On-target and nanoparticle-facilitated selective enrichment of peptides and proteins for analysis by MALDI-MS

Proteomics

Volumn 12, Issue 23-24, 2012, Pages 3438-3450

  Stolowitz, Mark L ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Immobilized metal ion affinity; MALDI MS; Metal oxide affinity; Nanoparticle; On target enrichment; Technology

Indexed keywords

ALPHA TUBULIN; ALUMINUM OXIDE; ANTIGEN; BETA 2 MICROGLOBULIN; C REACTIVE PROTEIN; EPITOPE; GLYCOPEPTIDE; HEMAGGLUTININ; INSULIN; MAGNETIC NANOPARTICLE; NANOPARTICLE; NITRILOTRIACETIC ACID; PHOSPHOPEPTIDE; REAGENT; TITANIUM; TITANIUM DIOXIDE; VASCULOTROPIN RECEPTOR; ZIRCONIUM;

ARTICLE; DRUG COATING; DRUG TARGETING; FRANCISELLA TULARENSIS; HUMAN; IMMUNOAFFINITY CHROMATOGRAPHY; ION EXCHANGE CHROMATOGRAPHY; MASS SPECTROMETER; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN IMMOBILIZATION; PROTEIN TARGETING; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; STAPHYLOCOCCUS AUREUS;

ANIMALS; HUMANS; NANOPARTICLES; PEPTIDES; PROTEINS; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SURFACE PROPERTIES;

EID: 84871301180     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200252     Document Type: Article

References (95)

1. Vestel, M., Modern MALDI time-of-flight mass spectrometry. J. Mass Spectrom. 2009, 44, 303-317.
2. Vestal, M., The future of biological mass spectrometry. J. Am. Soc. Mass Spectrom. 2011, 22, 953-959.
3. Caprioli, R., Farmer, T., Gile, J., Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF-MS. Anal. Chem. 1997, 69, 4751-4760.
4. Simpson, R., Greening, D. (Eds.), Serum/plasma proteomics: methods and protocols. Methods Mol. Biol. 2011, 728, 69-85.
5. Lu, J., Liu, S., Deng, C., Facile synthesis of alumina hollow spheres for on-plate-selective enrichment of phosphopeptides. Chem. Commun. 2011, 47, 5334-5336.
6. Chen, S.-Y., Juang, Y-M., Chien, M-W., Li, K-I. et al., Magnetic iron oxide nanoparticle enrichment of phosphopeptides on a radiate microstructure MALDI chip. Analyst 2011, 136, 4454-4459.
7. Oiao, L., Roussel, C., Wan, J., Yang, P. et al., Specific on-plate enrichment of phosphorylated peptides for direct MALDI-TOF MS analysis. J. Proteome Res. 2007, 6, 4763-4769.
8. Inuta, M., Arakawa, R., Kawasaki, H., Use of thermally annealed multilayer gold nanoparticle films in combination analysis of localized surface plasmon resonance sensing and MALDI mass spectrometry. Analyst 2011, 136, 1167-1176.
9. Hutchens, W., Yip, T., New desorption strategies for mass spectrometric analysis of macromolecules. Rapid Commun. Mass Spectrom. 1993, 7, 576-580.
10. Tang, N., Tornatore, P., Weinberger, S., Current developments in SELDI affinity technology. Mass Spectrom. Rev. 2004, 23, 34-44.
11. Wei, W., Martin, A., Johnson, P., Ward, D., 10 years of SELDI: what have we learnt? Curr. Proteomics 2010, 7, 15-25.
12. Law, K., Larkin, J., Recent advances in SALDI-MS techniques and their chemical and bioanalytical applications. Anal. Bioanal. Chem. 2011, 399, 2597-2622.
13. Chiang, C.-K., Chen, W-T., Chang, H-T., Nanoparticle-based mass spectrometry for the analysis of biomolecules. Chem. Soc. Rev. 2011, 40, 1269-1281.
