• 中国精品科技期刊
  • 中国高校百佳科技期刊
  • 中国中文核心期刊
  • 中国科学引文数据库核心期刊
Advanced Search
WU Weixin, YAN Jia, TAN Xiying, LI Bo, SU Mengxiang, YAN Fang, DI Bin. Advances in enrichment strategies for phosphoproteomics and its application in the research of disease[J]. Journal of China Pharmaceutical University, 2016, 47(1): 19-29. DOI: 10.11665/j.issn.1000-5048.20160103
Citation: WU Weixin, YAN Jia, TAN Xiying, LI Bo, SU Mengxiang, YAN Fang, DI Bin. Advances in enrichment strategies for phosphoproteomics and its application in the research of disease[J]. Journal of China Pharmaceutical University, 2016, 47(1): 19-29. DOI: 10.11665/j.issn.1000-5048.20160103

Advances in enrichment strategies for phosphoproteomics and its application in the research of disease

More Information
  • Protein phosphorylation is one of the most common post-translational modifications(PTMs)in various organisms, which plays critical roles in the regulation of intracellular biological processes such as cell proliferation, signal transduction, metabolismics and tumorigenesis. The understanding of phosphoproteomics is playing a great role in biomarker discovery, auxiliary treatment, as well as biological process exploration. However, the identification and characterization of phosphoproteins remain challenging due to their low abundance and the signal suppression of nonphosphorylated peptides. Thus, extraction of phosphorylated polypeptides from complex mixtures is a critical step in the success of phosphoproteomics experiments. Some strategies have been explored to promote enrichment specificity, detection sensitivity and enrichment capacity, such as design of new nanomaterials or combination of a variety of analytical methods. This review places special emphasis on the recent four-year advances for enrichment strategies that have been used for phosphoproteomics and summarize the application of phosphoproteomics in disease research.
  • [1]
    Wasinger VC,Cordwell SJ,Cerpa-Poljak A,et al.Progress with gene-product mapping of the Mollicutes:Mycoplasma genitalium[J].Electrophoresis,1995,16(7):1090-1094.
    [2]
    Zheng H,Hu P,Quinn DF,et al.Phosphotyrosine proteomic study of interferon signaling pathway using a combination of immunoprecipitation and immobilized metal affinity chromatography[J].Mol Cell Proteomics,2005,4(6):721-730.
    [3]
    Beausoleil SA,Jedrychowski M,Schwartz D,et al.Large-scale characterization of HeLa cell nuclear phosphoproteins[J].Proc Natl Acad Sci U S A,2004,101(33):12130-12135.
    [4]
    Zappacosta F,Scott GF,Huddleston MJ,et al.An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome[J].J Proteome Res,2015,14(2):997-1009.
    [5]
    Andersson L,Porath J. Isolation of phosphoproteins by immobilized metal(Fe3+)affinity chromatography[J].Anal Biochem,1986,154(1):250-254.
    [6]
    Hou C,Ma J,Tao D,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(8):4093-4101.
    [7]
    Elldrissi K,Eddarir S,Tokarski C,et al.Immobilized metal affinity chromatography using open tubular capillary for phosphoprotein analysis:comparison between polymer brush coating and surface functionalization[J].J Chromatogr B,2011,879(27):2852-2859.
    [8]
    Saeed A,Najam-ul-Haq M,Jabeen F,et al.High affinity phosphopeptides enrichment and desalting of biological materials on newly engineered poly(glycidyl propargyl ether/divinyl benzene)[J].Anal Chem,2013,85(19):8979-8986.
    [9]
    Wang ZG,Cheng G,Liu YL,et al.Novel core-shell Cerium(IV)-immobilized magnetic polymeric microspheres for selective enrichment and rapid separation of phosphopeptides[J].J Colloid Interf Sci,2014,417:217-226.
    [10]
    Ma W,Zhang Y,Li L,et al.Ti4+-immobilized magnetic composite microspheres for highly selective enrichment of phosphopeptides[J].Adv Funct Mater,2013,23(1):107-115.
    [11]
    Wang F,Zhang Y,Yang P,et al.Fabrication of polymeric microgels using reflux-precipitation polymerization and its application for phosphoprotein enrichment[J].J Mater Chem B,2014,2(17):2575-2582.
