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Ma J, Liang Z, Qiao X, Deng Q, Tao D, Zhang L, Zhang Y. Organic−Inorganic Hybrid Silica Monolith Based Immobilized Trypsin Reactor with High Enzymatic Activity. Anal Chem 2008; 80:2949-56. [DOI: 10.1021/ac702343a] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junfeng Ma
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaoqiang Qiao
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Qiliang Deng
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Dingyin Tao
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
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52
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Ji, Zhang Y, Zhou X, Kong J, Tang Y, Liu B. Enhanced Protein Digestion through the Confinement of Nanozeolite-Assembled Microchip Reactors. Anal Chem 2008; 80:2457-63. [DOI: 10.1021/ac702218v] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ji
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yahong Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xiaoqin Zhou
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yi Tang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Fudan University, Shanghai 200433, China
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53
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Migneault I, Dartiguenave C, Vinh J, Bertrand MJ, Waldron KC. Two Glutaraldehyde‐Immobilized Trypsin Preparations for Peptide Mapping by Capillary Zone Electrophoresis, Liquid Chromatography, and Mass Spectrometry. J LIQ CHROMATOGR R T 2008. [DOI: 10.1080/10826070801890413] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Isabelle Migneault
- a Department of Chemistry , Université de Montréal , Montréal, QC, Canada
- c Caprion Pharmaceuticals Inc. , Montreal, Canada
| | | | - Joëlle Vinh
- b Neurobiology and Cellular Diversity Laboratory , ESPCI/CNRS UMR , Paris, France
| | - Michel J. Bertrand
- a Department of Chemistry , Université de Montréal , Montréal, QC, Canada
| | - Karen C. Waldron
- a Department of Chemistry , Université de Montréal , Montréal, QC, Canada
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54
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Jiang X, Ye M, Zou H. Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis. Proteomics 2008; 8:686-705. [DOI: 10.1002/pmic.200700617] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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55
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Nicoli R, Gaud N, Stella C, Rudaz S, Veuthey JL. Trypsin immobilization on three monolithic disks for on-line protein digestion. J Pharm Biomed Anal 2007; 48:398-407. [PMID: 18242915 DOI: 10.1016/j.jpba.2007.12.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 12/13/2007] [Accepted: 12/13/2007] [Indexed: 11/28/2022]
Abstract
The preparation and characterization of three trypsin-based monolithic immobilized enzyme reactors (IMERs) developed to perform rapid on-line protein digestion and peptide mass fingerprinting (PMF) are described. Trypsin (EC 3.4.21.4) was covalently immobilized on epoxy, carbonyldiimidazole (CDI) and ethylenediamine (EDA) Convective Interaction Media (CIM) monolithic disks. The amount of immobilized enzyme, determined by spectrophotometric measurements at 280nm, was comprised between 0.9 and 1.5mg per disk. Apparent kinetic parameters Km* and Vmax*, as well as apparent immobilized trypsin BAEE-units, were estimated in flow-through conditions using N-alpha-benzoyl-L-arginine ethyl ester (BAEE) as a low molecular mass substrate. The on-line digestion of five proteins (cytochrome c, myoglobin, alpha1-acid glycoprotein, ovalbumin and albumin) was evaluated by inserting the IMERs into a liquid chromatography system coupled to an electrospray ionization ion-trap mass spectrometer (LC-ESI-MS/MS) through a switching valve. Results were compared to the in-solution digestion in terms of obtained scores, number of matched queries and sequence coverages. The most efficient IMER was obtained by immobilizing trypsin on a CIM EDA disk previously derivatized with glutaraldehyde, as a spacer moiety. The proteins were recognized by the database with satisfactory sequence coverage using a digestion time of only 5min. The repeatability of the digestion (R.S.D. of 5.4% on consecutive injections of myoglobin 12microM) and the long-term stability of this IMER were satisfactory since no loss of activity was observed after 250 injections.
