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Classification and Identification Tasks in Microbiology: Mass Spectrometric Methods Coming to the Aid

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Abstract

Mass spectrometry (MS) methods furnish the clue to many microbiological applications including advanced studies on the diversity and classification of prokaryotes. Mass spectral data contribute to the polyphasic taxonomy which considers genotypic characters together with structure-functional and ecological traits. Additionally, these methods contribute to reliable and rapid identification of microorganisms bypassing conventional manipulations which are materials and time consuming. MS based analyses of biomarkers can be performed at the level of whole cells, cell homogenates, subcellular fractions, and individual molecules. For this purpose, various MS methods can be employed, such as MALDI-TOF, ESI, SELDI, and BAMS. Of these, MALDI-TOF MS is the especially easy-to-use and rapid method with many analytical applications, primarily in proteomics which aims at comprehensive description of protein inventory in prokaryotes. An alternative for detection and comparison of biomarkers via MS is amplification and alignment of marker gene sequences. Two molecular approaches supplement each other under support of database resources. Microbiologists readily assimilate MS methods propelled by high performance analyzers and sensitive detectors. The review focuses at progressing application of MS methods in microbiology, with an emphasis on identification and comparative study of bacteria.

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REFERENCES

  1. Andersen, J.S., Svensson, B., and Roepstorff, P., Electrospray ionization and matrix assisted laser desorption/ionization mass spectrometry: powerful analytical tools in recombinant protein chemistry, Nat. Biotechnol., 1996, vol. 4, pp. 449–457.

    Article  Google Scholar 

  2. van Baar, B.L.M., Characterization of bacteria by matrix-assisted laser desorption/ionisation and electrospray mass spectrometry, FEMS Microbiol. Rev., 2000, vol. 24, pp. 193–219.

    Article  CAS  PubMed  Google Scholar 

  3. Barbuddhe, S.B., Maier, T., Schwarz, G., Kostrzewa, M., Hof, H., Domann, E., Chakraborty, T., and Hain, T., Ra-pid identification and typing of Listeria species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Appl. Environ. Microbiol., 2008, vol. 74, pp. 5402–5407.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Benagli, C., Demarta, A., Caminada, A., Ziegler, D., Petrini, O., and Tonolla, M., A rapid MALDI-TOF MS identification database at genospecies level for clinical and environmental Aeromonas strains, PLoS ONE, 2012, vol. 7, art. e48441.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Böhme, K., Fernández-No, I.C., Barros-Velázquez, J., Gallardo, J.M., Cañas, B., and Calo-Mata, P., SpectraBank: an open access tool for rapid microbial identification by MALDI-TOF MS fingerprinting, Electrophoresis, 2012, vol. 33, pp. 2138–2142.

    Article  CAS  PubMed  Google Scholar 

  6. de Bruyne, K., Slabbinck, B., Waegemann, W., Vauterin, P., De Baets, B., and Vandamme, P., Bacterial species identification from MALDI-TOF MS spectra through data analysis and machine learning, Syst. Appl. Microbiol., 2011, vol. 34, pp. 20–29.

    Article  CAS  PubMed  Google Scholar 

  7. Chao, Q.T., Lee, T.F., Teng, S.H., Peng, L.Y., Chen, P.H., Teng, L.J., and Hsueh, P.R., Comparison of accuracy of two conventional phenotypic methods and two MALDI-TOF systems with that of DNA sequencing analysis for correctly identifying clinically encountered yeasts, PLoS ONE, 2014, vol. 9, art. e109376.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen, K.-F., Blyn, L., Rothman, R.E., Ramachandran, P., Valsamakis, A., Ecker, D., Sampath, R., and Gaydos, C.A., RT-PCR and electrospray ionization mass spectrometry (RT-PCR/ESI-MS) for identifying acute viral upper respiratory tract infections, Diagn. Microbiol. Infect. Dis., 2011, vol. 69, pp. 179–186.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Chen, Y.-S., Liu, Y.-H., Teng, S.-H., Liao, C.H., Hung, C.C., Sheng, W.H., Teng, L.J., and Hsueh, P.R., Evaluation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Bruker Biotyper for identification of Penicillium marneffei, Paecilomyces species, Fusarium solani, Rhizopus species, and Pseudallesche-ria boydii, Front. Microbiol., 2015, vol. 6, https://doi.org/10.3389/fmicb.2015.00679

