蛋白质分离和鉴定的新技术新方法研究进展
Recent advances of technique and method on the protein separation and identification in the proteomic studies
-
摘要: 综述了国家重大科学研究计划"蛋白质分离和鉴定新技术新方法"课题的研究进展:高丰度蛋白质去除方面,采用强阳离子交换色谱(SCX)和反相色谱(RPLC),构建二维液相色谱分离系统;利用分子印迹技术制备高丰度蛋白质印迹聚合物.低丰度蛋白分离富集方面,采用新型功能材料磷酸化蛋白质/多肽、糖基化蛋白质/多肽、蛋白质/多肽实现对低丰度蛋白质的选择性富集.多维、多模式、阵列式的蛋白质高效分离方面,利用循环分离体积排阻色谱(csrSEC)和RPLC的联用构建多维分离系统;构建弱阴弱阳离子混合色谱-固定化酶反应器-RPLC-电喷雾质谱系统.高灵敏鉴定新技术新方法方面,发展液质联用接口技术,以中空纤维膜为根本,设计以此为核心的集成化样品预处理装置;新发展多肽衍生试剂,能够将肽段在质谱的检测灵敏度提高1-2个数量级;在靶体材料方面,采用复合核壳纳米功能靶体材料;在质谱数据处理方法方面,基于遗传算法发展筛选标准优化策略.这些新技术和新方法为蛋白质组研究提供了有效的方法.选择性吸附材料的研制为蛋白质组学研究中高丰度蛋白质去除和低丰度蛋白质富集提供了新的途径,进而避免了复杂体系对目标蛋白质鉴定的干扰.以多维、多模式、阵列式的蛋白质高效分离技术为核心构建的平台,实现了蛋白质组的高效、高通量、高可靠性分离;以液相色谱/质谱联用为核心的高灵敏鉴定的新技术新方法的发展,提高了低丰度蛋白质的质谱鉴定灵敏度和准确度.Abstract: The new techniques and methods of protein separation and identification in the program "Novel Techniques and Methods for Protein Separation and Identification",supported by "National Basic Research Program of China",were reviewed.For high-abundance proteins depletion,strong cation exchange (SCX) chromatography was coupled with reversed phase liquid chromatography (RPLC) to develop two dimensional liquid chromatography,and high abundance proteins were applied as the templates to developed molecularly imprinted materials.For low abundance protein enrichment selectively,novel functional materials were developed for selectively capturing significant post-translated proteins,such as phosphopeptides/proteins and glycopeptides/proteins.For multidimensional,multi-mode and array protein separation,column switch recycling size exclusion chromatography (csrSEC) was coupled with RPLC to develop multidimensional liquid chromatography,and weak anion and cation exchange chromatography mixed-bed microcolumn were integrated with the immobilized trypsin reactor and RPLC-ESI/MS/MS to develop at high-throughput proteome platform.During the study of high-sensitive identification techniques,an online integrated platform for sample pretreatment,which was based on the hollow fiber membrane interface for solvent exchange,was established.New reagents were developed for the peptide derivatization,which decreased the limit of detection of peptide on the mass spectrum by 10-100 times.Core-shell nanoparticles were employed on the plate materials directly for the matrix-assisted laser desorption/ionization mass (MALDI).A predictive genetic algorithm was implemented for the optimization of filtering criteria to maximize the number of identified peptides for mass spectrum database searching.The new technology and new method for proteomic study provides an effective method.The development of selective adsorption materials provides a new way for high abundance protein depletion and low abundance proteins enrichment of proteomics research,and avoids the interference of the target protein identification in complex system.The platform of multidimensional and mode,array type of protein efficient separation technology as the core is constructed and realized the protein group of high efficiency,high flux,high reliability separation.With the new technology and new method development of high performance liquid chromatography/mass spectrometry as the core of high sensitive identification,the sensitivity and accuracy of low abundance protein mass spectrum identification are improved.
-
-
[1]
Phizicky E,Bastiaens P I H,Zhu H,et al.Protein analysis on a proteomic scale[J].Nature,2003,422:208.
-
[2]
Cesari F.Proteomics getting the numbers right[J].Nat Rev Mol Cell Biol,2009(10):577.
-
[3]
Tyers M,Mann M.From genomics to proteomics[J].Nature,2003,422:193.
-
[4]
Issaq H J,Xiao Z,Veenstra T D.Serum and plasma proteomics[J].Chem Rev,2007,107:3601.
-
[5]
Blow N.Proteins and proteomics:Life on the surface[J].Nat Meth,2009(6):389.
-
[6]
Carter P J.Potent antibody therapeutics by design[J].Nat Rev Immunol,2006(6):343.