14. Zhang, L.-J., Lu, H-J., Yang, P-Y., Recent developments of nanoparticle-based enrichment methods for mass spectrometric analysis in proteomics. Sci. China Chem. 2010, 53, 695-703.
15. Hung, K.-C., Ding, H., Guo, B., Use of poly(tetrafluoroethylene) as a sample support for the MALDI-TOF analysis of DNA and proteins. Anal. Chem. 1999, 71, 518-521.
16. Yuan, X., Desiderio, D., Protein identification with Teflon and matrix-assisted laser desorption/ionization sample support. J. Mass Spectrom. 2002, 37, 512-524.
17. Wei, H., Dean, S., Parkin, M., Nolkrantz, K. et al., Microscale sample deposition onto hydrophobic target plates for trace level detection of neuropeptides in brain tissue by MALDI-MS. Mass Spectrom. Rev. 2005, 40, 1338-1346.
18. Schurenberg, M., Luebbert, C., Eickhoff, H., Kallum, M. et al., Prestructured MALDI-MS sample supports. Anal. Chem. 2000, 72, 3346-3442.
19. Oehlers, L., Perez, A., Walter, R., Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of 4-sulfophenyl isothiocyanate-derivatized peptides on AnchorChip sample supports using the sodium-tolerant matrix 2, 4, 6-trihydroxyacetophenone and diammonium citrate. Rapid Commun. Mass Spectrom. 2005, 19, 752-758.
20. Wu, Y.-C., Hsieh, C-H., Tam, M-F., Matrix-assisted laser desorption/ionization of peptides on AnchorChip targets with alpha-cyano-4-hydroxycinnamic acid and nitrocellulose as matrix. Rapid Commun. Mass Spectrom. 2006, 20, 309-312.
21. Zhang, X., Shi, L., Shu, S., Wang, Y. et al., An improved method of sample preparation on AnchorChip targets for MALDI-MS and MS/MS and its application in the liver proteome project. Proteomics 2007, 7, 2340-2349.
22. Navare, A., Nouzova, M., Noriega, F., Hernandez-Martinez, S. et al., On-chip solid-phase extraction pre-concentration/focusing substrates coupled to atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry for high sensitivity biomolecule analysis. Rapid Commun. Mass Spectrom. 2009, 23, 477-486.
23. Urban, P., Amantonico, A., Zenobi, R., Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets. Mass Spectrom. Rev. 2011, 30, 435-478.
24. Muck, A., Nesnerova, P., Pichova, I., Svatos, A., Fast prototyping of hydrophobic disposable polymer support arrays for matrix-assisted laser desorption/ionization-time of flight-mass spectrometry of proteins by atmospheric molding. Electrophoresis 2005, 26, 2835-2842.
25. Jia, W., Wu, H., Lu, H., Li, N. et al., Rapid and automatic on-plate desalting protocol for MALDI-MS: using imprinted hydrophobic polymer template. Proteomics 2007, 7, 2497-2506.
26. Ha, M., In, Y., Maeng, H., Zee, O. et al., Development of a matrix-prespotted plate for enhancing the reproducibility of serum glycan analysis by MALDI-TOF-MS. Mass Spectrom. Lett. 2011, 2, 61-64.
27. Zeng, Z., Wang, Y., Shi, S., Wang, L. et al., On-plate selective enrichment and self-desalting of peptides/proteins for direct MALDI MS analysis. Anal. Chem. 2011, 84, 2118-2123.
28. Muck, A., Nesnerova, P., Pichova, I., Ibanez, A. et al., Atmospheric molding of ionic copolymer MALDI-TOF/MS arrays: a new tool for protein identification/profiling. Electrophoresis 2006, 27, 4952-4959.
29. Cedervall, T., Lynch, I., Foy, M., Berggard, T. et al., Detailed identification of plasma proteins adsorbed on copolymer nanoparticles. Angew. Chem. 2007, 119, 5856-5858.