  10. Cheng, K., Chui, H., Domish, L., Hernandez, D., and Wang, G., Recent developments of mass spectrometry and proteomics applications in identification and typing of bacteria, Proteomics Clin. Appl., 2016, vol. 10, pp. 346−357.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Croxatto, A., Prod’hom, G., and Greub, G., Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology, FEMS Microbiol. Rev., 2012, vol. 36, pp. 380–407.

    Article  CAS  PubMed  Google Scholar 

  12. Dare, D., Microbial identification using MALDI-TOF MS, in Encyclopedia of Rapid Microbiological Methods, Vol. 3 (Miller, M.J., ed.), 2006, River Grove, IL: DHI Publ. LCC, pp. 19−56.

    Google Scholar 

  13. Dare, D., Sutton, H., Keys, C., Shah, H., McDowall, M., and Lunt, M., Exploring the potential for simultaneous rapid identification and typing of Staphylococcus aureus by matrix assisted laser desorption/ionization time-of-flight mass spectrometry, Int. J. Med. Microbiol., 2004, vol. 294, pp. 149–149.

    Article  CAS  Google Scholar 

  14. Del Chierico, F., Petrucca, A., Vernocchi, P., Bracaglia, G., Fiscarelli, E., Bernaschi, P., .Urbani, A., and Putignani, L., Proteomics boosts translational and clinical microbiology, J. Proteom., 2014, vol. 97, pp. 69−87.

    Article  CAS  Google Scholar 

  15. Dell, A., Fab-Mass spectrometry of carbohydrates, Adv. Carbohydr. Chem. Biochem., 1987, vol. 45, pp. 19–72.

    Article  CAS  PubMed  Google Scholar 

  16. Demirev, P.A. and Fenselau, C., Rapid characterization of microorganisms by mass spectrometry: an overview, Annu. Rev. Anal. Chem., 2008, vol. 1, pp. 71–93.

    Article  CAS  Google Scholar 

  17. Demirev, P. and Sandrin, T.R., Introduction, in Application of Mass Specrometry in Microbiology, Demirev, P. and Sandrin, T.R., Eds., 2016, Heidelberg: Springer I, pp. 1−10.

  18. Doan, N.T.L., van Hoorde, K., Cnokaert, M., De Brandt, E., Aerts, M., Le Thanh, B., and Vandamme, P., Validation of MALDI-TOF MS for rapid classification and identification of lactic acid bacteria, with a focus on isolates from traditional fermented foods in Northern Vietnam, Lett. Appl. Microbiol., 2012, vol. 55, pp. 265–273.

    Article  CAS  PubMed  Google Scholar 

  19. Dworzanski, J.P. and Snyder, A.P., Classification and identification of bacteria using mass spectrometry-based proteomics, Expert Rev. Proteomics, 2005, vol. 2, pp. 863–878.

    Article  CAS  PubMed  Google Scholar 

  20. El Khéchine, A., Couderc, C., Flaudrops, C. Raoult, D., and Drancourt, M., Matrix-assisted laser desorption/ioni-zation time-of-flight mass spectrometry identification of mycobacteria in routine clinical practice, PLoS ONE, 2011, vol. 6, art. e24720.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Emerson, D., Agulto, L., Liu, H., and Liu, L., Identifying and characterization of bacteria in an era of genomics and proteomics, BioScience, 2008, vol. 58, pp. 925–936.

