Mass spectrometry in high-throughput clinical biomarker assays: Multiple reaction monitoring

Topics in Current Chemistry

Volumn 336, Issue , 2014, Pages 117-138

  Parker, Carol E ^a   Domanski, Dominik ^a   Percy, Andrew J ^a   Chambers, Andrew G ^a   Camenzind, Alexander G ^a   Smith, Derek S ^a   Borchers, Christoph H ^a,b  

^a UNIVERSITY OF VICTORIA   (Canada)

^b UNIVERSITY OF VICTORIA   (Canada)

Author keywords

Clinical proteomics; Multiple reaction monitoring (MRM); Multiplex; Proteomics; Quantitation; Selected reaction monitoring (SRM)

Indexed keywords

BIOLOGICAL MARKER;

ARTICLE; HIGH THROUGHPUT SCREENING; HUMAN; MASS SPECTROMETRY; METHODOLOGY; PROTEOMICS; STATISTICAL ANALYSIS; TANDEM MASS SPECTROMETRY;

BIOLOGICAL MARKERS; DATA INTERPRETATION, STATISTICAL; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 84890894398     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128-2012-353     Document Type: Article

References (59)

1. Kondrat RW, McClusky GA, Cooks RG (1978) Anal Chem 50:2017
2. Yost RA, Enke CG (1978) J Am Chem Soc 100:2274
3. Harvan DJ, Hass JR, Schroeder JL, Corbett BJ (1981) Anal Chem 53:1755
4. Kuzyk MA, Parker CE, Borchers CH (2012) In: Backvall H (ed) Methods in molecular biology. Humana Press (in press
5. Kuzyk MA, Smith D, Yang J, Cross TJ, Jackson AM, Hardie DB, Anderson NL, Borchers CH (2009) Mol Cell Proteomics 8:1860
6. Stokvis E, Rosing H, Beijnen JH (2005) Rapid Commun Mass Spectrom 19:401
7. Regnier FE, Riggs L, Zhang RJ, Xiong L, Liu PR, Chakraborty A, Seeley E, Sioma C, Thompson RA (2002) J Mass Spectrom 37:133
8. Zhang R, Sioma CS, Thompson RA, Xiong L, Regnier FE (2002) Anal Chem 74:3662
9. Ong S, Mann M (2005) Nat Chem Biol 1:252
10. Elliott M, Smith D, Kuzyk M, Parker CE, Borchers CH (2009) J Mass Spectrom 44:1637
11. Hulmes JD, Bethea D, Ho K, Huang S-P, Ricci DL, Opiteck GJ, Hefta SA (2004) Clin Proteomics 1:17
12. Aguilar-Mahecha A, Kuzyk MA, Domanski D, Borchers CH, Basik M (2012) PLos One 7: E38290. doi:10.1371journal.pone.0038290
13. Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, Mehigh RJ, Cockrill SL, Scott GBI, Tammen H, Schulz-Knappe P, Speicher DW, Vitzthum F, Haab BB, Siest G, Chan DW (2005) Proteomics 5:3262
14. Tuck MK, Chan DW, Chia D, Godwin AK, Grizzle WE, Krueger KE, Rom W, Sanda M, Sorbara L, Stass S, Wang W, Brenner DE (2009) J Proteome Res 8:113
15. Proc JL, Kuzyk MA, Hardie DB, Yang J, Smith DS, Jackson AM, Parker CE, Borchers CH (2010) J Proteome Res 9:5422
16. Domanski D, Percy AJ, Yang J, Chambers AG, Hill JS, Cohen Freue GV, Borchers CH (2012) Proteomics 12:1222
17. Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P (2008) Proteomics Clin Appl 2:1386
18. Surinova S, Schiess R, Huttenhain R, Cerciello F, Wollscheid B, Aebersold R (2011) J Proteome Res 10:5
19. Wolters DA, Washburn MP, Yates JR III (2001) Anal Chem 73:5683
20. Asara JM, Christofk HR, Freimark LM, Cantley LC (2008) Proteomics 8:994
21. Silva JC, Gorenstein MV, Li G-Z, Vissers JPC, Geromanos SJ (2006) Mol Cell Proteomics 5:144
22. GE Healthcare (2011) About 2-D fluorescence difference gel electrophoresis (2-D DIGE). http://www.gelifesciences.com/aptrix/upp01077.nsf/ content/2d-electrophoresis~new-to-2d-dige. Accessed December 2011
23. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Mol Cell Proteomics 3:1154
24. Cohen Freue GV, Sasaki M, Meredith A, Gunther OP, Bergman A, Takhar M, Mui A, Balshaw RF, Ng RT, Opushneva N, Hollander Z, Li G, Borchers CH, Wilson-McManus J, McManus BM, Keown PA, McMaster WR (2010) Mol Cell Proteomics 9:1954
25. Keshishian H, Addona T, Burgess M, Mani DR, Shi X, Kuhn E, Sabatine MS, Gerszten RE, Carr SA (2009) Mol Cell Proteomics 8:2339
26. Washburn MP, Wolters D, Yates JR 3rd (2001) Nat Biotechnol 19:242
27. Kiyonami R, Schoen A, Prakash A, Peterman S, Zabrouskov V, Picotti P, Aebersold R, Huhmer A, Domon B (2011) Mol Cell Proteomics 10:M110.002931
