Quantification of microRNA by DNA-Peptide Probe and Liquid Chromatography-Tandem Mass Spectrometry-Based Quasi-Targeted Proteomics

Analytical Chemistry

Volumn 88, Issue 1, 2016, Pages 754-763

  Xu, Feifei ^a   Yang, Ting ^b   Chen, Yun ^a  

^a NANJING MEDICAL UNIVERSITY   (China)

^b MEDICAL SCHOOL OF NANJING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ASSAYS; DNA; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; POLYMERASE CHAIN REACTION; PROBES; PROTEINS; RNA;

CLINICAL PRACTICES; LIMIT OF QUANTIFICATIONS; LIQUID CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY; ORDERS OF MAGNITUDE; SUBSTRATE PEPTIDES; TARGETED PROTEOMICS; TRYPSIN DIGESTION; TRYPTIC CLEAVAGE;

PEPTIDES;

DNA PROBE; MICRORNA; PEPTIDE;

CHEMISTRY; DNA PROBE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; PROTEOMICS; SYNTHESIS; TANDEM MASS SPECTROMETRY; TUMOR CELL CULTURE;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DNA PROBES; HUMANS; MICRORNAS; PEPTIDES; PROTEOMICS; TANDEM MASS SPECTROMETRY; TUMOR CELLS, CULTURED;

EID: 84953439576     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/acs.analchem.5b03056     Document Type: Article

References (67)