-
[7]
Gao M X,Zhang J,Deng C H,et al.Novel strategy of high-abundance protein depletion using multidimensional liquid chromatography[J].J Proteome Res,2006(5):2853.
-
[8]
Gao M X,Deng C H,Yu W J,et al.Large scale depletion of the high-abundance proteins and analysis of middle-and low-abundance proteins in human liver proteome by multidimensional liquid chromatography[J].Proteomics,2008(8):939.
-
[9]
Liu J X,Deng Q L,Yang K G,et al.Macroporous molecularly imprinted monolithic polymer columns for protein recognition by liquid chromatography[J].J Sep Sci,2010,33:2757.
-
[10]
Liu J X,Yang K G,Deng Q L,et al.Preparation of a new type of affinity materials combining metal coordination with molecular imprinting[J].Chem Commun,2011,47:3969.
-
[11]
Yang K G,Zhang L H,Liang Z,et al.Protein-imprinted materials:rational design,application and challenges[J].Anal Bioanal Chem,2012,403:2173.
-
[12]
Qin L,He X-W,Zhang W,et al.Surface-modified polystyrene beads as photografting imprinted polymer matrix for chromatographic separation of proteins[J].J Chromatogr A,2009,1216:807.
-
[13]
Zhang L Y,Liang Z,Yang K G,et al.Mesoporous TiO2 aerogel for selective enrichment of phosphopeptides in rat liver mitochondria[J].Anal Chim Acta,2012,729:26.
-
[14]
Zhang L Y,Xu J,Sun L L,et al.Zirconium oxide aerogel for effective enrichment of phosphopeptides with high binding capacity[J].Anal Bioanal Chem,2011,399:3399.
-
[15]
Hou C Y,Ma J F,Tao D Y,et al.Organic-inorganic hybrid silica monolith based immobilized titanium ion affinity chromatography column for analysis of mitochondrial phosphoproteome[J].J Proteome Res,2010(9):4093.
-
[16]
Zhang L Y,Zhao Q,Liang Z,et al.Synthesis of adenosine functionalized metal immobilized magnetic nanoparticles for highly selective and sensitive enrichment of phosphopeptides[J].Chem Commun,2012,48:6274.
-
[17]
Zhao L A,Wu R A,Han G H,et al.The highly selective capture of phosphopeptides by zirconium phosphonate-modified magnetic nanoparticles for phosphoproteome analysis[J].J Am Soc Mass Spectrom,2008,19:1176.
-
[18]
Qu Y,Liu J,Yang K,et al.Boronic acid functionalized core-shell polymer nanoparticles prepared by distillation precipitation polymerization for glycopeptide enrichment[J].Chem-A European J,2012,18:9056.
-
[19]
Qu Y,Xia S,Yuan H,et al.Integrated sample pretreatment system for N-linked glycosylation site profiling with combination of hydrophilic interaction chromatography and PNGase F immobilized enzymatic reactor via a strong cation exchange precolumn[J].Anal Chem,2011,83:7457.
-
[20]
Qiao X Q,Sun L L,Wang L,et al.High sensitive protein detection by hollow fiber membrane interface based protein enrichment and in situ fluorescence derivatization[J].J of Chromatography B-Analytical Techs in the Biomedical and Life Sci,2011,879:1439.
-
[21]
Chen H M,Liu S S,Yang H L,et al.Selective separation and enrichment of peptides for MS analysis using the microspheres composed of Fe3O4@nSiO2 core and perpendicularly aligned mesoporous SiO2 shell[J].Proteomics,2010(10):930.
-
[22]
Liu S S,Chen H M,Lu X H,et al.Facile synthesis of copper(Ⅱ) Immobilized on magnetic mesoporous silica microspheres for selective enrichment of peptides for mass spectrometry analysis[J].Angewandte Chemie-Int Edition,2010,49:7557.
-
[23]
Gu X,Deng C H,Yan G Q,et al.Capillary array reversed-phase liquid chromatography-based multidimensional separation system coupled with MALDI-TOF-TOF-MS detection for high-throughput proteome analysis[J].J Proteome Res,2006(5):3186.
-
[24]
Yuan H M,Zhang L H,Zhang W B,et al.Columns switch recycling size exclusion chromatography for high resolution protein separation[J].J Chromatogr A,2009,1216:7024.
-
[25]
Hou C Y,Yuan H M,Qiao X Q,et al.Weak anion and cation exchange mixed-bed microcolumn for protein separation[J].J Sep Sci,2010,33:3299.
-
[26]
Jiang X N,Ye M L,Cheng K,et al.ArMone:A software suite specially designed for processing and analysis of phosphoproteome data[J].J Proteome Res,2010(9):2743.
-
[27]
Song C X,Ye M L,Han G H,et al.Reversed-phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides[J].Anal Chem,2010,82:53.