30. 8-functionalized magnetic nanoparticles for direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. J. Chromatog. A 2008, 1185, 93-101.
31. Shrivas, K., Wu, F., Modified silver nanoparticle as a hydrophobic affinity probe for analysis of peptides and proteins in biological samples by using liquid-liquid microextraction coupled to AP-MALDI-ion trap and MALDI-TOF mass spectrometry. Anal. Chem. 2008, 80, 2583-2589.
32. Kailasa, S. K., Wu, H. F., Surface modified silver selenide nanoparticles as extracting probes to improve peptide/protein detection via nanoparticles-based liquid phase microextraction coupled with MALDI mass spectrometry. Talanta 2010, 83, 527-534.
33. Bhat, A., Wu, H-F., Synthesis, characterization and application of modified Pd nanoparticles as preconcentration probes for selective enrichment/analysis of proteins via hydrophobic interactions from real-world samples using nanoparticle-laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2010, 24, 3547-3552.
34. Vanderpuije, B., Han, G., Rotell, V., Vachet, R., Mixed monolayer-protected gold nanoclusters as selective peptide extraction agents for MALDI-MS analysis. Anal. Chem. 2006, 78, 5491-5496.
35. Chang, S., Zheng, N., Chen, C., Chen, C. et al., Analysis of peptides and proteins affinity-bound to iron oxide nanoparticles by MALDI MS. J. Am. Soc. Mass Spectrom. 2007, 18, 910-918.
36. 2+-doped carbon nanotubes and CdS nanoparticles as the matrix, preconcentrating and accelerating probes of microwave enzymatic digestion of peptides and proteins for direct MALDI-MS analysis. J. Mass Spectom. 2010, 45, 1452-1460.
37. Wu, C., Han, C., Chang, H., Applications of surface-functionalized diamond nanoparticles for mass-spectrometry-based proteomics. J. Chin. Chem. Soc. 2010, 57, 583-594.
38. Ozohanics, O., Turiak, L., Drahos, L., Vekey, K., Comparison of glycopeptide/glycoprotein enrichment techniques. Rapid Commun. Mass Spectrom. 2012, 26, 215-217.
39. Jang, K., Kim, Y., Lee, K-S., Choi, I. et al., Method development for direct detection of glycoproteins on aminophenylboronic acid functionalized self-assembled monolayers by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 2009, 23, 3599-3602.
40. Tang, J., Liu, Y., Qi, D., Yao, G. et al., On-plate-selective enrichment of glycopeptides using boronic acid-modified gold nanoparticles for direct MALDI-QIT-TOF MS analysis. Proteomics 2009, 9, 5046-5055.
41. Xu, Y., Lijuan, L., Lu, H., Yang, P., On-plate enrichment of glycopeptides by using boronic acid functionalized gold-coated Si wafer. Proteomics 2010, 10, 1079-1086.
42. Shen, W.-W., Ma, C-N., Wang, S-F., Xiong, H-M. et al., SnO2@Poly(HEMA-co-St-co-VPBA) core-shell nanoparticles designed for selectively enriching glycopeptides followed by MALDI-MS analysis. Chem. Asian J. 2010, 5, 1185-1191.
43. Lin, P., Chen, S., Wang, K., Chen, M. et al., Fabrication of oriented antibody-conjugated magnetic nanoprobes and their immunoaffinity application. Anal. Chem. 2009, 81, 8774-8782.
44. Dunn, J., Reid, G., Bruening, M., Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Mass Spectrom. Rev. 2010, 29, 29-54.
45. Shen, J., Ahmed, T., Vogt, A., Wang, J. et al., Preparation and characterization of nitrilotriacetic-acid-terminated self-assembled monolayers on gold surfaces for matrix-assisted desorption ionization-time of flight-mass spectrometry analysis of proteins and peptides. Anal. Biochem. 2005, 345, 258-269.