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Affiliation(s)
- R Nicoli
- Laboratory of Analytical Pharmaceutical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20 Bd d'Yvoy, 1211 Geneva 4, Switzerland
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56
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Ma J, Zhang L, Liang Z, Zhang W, Zhang Y. Monolith-based immobilized enzyme reactors: Recent developments and applications for proteome analysis. J Sep Sci 2007; 30:3050-9. [DOI: 10.1002/jssc.200700362] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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57
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Wang F, Jiang X, Feng S, Tian R, Jiang X, Han G, Liu H, Ye M, Zou H. Automated injection of uncleaned samples using a ten-port switching valve and a strong cation-exchange trap column for proteome analysis. J Chromatogr A 2007; 1171:56-62. [DOI: 10.1016/j.chroma.2007.09.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Revised: 09/03/2007] [Accepted: 09/12/2007] [Indexed: 10/22/2022]
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58
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Qiao L, Liu Y, Hudson SP, Yang P, Magner E, Liu B. A Nanoporous Reactor for Efficient Proteolysis. Chemistry 2007; 14:151-7. [PMID: 17960551 DOI: 10.1002/chem.200701102] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liang Qiao
- Department of Chemistry, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
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59
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Stigter ECA, de Jong GJ, van Bennekom WP. Development of an open-tubular trypsin reactor for on-line digestion of proteins. Anal Bioanal Chem 2007; 389:1967-77. [PMID: 17899035 PMCID: PMC2117336 DOI: 10.1007/s00216-007-1584-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 08/06/2007] [Accepted: 08/24/2007] [Indexed: 11/08/2022]
Abstract
A study was initiated to construct a micro-reactor for protein digestion based on trypsin-coated fused-silica capillaries. Initially, surface plasmon resonance was used both for optimization of the surface chemistry applied in the preparation and for monitoring the amount of enzyme that was immobilized. The highest amount of trypsin was immobilized on dextran-coated SPR surfaces which allowed the covalent coupling of 11 ng mm−2 trypsin. Fused-silica capillaries were modified in a similar manner and the resulting open-tubular trypsin-reactors having a pH optimum of pH 8.5, display a high activity when operated at 37 °C and are stable for at least two weeks when used continuously. Trypsin auto-digestion fragments, sample carry-over, and loss of signal due to adsorption of the protein were not observed. On-line digestion without prior protein denaturation, followed by micro-LC separation and photodiode array detection, was tested with horse-heart cytochrome C and horse skeletal-muscle myoglobin. The complete digestion of 20 pmol μL−1 horse cytochrome C was observed when the average residence time of the protein sample in a 140 cm ×50 μm capillary immobilized enzyme reactor (IMER) was 165 s. Mass spectrometric identification of the injected protein on the basis of the tryptic peptides proved possible. Protein digestion was favorable with respect to reaction time and fragments formed when compared with other on-line and off-line procedures. These results and the easy preparation of this micro-reactor provide possibilities for miniaturized enzyme-reactors for on-line peptide mapping and inhibitor screening.
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Affiliation(s)
- E C A Stigter
- Division of Biomedical Analysis, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands.
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60
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Liu Y, Xue Y, Ji J, Chen X, Kong J, Yang P, Girault HH, Liu B. Gold Nanoparticle Assembly Microfluidic Reactor for Efficient On-line Proteolysis. Mol Cell Proteomics 2007; 6:1428-36. [PMID: 17519226 DOI: 10.1074/mcp.t600055-mcp200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A microchip reactor coated with a gold nanoparticle network entrapping trypsin was designed for the efficient on-line proteolysis of low level proteins and complex extracts originating from mouse macrophages. The nanostructured surface coating was assembled via a layer-by-layer electrostatic binding of poly(diallyldimethylammonium chloride) and gold nanoparticles. The assembly process was monitored by UV-visible spectroscopy, atomic force microscopy, and quartz crystal microbalance. The controlled adsorption of trypsin was theoretically studied on the basis of the Langmuir isotherm model, and the fitted Gamma(max) and K values were estimated to be 1.2 x 10(-7) mol/m(2) and 4.1 x 10(5) M(-1), respectively. An enzymatic kinetics assay confirmed that trypsin, which was entrapped in the biocompatible gold nanoparticle network with a high loading capacity, preserved its bioactivity. The maximum proteolytic rate of the adsorbed trypsin was 400 mM/(min.microg). Trace amounts of proteins down to femtomole per analysis were digested using the microchip reactor, and the resulting tryptic products were identified by MALDI-TOF MS/MS. The protein mixtures extracted from the mouse macrophages were efficiently identified by on-line digestion and LC-ESI-MS/MS analysis.