    Article  Google Scholar 

  22. Emonet, S., Shah, H.N., Cherkaoui, A., and Schrenzel, J., Application and use of various mass spectrometry methods in clinical microbiology, Clin. Microbiol. Infect., 2010, vol. 16, pp. 1604–1613.

    Article  CAS  PubMed  Google Scholar 

  23. Fagerquist, C.K., Amino acid sequence determination of protein biomarkers of Campylobacter upsaliensis and C. helveticus by ‘composite’ sequence proteomic analysis, J. Proteome Res., 2007, vol. 6, pp. 2539–2549.

    Article  CAS  PubMed  Google Scholar 

  24. Fathalli, A., Jenhani, A., Moreira, C., Welker, M., Romdhane, M., Antunes, A., and Vasconcelos, V., Molecular and phylogenetic characterization of potentially toxic cyanobacteria in Tunisian freshwaters, Syst. Appl. Microbiol., 2011, vol. 34, pp. 303–310.

    Article  CAS  PubMed  Google Scholar 

  25. Fenselau, C. and Demirev, P.A., Characterization of intact microorganisms by MALDI mass spectrometry, Mass Spectrom. Rev., 2001, vol. 20, pp. 157–171.

    Article  CAS  PubMed  Google Scholar 

  26. Fergenson, D.P., Pitesky, M.E., Tobias, H.J., Steele, P.T., Czerwieniec, G. A., Russell, S.C., Lebrilla, C.B., Horn, J.M., Coffee, K.R., Srivastava, A., Pillai, S.P., Shih, M.-T.P., Hall, H.L., Ramponi, A.J., Chang, J.T. et al., Reagentless identification of individual bioaerosol particles in millise-conds, Anal. Chem., 2003, vol. 76, pp. 373–378.

    Article  CAS  Google Scholar 

  27. Gaget, V., Welker, M., Rippka, R., and Tandeau de Marsac, N., A polyphasic approach leading to the revision of the genus Planktothrix (Cyanobacteria) and its type species, P. agardhii, and proposal for integrating the emended valid botanical taxa, as well as three new species, Planktothrix paucivesiculata sp. nov. ICNP, Planktothrix tepida sp. nov. ICNP, and Planktothrix serta sp. nov. ICNP, as genus and species names with nomenclatural standing under the ICNP, Syst. Appl. Microbiol., 2015, vol. 38, pp. 141–158.

    Article  PubMed  Google Scholar 

  28. Gillis, M., Vandamme, P., De Vos, P. et al., Polyphasic taxonomy, in Bergey’s Manual of Systematic Bacteriology, vol. 1, Boone, D.R. and Castenholz, R.W., Eds., 2001, New York: Springer, pp. 43−48.

    Google Scholar 

  29. Han, X.L. and Gross, R.W., Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics, J. Lipid Res., 2003, vol. 44, pp. 1071−1079.

    Article  CAS  PubMed  Google Scholar 

  30. Hettich, R.L., Sharma, R., Chourey, K., and Giannone, R.J., Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete in complex environmental communities, Curr. Opin. Microbiol., 2012, vol. 15, pp. 373−380.

    Article  CAS  PubMed  Google Scholar 

  31. Hiller, S., Krock, B., Cembella, A., and Luckas, B., Rapid detection of cyanobacterial toxins in precursor ion mode by liquid chromatography and tandem mass spectrometry, Int. J. Mass. Spectrom., 2007, vol. 42, pp. 1238−1250.

    Article  CAS  Google Scholar 

  32. Ho, Y.-P. and Reddy, P.M., Identification of pathogens by mass spectrometry, Clin. Chem., 2010, vol. 56, pp. 525–536.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hofstadler, S.A., Sampath, R., Blyn, L.B., Eshoo, M.E., Hall, T.A., Jiang, Y., Drader, J.J., Hannis, J.C., Sannes-Lowery, K.A., Cummins, L.L., Libby, B., Walcott, D.J., Schink, A., Massire, C., Ranken, R. et al., TIGER: the universal biosensor, Int. J. Mass Spectrom., 2005, vol. 242, pp. 23–41.