    [12]
    Li XS,Pan YN,Zhao Y,et al.Preparation of titanium-grafted magnetic mesoporous silica for the enrichment of endogenous serum phosphopeptides[J].J Chromatogr A,2013,1315:61-69.
    [13]
    Sun N,Deng C,Li Y,et al.Size-exclusive magnetic graphene/mesoporous silica composites with Titanium(IV)-immobilized pore walls for selective enrichment of endogenous phosphorylated peptides[J].ACS Appl Mater Inter,2014,6(14):11799-11804.
    [14]
    Shen F,Hu Y,Guan P,et al.Facile preparation of titanium phosphate-modified chitosan for selective capture of phosphopeptides[J].J Sep Sci,2013,36(3):540-547.
    [15]
    Shi C,Deng C,Zou SE,et al.Polydopamine-coated eppendorf tubes for Ti4+ immobilization for selective enrichment of phosphopeptides[J].Talanta,2014,127:88-93.
    [16]
    Wan J,Qian K,Qiao L,et al.TiO2-modified macroporous silica foams for advanced enrichment of multi-phosphorylated peptides[J].Chem Eur J,2009,15(11):2504-2508.
    [17]
    Bai Y,Qi L,Xu L,et al.Template-free synthesis of uniform mesoporous SnO2 nanospheres for efficient phosphopeptide enrichment[J].J Mater Chem B,2014,2(9):1121-1124.
    [18]
    Zhang L,Xu J,Sun L,et al.Zirconium oxide aerogel for effective enrichment of phosphopeptides with high binding capacity[J].Anal Bioanal Chem,2011,399(10):3399-3405.
    [19]
    Ma WF,Zhang Y,Li LL,et al.Tailor-made magnetic Fe3O4@ mTiO2 microspheres with a tunable mesoporous anatase shell for highly selective and effective enrichment of phosphopeptides[J].ACS Nano,2012,6(4):3179-3188.
    [20]
    Zhang Y,Ma W,Zhang C,et al.Titania composite microspheres endowed with a size-exclusive effect toward the highly specific revelation of phosphopeptidome[J].ACS Appl Mater Inter,2014,6(9):6290-6299.
    [21]
    Zhang Y,Li L,Ma W,et al.Two-in-one strategy for effective enrichment of phosphopeptides using magnetic mesoporous γ-Fe2O3 nanocrystal clusters[J].ACS Appl Mater Inter,2013,5(3):614-621.
    [22]
    Yan Y,Zhang X,Deng C. Designed synthesis of titania nanoparticles coated hierarchially ordered macro/mesoporous silica for selective enrichment of phosphopeptides[J].ACS Appl Mater Inter,2014,6(8):5467-5471.
    [23]
    Cheng G,Wang ZG,Liu YL,et al.Magnetic affinity microspheres with meso/macroporous shells for selective enrichment and fast separation of phosphorylated biomolecules[J].ACS Appl Mater Inter,2013,5(8):3182-3190.
    [24]
    Li H,Shi X,Qiao L,et al.Synthesis of a new type of echinus-like Fe3O4@ TiO2 core-shell-structured microspheres and their applications in selectively enriching phosphopeptides and removing phospholipids[J].J Chromatogr A,2013,1275:9-16.
    [25]
    Li W,Deng Q,Fang G,et al.Facile synthesis of Fe3O4@ TiO2-ZrO2 and its application in phosphopeptide enrichment[J].J Mater Chem B,2013,1(14):1947-1961.
    [26]
    Li LP,Zheng T,Xu LN,et al.SnO2-ZnSn(OH)6:a novel binary affinity probe for global phosphopeptide detection[J].Chem Commun,2013,49(17):1762-1764.
    [27]
    Wang F,Shi Z,Hu F,et al.Tuning of Ti-doped mesoporous silica for highly efficient enrichment of phosphopeptides in human placenta mitochondria[J].Anal Bioanal Chem,2013,405(5):1683-1693.
    [28]
    Huang X,Wang J,Liu C,et al.A novel rGR-TiO2-ZrO2 composite nanosheet for capturing phosphopeptides from biosamples[J].J Mater Chem B,2015,3(12):2505-2515.