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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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61
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Hu L, Ye M, Jiang X, Feng S, Zou H. Advances in hyphenated analytical techniques for shotgun proteome and peptidome analysis--a review. Anal Chim Acta 2007; 598:193-204. [PMID: 17719892 DOI: 10.1016/j.aca.2007.07.046] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 07/17/2007] [Accepted: 07/18/2007] [Indexed: 01/30/2023]
Abstract
Proteomics is defined as the analysis of part or all of the protein components of a complex biological system (a cell, organ or tissue) at a given moment. Due to the huge number of proteins encoded by the genome, novel analytical techniques must be developed to meet the need of large scale analysis. This has led to the hyphenation of multiple techniques to achieve this object. Here current status of the hyphenated analytical techniques of one-dimensional and multidimensional liquid chromatography-mass spectrometry for shotgun proteomic analysis is reviewed, and on-line techniques for automated sample preparation and injection are also covered. In addition, the hyphenated techniques for peptidome analysis are also covered.
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Affiliation(s)
- Lianghai Hu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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62
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Feng S, Ye M, Zhou H, Jiang X, Jiang X, Zou H, Gong B. Immobilized zirconium ion affinity chromatography for specific enrichment of phosphopeptides in phosphoproteome analysis. Mol Cell Proteomics 2007; 6:1656-65. [PMID: 17575324 DOI: 10.1074/mcp.t600071-mcp200] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Large scale characterization of phosphoproteins requires highly specific methods for purification of phosphopeptides because of the low abundance of phosphoproteins and substoichiometry of phosphorylation. Enrichment of phosphopeptides from complex peptide mixtures by IMAC is a popular way to perform phosphoproteome analysis. However, conventional IMAC adsorbents with iminodiacetic acid as the chelating group to immobilize Fe(3+) lack enough specificity for efficient phosphoproteome analysis. Here we report a novel IMAC adsorbent through Zr(4+) chelation to the phosphonate-modified poly(glycidyl methacrylate-co-ethylene dimethacrylate) polymer beads. The high specificity of Zr(4+)-IMAC adsorbent was demonstrated by effectively enriching phosphopeptides from the digest mixture of phosphoprotein (alpha- or beta-casein) and bovine serum albumin with molar ratio at 1:100. Zr(4+)-IMAC adsorbent was also successfully applied for the analysis of mouse liver phosphoproteome, resulting in the identification of 153 phosphopeptides (163 phosphorylation sites) from 133 proteins in mouse liver lysate. Significantly more phosphopeptides were identified than by the conventional Fe(3+)-IMAC approach, indicating the excellent performance of the Zr(4+)-IMAC approach. The high specificity of Zr(4+)-IMAC adsorbent was found to mainly result from the strong interaction between chelating Zr(4+) and phosphate group on phosphopeptides. Enrichment of phosphopeptides by Zr(4+)-IMAC provides a powerful approach for large scale phosphoproteome analysis.