    Article  CAS  Google Scholar 

  34. Honisch, C., Chen, Y., Mortimer, C., Arnold, C., Schmidt, O., van den Boom, D., Cantor, C.R., Shah, H.N., and Gharbia, S.E., Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing, Proc. Natl. Acad. Sci. U. S. A., 2007, vol. 7, pp. 10649–10654.

    Article  CAS  Google Scholar 

  35. Imanishi, S.Y., Nakayama, T., Asukabe, H., and Harada, K., Application of MALDI Biotyper to cyanobacterial profiling, Rapid Commun. Mass Spectrom., 2017, vol. 31, pp. 325–332.

    Article  CAS  PubMed  Google Scholar 

  36. Karas, M. and Hillenkamp, F., Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons, Anal. Chem., 1988, vol. 60, pp. 2299–2301.

    Article  CAS  PubMed  Google Scholar 

  37. Keys, C.J., Dare, D.J., Sutton, H., Wells, G., Lunt, M., McKenna, T., McDowall, M., and Shah, H.N., Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterization of bacteria implicated in human infectious diseases, Infect. Genet. Evol., 2004, vol. 4, pp. 221–242.

    Article  CAS  PubMed  Google Scholar 

  38. Khot, P.D. and Fisher, M.A., Novel approach for differentiating Shigella species and Escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry, J. Clin. Microbiol., 2013, vol. 51, pp. 3711–3716.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Kleefsman, I., Stowers, M.A., Verheijen, P.J.T., van Wuijckhuijse, A.L., Kientz, C.E., and Marijnissen, J.C.M., Bioaerosol analysis by single particle mass spectrometry, Part. Part. Syst. Charact., 2007, vol. 24, pp. 85–90.

    Article  CAS  Google Scholar 

  40. Lasch, P., Wahab, T., Weil, S., Pályi, B., Tomaso, H., Zange, S., Kiland Granerud, B., Drevinek, M., Kokotovic, B., Wittwer, M., Pflüger, V., Di Caro, A., Stämmler, M., Grunow, R., and Jacob, D., Identification of highly pathogenic microorganisms by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: results of an interlaboratory ring trial, J. Clin. Microbiol., 2015, vol. 53, pp. 2632−2640.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Lee, F., Ho, K.-C., Daniel, Y.-M., Liang, J., Chen, C., Gao, Y., and Chun-Lap Lo, S., Cellular Protein/Peptide Expression Profiles (PEPs): an alternative approach for easy identification of cyanobacterial species, JIOMICS, 2013, vol. 3, pp. 174−184.

    Google Scholar 

  42. Li, L., Han, J., Wang, Z., Liu, J., Wei, J., Xiong, S., and Zhao, Z., Mass spectrometry methodology in lipid analysis, Int. J. Mol. Sci., 2014, vol. 15, pp. 10492−10507.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Liu, H., Du, Z., Wang, J., and Yang, R., Universal sample preparation method for characterization of bacteria by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, Appl. Environ. Microbiol., 2007, vol. 73, pp. 1899–1907.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Lotz, A., Ferroni, A., Beretti, J.L., Dauphin, B., Carbonnelle, E., Guet-Revillet, H., Veziris, N., Heym, B., Jarlier, V., Gaillard, J.L., Pierre-Audigier, C., Frapy, E., Berche, P., Nassif, X., and Bille, E., Rapid identification of mycobacterial whole cells in solid and liquid culture media by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, J. Clin. Microbiol., 2010, vol. 48, pp. 4481–4486.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lundquist, M., Caspersen, M.B., Wikström, P., and Forsman, M., Discrimination of Francisella tularensis subspecies using surface enhanced laser desorption ionization mass spectrometry and multivariate data analysis, FEMS Microbiol. Lett., 2005, vol. 243, pp. 303–310.