1. Bartel, D. P. Cell 2004, 116, 281-297 10.1016/S0092-8674(04)00045-5
2. He, L.; Hannon, G. J. Nat. Rev. Genet. 2004, 5, 522-531 10.1038/nrg1379
3. Wegman, D. W.; Krylov, S. N. TrAC, Trends Anal. Chem. 2013, 44, 121-130 10.1016/j.trac.2012.10.014
4. Fix, L. N.; Shah, M.; Efferth, T.; Farwell, M. A.; Zhang, B. Cancer Genomics Proteomics 2010, 7, 261-277
5. Zhang, P.; Zhang, J.; Wang, C.; Liu, C.; Wang, H.; Li, Z. Anal. Chem. 2014, 86, 1076-1082 10.1021/ac4026384
6. Zhang, P.; Liu, Y.; Zhang, Y.; Liu, C.; Wang, Z.; Li, Z. Chem. Commun. (Cambridge, U. K.) 2013, 49, 10013-10015 10.1039/c3cc45760e
7. Jin, Z.; Geissler, D.; Qiu, X.; Wegner, K. D.; Hildebrandt, N. Angew. Chem., Int. Ed. 2015, 54, 10024-10029 10.1002/anie.201504887
8. Lu, J.; Tsourkas, A. Nucleic Acids Res. 2009, 37, e100 10.1093/nar/gkp482
9. Gao, Z.; Yang, Z. Anal. Chem. 2006, 78, 1470-1477 10.1021/ac051726m
10. Wyman, S. K.; Parkin, R. K.; Mitchell, P. S.; Fritz, B. R.; O'Briant, K.; Godwin, A. K.; Urban, N.; Drescher, C. W.; Knudsen, B. S.; Tewari, M. PLoS One 2009, 4, e5311 10.1371/journal.pone.0005311
11. Wang, T.; Viennois, E.; Merlin, D.; Wang, G. Anal. Chem. 2015, 87, 8173-8180 10.1021/acs.analchem.5b00780
12. Labib, M.; Khan, N.; Ghobadloo, S. M.; Cheng, J.; Pezacki, J. P.; Berezovski, M. V. J. Am. Chem. Soc. 2013, 135, 3027-3038 10.1021/ja308216z
13. Zhang, G. J.; Chua, J. H.; Chee, R. E.; Agarwal, A.; Wong, S. M. Biosens. Bioelectron. 2009, 24, 2504-2508 10.1016/j.bios.2008.12.035
14. Yin, B. C.; Liu, Y. Q.; Ye, B. C. J. Am. Chem. Soc. 2012, 134, 5064-5067 10.1021/ja300721s
15. Wang, Q.; Li, R. D.; Yin, B. C.; Ye, B. C. Analyst 2015, 140, 6306-6312 10.1039/C5AN01350J
16. Roy, S.; Soh, J. H.; Gao, Z. Lab Chip 2011, 11, 1886-1894 10.1039/c0lc00638f
17. Wegman, D. W.; Krylov, S. N. Angew. Chem., Int. Ed. 2011, 50, 10335-10339 10.1002/anie.201104693
18. Wegman, D. W.; Cherney, L. T.; Yousef, G. M.; Krylov, S. N. Anal. Chem. 2013, 85, 6518-6523 10.1021/ac401185g
19. Chaumpluk, P.; Kerman, K.; Takamura, Y.; Tamiya, E. Sci. Technol. Adv. Mater. 2007, 8, 323-330 10.1016/j.stam.2007.04.001
20. Shaner, N. C.; Lin, M. Z.; McKeown, M. R.; Steinbach, P. A.; Hazelwood, K. L.; Davidson, M. W.; Tsien, R. Y. Nat. Methods 2008, 5, 545-551 10.1038/nmeth.1209
21. Marx, H.; Lemeer, S.; Schliep, J. E.; Matheron, L.; Mohammed, S.; Cox, J.; Mann, M.; Heck, A. J.; Kuster, B. Nat. Biotechnol. 2013, 31, 557-564 10.1038/nbt.2585
22. Thomas, B.; Akoulitchev, A. V. Trends Biochem. Sci. 2006, 31, 173-181 10.1016/j.tibs.2006.01.004
23. Kiyonami, R.; Schoen, A.; Prakash, A.; Peterman, S.; Zabrouskov, V.; Picotti, P.; Aebersold, R.; Huhmer, A.; Domon, B. Mol. Cell. Proteomics 2011, 10, M110.002931 10.1074/mcp.M110.002931
24. Li, Q. Nat. Methods 2013, 10, 1.
25. Calvo, E.; Camafeita, E.; Fernandez-Gutierrez, B.; Lopez, J. A. Expert Rev. Proteomics 2011, 8, 165-173 10.1586/epr.11.11
26. Balogh, L. M.; Kimoto, E.; Chupka, J.; Zhang, H.; Lai, Y. J. Proteomics Bioinform. 2012, S4 10.4172/jpb.S4-003
27. Elschenbroich, S.; Kislinger, T. Mol. BioSyst. 2011, 7, 292-303 10.1039/C0MB00159G
28. Thompson, A.; Prescott, M.; Chelebi, N.; Smith, J.; Brown, T.; Schmidt, G. Nucleic Acids Res. 2007, 35, e28 10.1093/nar/gkl1123
29. Schurch, S.; Bernal-Mendez, E.; Leumann, C. J. J. Am. Soc. Mass Spectrom. 2002, 13, 936-945 10.1016/S1044-0305(02)00413-0
30. Matthiesen, R.; Kirpekar, F. Nucleic Acids Res. 2009, 37, e48 10.1093/nar/gkp139
31. de Bang, T. C.; Shah, P.; Cho, S. K.; Yang, S. W.; Husted, S. Anal. Chem. 2014, 86, 6823-6826 10.1021/ac5017166
32. Riley, J. A.; Brown, T.; Gale, N.; Herniman, J.; Langley, G. J. Analyst 2014, 139, 1088-1092 10.1039/c3an01825c
33. Kullolli, M.; Knouf, E.; Arampatzidou, M.; Tewari, M.; Pitteri, S. J. Am. Soc. Mass Spectrom. 2014, 25, 80-87 10.1007/s13361-013-0759-x
34. Si, M. L.; Zhu, S.; Wu, H.; Lu, Z.; Wu, F.; Mo, Y. Y. Oncogene 2007, 26, 2799-2803 10.1038/sj.onc.1210083
35. Gong, C.; Yao, Y.; Wang, Y.; Liu, B.; Wu, W.; Chen, J.; Su, F.; Yao, H.; Song, E. J. Biol. Chem. 2011, 286, 19127-19137 10.1074/jbc.M110.216887