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Affiliation(s)
- Shun Feng
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, China
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63
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Jiang X, Ye M, Jiang X, Liu G, Feng S, Cui L, Zou H. Method development of efficient protein extraction in bone tissue for proteome analysis. J Proteome Res 2007; 6:2287-94. [PMID: 17488005 DOI: 10.1021/pr070056t] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exploring bone proteome is an important and challenging task for understanding the mechanisms of physiological/pathological process of bone tissue. However, classical methods of protein extraction for soft tissues and cells are not applicable for bone tissue. Therefore, method development of efficient protein extraction is critical for bone proteome analysis. We found in this study that the protein extraction efficiency was improved significantly when bone tissue was demineralized by hydrochloric acid (HCl). A sequential protein extraction method was developed for large-scale proteome analysis of bone tissue. The bone tissue was first demineralized by HCl solution and then extracted using three different lysis buffers. As large amounts of acid soluble proteins also presented in the HCl solution, besides collection of proteins in the extracted lysis buffers, the proteins in the demineralized HCl solution were also collected for proteome analysis. Automated 2D-LC-MS/MS analysis of the collected protein fractions resulted in the identification of 6202 unique peptides which matched 2479 unique proteins. The identified proteins revealed a broad diversity in the protein identity and function. More than 40 bone-specific proteins and 15 potential protein biomarkers previously reported were observed in this study. It was demonstrated that the developed extraction method of proteins in bone tissue, which was also the first large-scale proteomic study of bone, was very efficient for comprehensive analysis of bone proteome and might be helpful for clarifying the mechanisms of bone diseases.
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Affiliation(s)
- Xiaogang Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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64
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Li Y, Xu X, Yan B, Deng C, Yu W, Yang P, Zhang X. Microchip Reactor Packed with Metal-Ion Chelated Magnetic Silica Microspheres for Highly Efficient Proteolysis. J Proteome Res 2007; 6:2367-75. [PMID: 17477555 DOI: 10.1021/pr060558r] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An easily replaceable and regenerable protease microreactor with metal-ion chelated adsorption of enzyme has been fabricated on chip. Magnetic microspheres with small size (approximately 200 nm in diameter) and strong magnetism were synthesized and were modified with tetraethyl orthosilicate. The metal chelating agent of iminodiacetic acid was then reacted with glycidoxypropyltrimethoxysilane before its immobilization onto the surface of magnetic silica microspheres (MS microspheres). The metal ion of copper and enzyme were subsequently adsorbed onto the surface. The prepared MS microspheres were then locally packed into the microchannel by the application of a strong magnetic field using a magnet to form an on-chip enzymatic microreactor. Capability of the proteolytic microreactor was demonstrated by cytochrome c and bovine serum albumin as model proteins. The digestion products were characterized using MALDI-TOF/TOF MS with sequence coverage of 77% and 21% observed, respectively. This microreactor was also applied to the analysis of one RPLC fraction of rat liver extract. After a database search, 23 unique peptides corresponding to 7 proteins were identified when one RPLC fraction of rat liver extract was digested by the microreactor. This opens a route for its future application in top-down proteomic analysis.
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Affiliation(s)
- Yan Li
- Department of Chemistry & Research Center of Proteome, Fudan University, Shanghai 200433, China
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65
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Gao M, Deng C, Lin S, Hu F, Tang J, Yao N, Zhang X. Recent developments and contributions from Chinese scientists in multidimensional separations for proteomics and traditional Chinese medicines. J Sep Sci 2007; 30:785-91. [PMID: 17536722 PMCID: PMC7167053 DOI: 10.1002/jssc.200600372] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2006] [Revised: 12/07/2006] [Indexed: 11/11/2022]
Abstract
The most basic task in proteomics remains the detection and identification of proteins from a biological sample, and the most traditional way to achieve this goal consists in protein separations performed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Yet the 2-D PAGE-mass spectrometry (MS) approach has its drawbacks with regard to automation, sensitivity, and throughput. Consequently, considerable effort has been devoted to the development of non-gel-based proteome separation technologies in an effort to alleviate the shortcomings of 2-D PAGE. In addition, traditional Chinese medicines (TCMs), due to their long period of clinical testing and reliable therapeutic efficacy, are attracting increased global attention. However, hundreds or even thousands of components are usually present in TCMs, which results in great difficulties of separation. As a mainstream separation tool, multidimensional liquid separation systems have shown powerful separation ability, high peak capacity, and excellent detectability in the analysis of complex samples including biological samples and TCMs, etc. Therefore, this review emphasizes the most recent advances in multidimensional liquid chromatography and capillary electrophoresis-based separation techniques, and the corresponding applications in proteomics and TCMs. In view of the significant contributions from Chinese scientists, this review focuses mainly on the work of Chinese scientists in the above fields.
