Share This Article:

MicrobMatcher: a microbial comparison software based on matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry

Abstract Full-Text HTML Download Download as PDF (Size:423KB) PP. 403-409
DOI: 10.4236/jbise.2011.45051    3,352 Downloads   6,537 Views   Citations

ABSTRACT

Matrix-assisted Laser Desorption/Ionization with Time-of-flight Mass Spectrometry (MALDI-TOFMS) was investigated as a method for the rapid identifica-tion of species. Current demand in microbial identi-fication is how to compare unknown strains to the known one quickly, semi-automatically and accurately. In this paper, we present a software tool that allows flexibly microbial matching in a user-friendly way, by letting the users to customize comparison parameters including: in vitro transcription enzyme, mass tolerance,minimum fragment length, intensity threshold and corresponding weights. We provide three spectral scoring functions to compute the affin-ity between the species. Therefore, the precision of microbial comparison increases. To test and verify this tool, we employed experimental spectral data based on MALDI-TOFMS and the gene sequences of E.coli and Salmonella. This software is written in Java for cross-platform intention.

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

Fu, Y. , Liu, F. and Ye, Y. (2011) MicrobMatcher: a microbial comparison software based on matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. Journal of Biomedical Science and Engineering, 4, 403-409. doi: 10.4236/jbise.2011.45051.

References

[1] Jarman, K.H., Cebula, S.T., Saenz, A.J., Petersen, C.E., Valentine, N.B., Kingsley, M.T. and Wahl, K.L. (2000) An algorithm for automated bacterial identification using matrix-assisted laser desorption/ionization mass spectrometry. Analytical Chemistry, 72, 1217-1223. doi:10.1021/ac990832j
[2] Jackson, G.W., McNichols, R.J., Fox, G.E. and Willson, R.C. (2007) Universal bacterial identification by mass spectrometry of 16S ribosomal RNA cleavage products. International Journal of Mass Spectrometry, 261, 218-226. doi:10.1016/j.ijms.2006.09.021
[3] Jackson, G.W., McNichols, R.J., Fox, G.E. and Willson, R.C. (2008) Toward universal flavivirus identification by mass cataloging. Journal of Molecular Diagnostics, 10, pp. 135-141. doi:10.2353/jmoldx.2008.070130
[4] Zhou, X.H., Gonnet, G., Hallett, M., Münchbach, M., Folkers, G. and James, P. (2001) Cell fingerprinting: An approach to classifying cells according to mass profiles of digests of protein extracts. Proteomics, 1, 683-690. doi:10.1002/1615-9861(200104)1:5<683::AID-PROT683>3.0.CO;2-3
[5] Ressom, H.W., Varghese, R.S., Drake, S.K., Hortin, G.L., Abdel-Hamid, M., Loffredo, C.A. and Goldman, R. (2007) Peak selection from MALDI-TOF mass spectra using ant colony optimization. Bioinformatics, 23, 619-626. doi:10.1093/bioinformatics/btl678
[6] Jackson, G.W., McNichols, R.J., Fox, G.E. and Willson R.C. (2007) Bacterial genotyping by 16S rRNA mass cataloging. BMC Bioinformatics, 7, 321. doi:10.1186/1471-2105-7-321
[7] Zhang, Z.D., Jackson, G.W., Fox, G.E. and Willson, R.C. (2006) Microbial identification by mass cataloging. BMC Bioinformatics, 7, 117. doi:10.1186/1471-2105-7-117
[8] Jones, N.C. and Pevzner, P.A. (2004) An introduction to bioinformatics algorithms, Chapter 6. MIT Press, Cambridge.

  
comments powered by Disqus

Copyright © 2019 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.