46. Dunn, J., Watson, J., Bruening, M., Detection of phosphopeptides using Fe(III)-nitrilotriacetate complexes immobilized on a MALDI plate. Anal. Chem. 2006, 78, 1574-1580.
47. Xu, S., Zhou, H., Pan, C., Fu, Y. et al., Iminodiacetic acid derivatized porous silicon as a matrix support for sample pretreatment and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. Rapid Commun. Mass Spectrom. 2006, 20, 1769-1775.
48. Dunn, J., Igrisan, E., Palumbo, A., Reid, G., Bruening, M., Phosphopeptide enrichment using MALDI plates modified with high-capacity polymer brushes. Anal. Chem. 2008, 80, 5727-5735.
49. Wang, W., Bruening, M., Phosphopeptide enrichment on functionalized polymer microspots for MALDI-MS analysis. Analyst 2009, 134, 512-518.
50. Blacken, G., Reactive landing of gas-phase ions as a tool for the fabrication of metal oxide surfaces for in situ phosphopeptide enrichment. J. Am. Soc. Mass Spectrom. 2009, 20, 915-926.
51. Torta, F., Fusi, M., Casari, C., Bottani, C., Bachi, A., Titanium dioxide coated MALDI plate for on target analysis of phosphopeptides. J. Proteome Res. 2009, 8, 1932-1942.
52. Niklew, M.-L., Hochkirch, U., Mellkyan, A., Moritz, T. et al., Phosphopeptide screening using nanocrystalline titanium dioxide films as affinity matrix-assisted laser desorption ionization targets in mass spectrometry. Anal. Chem. 2010, 82, 1047-1053.
53. 2-based experimental layout for on-target enrichment and separation of multi- and monophosphorylated peptides prior to analysis with matrix-assisted laser desorption-ionization mass spectrometry. Anal. Chem. 2010, 83, 761-766.
54. 2 arrays for on-plate selective enrichment of phosphopeptides and direct MALDI MS analysis. Anal. Chem. 2011, 83, 1624-1631.
55. Zhou, H., Xu, S., Ye, M., Feng, S. et al., Zirconium phosphonate-modified porous silicon for highly specific capture of phosphopeptides and MALDI-TOF MS analysis. J. Proteome Res. 2006, 5, 2431-2437.
56. Chen, C., Wang, L., Ho, Y., Use of polyethylenimine-modified magnetic nanoparticles for highly specific enrichment of phosphopeptides for mass spectrometric analysis. Anal. Bioanal. Chem. 2011, 399, 2795-2806.
57. Li, Y.-C., Lin, Y-S., Tsai, P-J., Chen, C-T. et al., Nitrilotriacetic acid-coated magnetic nanoparticles as affinity probes for enrichment of histidine-tagged proteins and phosphorylated peptides. Anal. Chem. 2007, 79, 7519-7525.
58. Wu, H., Hsu, C., Tsai, C., Lin, P. et al., Nanoprobe-based immobilized metal affinity chromatography for sensitive and complementary enrichment of multiply phosphorylated peptides. Proteomics 2011, 11, 2639-2653.
59. Chen, C. T., Chen, Y. C., Fe3O4TiO2 core/shell nanoparticles as affinity probes for the analysis of phosphopeptides using TiO2 surface-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 2005, 77, 5912-5919.
60. Li, Y., Xu, X., Qi, D., Deng, C. et al., Novel Fe3O4@TiO2 core-shell microspheres for selective enrichment of phosphopeptides in phosphoproteome analysis. J. Proteome Res. 2008, 7, 2526-2538.
61. Zneg, Y., Chen, H., Shiau, K., Hung, S. et al., Efficient enrichment of phosphopeptides by magnetic TiO2-coated carbon-encapsulated iron nanoparticles. Proteomics 2012, 12, 380-390.
62. Li, Y., Leng, T., Lin, H., Deng, C. et al., Preparation of Fe3O4@ZrO2 core-shell microspheres as affinity probes for selective enrichment and direct determination of phosphopeptides using matrix-assisted laser desorption ionization mass spectrometry. J. Proteome Res. 2007, 6, 4498-4510.
