Meta sequence analysis of human blood peptides and their parent proteins

Journal of Proteomics

Volumn 73, Issue 6, 2010, Pages 1163-1175

  Bowden, Peter ^a   Pendrak, Voitek ^a   Zhu, Peihong ^a   Marshall, John G ^a  

^a RYERSON UNIVERSITY   (Canada)

Author keywords

Blood; Database; Human; Peptide; Plasma; Protein; Serum

Indexed keywords

PEPTIDE; PLASMA PROTEIN; PROTEIN; PROTEOME; TRYPSIN;

AMINO ACID SEQUENCE; ARTICLE; HUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEIN CLEAVAGE; PROTEIN LOCALIZATION; SEQUENCE ANALYSIS; ALGORITHM; CHEMISTRY; ELECTROSPRAY MASS SPECTROMETRY; LABORATORY DIAGNOSIS; LIQUID CHROMATOGRAPHY; PROCEDURES; PROTEOMICS; STATISTICAL MODEL; TANDEM MASS SPECTROMETRY;

ALGORITHMS; BLOOD PROTEINS; CHROMATOGRAPHY, LIQUID; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; HUMANS; MODELS, STATISTICAL; PEPTIDES; PROTEINS; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY; TRYPSIN;

EID: 77950542338     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2010.02.007     Document Type: Article

References (89)

