Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes

International Journal of Mass Spectrometry

Volumn 259, Issue 1-3, 2007, Pages 147-160

  Hu, Zhang Zhi ^a   Valencia, Julio C ^b   Huang, Hongzhan ^a   Chi, An ^c   Shabanowitz, Jeffrey ^c   Hearing, Vincent J ^b   Appella, Ettore ^b   Wu, Cathy ^a  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Bioinformatics; Lysosome related organelle (LRO); Organelle proteome; Protein database; Proteomics

Indexed keywords

EID: 33750632498     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2006.09.024     Document Type: Article

References (67)

1. Brunet S., Thibault P., Gagnon E., Kearney P., Bergeron J.J., and Desjardins M. Trends Cell Biol. 13 (2003) 629
2. Kislinger T., Cox B., Kannan A., Chung C., Hu P., Ignatchenko A., Scott M.S., Gramolini A.O., Morris Q., Hallett M.T., Rossant J., Hughes T.R., Frey B., and Emili A. Cell 125 (2006) 173
3. Forner F., Foster L.J., Campanaro S., Valle G., and Mann M. Mol. Cell Proteom. 5 (2006) 608
4. Foster L.J., de Hoog C.L., Zhang Y., Zhang Y., Xie X., Mootha V.K., and Mann M. Cell 125 (2006) 187
5. Leung A.K., Andersen J.S., Mann M., and Lamond A.I. Biochem. J. 376 (2003) 553
6. Reichert A.S., and Neupert W. Trends Genet. 20 (2004) 555
7. Warnock D.E., Fahy E., and Taylor S.W. Mass Spectrom. Rev. 23 (2004) 259
8. Yates J.R. Annu. Rev. Biophys. Biomol. Struct. 33 (2004) 297
9. Hinsby A.M., Kiemer L., Karlberg E.O., Lage K., Fausboll A., Juncker A.S., Andersen J.S., Mann M., and Brunak S. Mol. Cell 22 (2006) 285
10. Dreger M. Mass Spectrom. Rev. 22 (2003) 27
11. Wu C.H., Apweiler R., Bairoch A., Natale D.A., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Mazumder R., O'Donovan C., Redaschi N., and Suzek B. Nucl. Acids Res. 34 Database issue (2006) D187
12. Prokisch H., Andreoli C., Ahting U., Heiss K., Ruepp A., Scharfe C., and Meitinger T. Nucl. Acids Res. 34 Database issue (2006) D705
13. Wiwatwattana N., and Kumar A. Nucl. Acids Res. 33 Database issue (2005) D598
14. Chou K.C. Curr. Protein Pept. Sci. 1 (2000) 171
15. Emanuelsson O., and von Heijne G. Biochim. Biophys. Acta 1541 (2001) 114
16. Feng Z.P. In Silico Biol. 2 (2002) 291
17. Donnes P., and Hoglund A. Genom. Proteom Bioinform. 2 (2004) 209
18. Schneider G., and Fechner U. Proteomics 4 (2004) 1571
19. Li W., Amri H., Huang H., Wu C., and Papadopoulos V. J. Androl. 25 (2004) 900
20. Wu C.H., Huang H., Nikolskaya A., Hu Z., and Barker W.C. Comput. Biol. Chem. 28 (2004) 87
21. A. Chi, J.C. Valencia, Z.Z. Hu, H. Watabe, H. Yamaguchi, N. Mangini, H. Huang, V.A. Canfield, K. Cheng, J. Shabanowitz, V.J. Hearing, C.H. Wu, E. Appella, D.F. Hunt, J. Prot. Res. (2006).
22. Yu W.H., and Forte M. J. Bioenerg. Biomembr. 28 (1996) 93