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Affiliation(s)
- Mingxia Gao
- Department of Chemistry, Fudan University, Shanghai, China. Fax: +86‐21‐6564‐1740
- Research Center of Proteome, Fudan University, Shanghai, China
| | - Chunhui Deng
- Department of Chemistry, Fudan University, Shanghai, China. Fax: +86‐21‐6564‐1740
- Research Center of Proteome, Fudan University, Shanghai, China
| | - Shuang Lin
- Department of Chemistry, Fudan University, Shanghai, China. Fax: +86‐21‐6564‐1740
- Research Center of Proteome, Fudan University, Shanghai, China
| | - Fengli Hu
- Department of Chemistry, Fudan University, Shanghai, China. Fax: +86‐21‐6564‐1740
- Research Center of Proteome, Fudan University, Shanghai, China
| | - Jia Tang
- Department of Chemistry, Fudan University, Shanghai, China. Fax: +86‐21‐6564‐1740
- Research Center of Proteome, Fudan University, Shanghai, China
| | - Ning Yao
- Department of Chemistry, Fudan University, Shanghai, China. Fax: +86‐21‐6564‐1740
- Research Center of Proteome, Fudan University, Shanghai, China
| | - Xiangmin Zhang
- Research Center of Proteome, Fudan University, Shanghai, China
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66
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Zhu G, Zhang L, Yuan H, Liang Z, Zhang W, Zhang Y. Recent development of monolithic materials as matrices in microcolumn separation systems. J Sep Sci 2007; 30:792-803. [PMID: 17536723 DOI: 10.1002/jssc.200600496] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This review summarizes the development of monolithic materials, including both organic and inorganic polymers, according mainly to the papers published in the past two years. Due to their good permeability, fast mass transfer, high stability, and their ease of modification, such materials have been widely used in microcolumn separation systems, not only as stationary phases for CEC and capillary HPLC, but also as substances for sample concentration and enzyme reactor. All the research results demonstrate that monolithic materials in microseparation systems can be expected to play an increasingly important role in the analysis of complex samples.
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Affiliation(s)
- Guijie Zhu
- National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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67
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Jiang X, Feng S, Tian R, Han G, Jiang X, Ye M, Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome analysis by using a strong cation exchange trap column. Proteomics 2007; 7:528-539. [PMID: 17309098 DOI: 10.1002/pmic.200600661] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An approach was developed to automate sample introduction for nanoflow LC-MS/MS (microLC-MS/MS) analysis using a strong cation exchange (SCX) trap column. The system consisted of a 100 microm id x 2 cm SCX trap column and a 75 microm id x 12 cm C18 RP analytical column. During the sample loading step, the flow passing through the SCX trap column was directed to waste for loading a large volume of sample at high flow rate. Then the peptides bound on the SCX trap column were eluted onto the RP analytical column by a high salt buffer followed by RP chromatographic separation of the peptides at nanoliter flow rate. It was observed that higher performance of separation could be achieved with the system using SCX trap column than with the system using C18 trap column. The high proteomic coverage using this approach was demonstrated in the analysis of tryptic digest of BSA and yeast cell lysate. In addition, this system was also applied to two-dimensional separation of tryptic digest of human hepatocellular carcinoma cell line SMMC-7721 for large scale proteome analysis. This system was fully automated and required minimum changes on current microLC-MS/MS system. This system represented a promising platform for routine proteome analysis.