    Article  CAS  PubMed  Google Scholar 

  46. Maiden, M.C.J., Multilocus sequence typing in bacteria, Annu. Rev. Microbiol., 2006, vol. 60, pp. 561−588.

    Article  CAS  PubMed  Google Scholar 

  47. Marvin, L.F., Roberts, M.A., and Fay, L.B., Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in clinical chemistry, Clin. Chim. Acta, 2003, vol. 337, pp. 11–21.

    Article  CAS  PubMed  Google Scholar 

  48. Mellmann, A., Cloud, J., Maier, T., Keckevoet, U., Ramminger, I., Iwen, P., Dunn, J., Hall, G., Wilson, D., Lasala, P., Kostrzewa, M., and Harmsen, D., Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria, J. Clin. Microbiol., 2008, vol. 46, pp. 1946–1954.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Moura, H., Woolfitt, A.R., Carvalho, M.G., Pavlopoulos, A., Teixeira, L.M., Satten, G.A., and Barr, J.R., MALDI-TOF mass spectrometry as a tool for differentiation of invasive and noninvasive Streptococcus pyogenes isolates, FEMS Immunol. Med. Microbiol., 2008, vol. 53, pp. 333–342.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Murphy, R.C. and Gaskell, S.J., New applications of mass spectrometry in lipid analysis, J. Biol. Chem., 2011, vol. 286, pp. 25427−25433.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Murray, P.R., What is new in clinical microbiology − microbial identification by MALDI-TOF mass spectrometry? J. Mol. Diagnost., 2012, vol. 14, pp. 419–423.

    Article  CAS  Google Scholar 

  52. Nordhoff, E., Kirpekar, F., and Roepstorff, P., Mass spectrometry of nucleic acids, Mass Spectrom. Rev., 1996, vol. 15, pp. 67–138.

    Article  CAS  PubMed  Google Scholar 

  53. Oehrie, S.A., Southwell, B., and Westrick, J., Detection of various freshwater cyanobacterial toxins using ultra-performance liquid chromatography and tandem mass spectrometry, Toxicon, 2010, vol. 55, pp. 965−972.

    Article  CAS  Google Scholar 

  54. Panda, A., Kurapati, S., Samantaray, J.C., Srinivasan, A., and Khalil, S., MALDI-TOF mass spectrometry proteomic based identification of clinical bacterial isolates, Indian J. Med. Res., 2014, vol. 40, pp. 770–777.

    Google Scholar 

  55. Pineda, F.J., Antoine, M.D., Demirev, P.A., Feldman, A.B., Jackman, J., Longenecker, M., and Lin, J.S., Microorga-nism identification by matrix-assisted laser/desorption ionization mass spectrometry and model-derived ribosomal protein biomarkers, Anal. Chem., 2003, vol. 75, pp. 3817–3822.

    Article  CAS  PubMed  Google Scholar 

  56. Pinevich, A.V., Proposal to consistently apply the International Code of Nomenclature of Prokaryotes (ICNP) to names of the oxygenic photosynthetic bacteria (cyanobacteria), including those validly published under the International Code of Botanical Nomenclature (ICBN)/International Code of Nomenclature for algae, fungi and plants (ICN), and proposal to change Principle 2 of the ICNP, Int. J. Syst. Evol. Microbiol. 2015, vol. 65, pp. 1070−1074.

    Article  PubMed  Google Scholar 

  57. Puddick, J. and Prinsep, M.R., MALDI-TOF mass spectrometry of cyanobacteria: a global approach to the disco-very of novel secondary metabolites, Chem. New Zeal., 2008, vol. 72, pp. 25−28.

    CAS  Google Scholar 

  58. Rahi, P., Prakash, O., and Shouche, Y.S., Matrix-assisted laser desorption/ionization time-of-flight mass-spectro-metry (MALDI-TOF MS) based microbial identifications: challenges and scopes for microbial ecologists, Front. M-icrobiol., 2016, vol. 7, https://doi.org/10.3389/fmicb.2016.01359

  59. Ross, M.M., Neihof, R.A., and Campana, J.E., Direct fatty-acid profiling of complex lipids in intact algae by fast-atom-bombardment mass-spectrometry, Anal. Chim. Acta, 1986, vol. 181, pp. 149–157.