    [29]
    Xu LN,Li LP,Jin L,et al.Guanidyl-functionalized graphene as a bifunctional adsorbent for selective enrichment of phosphopeptides[J].Chem Commun,2014,50(75):10963-10966.
    [30]
    Wang M,Deng C,Li Y,et al.Magnetic binary metal oxides affinity probe for highly selective enrichment of phosphopeptides[J].ACS Appl Mater Inter,2014,6(14):11775-11782.
    [31]
    Yan Y,Lu J,Deng C,et al.Facile synthesis of titania nanoparticles coated carbon nanotubes for selective enrichment of phosphopeptides for mass spectrometry analysis[J].Talanta,2013,107:30-35.
    [32]
    Wang ST,Wang MY,Su X,et al.Facile preparation of SiO2/TiO2 composite monolithic capillary column and its application in enrichment of phosphopeptides[J].Anal Chem,2012,84(18):7763-7770.
    [33]
    He XM,Zhu GT,Li XS,et al.Rapid enrichment of phosphopeptides by SiO2-TiO2 composite fibers[J].Analyst,2013,138(18):5495-5502.
    [34]
    Tan YJ,Sui D,Wang WH,et al.Phosphopeptide enrichment with TiO2-modified membranes and investigation of tau protein phosphorylation[J].Anal Chem,2013,85(12):5699-5706.
    [35]
    Jabeen F,Najam-ul-Haq M,Rainer M,et al.Newly fabricated magnetic lanthanide oxides core-shell nanoparticles in phosphoproteomics[J].Anal Chem,2015,87(9):4726-4732.
    [36]
    Min Q,Li S,Chen X,et al.Magnetite/ceria-codecorated titanoniobate nanosheet:a 2D catalytic nanoprobe for efficient enrichment and programmed dephosphorylation of phosphopeptides[J].ACS Appl Mater Inter, 2015,7(18):9563-9572.
    [37]
    Thingholm TE,Jensen ON,Robinson PJ,et al.SIMAC(sequential elution from IMAC),a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides[J].Mol Cell Proteomics,2008,7(4):661-671.
    [38]
    Yu QW,Li XS,Xiao Y,et al.Sequential enrichment with titania-coated magnetic mesoporous hollow silica microspheres and zirconium arsenate-modified magnetic nanoparticles for the study of phosphoproteome of HL60 cells[J].J Chromatogr A,2014,1365:54-60.
    [39]
    Tape CJ,Worboys JD,Sinclair J,et al.Reproducible automated phosphopeptide enrichment using magnetic TiO2 and Ti-IMAC[J].Anal Chem,2014,86(20):10296-10302.
    [40]
    Eriksson AI, Bartsch M, Bergquist J, et al. On-target titanium dioxide-based enrichment for characterization of phosphorylations in the Adenovirus pIIIa protein[J].J Chromatogr A,2013,1317:105-109.
    [41]
    Tsougeni K,Zerefos P,Tserepi A,et al.TiO2-ZrO2 affinity chromatography polymeric microchip for phosphopeptide enrichment and separation[J].Lab Chip,2011,11(18):3113-3120.
    [42]
    Tang LA,Wang J,Lim TK,et al.High-performance graphene-titania platform for detection of phosphopeptides in cancer cells[J].Anal Chem,2012,84(15):6693-6700.
    [43]
    Min Q, Chen X, Zhang X, et al. Tailoring of a TiO2 nanotube array-integrated portable microdevice for efficient on-chip enrichment and isotope labeling of serum phosphopeptides[J].Lab Chip,2013,13(19):3853-3861.
    [44]
    Vormbrock I,Kaber G,Hartwig S,et al.Targeting phosphoprotein profiling by combination of hydroxyapatite-based phosphoprotein enrichment and SELDI-TOF MS[J].Arch Physiol Biochem,2010,116(4/5):181-187.
    [45]
    Yu Q,Li XS,Yuan BF,et al.Preparation of magnetic hydroxyapatite clusters and their application in the enrichment of phosphopeptides[J].J Sep Sci,2014,37(5):580-586.
    [46]
    Xu CF,Lu Y,Ma J,et al.Identification of phosphopeptides by MALDI Q-TOF MS in positive and negative ion modes after methyl esterification[J].Mol Cell Proteomics,2005,4(6):809-818.
