Rapid differentiation of new isolates with MALDI-TOF mass spectrometry via discriminant function analysis based on principal components

Berna Sariyar-Akbulut

Korean Journal of Chemical Engineering, Vol.26, No.6, 1645-1651, November, 2009

DOI10.1007/s11814-009-0243-2 Export Citation

Rapid differentiation of new isolates with MALDI-TOF mass spectrometry via discriminant function analysis based on principal components

Berna Sariyar-Akbulut^†

Department of Bioengineering, Marmara University, Kadikoy 34722, Istanbul, Turkey

E-mail:

Discriminant function analysis based on principal components was applied to the spectral outputs of whole cell suspensions of nine isolates from matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. First, based on the salt tolerance and whole cell proteins, the similarity of the isolates to moderate halophiles was established. Intact microorganisms were then inferentially clustered by MALDI-TOF mass spectroscopy taking four type strains as precursors. Two of these type strains were moderate halophilic bacteria (Halomonas salina and Halomonas halophila), one was a mesophilic bacteria (Escherichia coli), and one was a halophilic archaea (Haloarcula vallismortis). Results showed that the isolates were significantly similar to halophiles but were different from a mesophile. This investigation demonstrates the feasibility of using whole cell suspensions for rapid differentiation prior to extensive experimentation.

Keywords:Hierarchical Clustering;Discriminant Function Analysis;Principal Component Analysis;Intact Microorganisms;MALDI-TOF-MS

[References]

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[3] Roepstorff P, Curr. Opin. Biotech., 8, 6 (1997)

[4] Black GE, Fox A (1996) In: Snyder PA (ed.) Biochemical and Biotechnological Applications of Electrospray Ionization Mass Spectrometry, Vol. DCXIX. American Chemical Society, Washington DC, 81-105 (1996)

[5] Vanlaere E, Sergeant K, Dawyndt P, Kallow W, Erhard M, Sutton H, Dare D, Devreese B, Samyn B, Vandamme P, J. Microbiological Methods, 75, 279 (2008)

[6] Dieckmann R, Graeber I, Kaesler I, Szewzyk U, von Dohren H, Appl. Microbiol. Biotechnol., 67(4), 539 (2005)

[7] Keys CJ, Dare DJ, Sutton H, Wells G, Lunt M, McKenna K, McDowall M, Shah HN, Infect. Genet. Evol., 4, 221 (2004)

[8] Kumar MP, Vairamani M, Raju RP, Lobo C, Abumani N, Kumar CP, Menon T, Shanmugasundaram S, Indian J. Med. Res., 119, 283 (2004)

[9] Pribil P, Fenselau C, Anal. Chem., 77, 6092 (2005)

[10] Ruelle V, Moualij B, Zorzi W, Ledent P, Pauw ED, Rapid Commun. Mass Spectrom., 18, 2013 (2004)

[11] Van Baar BL, Fems Microbiol. Rev., 24, 193 (2000)

[12] Dalluge JJ, Fresenius J. Anal. Chem., 366, 701 (2000)

[13] Fox A, J. Clin. Microbiol., 44, 2677 (2006)

[14] Kell DB, Brown M, Davey HM, Dunn WB, Spasic I, Oliver SG, Nat. Rev. Microbiol., 3, 557 (2005)

[15] Siegrist TJ, Anderson PD, Huen WE, Kleinheinz GT, Mcdermott CM, Sandrin TR, J. Microbiol. Methods, 68, 554 (2007)

[16] Mandrell RE, Harden LA, Bates A, Miller WG, Haddon WF, Fagerquist CK, Appl. Environ. Microbiol., 71, 6292 (2005)

[17] Goodacre R, Heald JK, Kell DB, FEMS Microbiol. Lett., 176, 17 (1999)

[18] Allen J, Davey HM, Broashurst D, Heald JK, Rowland JJ, Oliver SG, Nat. Biotechnol., 21, 692 (2003)

[19] Timmins EM, Howell AS, Alsberg BK, Noble WC, Goodacre R, J. Clin. Microbiol., 36, 367 (1998)

[20] Vaidyanathan S, Rowland JJ, Kell DB, Goodacre R, Anal. Chem., 73, 4134 (2001)

[21] Zhao H, Parry RL, Ellis DI, Griffith GW, Goodacre R, Vib. Spectrosc., 40, 213 (2006)

[22] O’Farrel PZ, Goodman HM, O’Farrel PH, Cell, 12, 1133 (1977)

[23] Laemmli UK, Nature, 227, 680 (1970)

[24] Blum H, Beier H, Gross HJ, Electrophoresis, 8, 93 (1987)

[25] Bakshi BR, AIChE J., 44, 1596 (1987)

[26] Eriksson L, Johansson E, Kettaneh-Wold N, Wold S, Multiand megavariate data analysis; principles and applications, Umetrics AB, Umea, Sweden (Chapter 3) (2001)

[27] http://www2.chass.ncsu.edu/garson/pa765/discrim.htm.

[28] http://www.statsoft.com/textbook/stathome.html.

[29] Dixon WJ, Biomedical computer programs, Los Angeles:University of California Press (1975)

[30] MacFie HJH, Gutteridge CS, Norris JR, J. Gen. Microbiol., 104, 67 (1978)

[31] http://personalpages.manchester.ac.uk/staff/Roy.Goodacre.

[32] Jain AK, Murty MN, Flynn PJ, ACM Comput. Surv., 31, 264 (1999)

[33] Akman U, Okay N, Oner Hortacsu O, Korean J. Chem. Eng., 25(2), 329 (2008)

[34] Galinski EA, Louis P, Compatible solutes: ectoine production and gene expression, In: Oren A (ed), Microbiology and biogeochemistry of hyper-saline environments, CRC Press, Inc. Boca Raton, Fla., 187-202 (1999)

[35] Lanyi JK, Bacteriological Reviewa, 38, 272 (1974)

[36] Reistad R, Arch. Mikrobiol., 71, 353 (1970)

[37] Ventosa A, Nieto JJ, Oren A, Microbiol. Mol. Biol. R., 62, 504 (1998)

[38] Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K, J. Mol. Biol., 327, 347 (2003)

[39] Yeung KY, Ruzzo WL, Bioinformatics, 17, 763 (2001)