    Article  CAS  Google Scholar 

  60. Rosselló-Mora, R. and Amann, A., The species concept for prokaryotes, FEMS Microbiol. Rev., 2001, vol. 25, pp. 30−67.

    Article  Google Scholar 

  61. Russell, S.C., Czerwieniec, G., Lebrilla, C., Steele, P., Riot, V., Coffee, K., Frank, M., and Gard, E.E., Achieving high detection sensitivity (14 zmol) of biomolecular ions in bioaerosol mass spectrometry, Anal. Chem., 2005, vol. 77, pp. 4734–4741.

    Article  CAS  PubMed  Google Scholar 

  62. Rychert, J., Burnham, C.-A.D., Bythrow, M., Garner, O.B., Ginocchio, C.C., Jennemann, R., Lewinski, M.A., Manji, R., Mochon, A.B., Procop, G.W., Richter, S.S., Sercia, L., Westblade, L.F., Ferraro, M.J., and Branda, J.A., Multicenter evaluation of the Vitek MS matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for identification of Gram-positive aerobic bacteria, J. Clin. Microbiol., 2013, vol. 51, pp. 2225–2231.

    Article  PubMed  PubMed Central  Google Scholar 

  63. Sampath, R., Russell, K.L., Massire, C., Eshoo, M.W., Harpin, V., Blyn, L.B., Melton, R., Ivy, C., Pennella, T., Li, F., Levene, H., Hall, T.A., Libby, B., Fan, N., Walcott, D.J. et al., Global surveillance of emerging influenza virus genotypes by mass spectrometry, PLoS ONE, 2007, vol. 2, art. e489.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Sandrin, T.R., Goldstein, J.E., and Schumaker, S., MALDI-TOF MS profiling of bacteria at strain level, Mass Spectrom. Rev., 2013, vol. 32, pp. 188–217.

    Article  CAS  PubMed  Google Scholar 

  65. Santosa, C., Lima, N., Sampaio, P., and Pais, C., Matrix-assisted laser desorption/ionization time-of-flight intact cell mass spectrometry to detect emerging pathogenic Candida species, Diagn. Microbiol. Infect. Disease, 2011, vol. 71, pp. 204–308.

    Google Scholar 

  66. Seng, P., Abat, C., Rolain, J.M., Colson, P., Lagier, J.C., Gouriet, F., Fournier, P.E., Drancourt, M., La Scola, B., and Raoult, D., Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, J. Clin. Microbiol., 2013, vol. 51, pp. 2182–2194.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Shih, C.J., Chen, S.C., Weng, C.Y., Lai, M.C., and Yang, Y.L., Rapid identification of haloarchaea and methanoarchaea using the matrix assisted laser desorption/ionization time-of-flight mass spectrometry, Sci. Rep., 2015, vol. 5, https://doi.org/10.1038/srep16326

  68. Singhal, N., Kumar, M., Kanaujia, P.K., and Virdi, J.S., MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis, Front. Microbiol., 2015, vol. 6, https://doi.org/10.3389/fmicb.2015.00791

  69. Spinali, S., van Belkum, A., Goering, R.V., Girard, V., Welker, M., Van Nuenen, M., Pincus, D.H., Arsac, M., and Durand, G., Microbial typing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: do we need guidance for data interpretation? J. Clin. Microbiol., 2015, vol. 53, pp. 760–765.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Sun, L.-W., Jiang, W.-J., Sato, H., Kawachi, M., and Lu, X.W., Rapid classification and identification of Microcystis aeruginosa strains using MALDI-TOF MS and polygenetic analysis, PLoS ONE, 2016, vol. 11, https://doi.org/10.1371/journal.pone.0156275

  71. Sun, L.-W., Teramoto, K., Sato, H., Torimura, M., Tao, H., and Shintani, T., Characterization of ribosomal proteins as biomarkers for matrix-assisted laser desorption/ionization mass spectral identification of Lactobacillus plantarum, Rapid Commun. Mass Spectrom., 2006, vol. 20, pp. 3789–3798.

