of reactive monoliths prepared from silica as well as from organic polymers in the form of disks, columns, and capillaries. All these monoliths were prepared by direct formation from reactive precursors or activation of preformed inactive structures. Interestingly, most of the applications of monolithic enzyme reactors target proteolytic digestion of proteins for proteomic analysis.
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Affiliation(s)
- Jana Krenkova
- The Molecular Foundry, E. O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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47
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Yang Y, Boysen RI, Harris SJ, Hearn MTW. Peptide mapping with mobile phases of intermediate pH value using capillary reversed-phase high-performance liquid chromatography/electrospray ionisation tandem mass spectrometry. J Chromatogr A 2009; 1216:3767-73. [PMID: 19285675 DOI: 10.1016/j.chroma.2009.02.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 02/12/2009] [Accepted: 02/13/2009] [Indexed: 11/29/2022]
Abstract
This investigation describes the separation of tryptic peptides by capillary reversed-phase high-performance liquid chromatography (RP-HPLC) with eluents in the intermediate pH range, followed by in-line electrospray ionisation tandem mass spectrometry (ESI-MS/MS) analysis. For these purposes, gradient elution procedures with an aqueous eluent containing 20 mM ammonium formate, and an increasing content of acetonitrile or methanol, were employed. Compared to the analysis of the same tryptic peptides under low-pH conditions with an ion-pairing reagent, the increase in the pH with the 20 mM ammonium formate mobile phase led to significant changes in both peptide retention to the reversed-phase column and the collision-induced dissociation at the MS/MS stage as a consequence of the changes in the physico-chemical properties of these peptides, such as their overall charge, polarity and relative hydrophobicity. Thus, improved selectivity for the peptide separation and favourable tandem mass spectrometry analysis could be obtained with eluents in this intermediate pH range. The number of tryptic peptides identified by the new approach for the proteins investigated were significantly higher than that obtained by the conventional low-pH methods. Moreover, analysis of protein digests at very low concentrations was also performed under both acidic and intermediate pH conditions and similar improvements in selectivity and MS/MS detection limits were observed, i.e. identification of more distinct peptides and higher sequence coverage of the protein was obtained when eluents of intermediate pH were employed. This study therefore highlights the potential of conducting peptide mapping in the intermediate pH range to achieve more reliable and sensitive protein identifications with capillary RP-HPLC-ESI-MS/MS.
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Affiliation(s)
- Yuanzhong Yang
- Australian Research Council Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria 3800, Australia
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48
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Ma J, Zhang L, Liang Z, Zhang W, Zhang Y. Recent advances in immobilized enzymatic reactors and their applications in proteome analysis. Anal Chim Acta 2009; 632:1-8. [DOI: 10.1016/j.aca.2007.08.045] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Revised: 08/26/2007] [Accepted: 08/28/2007] [Indexed: 11/26/2022]
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49
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Jiang X, Dong J, Wang F, Feng S, Ye M, Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome and peptide profiling analysis by using a monolithic analytical capillary column. Electrophoresis 2008; 29:1612-8. [DOI: 10.1002/elps.200700513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Xu X, Wang X, Liu Y, Liu B, Wu H, Yang P. Trypsin entrapped in poly(diallyldimethylammonium chloride) silica sol-gel microreactor coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1257-1264. [PMID: 18383213 DOI: 10.1002/rcm.3478] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An enzyme-immobilized capillary microreactor for rapid protein digestion and proteomics analysis is reported. The inner surface of the fused-silica capillary was coated with poly(diallyldimethylammonium chloride) (PDDA)-entrapped silica sol-gel matrix, followed by assembly of trypsin onto the PDDA-modified surface via electrostatic adsorption. The immobilization parameters such as PDDA content in the sol-gel matrix, trypsin concentration and pH were investigated in detail. Protein samples including beta-casein, myoglobin and cytochrome c could be effectively digested and electrophoretically separated simultaneously in such a modified capillary. Just 2.26 ng (corresponding to 0.10-0.14 picomole) of sample was sufficient for on-line capillary electrophoresis peptide mapping. The efficiency of the digestion was further demonstrated by digestion of a human liver cytoplasm sample and 253 proteins were identified in one unique run.
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Affiliation(s)
- Xuejiao Xu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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