23. Shoshan-Barmatz V., Zalk R., Gincel D., and Vardi N. Biochim. Biophys. Acta 1657 (2004) 105
24. Seachrist J.L., and Ferguson S.S. Life Sci. 74 (2003) 225
25. Helip-Wooley A., and Thoene J.G. Exp. Cell Res. 292 (2004) 89
26. Speight P., and Silverman M. Traffic 6 (2005) 858
27. Amillet J.M., Ferbus D., Real F.X., Antony C., Muleris M., Gress T.M., and Goubin G. Hum. Pathol. 37 (2006) 256
28. Colucci A.M., Campana M.C., Bellopede M., and Bucci C. Biochem. Biophys. Res. Commun. 334 (2005) 128
29. Kushimoto T., Basrur V., Valencia J., Matsunaga J., Vieira W.D., Ferrans V.J., Muller J., Appella E., and Hearing V.J. Proc. Natl. Acad. Sci. USA 98 (2001) 10698
30. Valencia J.C., Watabe H., Chi A., Rouzaud F., Chen K.G., Vieira W.D., Takahashi K., Yamaguchi Y., Berens W., Nagashima K., Shabanowitz J., Hunt D.F., Appella E., and Hearing V.J. J. Cell Sci. 119 (2006) 1080
31. Bahadoran P., Busca R., Chiaverini C., Westbroek W., Lambert J., Bille K., Valony G., Fukuda M., Naeyaert J.M., Ortonne J.P., and Ballotti R. J. Biol. Chem. 278 (2003) 11386
32. Loftus S.K., Larson D.M., Baxter L.L., Antonellis A., Chen Y., Wu X., Jiang Y., Bittner M., Hammer III J.A., and Pavan W.J. Proc. Natl. Acad. Sci. USA 99 (2002) 4471
33. Barral D.C., Ramalho J.S., Anders R., Hume A.N., Knapton H.J., Tolmachova T., Collinson L.M., Goulding D., Authi K.S., and Seabra M.C. J. Clin. Invest. 110 2 (2002 July) 247
34. Osanai K., Iguchi M., Takahashi K., Nambu Y., Sakuma T., Toga H., Ohya N., Shimizu H., Fisher J.H., and Voelker D.R. Am. J. Pathol. 158 (2001) 1665
35. Rastaldi M.P., Armelloni S., Berra S., Li M., Pesaresi M., Poczewski H., Langer B., Kerjaschki D., Henger A., Blattner S.M., Kretzler M., Wanke R., and D'Amico G. Am. J. Pathol. 163 (2003) 889
36. Yang M., Chen T., Han C., Li N., Wan T., and Cao X. Biochem. Biophys. Res. Commun. 318 (2004) 792
37. Ni X., Ma Y., Cheng H., Jiang M., Guo L., Ji C., Gu S., Cao Y., Xie Y., and Mao Y. J. Hum. Genet. 47 (2002) 548
38. Chavez R.A., Miller S.G., and Moore H.P. J. Cell Biol. 133 (1996) 1177
39. Tang L.H., Gumkowski F.D., Sengupta D., Modlin I.M., and Jamieson J.D. Gastroenterology 110 (1996) 809
40. Opdam F.J., Echard A., Croes H.J., van den Hurk J.A., van de Vorstenbosch R.A., Ginsel L.A., Goud B., and Fransen J.A. J. Cell Sci. 113 (2000) 2725
41. Strick D.J., Francescutti D.M., Zhao Y., and Elferink L.A. J. Biol. Chem. 277 (2002) 32722
42. Sudhof T.C. J. Biol. Chem. 277 (2002) 7629
43. Li C., Ullrich B., Zhang J.Z., Anderson R.G., Brose N., and Sudhof T.C. Nature 375 6532 (1995) 594
44. Arantes R.M., and Andrews N.W. J. Neurosci. 26 (2006) 4630
45. Lamason R.L., Mohideen M.A., Mest J.R., Wong A.C., Norton H.L., Aros M.C., Jurynec M.J., Mao X., Humphreville V.R., Humbert J.E., Sinha S., Moore J.L., Jagadeeswaran P., Zhao W., Ning G., Makalowska I., McKeigue P.M., O'donnell D., Kittles R., Parra E.J., Mangini N.J., Grunwald D.J., Shriver M.D., Canfield V.A., and Cheng K.C. Science 310 5755 (2005) 1782
46. Watabe H., Valencia J.C., Yasumoto K., Kushimoto T., Ando H., Muller J., Vieira W.D., Mizoguchi M., Appella E., and Hearing V.J. J. Biol. Chem. 279 (2004) 7971
47. Isoldi M.C., Pereira E.A., Visconti M.A., and Castrucci A.M. Braz. J. Med. Biol. Res. 37 (2004) 559
48. Izumi Y., Sawada H., Yamamoto N., Kume T., Katsuki H., Shimohama S., and Akaike A. J. Neurosci. Res. 82 (2005) 126
49. Berson J.F., Harper D.C., Tenza D., Raposo G., and Marks M.S. Mol. Biol. Cell. 12 (2001) 3451
50. Gruenberg J. Nat. Rev. Mol. Cell Biol. 2 (2001) 721
51. Gruenberg J., and Stenmark H. Nat. Rev. Mol. Cell Biol. 5 (2004) 317
52. Huizing M., Anikster Y., and Gahl W.A. Thromb. Haemost. 86 (2001) 233
53. Jensen R.E., Dunn C.D., Youngman M.J., and Sesaki H. Trends Cell Biol. 14 (2004) 215
54. Andersen J.S., Lam Y.W., Leung A.K., Ong S.E., Lyon C.E., Lamond A.I., and Mann M. Nature 433 7021 (2005) 77
55. Chiariello M., Bruni C.B., and Bucci C. FEBS Lett. 453 (1999) 20
56. Bucci C., Lutcke A., Steele-Mortimer O., Olkkonen V.M., Dupree P., Chiariello M., Bruni C.B., Simons K., and Zerial M. FEBS Lett. 366 (1995) 65
57. Barbieri M.A., Roberts R.L., Gumusboga A., Highfield H., Alvarez-Dominguez C., Wells A., and Stahl P.D. J. Cell Biol. 151 (2000) 539
58. Knoblach B., Keller B.O., Groenendyk J., Aldred S., Zheng J., Lemire B.D., Li L., and Michalak M. Mol. Cell Proteom. 2 (2003) 1104
59. Bagshaw R.D., Mahuran D.J., and Callahan J.W. Mol. Cell Proteom. 4 (2005) 133
60. Taylor S.W., Fahy E., Zhang B., Glenn G.M., Warnock D.E., Wiley S., Murphy A.N., Gaucher S.P., Capaldi R.A., Gibson B.W., and Ghosh S.S. Nat. Biotechnol. 21 (2003) 281
61. Gaucher S.P., Taylor S.W., Fahy E., Zhang B., Warnock D.E., Ghosh S.S., and Gibson B.W. J. Proteome. Res. 3 (2004) 495
62. Martens L., Van Damme P., Van Damme J., Staes A., Timmerman E., Ghesquiere B., Thomas G.R., Vandekerckhove J., and Gevaert K. Proteomics 5 (2005) 3193
63. Tribl F., Gerlach M., Marcus K., Asan E., Tatschner T., Arzberger T., Meyer H.E., Bringmann G., and Riederer P. Mol. Cell Proteom. 4 (2005) 945
64. Witzmann F.A., Arnold R.J., Bai F., Hrncirova P., Kimpel M.W., Mechref Y.S., McBride W.J., Novotny M.V., Pedrick N.M., Ringham H.N., and Simon J.R. Proteomics 5 (2005) 2177
65. Morciano M., Burre J., Corvey C., Karas M., Zimmermann H., and Volknandt W. J. Neurochem. 95 (2005) 1732
66. Mears R., Craven R.A., Hanrahan S., Totty N., Upton C., Young S.L., Patel P., Selby P.J., and Banks R.E. Proteomics 4 (2004) 4019
67. Pisitkun T., Shen R.F., and Knepper M.A. Proc. Natl. Acad. Sci. USA 101 (2004) 13368