1. Anderson N.L., and Anderson N.G. Mol Cell Proteomics 2 (2003) 50
2. Cohen S.N., and Chang A.C. Mol Gen Genet 134 (1974) 133-141
3. Sanger F., Nicklen S., and Coulson A.R. Proc Natl Acad Sci U S A 74 (1977) 5463-5467
4. Brutlag D., Atkinson M.R., Setlow P., and Kornberg A. Biochem Biophys Res Commun 37 (1969) 982-989
5. Mullis K.B. Ann Biol Clin (Paris) 48 (1990) 579-582
6. McCombie W.R., Adams M.D., Kelley J.M., FitzGerald M.G., Utterback T.R., Khan M., Dubnick M., Kerlavage A.R., Venter J.C., and Fields C. Nat Genet 1 (1992) 124-131
7. Adams M.D., Soares M.B., Kerlavage A.R., Fields C., and Venter J.C. Nat Genet 4 (1993) 373-380
8. Brenner S., Johnson M., Bridgham J., Golda G., Lloyd D.H., Johnson D., Luo S., McCurdy S., Foy M., Ewan M., Roth R., George D., Eletr S., Albrecht G., Vermaas E., Williams S.R., Moon K., Burcham T., Pallas M., DuBridge R.B., Kirchner J., Fearon K., Mao J., and Corcoran K. Nat Biotechnol 18 (2000) 630-634
9. Sanchez-Carbayo M., Socci N.D., Charytonowicz E., Lu M., Prystowsky M., Childs G., and Cordon-Cardo C. Cancer Res 62 (2002) 6973-6980
10. Smith L.M., Sanders J.Z., Kaiser R.J., Hughes P., Dodd C., Connell C.R., Heiner C., Kent S.B., and Hood L.E. Nature 321 (1986) 674-679
11. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C., et al. Science 291 (2001) 1304-1351
12. Soll D., Ohtsuka E., Jones D.S., Lohrmann R., Hayatsu H., Nishimura S., and Khorana H.G. Proc Natl Acad Sci U S A 54 (1965) 1378-1385
13. Zhang M.Q. Proc Natl Acad Sci U S A 94 (1997) 565-568
14. Knapp K., and Chen Y.P. Nucleic Acids Res 35 (2007) 317-324
15. Hutchinson G.B., and Hayden M.R. Nucleic Acids Res 20 (1992) 3453-3462
16. Cech T.R., Zaug A.J., and Grabowski P.J. Cell 27 (1981) 487-496
17. Pawson T., and Nash P. Science 300 (2003) 445-452
18. Machida K., Thompson C.M., Dierck K., Jablonowski K., Karkkainen S., Liu B., Zhang H., Nash P.D., Newman D.K., Nollau P., Pawson T., Renkema G.H., Saksela K., Schiller M.R., Shin D.G., and Mayer B.J. Mol Cell 26 (2007) 899-915
19. McClintock B. Genetics 26 (1941) 234-282
20. Strekalov A.A. Sov Genet 7 (1973) 919-929
21. Urbain J. Rev Fr Etud Clin Biol 14 (1969) 735-740
22. Ono S. J Med Genet 9 (1972) 254-263
23. Tonegawa S., Steinberg C., Dube S., and Bernardini A. Proc Natl Acad Sci U S A 71 (1974) 4027-4031
24. Lonai P., Rechavi G., Arman E., and Givol D. Embo J 2 (1983) 781-786
25. Kavaler J., Davis M.M., and Chien Y. Nature 310 (1984) 421-423
26. Hagen M., and Cech T.R. Embo J 18 (1999) 6491-6500
27. Schmucker D., Clemens J.C., Shu H., Worby C.A., Xiao J., Muda M., Dixon J.E., and Zipursky S.L. Cell 101 (2000) 671-684
28. Kersey P.J., Duarte J., Williams A., Karavidopoulou Y., Birney E., and Apweiler R. Proteomics 4 (2004) 1985-1988
29. Maglott D.R., Katz K.S., Sicotte H., and Pruitt K.D. Nucleic Acids Res 28 (2000) 126-128
30. Codd E.F. MD Comput 15 (1998) 162-166
31. Marshall J., Jankowski A., Furesz S., Kireeva I., Barker L., Dombrovsky M., Zhu W., Jacks K., Ingratta L., Bruin J., Kristensen E., Zhang R., Stanton E., Takahashi M., and Jackowski G. J Proteome Res 3 (2004) 364-382
32. Chelius D., Huhmer A.F., Shieh C.H., Lehmberg E., Traina J.A., Slattery T.K., and Pungor Jr. E. J Proteome Res 1 (2002) 501-513
33. Moore R.E., Young M.K., and Lee T.D. J Am Soc Mass Spectrom 13 (2002) 378-386
34. Tucholska M., Bowden P., Jacks K., Zhu P., Furesz S., Dumbrovsky M., and Marshall J. J Proteome Res 8 (2009) 1143-1155
35. Yan W., Lee H., Deutsch E.W., Lazaro C.A., Tang W., Chen E., Fausto N., Katze M.G., and Aebersold R. Mol Cell Proteomics 3 (2004) 1039-1041