    Article  CAS  PubMed  Google Scholar 

  72. Tanaka, K., Waki, H., Ido, Y., Akita, S., Yoshida, Y., Yoshida, T., and Matsuo, T., Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry, Rapid Commun. Mass Spectrom., 1988, vol. 2, pp. 151–153.

    Article  CAS  Google Scholar 

  73. Thulasiraman, V., McCutchen-Maloney, S.L., Motin, V.L., and Garcia, E., Detection and identification of virulence factors in Yersinia pestis using SELDI ProteinChip system, BioTechniques, 2000, vol. 30, pp. 428–432.

    Article  Google Scholar 

  74. Tobias, H.J., Schafer, M.P., Pitesky, M., Fergenson, D.P., Horn, J., Frank, M., and Gard, E.E., Bioaerosol mass spectrometry for rapid detection of individual airborne Mycobacterium tuberculosis H37Ra particles, Appl. Environ. Microbiol., 2005, vol. 71, pp. 6086–6095.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Tshikhudo, P., Nnzeru, R., Ntushelo, K., and Mudau, F., Bacterial species identification getting easier, Afr. J. Biotechnol., 2013, vol. 12, pp. 5975−5982.

    Article  CAS  Google Scholar 

  76. Vandamme, P., Pot, B., Gillis, M., de Vos, P., Kersters, K., and Swings, J., Polyphasic taxonomy, a consensus approach to bacterial systematics, Microbiol. Rev., 1996, vol. 60, pp. 407−438.

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Vanlaere, E., Sergeant, K., Dawyndt, W., Kallow, W., Erhard, M., Sutton, H., Dare, D., Devreese, B., Samyn, B., and Vandamme, P., Matrix assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells allows rapid identification of Burkholderia cepacia complex species, J. Microbiol. Meth., 2006, vol. 75, pp. 279–286.

    Article  CAS  Google Scholar 

  78. Van Lear, G.E. and McLafferty, F.W., Biochemical aspects of high-resolution mass spectrometry, Annu. Rev. Biochem., 1969, vol. 38, pp. 289−322.

    Article  CAS  Google Scholar 

  79. Vargha, M., Takáts, Z., Konopka, A., and Nakatsua, C.H., Optimization of MALDI-TOF MS for strain level differentiation of Arthrobacter isolates, J. Microbiol. Meth., 2006, vol. 66, pp. 399–409.

    Article  CAS  Google Scholar 

  80. Velichko, N.V., Emelijanova, M.S., Averina, S.G., Pinevich, A.A., and Pinevich, A.V., Taxonomic attribution of “Oscillatoriales” strains within the bacteriological system of cyanobacteria: identification algorithm for operational ge-nera, Microbiology (Moscow), 2018, vol. 87, pp. 393−406.

    Article  CAS  Google Scholar 

  81. Verroken, A., Janssens, M., Berhin, C., Bogaerts, P., Huang, T.D., Wauters, G., and Glupczynski, Y., Evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for identification of Nocardia species, J. Clin. Microbiol., 2010, vol. 48, pp. 4015–4021.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Wang, H., Chen. Y.-L., Teng, S.-H., Xu, Z.P., Xu, Y.C., and Hsueh, P.R., Evaluation of the Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for identification of clinical and environmental isolates of Burkholderia pseudomallei, Front. M-icrobiol., 2016, vol. 7, pp. 415–423.

    Google Scholar 

  83. Warscheid, B. and Fenselau, C., A targeted proteomics approach to the rapid identification of bacterial cell mixtures by matrix-assisted laser desorption/ionization mass spectrometry, Proteomics, 2004, vol. 4, pp. 2877–2892.