-
[28]
Wang F J,Song C X,Cheng K,et al.Perspectives of comprehensive phosphoproteome analysis using shotgun strategy[J].Anal Chem,2011,83:8078.
-
[29]
Ma J F,Zhang L H,Liang Z,et al.Immobilized enzyme reactors in proteomics[J].Trac-Trends in Analytical Chem,2011,30:691.
-
[30]
Ma J F,Hou C Y,Liang Y,et al.Efficient proteolysis using a regenerable metalion chelate immobilized enzyme reactor supported on organic-inorganic hybrid silica monolith[J].Proteomics,2011(11):991.
-
[31]
Liang Y,Tao D Y,Ma J F,et al.Hydrophilic monolith based immobilized enzyme reactors in capillary and on microchip for high-throughput proteomic analysis[J].J Chromatogr A,2011,1218:2898.
-
[32]
Wu S,Sun L,Ma J,et al.High throughput tryptic digestion via poly (acrylamide-co-methylenebisacrylamide) monolith based immobilized enzyme reactor[J].Talanta,2011,83:1748.
-
[33]
Gao M X,Deng C H,Zhang X M.Magnetic nanoparticles-based digestion and enrichment methods in proteomics analysis[J].Expert Rev Proteomics,2011,8:379.
-
[34]
Lin S,Yun D,Qi D W,et al.Novel microwave-assisted digestion by trypsin-immobilized magnetic nanoparticles for proteomic analysis[J].J Proteome Res,2008(7):1297.
-
[35]
Liu J Y,Lin S,Qi D W,et al.On-chip enzymatic microreactor using trypsin-immobilized superparamagnetic nanoparticles for highly efficient proteolysis[J].J Chromatogr A,2007,1176:169.
-
[36]
Yuan H M,Zhou Y,Xia S M,et al.Integrated platform for proteome profiling with combination of microreversed phase based protein and peptide separation via online solvent exchange and protein digestion[J].Anal Chem,2012,84:5124.
-
[37]
Wang F J,Ye M L,Dong J,et al.Improvement of performance in label-free quantitative proteome analysis with monolithic electrospray ionization emitter[J].J Sep Sci,2008,31:2589.
-
[38]
Wang F J,Dong J,Ye M L,et al.Integration of monolithic frit into the particulate capillary (IMFPC) column in shotgun proteome analysis[J].Anal Chim Acta,2009,652:324.
-
[39]
Xue Y F,Wei J Y,Han H H,et al.Application of open tubular capillary columns coated with zirconium phosphonate for enrichment of phosphopeptides[J].J of Chromatography B-Analytical Tech in the Biomedical and Life Sci,2009,877:757.
-
[40]
Qiao X Q,Sun L L,Chen L F,et al.Piperazines for peptide carboxyl group derivatization:Effect of derivatization reagents and properties of peptides on signal enhancement in matrix-assisted laser desorption/ionization mass spectrometry[J].Rapid Commun Mass Spectrom,2011,25:639.
-
[41]
Qiao X Q,Wang L,Ma J F,et al.High sensitivity analysis of water-soluble,cyanine dye labeled proteins by high-performance liquid chromatography with fluorescence detection[J].Anal Chim Acta,2009,640:114.
-
[42]
Shen W W,Xiong H M,Xu Y,et al.ZnO-poly(methyl methacrylate) nanobeads for enriching and desalting low-abundant proteins followed by directly MALDI-TOF MS analysis[J].Anal Chem,2008,80:6758.
-
[43]
Tang J,Liu Y C,Qi D W,et al.On-plate-selective enrichment of glycopeptides using boronic acid-modified gold nanoparticles for direct MALDI-QIT-TOF MS analysis[J].Proteomics,2009(9):5046.
-
[44]
Jiang X N,Jiang X G,Han G H,et al.Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics[J].BMC Bioinformatics,2007(8):323.
-
[45]
Jiang X N,Han G H,Feng S,et al.Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy[J].J Proteome Res,2008(7):1640.
-
[46]
Jiang X N,Dong X L,Ye M L,et al.Instance based algorithm for posterior probability calculation by target-decoy strategy to improve protein identifications[J].Anal Chem,2008,80:9326.
-
[47]
Han G H,Ye M L,Jiang X N,et al.Comprehensive and reliable phosphorylation site mapping of individual phosphoproteins by combination of multiple stage mass spectrometric analysis with a target-decoy database search[J].Anal Chem,2009,81:5794.
-
[48]
Jiang X N,Ye M L,Han G H,et al.Classification filtering strategy to improve the coverage and sensitivity of phosphoproteome analysis[J].Anal Chem,2010,82:6168.
-
[1]
-
点击查看大图
计量
- PDF下载量: 30
- 文章访问数: 1313
- 引证文献数: 0
下载:
