Typing of unknown microorganisms based on quantitative analysis of fatty acids by mass spectrometry and hierarchical clustering

Analytica Chimica Acta

Volumn 684, Issue 1-2, 2011, Pages 8-16

  Li, Tingting ^a   Dai, Ling ^a   Li, Lun ^a   Hu, Xuejiao ^a   Dong, Linjie ^a   Li, Jianjian ^a   Salim, Sule Khalfan ^a   Fu, Jieying ^a   Zhong, Hongying ^a  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

Author keywords

Fatty acids; Hierarchical clustering; Mass spectrometry; Microorganism identification; Stable isotope labeling

Indexed keywords

HEXANE; ISOTOPES; MASS SPECTROMETRY; METHANOL; MICROORGANISMS; SPECTROMETRY;

BIOSYNTHETIC PATHWAY; EUCLIDEAN DISTANCE; FATTY ACID METHYL-ESTERS; HIER-ARCHICAL CLUSTERING; PROTEOME DATABASE; RAPID IDENTIFICATION; STABLE-ISOTOPE LABELING; ULTRA-SONICATION;

FATTY ACIDS;

FATTY ACID; FATTY ACID ESTER;

ARTICLE; CELL LYSATE; CLUSTER ANALYSIS; FUNGUS IDENTIFICATION; HIERARCHICAL CLUSTERING; ISOTOPE CODED FATTY ACID TRANSMETHYLATION; ISOTOPE LABELING; MASS SPECTROMETRY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SPECIES DIFFERENCE; ULTRASOUND;

ANIMALIA; BACTERIA (MICROORGANISMS); FUNGI;

EID: 78650180016     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2010.10.047     Document Type: Article

References (64)

1. Crist A.E., Johnson L.M., Burke P.J. J. Clin. Microbiol. 1996, 34:2408-2413.
2. Budowle B., Schutzer S.E., Einseln A., Kelley L.C., Walsh A.C., Smith J.A.L., Marrone B.L., Robertson J., Canpos J. Science 2003, 301:1852-1853.
3. Binder S., Levitt A.M., Sacks J.J., Hughes J.M. Science 1999, 284:1311-1313.
4. Abee T., Schaik W.V., Siezen R.J. Trends Biotech. 2004, 22:650-653.
5. Strange R.N. Annu. Rev. 2005, 43:83-116.
6. Beveridge T.J. Biotech. Histochem. 2001, 71:111-118.
7. Aldridge C., Jones P.W., Gibson S., Lanham J., Meyer M., Vannest R., Charles R. J. Clin. Microbiol. 1977, 6:406-413.
8. Miller J.M., Rhoden D.L. J. Clin. Microbiol. 1991, 29:1143-1147.
9. Olive D.M., Bean P. J. Clin. Microbiol. 1999, 37:1661-1669.
10. Healy M., Huong J., Bittner T., Lising M., Frye S., Raza S., Schrock R., Manry J., Benwick A., Nieto R., Woods C., Versalovic J., Lupski J.R. J. Clin. Microbiol. 2005, 43:199-207.
11. Fenselau C., Demirev P.A. Mass Spectrom. Rev. 2001, 20:157-171.
12. Wunschel D.S., Hill E.A., McLean J.S., Jarman K., Gorby Y.A., Valentine N., Wahl K.J. Microbiol. Methods 2005, 62:259-271.
13. Ho Y.P., Reddy P.M. Clin. Chem. 2010, 56:525-536.
14. Sauer S., Kliem M. Nat. Rev. Microbiol. 2010, 8:74-82.
15. Demirev P.A., Ho Y.P., Ryzhov V., Fenselau G. Anal. Chem. 1999, 71:2732-2738.
16. Demirev P.A., Feldman A.B., Kowalski P., Lin J.S. Anal. Chem. 2005, 7455-7461.
17. Fagerquist C.K., Garbus B.R., Williams K.E., Bates A.H., Boyle S., Harden L.A. Appl. Environ. Microbiol. 2009, 75:4341-4353.
18. Tao L., Yue X., Snyder A.P., Li L. Anal. Chem. 2004, 76:6609-6617.
19. Wynne C., Fenselau C., Demirev P.A., Edwards N. Anal. Chem. 2009, 81:9633-9642.
20. Jabbour R.E., Wade M.M., Deshpande S.V., Stanford M.F., Wick C.H., Zulich A.W., Snyder A.P. J. Proteome Res. 2010, 9:3647-3655.
21. Jabbour R.E., Deshpande S.V., Wade M.M., Stanford M.F., Wick C.H., Zulich A.W., Skowronski E.W., Snyder A.P. Appl. Environ. Microbiol. 2010, 76:3637-3644.
22. Saito N., Ohashi Y., Soga T., Tomita M. Curr. Opin. Microbiol. 2010, 13:358-362.
23. Bolten C.J., Kiefer P., Letisse F., Portais J.C., Wittmann C. Anal. Chem. 2007, 79:3843-3849.
24. Dettmer K., Aronov P.A., Hammock B.D. Mass Spectrom. Rev. 2007, 26:51-78.
25. Kohlstedt M., Becker J., Wittmann C. Appl. Microbiol. Biotech. 2010, 88:1065-1075.
26. Abel K., de Schmertzing H., Peterson J.I. J. Bacteriol. 1963, 85:1039-1044.
27. Eerola E., Lehtonen O.P. J. Clin. Microbiol. 1988, 9:1745-1753.
28. Moss C.W., Dees S.B. J. Chromatogr. 1975, 112:595-604.
29. Mukwaya G.M., Welch D.F. J. Clin. Microbiol. 1989, 27:2640-2646.
30. Spitsmeister M., Adamberg K., Vilu R. J. Microbiol. Methods 2010, 82:288-295.
31. Stead D.E., Sellwood J.E., Wilson J., Viney I. J. Appl. Microbiol. 1992, 72:315-321.
32. Li J., Yue Y., Li T., Hu X., Zhong H. Anal. Chim. Acta 2009, 650:221-226.
33. Li J., Yue Y., Hu X., Zhong H. Anal. Chem. 2009, 81:5080-5087.
34. German J.B., Roberts M.A., Watkins S.M. J. Nutr. 2003, 133:2078S-2083S.
35. Mortishine-Smith R.J., Skiles G.L., Lawrence J.W., Spence S., Nicholls A.W., Johnson B.A., Nicholson J.K. Chem. Res. Toxicol. 2004, 17:165-173.
36. Farmer E.E. Plant Mol. Biol. 1994, 26:1423-1437.
37. Farmer E.E. Science 1997, 276:912-913.
38. Kang J.X., Leaf A. Proc. Natl. Acad. Sci. U.S.A. 1996, 937:3542-3546.
39. Aderson M.P., Welsh M.J. Proc. Natl. Acad. Sci. U.S.A. 1990, 87:7334-7338.
40. Gottlicher M., Widmark E., Li Q., Gustafsson J.A. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:4653-4657.
41. Keller H., Dreyer C., Medin J., Mahfoudi A., Ozato K., Wahli W. Proc. Natl. Acad. Sci. U.S.A. 1993, 90:2160-2164.
42. Ostrosky-Zeichner L., Casadevall A., Galgiani J.N., Odds F.C., Rex J.H. Nat. Rev. Drug Discov. 2010, 9:719-727.
43. Caraux G., Pinloche S. Bioinformatics 2005, 21:1280-1281.
44. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:14863-14868.
45. Ho C.H., Magtanong L., Barker S.L., Gresham D., Nishimura S., Natarajan P., Koh J.L.Y., Porter J., Gray C.A., Anderson R.J., Giaever G., Nislow C., Anderews B., Botstein D., Graham T.R., Yoshida M., Boone C. Nat. Biotech. 2009, 27:369-377.
46. Brown H.A., Murph R.C. Nat. Chem. Biol. 2009, 5:602-606.
47. Cotter D., Maer A., Guda C., Saunder B., Subramaniam A. Nucl. Acids Res. 2006, 34:D507-D510.
48. Sud M., Fahy E., Cotter D., Brown A., Dennis E.A., Glass C.K., Merrill A.H., Murph R.C., Raetz C.R.H., Russell D.W., Subramaniam S. Nucl. Acids Res. 2007, 35:D527-D532.
49. Fahy E., Subramaniam S., Brown H.A., Glass C.K., Merrill A.H., Murph R.C., Raetz C.R.H., Russell D.W., Seyama Y., Shaw W., Shimizn T., Spener F., Van Meer G., VanNienwenhze M.S., White S.H., Witztum J.L., Dennis E.A. J. Lipids Res. 2005, 46:839-861.
50. Fahy E., Subramaniam S., Murph R.C., Nishijima M., Raetz C.R.H., Shimizn T., Spener F., VanMeer G., Wakelam M.J.O., Dennis E.A. J. Lipids Res. 2009, 50:S9-S14.
51. Junker B.H., Klukas C., Schreiber F. Bioinformatics 2006, 7:109-122.
52. Byrnes R.W., Cotter D., Maer A., Li J., Nadeau D., Subramaniam S. BMC Sys. Biol. 2009, 3:99. doi:10. 1186/1752-0509-3-99.
53. Ackman R.G., Burgher R.D., Sipos J.C. Nature 1963, 200:777-778.
54. Ackman R.G., Burgher R.D. Anal. Chem. 1963, 35:647-652.
55. Arnold R.J., Karty J.A., Ellington A.D., Reilly J.P. Anal. Chem. 1999, 71:1990-1996.
56. Jarman K.H., Cebula S.T., Saenz A.J., Petersen C.E., Valentine N.B., Kingsley M.T., Wahl K.L. Anal. Chem. 2000, 72:1217-1223.
57. Gacer A., Trofa D., Schafer W., Nosanchuk J.D. J. Clin. Invest. 2007, 117:3049-3058.
58. Nguyen L.N., Trofa D., Nosanchuk J.D. PloS One 2009, 4:e8421.
59. Hayes J.D., Wolf C.R. Molecular Genetics of Drug Resistance 1997, Hardwood Academic Publishers, Amsterdam.
60. Swain E., Baudry K., Stukey J., McDonough V., Germann M., Nickels J.T. Biol. Chem. 2002, 277:26177-26184.
61. Eisenkolb M., Zenzmaier C., Leitner E., Schneiter R. Mol. Biol. Cell 2002, 13:4414-4428.
62. Valachovic M., Wilcox L.I., Sturley S.L., Bard M. Lipids 2004, 39:747-752.
63. Veen M., Lang C. Biochem. Soc. Trans. 2005, 33:1178-1181.
64. Bammert G.F., Fostel J.M. Antimicrob. Agents Chemother. 2000, 44:1255-1265.