36. Kutanzi, K. R.; Yurchenko, O. V.; Beland, F. A.; Checkhun, V. F.; Pogribny, I. P. Clin. Epigenet. 2011, 2, 171-185 10.1007/s13148-011-0040-8
37. van den Brand, M.; Hoevenaars, B. M.; Sigmans, J. H.; Meijer, J. W.; van Cleef, P. H.; Groenen, P. J.; Hebeda, K. M.; van Krieken, J. H. Histopathology 2014, 65, 651-657 10.1111/his.12446
38. Biopharmaceutics Coordinating Committee in CDER. Guidance for industry-bioanalytical method validation, 2001; available at: http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm070107.pdf (accessed: May 28, 2015).
39. Barnidge, D. R.; Dratz, E. A.; Martin, T.; Bonilla, L. E.; Moran, L. B.; Lindall, A. Anal. Chem. 2003, 75, 445-451 10.1021/ac026154+
40. Xu, F.; Yang, T.; Fang, D.; Xu, Q.; Chen, Y. J. Proteomics 2014, 108, 188-197 10.1016/j.jprot.2014.05.016
41. Xu, Q.; Zhu, M.; Yang, T.; Xu, F.; Liu, Y.; Chen, Y. Clin. Chim. Acta 2015, 448, 118-123 10.1016/j.cca.2015.05.022
42. Uchida, Y.; Tachikawa, M.; Obuchi, W.; Hoshi, Y.; Tomioka, Y.; Ohtsuki, S.; Terasaki, T. Fluids Barriers CNS 2013, 10, 21 10.1186/2045-8118-10-21
43. Kamiie, J.; Ohtsuki, S.; Iwase, R.; Ohmine, K.; Katsukura, Y.; Yanai, K.; Sekine, Y.; Uchida, Y.; Ito, S.; Terasaki, T. Pharm. Res. 2008, 25, 1469-1483 10.1007/s11095-008-9532-4
44. Fusaro, V. A.; Mani, D. R.; Mesirov, J. P.; Carr, S. A. Nat. Biotechnol. 2009, 27, 190-198 10.1038/nbt.1524
45. Xu, F.; Yang, T.; Sheng, Y.; Zhong, T.; Yang, M.; Chen, Y. J. Proteome Res. 2014, 13, 5452-5460 10.1021/pr500339u
46. Yang, T.; Xu, F.; Zhao, Y.; Wang, S.; Yang, M.; Chen, Y. Proteomics: Clin. Appl. 2014, 8, 773-782 10.1002/prca.201300109
47. Kuhn, E.; Wu, J.; Karl, J.; Liao, H.; Zolg, W.; Guild, B. Proteomics 2004, 4, 1175-1186 10.1002/pmic.200300670
48. Waters, available at: http://www.waters.com/webassets/cms/library/docs/720004507en.pdf (accessed May 28, 2015).
49. Nitin, N.; Santangelo, P. J.; Kim, G.; Nie, S.; Bao, G. Nucleic Acids Res. 2004, 32, e58 10.1093/nar/gnh063
50. Riccelli, P. V.; Merante, F.; Leung, K. T.; Bortolin, S.; Zastawny, R. L.; Janeczko, R.; Benight, A. S. Nucleic Acids Res. 2001, 29, 996-1004 10.1093/nar/29.4.996
51. Kim, D.; Herr, A. E. Biomicrofluidics 2013, 7, 041501 10.1063/1.4816934
52. Sigma; available at: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product-Information-Sheet/1/s1638pis.pdf (accessed May 28, 2015).
53. Steinberg, G.; Stromsborg, K.; Thomas, L.; Barker, D.; Zhao, C. Biopolymers 2004, 73, 597-605 10.1002/bip.20006
54. Gingeras, T. R.; Kwoh, D. Y.; Davis, G. R. Nucleic Acids Res. 1987, 15, 5373-5390 10.1093/nar/15.13.5373
55. Bartosik, M.; Hrstka, R.; Palecek, E.; Vojtesek, B. Anal. Chim. Acta 2014, 813, 35-40 10.1016/j.aca.2014.01.023
56. Tombelli, S.; Minunni, M.; Luzi, E.; Mascini, M. Bioelectrochemistry 2005, 67, 135-141 10.1016/j.bioelechem.2004.04.011
57. Javaherian, S.; Musheev, M. U.; Kanoatov, M.; Berezovski, M. V.; Krylov, S. N. Nucleic Acids Res. 2009, 37, e62 10.1093/nar/gkp176
58. Liu, Y.; Huttenhain, R.; Collins, B.; Aebersold, R. Expert Rev. Mol. Diagn. 2013, 13, 811-825 10.1586/14737159.2013.845089
59. Ye, X.; Blonder, J.; Veenstra, T. D. Briefings Funct. Genomics Proteomics 2009, 8, 126-135 10.1093/bfgp/eln050
60. Harlan, R.; Zhang, H. Expert Rev. Proteomics 2014, 11, 657-661 10.1586/14789450.2014.976558
61. Tetu, B.; Brisson, J.; Landry, J.; Huot, J. Breast Cancer Res. Treat. 1995, 36, 93-97 10.1007/BF00690189
62. Kanagasabai, R.; Krishnamurthy, K.; Druhan, L. J.; Ilangovan, G. J. Biol. Chem. 2011, 286, 33289-33300.
63. Wegman, D. W.; Ghasemi, F.; Khorshidi, A.; Yang, B. B.; Liu, S. K.; Yousef, G. M.; Krylov, S. N. Anal. Chem. 2015, 87, 1404-1410 10.1021/ac504406s
64. Mauroy, A.; Van der Poel, W. H.; der Honing, R. H.; Thys, C.; Thiry, E. BMC Vet. Res. 2012, 8, 193 10.1186/1746-6148-8-193
65. Wong, M. L.; Medrano, J. F. BioTechniques 2005, 39, 75-85 10.2144/05391RV01
66. Pfaffl, M. W.; Tichopad, A.; Prgomet, C.; Neuvians, T. P. Biotechnol. Lett. 2004, 26, 509-515 10.1023/B:BILE.0000019559.84305.47
67. Wu, D. Y.; Ugozzoli, L.; Pal, B. K.; Qian, J.; Wallace, R. B. DNA Cell Biol. 1991, 10, 233-238 10.1089/dna.1991.10.233