    Article  CAS  PubMed  Google Scholar 

  84. Welker, M., Proteomics for routine identification of microorganisms, Proteomics, 2011, vol. 11, pp. 3143–3153.

    Article  CAS  PubMed  Google Scholar 

  85. Welker, M. and Erhard, M., Consistency between chemotyping of single filaments of Planktothrix rubescens (cyanobacteria) by MALDI-TOF and the peptide patterns of strains determined by HPLC-MS, J. Mass Spectrom., 2007, vol. 42, pp. 1062–1068.

    Article  CAS  PubMed  Google Scholar 

  86. Welker, M. and Moore, E.M., Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology, Syst. Appl. Microbiol., 2011, vol. 34, pp. 2–11.

    Article  CAS  PubMed  Google Scholar 

  87. Whitehouse, C.M., Dreyer, R.N., Yamashita, M., and Fenn, J.B., Electrospray interface for liquid chromatographs and mass spectrometers, Anal. Chem., 1985, vol. 57, pp. 675–679.

    Article  CAS  PubMed  Google Scholar 

  88. von Wintzingerode, F., Bocker, S., Schlotelburg, C., Chiu, N.H., Storm, N., Jurinke, C., Cantor, C.R., Göbel, U.B., and van den Boom, D., Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification, Proc. Natl. Acad. Sci. U. S. A., 2002, vol. 99, pp. 7039–7044.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. van Wuijckhuijse, A.L., Stowers, M.A., Kleefsman, W.A., van Baar, B.L.M., Kientz, Ch.E., and Marijnissen, J.C.M., Matrix-assisted laser desorption/ionization aerosol time-of-flight mass spectrometry for the analysis of bioaerosols: development of a fast detector for airborne biological pathogens, J. Aerosol Sci., 2005, vol. 36, pp. 677–687.

    Article  CAS  Google Scholar 

  90. Xiao, D., Yang, Y., Jiang, W., Zhang, H., Liu, H., Yu, H., Xie, C., Zhong, M., Chen, L., and Huang, W., Direct common gram-negative bacterial identification from positive blood culture bottles by SELDI-TOF MS, J. Microbiol. Meth., 2014, vol. 105, pp. 116–120.

    Article  CAS  Google Scholar 

  91. Yip, T.-T. and Lomas, L., SELDI ProteinChip array in oncoproteomic research, Cancer Res., 2002, vol. 1, pp. 273–279.

    CAS  Google Scholar 

  92. Zawadowicz, M.A., Froyd, K.D., Murphy, D.M., and Cziczo, D.J., Improved identification of primary biological aerosol particles using single-particle mass spectrometry, Atmos. Chem. Phys., 2017, vol. 17, pp. 7193–7212.

    Article  CAS  Google Scholar 

  93. Zhang, L., Smart, S., and Sandrin, T.R., Biomarker- and similarity coefficient-based approaches to bacterial mixture characterization using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), Sci. Rep., 2015, vol. 5, art. e15834.

    Article  CAS  Google Scholar 

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ACKNOWLEDGMENTS

We especially thank the anonymous reviewer for criticism and offering valuable suggestions that have strongly improved the manuscript. Conceptual editing by Dr. A.A. Selyutin (Department of General and Inorganic Chemistry, St. Petersburg State University) is gratefully acknowledged.

Funding

This study was supported by grant 16-04-00174 from the Russian Foundation for Fundamental Research, and St. Petersburg University Grant 1.40.540.2017.

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  1. Saint Petersburg State University, 199034, St. Petersburg, Russia

    N. V. Velichko & A. V. Pinevich

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  1. N. V. Velichko
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Velichko, N.V., Pinevich, A.V. Classification and Identification Tasks in Microbiology: Mass Spectrometric Methods Coming to the Aid. Microbiology 88, 534–547 (2019). https://doi.org/10.1134/S0026261719050151

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