63. Lo, C.-Y., Chen, W-Y., Chen, C-T., Chen, Y-C., Rapid enrichment of phosphopeptides from tryptic digests of proteins using iron oxide nanocomposites of magnetic particles coated with zirconia as the concentrating probes. J. Proteome Res. 2007, 6, 887-893.
64. Chen, C.-T., Chen, W-Y., Tsai, P-J., Chien, K-Y. et al., Rapid enrichment of phosphopeptides and phosphoproteins from complex samples using magnetic particles coated with alumina as the concentrating probes for MALDI MS analysis. J. Proteome Res. 2007, 6, 316-325.
65. Zhao, L., Wu, R., Han, G., Zhou, H. et al., The highly selective capture of phosphopeptides by zirconium phosphonate-modified magnetic nanoparticles for phosphoproteome analysis. J. Am. Soc. Mass Spectrom. 2008, 19, 1176-1186.
66. Lin, H., Chen, W., Chen, Y., Iron oxide/tantalum oxide core-shell magnetic nanoparticle-based microwave-assisted extraction for phosphopeptide enrichment from complex samples for MALDI MS analysis. Anal. Bioana. Chem. 2009, 394, 2129-2136.
67. Kwon, Y., Han, Z., Kartan, E., Mrksich, M., Kay, B., Antibody arrays by cutinase-mediated immobilization on self-assembled monolayers. Anal. Chem. 2004, 76, 5713-5720.
68. Faccenda, A., Bonham, C., Vacratsis, P., Zhang, X., Mutus, B., Gold nanoparticle enrichment method for identifying S-nitrosylation and S-glutathionylation sites in proteins. J. Amer. Chem. Soc. 2010, 132, 11392-11394.
69. Brockman, A., Orlando, R., Probe immobilized affinity-chromatography mass-spectrometry. Anal. Chem. 1995, 67, 4581-4585.
70. Brockman, A. H., Orlando, R., New immobilization chemistry for probe affinity mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 10, 1688-1692.
71. Nelson, R., Krone, J., Bieber, A., Williams, P., Mass spectrometric immunoassay. Anal. Chem. 1995, 67, 1153-1158.
72. Nelson, R. W., Borges, C. R., Mass spectrometric immunoassay revisited. J. Am. Soc. Mass Spectrom. 2011, 22, 960-968.
73. Sparbier, K., Wenzel, T., Dihazi, H., Blaschke, S. et al., Immuno-MALDI-TOF MS: new perspectives for clinical applications of mass spectrometry. Proteomics 2009, 9, 1442-1450.
74. Neubert, H., Jacoby, E., Bansal, S., Iles, R. et al., Enhanced affinity capture MALDI-TOF MS: orientation of an immunoglobulin G using recombinant protein G. Anal. Chem. 2002, 74, 3677-3683.
75. Seok, H.-J., Hong, M-Y., Kim, Y-J., Han, M-K. et al., Mass spectrometric analysis of affinity-captured proteins on a dendrimer-based immunosensing surface: investigation of on-chip proteolytic digestion. Anal. Biochem. 2005, 337, 294-307.
76. Wang, R., Kreuzer, H., Grunze, M., Molecular conformation and solvation of oligo (ethylene glycol)-terminated self-assembled monolayers and their resistance to protein adsorption. J. Phys. Chem. B 1997, 101, 9767-9773.
77. Harder, P., Grunze, M., Dahint, R., Whitesides, G. M. et al., Molecular conformation of oligo (ethylene glycol)-terminated self-assembled monolayers on gold and silver surfaces determines their ability to resist protein adsorption. J. Phys. Chem. B 1998, 102, 426-436.
78. Patrie, S., Mrksich, M., Self-assembled monolayers for MALDI-TOF mass spectrometry for immunoassays of human protein antigens. Anal. Chem. 2007, 79, 5878-5887.