36. Adkins J.N., Varnum S.M., Auberry K.J., Moore R.J., Angell N.H., Smith R.D., Springer D.L., and Pounds J.G. Mol Cell Proteomics 1 (2002) 947-955
37. Tirumalai R.S., Chan K.C., Prieto D.A., Issaq H.J., Conrads T.P., and Veenstra T.D. Mol Cell Proteomics 2 (2003) 1096-1103
38. Olsen J.V., Ong S.E., and Mann M. Mol Cell Proteomics 3 (2004) 608-614
39. Zhu P.-H., K.K., Jankowski A., and Marshall J. Mol Cell Proteomics 3 (2004) S235
40. Shen Y., Jacobs J.M., Camp II D.G., Fang R., Moore R.J., Smith R.D., Xiao W., Davis R.W., and Tompkins R.G. Anal Chem 76 (2004) 1134-1144
41. Shen Y., Kim J., Strittmatter E.F., Jacobs J.M., Camp II D.G., Fang R., Tolie N., Moore R.J., and Smith R.D. Proteomics. (2005)
42. Chan K., Lucas D.A., Hise D., Schaefer C.F., Xiao Z., Janini G.M., Beutow K.H., Issaq HJ., Veenstra T.D., and Conrads T.P. Clin Proteomics 1 (2004) 101-225
43. Jin W.H., Dai J., Li S.J., Xia Q.C., Zou H.F., and Zeng R. J Proteome Res 4 (2005) 613-619
44. Omenn G.S., States D.J., Adamski M., Blackwell T.W., Menon R., Hermjakob H., Apweiler R., Haab B.B., Simpson R.J., Eddes J.S., Kapp E.A., Moritz R.L., Chan D.W., Rai A.J., Admon A., Aebersold R., Eng J., Hancock W.S., Hefta S.A., Meyer H., Paik Y.K., Yoo J.S., Ping P., Pounds J., Adkins J., Qian X., Wang R., Wasinger V., Wu C.Y., Zhao X., Zeng R., Archakov A., Tsugita A., Beer I., Pandey A., Pisano M., Andrews P., Tammen H., Speicher D.W., and Hanash S.M. Proteomics 5 (2005) 3226-3245
45. States D.J., Omenn G.S., Blackwell T.W., Fermin D., Eng J., Speicher D.W., and Hanash S.M. Nat Biotechnol 24 (2006) 333-338
46. Liu T., Qian W.J., Mottaz H.M., Gritsenko M.A., Norbeck A.D., Moore R.J., Purvine S.O., Camp II D.G., and Smith R.D. Mol Cell Proteomics 5 (2006) 2167-2174
47. Whiteaker J.R., Zhang H., Eng J.K., Fang R., Piening B.D., Feng L.C., Lorentzen T.D., Schoenherr R.M., Keane J.F., Holzman T., Fitzgibbon M., Lin C., Cooke K., Liu T., Camp II D.G., Anderson L., Watts J., Smith R.D., McIntosh M.W., and Paulovich A.G. J Proteome Res 6 (2007) 828-836
48. Sennels L., Salek M., Lomas L., Boschetti E., Righetti P.G., and Rappsilber J. J Proteome Res 6 (2007) 4055-4062
49. Faca V., Pitteri S.J., Newcomb L., Glukhova V., Phanstiel D., Krasnoselsky A., Zhang Q., Struthers J., Wang H., Eng J., Fitzgibbon M., McIntosh M., and Hanash S. J Proteome Res 6 (2007) 3558-3565
50. Tanaka Y., Akiyama H., Kuroda T., Jung G., Tanahashi K., Sugaya H., Utsumi J., Kawasaki H., and Hirano H. Proteomics 6 (2006) 4845-4855
51. Davis M.T., Stahl D.C., Hefta S.A., and Lee T.D. Anal Chem 67 (1995) 4549-4556
52. Anderson N.L., Polanski M., Pieper R., Gatlin T., Tirumalai R.S., Conrads T.P., Veenstra T.D., Adkins J.N., Pounds J.G., Fagan R., and Lobley A. Mol Cell Proteomics 3 (2004) 311-326
53. Ping P., Vondriska T.M., Creighton C.J., Gandhi T.K., Yang Z., Menon R., Kwon M.S., Cho S.Y., Drwal G., Kellmann M., Peri S., Suresh S., Gronborg M., Molina H., Chaerkady R., Rekha B., Shet A.S., Gerszten R.E., Wu H., Raftery M., Wasinger V., Schulz-Knappe P., Hanash S.M., Paik Y.K., Hancock W.S., States D.J., Omenn G.S., and Pandey A. Proteomics 5 (2005) 3506-3519
54. Peihong Zhu P.B., Pendrak V., Herbert Thiele Du., Zhang M., Diamandis EleftheriosP., and Marshall J. Clinical Proteomics 2 (2007) 1-20
55. Brenner S.E., Chothia C., and Hubbard T.J. Proc Natl Acad Sci U S A 95 (1998) 6073-6078
56. Field H.I., Fenyo D., and Beavis R.C. Proteomics 2 (2002) 36-47
57. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Nucleic Acids Res 25 (1997) 3389-3402
58. Pruitt K.D., Tatusova T., and Maglott D.R. Nucleic Acids Res 35 (2007) D61-D65
59. Titulaer M.K., Siccama I., Dekker L.J., van Rijswijk A.L., Heeren R.M., Sillevis Smitt P.A., and Luider T.M. BMC Bioinformatics 7 (2006) 403
60. Rauch A., Bellew M., Eng J., Fitzgibbon M., Holzman T., Hussey P., Igra M., Maclean B., Lin C.W., Detter A., Fang R., Faca V., Gafken P., Zhang H., Whiteaker J., States D., Hanash S., Paulovich A., and McIntosh M.W. J Proteome Res 5 (2006) 112-121
61. Babnigg G., and Giometti C.S. Proteomics 6 (2006) 4514-4522
62. Anderson L., and Hunter C.L. Mol Cell Proteomics 5 (2006) 573-588
63. Keshishian H., Addona T., Burgess M., Kuhn E., and Carr S.A. Mol Cell Proteomics 6 (2007) 2212-2229
64. Kulasingam V., Smith C.R., Batruch I., Buckler A., Jeffery D.A., and Diamandis E.P. J Proteome Res 7 (2008) 640-647
65. Keller A., Purvine S., Nesvizhskii A.I., Stolyar S., Goodlett D.R., and Kolker E. Omics 6 (2002) 207-212
66. Keller A., Nesvizhskii A.I., Kolker E., and Aebersold R. Anal Chem 74 (2002) 5383-5392
67. Nesvizhskii A.I., Keller A., Kolker E., and Aebersold R. Anal Chem 75 (2003) 4646-4658
68. Schenk S., Schoenhals G.J., de Souza G., and Mann M. BMC Med Genomics 1 (2008) 41
69. Cargile B.J., Bundy J.L., and Stephenson Jr. J.L. J Proteome Res 3 (2004) 1082-1085
70. Zhu P., Bowden P., Pendrak V., Thiele H., Zhang D., Siu M., Diamandis E.P., and J. M. Clinical Proteomics 2 (2006) 185-203
71. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., and Sherlock G. Nat Genet 25 (2000) 25-29
72. Liu X., Valentine S.J., Plasencia M.D., Trimpin S., Naylor S., and Clemmer D.E. J Am Soc Mass Spectrom 18 (2007) 1249-1264
73. Perkins D.N., Pappin D.J., Creasy D.M., and Cottrell J.S. Electrophoresis 20 (1999) 3551-3567 [pii]
74. Eng JimmyK., A. L. M., and Yates III JohnR. Am Soc Mass Spectrom 5 (1994) 979-989
75. Yates III J.R., Eng J.K., McCormack A.L., and Schieltz D. Anal Chem 67 (1995) 1426-1436
76. Craig R., and Beavis R.C. Bioinformatics 20 (2004) 1466-1467
77. Zhang H., Liu A.Y., Loriaux P., Wollscheid B., Zhou Y., Watts J.D., and Aebersold R. Mol Cell Proteomics 6 (2007) 64-71
78. Craig R., Cortens J.P., and Beavis R.C. J Proteome Res 3 (2004) 1234-1242
79. Belov L., Huang P., Chrisp J.S., Mulligan S.P., and Christopherson R.I. J Immunol Methods 305 (2005) 10-19
80. Hortin G.L. Clin Chem 52 (2006) 1223-1237
81. Edman P., and Begg G. Eur J Biochem 1 (1967) 80-91
82. Falkner J.A., Kachman M., Veine D.M., Walker A., Strahler J.R., and Andrews P.C. J Am Soc Mass Spectrom 18 (2007) 850-855
83. Declan Williams P.Z., Bowden P., Stacey C., McDonell M., Kowalski P., Kowalski J., Evans K., Diamandis Eleftherios P., Michael Siu K.W., and Marshall J. Clin Proteomics 2 (2007) 67-89
84. Tucholska M., Scozzaro S., Williams D., Ackloo S., Lock C., Siu K.W., Evans K.R., and Marshall J.G. Anal Biochem 370 (2007) 228-245
85. Marshall J., Kupchak P., Zhu W., Yantha J., Vrees T., Furesz S., Jacks K., Smith C., Kireeva I., Zhang R., Takahashi M., Stanton E., and Jackowski G. J Proteome Res 2 (2003) 361-372
86. Nesvizhskii A.I. Methods Mol Biol 367 (2007) 87-119
87. Belov M.E., Clowers B.H., Prior D.C., Danielson III W.F., Liyu A.V., Petritis B.O., and Smith R.D. Anal Chem 80 (2008) 5873-5883
88. Anderson N.L., and Anderson N.G. Mol Cell Proteomics 1 (2002) 845-867
89. Valentine S.J., Plasencia M.D., Liu X., Krishnan M., Naylor S., Udseth H.R., Smith R.D., and Clemmer D.E. J Proteome Res 5 (2006) 2977-2984