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Affiliation(s)
- Xiaogang Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- School of Medicine, Suzhou University, Suzhou, Jiangsu, China
| | - Shun Feng
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ruijun Tian
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Guanghui Han
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xinning Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingliang Ye
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hanfa Zou
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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68
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Feng S, Pan C, Jiang X, Xu S, Zhou H, Ye M, Zou H. Fe3+ immobilized metal affinity chromatography with silica monolithic capillary column for phosphoproteome analysis. Proteomics 2007; 7:351-60. [PMID: 17177250 DOI: 10.1002/pmic.200600045] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Immobilized metal affinity chromatography (IMAC) is a commonly used technique for phosphoproteome analysis due to its high affinity for adsorption of phosphopeptides. Miniaturization of IMAC column is essential for the analysis of a small amount of sample. Nanoscale IMAC column was prepared by chemical modification of silica monolith with iminodiacetic acid (IDA) followed by the immobilization of Fe3+ ion inside the capillary. It was demonstrated that Fe3+-IDA silica monolithic IMAC capillary column could specifically capture the phosphopeptides from tryptic digest of alpha-casein with analysis by MALDI-TOF MS. The silica monolithic IMAC capillary column was manually coupled with nanoflow RPLC/nanospray ESI mass spectrometer (muRPLC-nanoESI MS) for phosphoproteome analysis. The system was validated by analysis of standard phosphoproteins and then it was applied to the analysis of protein phosphorylation in mouse liver lysate. Besides MS/MS spectra, MS/MS/MS spectra were also collected for neutral loss peak. After database search and manual validation with conservative criteria, 29 singly phosphorylated peptides were identified by analyzing a tryptic digest of only 12 mug mouse liver lysate. The results demonstrated that the silica monolithic IMAC capillary column coupled with muRPLC-nanoESI MS was very suitable for the phosphoproteome analysis of minute sample.
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Affiliation(s)
- Shun Feng
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, China
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69
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Jiang X, Jiang X, Feng S, Tian R, Ye M, Zou H. Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. J Proteome Res 2007; 6:1038-47. [PMID: 17266348 DOI: 10.1021/pr0605318] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There are vast archives of formalin-fixed tissues spanning many conceivable conditions such as different diseases, time courses, and different treatment and allowing acquisition of the necessary numbers of samples to carry out biomarker discovery study. However, the conventional protein analysis approach is not applicable for the analysis of proteins in the formalin-fixed tissue because the formalin fixation process resulted in the cross-linking of proteins, and thus, intact proteins cannot be efficiently extracted. In this study, several protocols were investigated to extract proteins from formalin-fixed mouse liver tissue for shotgun proteome analysis. It was found that incubation of tissue in a lysis buffer containing 6 M guanidine hydrochloride at high temperature led to the highest protein yield and the largest number of proteins identified. The peptides and proteins identified from formalin-fixed tissue were first comprehensively compared with those identified from frozen-fresh tissue. It was found that a majority of peptides identified from fixed tissue were unmodified and proteome coverage for the analysis of fixed tissue was not obviously compromised by the formalin fixation process. Valuable proteome information could be obtained by shotgun proteome analysis of formalin-fixed tissue, which presents a new approach for disease biomarker discovery.
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Affiliation(s)
- Xiaogang Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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70
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Jeng J, Lin MF, Cheng FY, Yeh CS, Shiea J. Using high-concentration trypsin-immobilized magnetic nanoparticles for rapid in situ protein digestion at elevated temperature. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3060-8. [PMID: 17705254 DOI: 10.1002/rcm.3191] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We describe an innovative approach - using a high concentration of trypsin-modified magnetic nanoparticles (TMNPs) - for the rapid and efficient digestion of proteins at elevated temperature. The required digestion time could be reduced to less than 10 s. After digestion, the TMNPs were collected magnetically from the sample solution for reuse and the digested peptides were characterized using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Protein digestion was optimized when using the TMNPs (5 microg/microL) at 57 degrees C; a significantly high peptide coverage was achieved for protein identification (e.g., 98% for lysozyme). Although a high concentration of TMNPs was used for digestion, the short digestion time led to much lower amounts of trypsin peptides being produced through self-digestion. As a result, interference in the mass spectrometric detection of the peptide ions was reduced significantly.
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Affiliation(s)
- Jingyueh Jeng
- Department of Biotechnology, Chia Nan University of Pharmacy & Science, 60, Erh-Jen RD., Sec.1, Jen-Te, Tainan 717, Taiwan
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Ye M, Jiang X, Feng S, Tian R, Zou H. Advances in chromatographic techniques and methods in shotgun proteome analysis. Trends Analyt Chem 2007. [DOI: 10.1016/j.trac.2006.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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72
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:1520-1531. [PMID: 17103385 DOI: 10.1002/jms.958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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