28. Domanski D, Cohen Freue G, Sojo L, Kuzyk MA, Parker CE, Goldberg YP, Borchers CH (2011) J Proteomics. doi:10.1016/j.jprot.2011.11.022
29. Bystrom CE, Salameh W, Reitz R, Clarke NJ (2010) Clin Chem 56:1561
30. Hoofnagle AN, Becker JO, Wener MH, Heinecke JW (2008) Clin Chem 54:1796
31. Anderson NL, Anderson NG (2002) Mol Cell Proteomics 1:845
32. Domanski D, Smith DS, Miller CA, Yang Y, Jackson AM, Cohen Freue G, Hill JS, Parker CE, Borchers CH (2011) Clin Lab Med 31:371
33. Farrah T, Deutsch EW, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmstrom J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R (2011) Mol Cell Proteomics 10. doi:10.1074/mcp.M110.006353
34. Chen Y-T, Chen H-W, Domanski D, Smith DS, Liang K-H, Wu C-C, Chen C-L, Chung T, Chen M-C, Chang Y-S, Parker CE, Borchers CH, Yu J-S (2012) Proteomics. doi:10.1016/j. jprot.2011.12.031
35. Remily-Wood ER, Liu RZ, Xiang Y, Chen Y, Thomas CE, Rajyaguru N, Kaufman LM, Ochoa JE, Hazlehurst L, Pinilla-Ibarz J, Lancet J, Zhang G, Haura E, Shibata D, Yeatman T, Smalley KSM, Dalton WS, Huang E, Scott E, Bloom GC, Eschrich SA, Koomen JM (2011) Proteomics Clin Appl. doi:10.1002/prca.201000115
36. Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW (2004) J Proteome Res 3:235
37. Whiteaker JR, Zhao L, Anderson L, Paulovich AG (2010) Mol Cell Proteomics 9:184
38. Anderson NL, Jackson A, Smith D, Hardie D, Borchers C, Pearson TW (2009) Mol Cell Proteomics 8:995
39. Whiteaker JR, Zhao L, Abbatiello SE, Burgess M, Kuhn E, Lin C, Pope M, Razavi M, Anderson NL, Pearson TW, Carr SA, Paulovich AG (2011) Mol Cell Proteomics 10: M110.005645
40. Wu J, Pungaliya P, Kraynov E, Bates B (2012) Biomarkers 17:125
41. Anderson DS, Kirchner M, Kellogg M, Kalish LA, Jeong JY, Vanasse G, Berliner N, Fleming MD, Steen H (2011) Anal Chem 83:8357
42. Jiang J, Parker CE, Hoadley KA, Perou CM, Boysen G, Borchers CH (2007) Proteomics Clin Appl 1:1651
43. Jiang J, Parker CE, Fuller JR, Kawula TH, Borchers CH (2007) Anal Chim Acta 605:70
44. Reid JD, Holmes DT, Mason DR, Shah B, Borchers CH (2010) J Am Soc Mass Spectrom 21:1680
45. Shah B, Reid JD, Kuzyk MJ, Parker CE, Borchers CH (2012) Methods in molecular biology (in press
46. Reed GF, Lynn F, Mead BD (2002) Clin Diagn Lab Immunol 9:1235
47. Green DM, Swets JM (1966) Signal detection theory and psychophysics. Wiley, New York
48. Shariat SF, Semjonow A, Lilja H, Savage C, Vickers AJ, Bjartell A (2011) Acta Oncol 50:61
49. Receiver Operating Characteristic (2011) http://en.wikipedia.org/wiki/ Receiver-operating- characteristic. Accessed December 2011
50. Kroot JJC, Kemna EHJM, Bansal SS, Busbridge M, Campostrini N, Girelli D, Hider RC, Koliaraki V, Mamalaki A, Olbina G, Tomosugi N, Tselepis C, Ward DG, Ganz T, Hendriks JCM, Swinkels DW (2009) Haematologica 94:1748
51. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham A-JL, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA (2009) Nat Biotechnol 27:633
52. HUPO (2011) The Human Proteome Project. http://www.hupo.org/research/hpp/ . Accessed December 2011
53. Anderson NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M, Aebersold R, Carr SA (2009) Mol Cell Proteomics 8:883
54. HUPO (2010) The HUPO standards initiative. http://www.hupo.org/research/ psi/. Accessed December 2011
55. HUPO (2011) The HUPO proteomics standards initiative. Accessed December 2011
56. Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers C, Corthals GL, Costello CE, Deutsch EW, Domon B, Hanock W, He F, Hochstrasser D, Marko- Varga G, Salekdeh GH, Sechi S, Snyder M, Srivastava S, Uhlen M, Hu CH, Yamamoto T, Paik YK, Omenn GS (2011) Mol Cell Proteomics 10:M111.00993
57. Omenn GS (2004) Proteomics 4:1235
58. Kinter M, Sherman NE (2005) Protein sequencing and identification using tandem mass spectrometry, John Wiley & Sons, USA, p. 58.
59. Percy AJ, Chambers AG, Yang J, Domanski D, Borchers CH (2012) Anal Bioanal Chem doi:10.1007/s00216-00012-06010-y