    [47]
    de Graaf EL,Giansanti P,Altelaar AF,et al.Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution[J].Mol Cell Proteomics,2014,13(9):2426-2434.
    [48]
    Luerman GC,Powell DW,Uriarte SM,et al.Identification of phosphoproteins associated with human neutrophil granules following chemotactic peptide stimulation[J].Mol Cell Proteomics,2011,10(3):M110. 001552.
    [49]
    Zawadzka AM,Schilling B,Cusack MP,et al.Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma[J].Mol Cell Proteomics,2014,13(4):1034-1049.
    [50]
    Dillon R,Nilsson CL,Shi SD,et al.Discovery of a novel B-Raf fusion protein related to c-Met drug resistance[J].J Proteome Res,2011,10(11):5084-5094.
    [51]
    Yang Y,Chen Y,Saha MN,et al.Targeting phospho-MARCKS overcomes drug-resistance and induces antitumor activity in preclinical models of multiple myeloma[J].Leukemia,2015,29(3):715-726.
  • Related Articles

    [1]LI Xueyan, CHEN Na, JIANG Cheng. Research progress of KRAS inhibitors[J]. Journal of China Pharmaceutical University, 2024, 55(2): 257-269. DOI: 10.11665/j.issn.1000-5048.2024010801
    [2]YANG Wanwan, YE Fangyu, WU Yujia, WANG Haochen, ZHAO Li. Research progress of PARP inhibitors in cancers and their drug resistance[J]. Journal of China Pharmaceutical University, 2022, 53(5): 525-534. DOI: 10.11665/j.issn.1000-5048.20220503
    [3]YANG Qian, WANG Xiaojian. Research progress of sphingosine kinase 1 inhibitors[J]. Journal of China Pharmaceutical University, 2021, 52(6): 759-768. DOI: 10.11665/j.issn.1000-5048.20210615
    [4]ZHAN Kangning, QUAN Xu, HUANG Zhangjian, ZHAO Liwen. Research progress of protein arginine methyltransferase 5 inhibitors[J]. Journal of China Pharmaceutical University, 2021, 52(3): 371-378. DOI: 10.11665/j.issn.1000-5048.20210315
    [5]LI Zhiyan, LIU Jie, LI Bingyan, JIANG Cheng. Design, synthesis and evaluation of peptidomimetics targeting the polo-box domain of polo-like kinase 1[J]. Journal of China Pharmaceutical University, 2020, 51(3): 287-294. DOI: 10.11665/j.issn.1000-5048.20200305
    [6]LIANG Tingting, WANG Wenjie, HE Guangchao, HE Guangchao, XU Yungen. Research progress of ERK small molecule inhibitors[J]. Journal of China Pharmaceutical University, 2020, 51(3): 260-269. DOI: 10.11665/j.issn.1000-5048.20200302
    [7]SHI Jinyu, BAI Ying, PENG Kewen, ZHANG Wenhui, ZHU Qihua, XU Yungen. Research progress of PARP-1 inhibitors in combination with other drugs to overcome drug resistance[J]. Journal of China Pharmaceutical University, 2019, 50(5): 523-530. DOI: 10.11665/j.issn.1000-5048.20190503
    [8]WANG Tianshuai, YU Junjie, ZHANG Yan, ZENG Jinjin, CUI Jingxin. Advances in platinum-intercalators of DNA as antitumor agents[J]. Journal of China Pharmaceutical University, 2019, 50(5): 505-515. DOI: 10.11665/j.issn.1000-5048.20190501
    [9]GUO Yahui, LU Peng, WANG Yubin, ZHANG Huibin. Progress in the researches for antitumor NEDD8 activating enzyme inhibitors[J]. Journal of China Pharmaceutical University, 2017, 48(6): 646-653. DOI: 10.11665/j.issn.1000-5048.20170603
    [10]KONG Kai-lai, LU Shuai, GAO Yi-ping, YANG Pei, TANG Wei-fang, LU Tao. Advances on the study of PLK1 inhibitors as antitumor agents[J]. Journal of China Pharmaceutical University, 2011, 42(1): 9-15.

Catalog

    Article views (1536) PDF downloads (3329) Cited by()

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return