79. Brauer, H., Lampe, P., Yasui, Y., Hamajima, N., Stolowitz, M., Biochips that sequentially capture and focus antigens for immunoaffinity MALDI-TOF MS: a new tool for biomarker verification. Proteomics 2010, 10, 3922-3927.
80. Ha, N., Kim, S., Lee, T., Han, S., Rapid characterization of protein chips using microwave-assisted protein tryptic digestion and MALDI mass spectrometry. Langmuir 2011, 27, 10098-10105.
81. Kim, Y., Yi, S., Lee, C., Jung, Y., Chung, B., Gold patterned biochips for on-chip immuno-MALDI-TOF MS: SPR imaging coupled multi-protein MS analysis. Analyst 2012, 137, 386-392.
82. Raska, C., Parker, C., Sunarborg, S., Pope, R. et al., Rapid and selective identification of etitope-containing peptides by direct matrix-assisted laser desorption/ionization tandem mass spectrometry of peptides affinity-bound to antibody beads. J. Am. Soc. Mass Spectrom. 2003, 14, 1076-1085.
83. Warren, E., Jiang, J., Parker, C., Borchers, C., Absolute quantitation of cancer-related proteins using an MS-based peptide chip. BioTechniques 2005, 38, S7-S11.
84. Jiang, J. P. C., Fuller, J., Kawula, T., Borchers, C., Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis. Proteomics 2007, 1, 1651-1659.
85. Reid, J., Holmes, D., Mason, D., Shah, B., Borchers, C., Toward the development of an immmuno MALDI (iMALDI) mass spectrometry assay for the diagnosis of hypertension. J. Am. Soc. Mass Spectrom. 2010, 21, 1680-1686.
86. Warren, E., Elms, P., Parker, C., Borchers, C., Development of a protein chip: a MS-based method for quantitation of protein expression and modification levels using an immunoaffinity approach. Anal. Chem. 2004, 76, 4082-4092.
87. Jiang, J., Parker, C., Fuller, J., Kawula, T., Borchers, C., An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularensis. Analytica. Chimica. Acta 2007, 605, 70-79.
88. Chou, P., Chen, S., Liao, H., Lin, P. et al., Nanoprobe-based affinity mass spectrometry for selected protein profiling in human plasma. Anal. Chem. 2005, 77, 5990-5997.
89. Lin, P., Chou, P., Chen, S., Liao, H. et al., Ethylene glycol-protected magnetic nanoparticles for a multiplexed immunoassay in human plasma. Small 2006, 2, 485-489.
90. Wang, K., Chuang, S., Lin, P., Huang, L. et al., Multiplexed immunoassay: quantitation and profiling of serum biomarkers using magnetic nanoprobes and MALDI-TOF MS. Anal. Chem. 2008, 80, 6159-6167.
91. Zhang, X., Zhu, S., Deng, C., Zhang, X., An aptamer based on-plate microarray for high-throughput insulin detection by MALDI-TOF MS. Chem. Commun. 2012, 48, 2689-2691.
92. Johnson, E., Ellis, W., Powers, L., Wysocki, V., Affinity capture mass spectrometry of biomarker proteins using peptide ligands from biopanning. Anal. Chem. 2009, 81, 5999-6005.
93. Lee, J., Ryoo, R., Kim, S., Ahn, J. et al., Quantitation of surface-bound proteins on biochips using MALDI-TOF MS. Anal. Sci. 2011, 27, 1127-1131.
94. Gavin, I., Kukhtin, A., Glesne, D., Schabacker, D., Chandler, D., Analysis of protein interaction and function with a 3-dimensional MALDI-MS protein array. BioTechniques 2005, 39, 1-8.
95. Gurard-Levin, Z., Mrksich, M., Combining self-assembled monolayers and mass spectrometry for applications in biochips. Annu. Rev. Anal. Chem. 2008, 1, 767-800.